PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Salvianolic acid B plays an anti-obesity role in high fat diet-induced obese mice by regulating the expression of mRNA, circRNA, and lncRNA
items: Remote sensing pipeline for tree segmentation and classification in a mixed softwood and hardwood system
items: A data science challenge for converting airborne remote sensing data into ecological information
items: https://peerj.com/articles/6022
items: Remote sensing tree classification with a multilayer perceptron
items: Hyperspectral tree crown classification using the multiple instance adaptive cosine estimator
items: Active management is required to turn the tide for depleted Ostrea edulis stocks from the effects of overfishing, disease and invasive species
items: Incidence of acute kidney disease after receiving hematopoietic stem cell transplantation: a single-center retrospective study
items: Quantitative heterodonty in Crocodylia: assessing size and shape across modern and extinct taxa
items: A population-based study on prevalence and risk factors of gastroesophageal reflux disease in the Tibet Autonomous Region, China
items: Effects of root phenotypic changes on the deep rooting of Populus euphratica seedlings under drought stresses
items: TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11
items: Winter temperature predicts prolonged diapause in pine processionary moth species across their geographic range
items: Recruitment of cognitive control regions during effortful self-control is associated with altered brain activity in control and reward systems in dieters during subsequent exposure to food commercials
items: Repeated ethanol exposure increases anxiety-like behaviour in zebrafish during withdrawal
items: A novel and enigmatic two-holed shell aperture in a new species of suspension-feeding worm-snail (Vermetidae)
items: Chemical composition, antioxidant and hepatoprotective activities of methanol extracts from leaves of Terminalia bellirica and Terminalia sericea (Combretaceae)
items: The nectar report: quantitative review of nectar sugar concentrations offered by bee visited flowers in agricultural and non-agricultural landscapes
items: Identification of a novel potassium channel (GiK) as a potential drug target in Giardia lamblia: Computational descriptions of binding sites
items: Trends in fragmentation and connectivity of Paspalum quadrifarium grasslands in the Buenos Aires province, Argentina
items: Considerations for studying transmission of antimicrobial resistant enteric bacteria between wild birds and the environment on intensive dairy and beef cattle operations
items: Phylogeny and circumscription of Dasyphyllum (Asteraceae: Barnadesioideae) based on molecular data with the recognition of a new genus, Archidasyphyllum
items: Change of soil microbial community under long-term fertilization in a reclaimed sandy agricultural ecosystem
items: TRPV1 protects renal ischemia-reperfusion injury in diet-induced obese mice by enhancing CGRP release and increasing renal blood flow
items: Revision of the Afro-Madagascan genus Costularia (Schoeneae, Cyperaceae): infrageneric relationships and species delimitation
items: Validation of reference genes for gene expression studies in tartary buckwheat (Fagopyrum tataricum Gaertn.) using quantitative real-time PCR
items: A new glassfrog (Centrolenidae) from the Chocó-Andean Río Manduriacu Reserve, Ecuador, endangered by mining
items: Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures in Sulfolobus acidocaldarius
items: Effects of stigmata maydis on the methicillin resistant Staphylococus aureus biofilm formation
items: Optimizing plant density and nitrogen application to manipulate tiller growth and increase grain yield and nitrogen-use efficiency in winter wheat
items: Heat stress compromises epithelial integrity in the coral, Acropora hyacinthus
items: Psychological flexibility and attitudes toward evidence-based interventions by amyotrophic lateral sclerosis patients
items: Genetic diversity of Simao pine in China revealed by SRAP markers
items: Oxidative stress and the presence of bacteria increase gene expression of the antimicrobial peptide aclasin, a fungal CSαβ defensin in Aspergillus clavatus
items: Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis
items: Some methods to improve the utility of conditioned Latin hypercube sampling
items: A simulation framework for evaluating multi-stage sampling designs in populations with spatially structured traits
items: Association between maternal pre-delivery body mass index and offspring overweight/obesity at 1 and 2 years of age among residents of a suburb in Taiwan
items: Integrative taxonomic reassessment of Odontophrynus populations in Argentina and phylogenetic relationships within Odontophrynidae (Anura)
items: Evaluating the utility of camera traps in field studies of predation
items: Success of concrete and crab traps in facilitating Eastern oyster recruitment and reef development
items: Tumor mutational profile of triple negative breast cancer patients in Thailand revealed distinctive genetic alteration in chromatin remodeling gene
items: Effects of narrow linear clearings on movement and habitat use in a boreal forest mammal community during winter
items: Emergence of visible light optical properties of L-phenylalanine aggregates
items: The impact on life cycle carbon footprint of converting from disposable to reusable sharps containers in a large US hospital geographically distant from manufacturing and processing facilities
items: A second HD mating type sublocus of Flammulina velutipes is at least di-allelic and active: new primers for identification of HD-a and HD-b subloci
items: Grazing exclosures solely are not the best methods for sustaining alpine grasslands
items: The tetrapod fauna of the upper Permian Naobaogou Formation of China: 3. Jiufengia jiai gen. et sp. nov., a large akidnognathid therocephalian
items: Epidemiology and spatial distribution of bluetongue virus in Xinjiang, China
items: Experimental investigation on the effects of website aesthetics on user performance in different virtual tasks
items: From data compilation to model validation: a comprehensive analysis of a full deep-sea ecosystem model of the Chatham Rise
items: Tracking down the lizards from Gravenhorst's collection at the University of Wrocław: type specimens of Callopistes maculatus Gravenhorst, 1838 and three Liolaemus species rediscovered
items: The response of sulfur dioxygenase to sulfide in the body wall of Urechis unincinctus
items: Diversity, spatial distribution and activity of fungi in freshwater ecosystems
items: What does a Pacman eat? Macrophagy and necrophagy in a generalist predator (Ceratophrys stolzmanni)
items: Lower rotational inertia and larger leg muscles indicate more rapid turns in tyrannosaurids than in other large theropods
items: Comparative study on the composition of four different varieties of garlic
items: The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont
items: Distribution and status of living colonies of Acropora spp. in the reef crests of a protected marine area of the Caribbean (Jardines de la Reina National Park, Cuba)
items: Seasonal variations of the ichthyoplankton assemblage in the Yangtze Estuary and its relationship with environmental factors
items: Dual mechanism of TRKB activation by anandamide through CB1 and TRPV1 receptors
items: Subjective wellbeing at different spatial scales for individuals satisfied and dissatisfied with life
items: Carbon and nitrogen isotopic composition of commercial dog food in Brazil
items: Genome organization and molecular characterization of the three Formica exsecta viruses—FeV1, FeV2 and FeV4
items: Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses
items: Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach
items: Fecal microbiota transplantation research output from 2004 to 2017: a bibliometric analysis
items: Variation in pelvic shape and size in Eastern European males: a computed tomography comparative study
items: Enhancing fitness, enjoyment, and physical self-efficacy in primary school children: a DEDIPAC naturalistic study
items: A community-level investigation following a yellow fever virus outbreak in South Omo Zone, South-West Ethiopia
items: Yeasts producing zeatin
items: Alternative reproductive strategies in black-winged territorial males of Paraphlebia zoe (Odonata, Thaumatoneuridae)

Salvianolic acid B plays an anti-obesity role in high fat diet-induced obese mice by regulating the expression of mRNA, circRNA, and lncRNA
type: item
type: AcademicArticle
description: Background Adipose tissue plays a central role in obesity-related metabolic diseases such as type 2 diabetes. Salvianolic acid B (Sal B), a water-soluble ingredient derived from Salvia miltiorrhiza, has been shown to reduce obesity and obesity-related metabolic diseases by suppressing adipogenesis. However, the role of Sal B in white adipose tissue (WAT) is not yet clear. Methods Illumina Hiseq 4000 was used to study the effects of Sal B on the expression of long non-coding RNA (lncRNA) and circular RNA (circRNA) in epididymal white adipose tissue induced by a high fat diet in obese mice. Results RNA-Seq data showed that 234 lncRNAs, 19 circRNAs, and 132 mRNAs were differentially expressed in WAT under Sal B treatment. The up-regulated protein-coding genes in WAT of the Sal B-treated group were involved in the insulin resistance pathway, while the down-regulated genes mainly participated in the IL-17 signaling pathway. Other pathways may play an important role in the formation and differentiation of adipose tissue, such as B cell receptor signaling. Analysis of the lncRNA–mRNA network provides potential targets for lncRNAs in energy metabolism. We speculate that Sal B may serve as a potential therapeutic approach for obesity.
format: application/pdf
format: text/html
creator: Tian An
creator: Jing Zhang
creator: Bohan Lv
creator: Yufei Liu
creator: Jiangpinghao Huang
creator: Juan Lian
creator: Yanxiang Wu
creator: Sihua Gao
creator: Guangjian Jiang
subject: Molecular Biology
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6506
publisher: PeerJ Inc.
rights: © 2019 An et al.
abstract: Background Adipose tissue plays a central role in obesity-related metabolic diseases such as type 2 diabetes. Salvianolic acid B (Sal B), a water-soluble ingredient derived from Salvia miltiorrhiza, has been shown to reduce obesity and obesity-related metabolic diseases by suppressing adipogenesis. However, the role of Sal B in white adipose tissue (WAT) is not yet clear. Methods Illumina Hiseq 4000 was used to study the effects of Sal B on the expression of long non-coding RNA (lncRNA) and circular RNA (circRNA) in epididymal white adipose tissue induced by a high fat diet in obese mice. Results RNA-Seq data showed that 234 lncRNAs, 19 circRNAs, and 132 mRNAs were differentially expressed in WAT under Sal B treatment. The up-regulated protein-coding genes in WAT of the Sal B-treated group were involved in the insulin resistance pathway, while the down-regulated genes mainly participated in the IL-17 signaling pathway. Other pathways may play an important role in the formation and differentiation of adipose tissue, such as B cell receptor signaling. Analysis of the lncRNA–mRNA network provides potential targets for lncRNAs in energy metabolism. We speculate that Sal B may serve as a potential therapeutic approach for obesity.
bibliographic citation: An et al. (2019) Salvianolic acid B plays an anti-obesity role in high fat diet-induced obese mice by regulating the expression of mRNA, circRNA, and lncRNA. PeerJ 7:e6506 https://doi.org/10.7717/peerj.6506
date submitted: 2018-12-06
date accepted: 2019-01-23
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: An
  given name: Tian
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Lv
  given name: Bohan
author list: Agent
  family name: Liu
  given name: Yufei
author list: Agent
  family name: Huang
  given name: Jiangpinghao
author list: Agent
  family name: Lian
  given name: Juan
author list: Agent
  family name: Wu
  given name: Yanxiang
author list: Agent
  family name: Gao
  given name: Sihua
author list: Agent
  family name: Jiang
  given name: Guangjian
doi: 10.7717/peerj.6506
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 An et al.
attribution name: An et al.

Remote sensing pipeline for tree segmentation and classification in a mixed softwood and hardwood system
type: item
type: AcademicArticle
description: The National Institute of Standards and Technology data science evaluation plant identification challenge is a new periodic competition focused on improving and generalizing remote sensing processing methods for forest landscapes. I created a pipeline to perform three remote sensing tasks. First, a marker-controlled watershed segmentation thresholded by vegetation index and height was performed to identify individual tree crowns within the canopy height model. Second, remote sensing data for segmented crowns was aligned with ground measurements by choosing the set of pairings which minimized error in position and in crown area as predicted by stem height. Third, species classification was performed by reducing the dataset’s dimensionality through principle component analysis and then constructing a set of maximum likelihood classifiers to estimate species likelihoods for each tree. Of the three algorithms, the classification routine exhibited the strongest relative performance, with the segmentation algorithm performing the least well.
format: application/pdf
format: text/html
creator: Conor A. McMahon
subject: Biogeography
subject: Ecology
subject: Natural Resource Management
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5837
publisher: PeerJ Inc.
rights: © 2019 McMahon
abstract: The National Institute of Standards and Technology data science evaluation plant identification challenge is a new periodic competition focused on improving and generalizing remote sensing processing methods for forest landscapes. I created a pipeline to perform three remote sensing tasks. First, a marker-controlled watershed segmentation thresholded by vegetation index and height was performed to identify individual tree crowns within the canopy height model. Second, remote sensing data for segmented crowns was aligned with ground measurements by choosing the set of pairings which minimized error in position and in crown area as predicted by stem height. Third, species classification was performed by reducing the dataset’s dimensionality through principle component analysis and then constructing a set of maximum likelihood classifiers to estimate species likelihoods for each tree. Of the three algorithms, the classification routine exhibited the strongest relative performance, with the segmentation algorithm performing the least well.
bibliographic citation: McMahon (2019) Remote sensing pipeline for tree segmentation and classification in a mixed softwood and hardwood system. PeerJ 6:e5837 https://doi.org/10.7717/peerj.5837
date submitted: 2018-06-04
date accepted: 2018-09-27
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McMahon
  given name: Conor A.
doi: 10.7717/peerj.5837
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 McMahon
attribution name: McMahon

A data science challenge for converting airborne remote sensing data into ecological information
type: item
type: AcademicArticle
description: Ecology has reached the point where data science competitions, in which multiple groups solve the same problem using the same data by different methods, will be productive for advancing quantitative methods for tasks such as species identification from remote sensing images. We ran a competition to help improve three tasks that are central to converting images into information on individual trees: (1) crown segmentation, for identifying the location and size of individual trees; (2) alignment, to match ground truthed trees with remote sensing; and (3) species classification of individual trees. Six teams (composed of 16 individual participants) submitted predictions for one or more tasks. The crown segmentation task proved to be the most challenging, with the highest-performing algorithm yielding only 34% overlap between remotely sensed crowns and the ground truthed trees. However, most algorithms performed better on large trees. For the alignment task, an algorithm based on minimizing the difference, in terms of both position and tree size, between ground truthed and remotely sensed crowns yielded a perfect alignment. In hindsight, this task was over simplified by only including targeted trees instead of all possible remotely sensed crowns. Several algorithms performed well for species classification, with the highest-performing algorithm correctly classifying 92% of individuals and performing well on both common and rare species. Comparisons of results across algorithms provided a number of insights for improving the overall accuracy in extracting ecological information from remote sensing. Our experience suggests that this kind of competition can benefit methods development in ecology and biology more broadly.
format: application/pdf
format: text/html
creator: Sergio Marconi
creator: Sarah J. Graves
creator: Dihong Gong
creator: Morteza Shahriari Nia
creator: Marion Le Bras
creator: Bonnie J. Dorr
creator: Peter Fontana
creator: Justin Gearhart
creator: Craig Greenberg
creator: Dave J. Harris
creator: Sugumar Arvind Kumar
creator: Agarwal Nishant
creator: Joshi Prarabdh
creator: Sundeep U. Rege
creator: Stephanie Ann Bohlman
creator: Ethan P. White
creator: Daisy Zhe Wang
subject: Ecology
subject: Data Mining and Machine Learning
subject: Data Science
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5843
publisher: PeerJ Inc.
rights: © 2019 Marconi et al.
abstract: Ecology has reached the point where data science competitions, in which multiple groups solve the same problem using the same data by different methods, will be productive for advancing quantitative methods for tasks such as species identification from remote sensing images. We ran a competition to help improve three tasks that are central to converting images into information on individual trees: (1) crown segmentation, for identifying the location and size of individual trees; (2) alignment, to match ground truthed trees with remote sensing; and (3) species classification of individual trees. Six teams (composed of 16 individual participants) submitted predictions for one or more tasks. The crown segmentation task proved to be the most challenging, with the highest-performing algorithm yielding only 34% overlap between remotely sensed crowns and the ground truthed trees. However, most algorithms performed better on large trees. For the alignment task, an algorithm based on minimizing the difference, in terms of both position and tree size, between ground truthed and remotely sensed crowns yielded a perfect alignment. In hindsight, this task was over simplified by only including targeted trees instead of all possible remotely sensed crowns. Several algorithms performed well for species classification, with the highest-performing algorithm correctly classifying 92% of individuals and performing well on both common and rare species. Comparisons of results across algorithms provided a number of insights for improving the overall accuracy in extracting ecological information from remote sensing. Our experience suggests that this kind of competition can benefit methods development in ecology and biology more broadly.
bibliographic citation: Marconi et al. (2019) A data science challenge for converting airborne remote sensing data into ecological information. PeerJ 6:e5843 https://doi.org/10.7717/peerj.5843
date submitted: 2018-05-29
date accepted: 2018-09-27
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marconi
  given name: Sergio
author list: Agent
  family name: Graves
  given name: Sarah J.
author list: Agent
  family name: Gong
  given name: Dihong
author list: Agent
  family name: Nia
  given name: Morteza Shahriari
author list: Agent
  family name: Le Bras
  given name: Marion
author list: Agent
  family name: Dorr
  given name: Bonnie J.
author list: Agent
  family name: Fontana
  given name: Peter
author list: Agent
  family name: Gearhart
  given name: Justin
author list: Agent
  family name: Greenberg
  given name: Craig
author list: Agent
  family name: Harris
  given name: Dave J.
author list: Agent
  family name: Kumar
  given name: Sugumar Arvind
author list: Agent
  family name: Nishant
  given name: Agarwal
author list: Agent
  family name: Prarabdh
  given name: Joshi
author list: Agent
  family name: Rege
  given name: Sundeep U.
author list: Agent
  family name: Bohlman
  given name: Stephanie Ann
author list: Agent
  family name: White
  given name: Ethan P.
author list: Agent
  family name: Wang
  given name: Daisy Zhe
doi: 10.7717/peerj.5843
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 Marconi et al.
attribution name: Marconi et al.

https://peerj.com/articles/6022
type: item
type: AcademicArticle
title: The effects of Pilates vs. aerobic training on cardiorespiratory fitness, isokinetic muscular strength, body composition, and functional tasks outcomes for individuals who are overweight/obese: a clinical trial
description: Background Some studies have been conducted to verify the effects of Pilates for individuals who are obese, but conclusive results are not yet available due to methodological concerns. The present study aims to verify and compare the effects of Pilates and aerobic training on cardiorespiratory fitness, isokinetic muscular strength, body composition, and functional task outcomes for individuals who are overweight/obese. Methods Of the sixty participants, seventeen were allocated to the control group, since the intervention protocol (Pilates or walking sessions) was during their working hours. The remaining 44 participants were randomly allocated to one of two experimental groups (Pilates (n = 22)) or aerobic groups (n = 21).The Pilates and aerobic groups attended 60-min exercise sessions, three times per week for 8 weeks. The aerobic group performed walking training at a heart rate corresponding to the ventilatory threshold. The Pilates group performed exercises on the floor, resistance apparatus, and 1-kg dumbbells. The control group received no intervention. All volunteers were evaluated at the beginning and end of the intervention. The following assessments were conducted: food intake, cardiorespiratory maximal treadmill test, isokinetic strength testing, body composition and anthropometry, abdominal endurance test, trunk extensor endurance test, flexibility test and functional (stair and chair) tests. Results There was no significant difference pre- and post-intervention in calorie intake [F(2, 57) = 0.02744, p = 0.97)]. A significant improvement in oxygen uptake at ventilatory threshold (p = 0.001; d = 0.60), respiratory compensation point (p = 0.01; d = 0.48), and maximum effort (p = 0.01; d = 0.33) was observed only in the Pilates group. Isokinetic peak torque for knee flexor and extensor muscles did not change for any groups. Lean mass (p = 0.0005; d = 0.19) and fat mass (p = 0.0001; d = 0.19) improved only in the Pilates group. Waist and hip circumference me…
format: application/pdf
format: text/html
creator: Angeles Bonal Rosell Rayes
creator: Claudio Andre B. de Lira
creator: Ricardo B. Viana
creator: Ana A. Benedito-Silva
creator: Rodrigo L. Vancini
creator: Naryana Mascarin
creator: Marilia S. Andrade
subject: Clinical Trials
subject: Kinesiology
description: doi:10.7717/peerj.6022
publisher: PeerJ Inc.
rights: © 2019 Rayes et al.
abstract: Background Some studies have been conducted to verify the effects of Pilates for individuals who are obese, but conclusive results are not yet available due to methodological concerns. The present study aims to verify and compare the effects of Pilates and aerobic training on cardiorespiratory fitness, isokinetic muscular strength, body composition, and functional task outcomes for individuals who are overweight/obese. Methods Of the sixty participants, seventeen were allocated to the control group, since the intervention protocol (Pilates or walking sessions) was during their working hours. The remaining 44 participants were randomly allocated to one of two experimental groups (Pilates (n = 22)) or aerobic groups (n = 21).The Pilates and aerobic groups attended 60-min exercise sessions, three times per week for 8 weeks. The aerobic group performed walking training at a heart rate corresponding to the ventilatory threshold. The Pilates group performed exercises on the floor, resistance apparatus, and 1-kg dumbbells. The control group received no intervention. All volunteers were evaluated at the beginning and end of the intervention. The following assessments were conducted: food intake, cardiorespiratory maximal treadmill test, isokinetic strength testing, body composition and anthropometry, abdominal endurance test, trunk extensor endurance test, flexibility test and functional (stair and chair) tests. Results There was no significant difference pre- and post-intervention in calorie intake [F(2, 57) = 0.02744, p = 0.97)]. A significant improvement in oxygen uptake at ventilatory threshold (p = 0.001; d = 0.60), respiratory compensation point (p = 0.01; d = 0.48), and maximum effort (p = 0.01; d = 0.33) was observed only in the Pilates group. Isokinetic peak torque for knee flexor and extensor muscles did not change for any groups. Lean mass (p = 0.0005; d = 0.19) and fat mass (p = 0.0001; d = 0.19) improved only in the Pilates group. Waist and hip circumference me…
bibliographic citation: Rayes et al. (2019) The effects of Pilates vs. aerobic training on cardiorespiratory fitness, isokinetic muscular strength, body composition, and functional tasks outcomes for individuals who are overweight/obese: a clinical trial. PeerJ 7:e6022 https://doi.org/10.7717/peerj.6022
date submitted: 2018-07-19
date accepted: 2018-10-29
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rayes
  given name: Angeles Bonal Rosell
author list: Agent
  family name: de Lira
  given name: Claudio Andre B.
author list: Agent
  family name: Viana
  given name: Ricardo B.
author list: Agent
  family name: Benedito-Silva
  given name: Ana A.
author list: Agent
  family name: Vancini
  given name: Rodrigo L.
author list: Agent
  family name: Mascarin
  given name: Naryana
author list: Agent
  family name: Andrade
  given name: Marilia S.
doi: 10.7717/peerj.6022
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: ©2019 Rayes et al.
attribution name: Rayes et al.

Remote sensing tree classification with a multilayer perceptron
type: item
type: AcademicArticle
description: To accelerate scientific progress on remote tree classification—as well as biodiversity and ecology sampling—The National Institute of Science and Technology created a community-based competition where scientists were invited to contribute informatics methods for classifying tree species and genus using crown-level images of trees. We classified tree species and genus at the pixel level using hyperspectral and LiDAR observations. We compared three algorithms that have been implemented extensively across a broad range of research applications: support vector machines, random forests, and multilayer perceptron. At the pixel level, the multilayer perceptron algorithm classified species or genus with high accuracy (92.7% and 95.9%, respectively) on the training data and performed better than the other two algorithms (85.8–93.5%). This indicates promise for the use of the multilayer perceptron (MLP) algorithm for tree-species classification based on hyperspectral and LiDAR observations and coincides with a growing body of research in which neural network-based algorithms outperform other types of classification algorithm for machine vision. To aggregate patterns across the images, we used an ensemble approach that averages the pixel-level outputs of the MLP algorithm to classify species at the crown level. The average accuracy of these classifications on the test set was 68.8% for the nine species.
format: application/pdf
format: text/html
creator: G Rex Sumsion
creator: Michael S. Bradshaw
creator: Kimball T. Hill
creator: Lucas D.G. Pinto
creator: Stephen R. Piccolo
subject: Ecology
subject: Data Mining and Machine Learning
subject: Forestry
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6101
publisher: PeerJ Inc.
rights: © 2019 Sumsion et al.
abstract: To accelerate scientific progress on remote tree classification—as well as biodiversity and ecology sampling—The National Institute of Science and Technology created a community-based competition where scientists were invited to contribute informatics methods for classifying tree species and genus using crown-level images of trees. We classified tree species and genus at the pixel level using hyperspectral and LiDAR observations. We compared three algorithms that have been implemented extensively across a broad range of research applications: support vector machines, random forests, and multilayer perceptron. At the pixel level, the multilayer perceptron algorithm classified species or genus with high accuracy (92.7% and 95.9%, respectively) on the training data and performed better than the other two algorithms (85.8–93.5%). This indicates promise for the use of the multilayer perceptron (MLP) algorithm for tree-species classification based on hyperspectral and LiDAR observations and coincides with a growing body of research in which neural network-based algorithms outperform other types of classification algorithm for machine vision. To aggregate patterns across the images, we used an ensemble approach that averages the pixel-level outputs of the MLP algorithm to classify species at the crown level. The average accuracy of these classifications on the test set was 68.8% for the nine species.
bibliographic citation: Sumsion et al. (2019) Remote sensing tree classification with a multilayer perceptron. PeerJ 7:e6101 https://doi.org/10.7717/peerj.6101
date submitted: 2018-06-01
date accepted: 2018-11-12
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sumsion
  given name: G Rex
author list: Agent
  family name: Bradshaw
  given name: Michael S.
author list: Agent
  family name: Hill
  given name: Kimball T.
author list: Agent
  family name: Pinto
  given name: Lucas D.G.
author list: Agent
  family name: Piccolo
  given name: Stephen R.
doi: 10.7717/peerj.6101
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: ©2019 Sumsion et al.
attribution name: Sumsion et al.

Hyperspectral tree crown classification using the multiple instance adaptive cosine estimator
type: item
type: AcademicArticle
description: Tree species classification using hyperspectral imagery is a challenging task due to the high spectral similarity between species and large intra-species variability. This paper proposes a solution using the Multiple Instance Adaptive Cosine Estimator (MI-ACE) algorithm. MI-ACE estimates a discriminative target signature to differentiate between a pair of tree species while accounting for label uncertainty. Multi-class species classification is achieved by training a set of one-vs-one MI-ACE classifiers corresponding to the classification between each pair of tree species and a majority voting on the classification results from all classifiers. Additionally, the performance of MI-ACE does not rely on parameter settings that require tuning resulting in a method that is easy to use in application. Results presented are using training and testing data provided by a data analysis competition aimed at encouraging the development of methods for extracting ecological information through remote sensing obtained through participation in the competition. The experimental results using one-vs-one MI-ACE technique composed of a hierarchical classification, where a tree crown is first classified to one of the genus classes and one of the species classes. The species-level rank-1 classification accuracy is 86.4% and cross entropy is 0.9395 on the testing data, provided by the competition organizer, without the release of ground truth for testing data. Similarly, the same evaluation metrics are computed on the training data, where the rank-1 classification accuracy is 95.62% and the cross entropy is 0.2649. The results show that the presented approach can not only classify the majority species classes, but also classify the rare species classes.
format: application/pdf
format: text/html
creator: Sheng Zou
creator: Paul Gader
creator: Alina Zare
subject: Plant Science
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.6405
publisher: PeerJ Inc.
rights: © 2019 Zou et al.
abstract: Tree species classification using hyperspectral imagery is a challenging task due to the high spectral similarity between species and large intra-species variability. This paper proposes a solution using the Multiple Instance Adaptive Cosine Estimator (MI-ACE) algorithm. MI-ACE estimates a discriminative target signature to differentiate between a pair of tree species while accounting for label uncertainty. Multi-class species classification is achieved by training a set of one-vs-one MI-ACE classifiers corresponding to the classification between each pair of tree species and a majority voting on the classification results from all classifiers. Additionally, the performance of MI-ACE does not rely on parameter settings that require tuning resulting in a method that is easy to use in application. Results presented are using training and testing data provided by a data analysis competition aimed at encouraging the development of methods for extracting ecological information through remote sensing obtained through participation in the competition. The experimental results using one-vs-one MI-ACE technique composed of a hierarchical classification, where a tree crown is first classified to one of the genus classes and one of the species classes. The species-level rank-1 classification accuracy is 86.4% and cross entropy is 0.9395 on the testing data, provided by the competition organizer, without the release of ground truth for testing data. Similarly, the same evaluation metrics are computed on the training data, where the rank-1 classification accuracy is 95.62% and the cross entropy is 0.2649. The results show that the presented approach can not only classify the majority species classes, but also classify the rare species classes.
bibliographic citation: Zou et al. (2019) Hyperspectral tree crown classification using the multiple instance adaptive cosine estimator. PeerJ 7:e6405 https://doi.org/10.7717/peerj.6405
date submitted: 2018-07-26
date accepted: 2019-01-08
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Sheng
author list: Agent
  family name: Gader
  given name: Paul
author list: Agent
  family name: Zare
  given name: Alina
doi: 10.7717/peerj.6405
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: ©2019 Zou et al.
attribution name: Zou et al.

Active management is required to turn the tide for depleted Ostrea edulis stocks from the effects of overfishing, disease and invasive species
type: item
type: AcademicArticle
description: The decline of the European oyster Ostrea edulis across its biogeographic range has been driven largely by over-fishing and anthropogenic habitat destruction, often to the point of functional extinction. However, other negatively interacting factors attributing to this catastrophic decline include disease, invasive species and pollution. In addition, a relatively complex life history characterized by sporadic spawning renders O. edulis biologically vulnerable to overexploitation. As a viviparous species, successful reproduction in O. edulis populations is density dependent to a greater degree than broadcast spawning oviparous species such as the Pacific oyster Crassostrea (Magallana) gigas. Here, we report on the benthic assemblage of O. edulis and the invasive gastropod Crepidula fornicata across three actively managed South coast harbors in one of the few remaining O. edulis fisheries in the UK. Long-term data reveals that numbers of O. edulis sampled within Chichester Harbour have decreased by 96%, in contrast numbers of C. fornicata sampled have increased by 441% over a 19-year period. The recent survey data also recorded extremely low densities of O. edulis, and extremely high densities of C. fornicata, within Portsmouth and Langstone Harbours. The native oyster’s failure to recover, despite fishery closures, suggests competitive exclusion by C. fornicata is preventing recovery of O. edulis, which is thought to be due to a lack of habitat heterogeneity or suitable settlement substrate. Large scale population data reveals that mean O. edulis shell length and width has decreased significantly across all years and site groups from 2015 to 2017, with a narrowing demographic structure. An absence of juveniles and lack of multiple cohorts in the remaining population suggests that the limited fishing effort exceeds biological output and recruitment is poor. In the Langstone & Chichester 2017 sample 98% of the population is assigned to a single cohort (modal mean 71.20…
format: application/pdf
format: text/html
creator: Luke Helmer
creator: Paul Farrell
creator: Ian Hendy
creator: Simon Harding
creator: Morven Robertson
creator: Joanne Preston
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.6431
publisher: PeerJ Inc.
rights: © 2019 Helmer et al.
abstract: The decline of the European oyster Ostrea edulis across its biogeographic range has been driven largely by over-fishing and anthropogenic habitat destruction, often to the point of functional extinction. However, other negatively interacting factors attributing to this catastrophic decline include disease, invasive species and pollution. In addition, a relatively complex life history characterized by sporadic spawning renders O. edulis biologically vulnerable to overexploitation. As a viviparous species, successful reproduction in O. edulis populations is density dependent to a greater degree than broadcast spawning oviparous species such as the Pacific oyster Crassostrea (Magallana) gigas. Here, we report on the benthic assemblage of O. edulis and the invasive gastropod Crepidula fornicata across three actively managed South coast harbors in one of the few remaining O. edulis fisheries in the UK. Long-term data reveals that numbers of O. edulis sampled within Chichester Harbour have decreased by 96%, in contrast numbers of C. fornicata sampled have increased by 441% over a 19-year period. The recent survey data also recorded extremely low densities of O. edulis, and extremely high densities of C. fornicata, within Portsmouth and Langstone Harbours. The native oyster’s failure to recover, despite fishery closures, suggests competitive exclusion by C. fornicata is preventing recovery of O. edulis, which is thought to be due to a lack of habitat heterogeneity or suitable settlement substrate. Large scale population data reveals that mean O. edulis shell length and width has decreased significantly across all years and site groups from 2015 to 2017, with a narrowing demographic structure. An absence of juveniles and lack of multiple cohorts in the remaining population suggests that the limited fishing effort exceeds biological output and recruitment is poor. In the Langstone & Chichester 2017 sample 98% of the population is assigned to a single cohort (modal mean 71.20…
bibliographic citation: Helmer et al. (2019) Active management is required to turn the tide for depleted Ostrea edulis stocks from the effects of overfishing, disease and invasive species. PeerJ 7:e6431 https://doi.org/10.7717/peerj.6431
date submitted: 2018-07-24
date accepted: 2019-01-10
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Helmer
  given name: Luke
author list: Agent
  family name: Farrell
  given name: Paul
author list: Agent
  family name: Hendy
  given name: Ian
author list: Agent
  family name: Harding
  given name: Simon
author list: Agent
  family name: Robertson
  given name: Morven
author list: Agent
  family name: Preston
  given name: Joanne
doi: 10.7717/peerj.6431
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 Helmer et al.
attribution name: Helmer et al.

Incidence of acute kidney disease after receiving hematopoietic stem cell transplantation: a single-center retrospective study
type: item
type: AcademicArticle
description: Background Previous reports have shown that acute kidney injury (AKI) is common after hematopoietic stem cell transplantation (HSCT), which is a crucial treatment for patients with hematological disorders. AKI could increase mortality and induce adverse effects including the development of chronic kidney disease. The incidence of AKI in association with HSCT reportedly varies significantly because several definitions of AKI have been adopted. Acute kidney disease (AKD) is a new concept that can clinically define both AKI and persistent decreases in glomerular filtration rate (GFR) state. We conducted a retrospective cohort study to determine the incidence of AKD after HSCT. Methods This study included 108 patients aged between 16 and 70 years undergoing HSCT. In this study, AKD included clinical condition of AKI or subacute decreases in GFR. AKI was defined according to the Kidney Disease: Improving Global Outcomes guidelines based on serum creatinine. However, urine output data were not included to define AKI because the database lacked some of these data. Comparisons were made between groups using the Mann–Whitney U test. Results Acute kidney disease occurred in 17 patients (15.7%). There were significant differences between the AKD and non-AKD with respect to ABO-incompatible HSCT (p = 0.001) and incidence of acute graft versus host disease (GVHD) after HSCT (p < 0.001). The 100-day overall survival of patients with AKD and without AKD after HSCT was 70.6% and 79.8%, respectively (p = 0.409). Discussion ABO-incompatible HSCT and acute GVHD after HSCT were risk factors for the incidence of AKD. However, we could not find a significant association between AKD after HSCT and mortality.
format: application/pdf
format: text/html
creator: Akira Mima
creator: Kousuke Tansho
creator: Dai Nagahara
creator: Kazuo Tsubaki
subject: Hematology
subject: Nephrology
description: doi:10.7717/peerj.6467
publisher: PeerJ Inc.
rights: © 2019 Mima et al.
abstract: Background Previous reports have shown that acute kidney injury (AKI) is common after hematopoietic stem cell transplantation (HSCT), which is a crucial treatment for patients with hematological disorders. AKI could increase mortality and induce adverse effects including the development of chronic kidney disease. The incidence of AKI in association with HSCT reportedly varies significantly because several definitions of AKI have been adopted. Acute kidney disease (AKD) is a new concept that can clinically define both AKI and persistent decreases in glomerular filtration rate (GFR) state. We conducted a retrospective cohort study to determine the incidence of AKD after HSCT. Methods This study included 108 patients aged between 16 and 70 years undergoing HSCT. In this study, AKD included clinical condition of AKI or subacute decreases in GFR. AKI was defined according to the Kidney Disease: Improving Global Outcomes guidelines based on serum creatinine. However, urine output data were not included to define AKI because the database lacked some of these data. Comparisons were made between groups using the Mann–Whitney U test. Results Acute kidney disease occurred in 17 patients (15.7%). There were significant differences between the AKD and non-AKD with respect to ABO-incompatible HSCT (p = 0.001) and incidence of acute graft versus host disease (GVHD) after HSCT (p < 0.001). The 100-day overall survival of patients with AKD and without AKD after HSCT was 70.6% and 79.8%, respectively (p = 0.409). Discussion ABO-incompatible HSCT and acute GVHD after HSCT were risk factors for the incidence of AKD. However, we could not find a significant association between AKD after HSCT and mortality.
bibliographic citation: Mima et al. (2019) Incidence of acute kidney disease after receiving hematopoietic stem cell transplantation: a single-center retrospective study. PeerJ 7:e6467 https://doi.org/10.7717/peerj.6467
date submitted: 2018-10-08
date accepted: 2019-01-17
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mima
  given name: Akira
author list: Agent
  family name: Tansho
  given name: Kousuke
author list: Agent
  family name: Nagahara
  given name: Dai
author list: Agent
  family name: Tsubaki
  given name: Kazuo
doi: 10.7717/peerj.6467
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 Mima et al.
attribution name: Mima et al.

Quantitative heterodonty in Crocodylia: assessing size and shape across modern and extinct taxa
type: item
type: AcademicArticle
description: Heterodonty in Crocodylia and closely related taxa has not been defined quantitatively, as the teeth rarely have been measured. This has resulted in a range of qualitative descriptors, with little consensus on the condition of dental morphology in the clade. The purpose of this study is to present a method for the quantification of both size- and shape-heterodonty in members of Crocodylia. Data were collected from dry skeletal and fossil specimens of 34 crown crocodylians and one crocodyliform, resulting in 21 species total. Digital photographs were taken of each tooth and the skull, and the margins of both were converted into landmarks and semilandmarks. We expressed heterodonty through Foote’s morphological disparity, and a principal components analysis quantified shape variance. All specimens sampled were heterodont to varying degrees, with the majority of the shape variance represented by a ‘caniniform’ to ‘molariform’ transition. Heterodonty varied significantly between positions; size undulated whereas shape was significantly linear from mesial to distal. Size and shape appeared to be primarily decoupled. Skull shape correlated significantly with tooth shape. High size-heterodonty often correlated with relatively large caniniform teeth, reflecting a prioritization of securing prey. Large, highly molariform, distal teeth may be a consequence of high-frequency durophagy combined with prey size. The slender-snouted skull shape correlated with a caniniform arcade with low heterodonty. This was reminiscent of other underwater-feeding tetrapods, as they often focus on small prey that requires minimal processing. Several extinct taxa were very molariform, which was associated with low heterodonty. The terrestrial peirosaurid shared similarities with large modern crocodylian taxa, but may have processed prey differently. Disparity measures can be inflated or deflated if certain teeth are absent from the tooth row, and regression analysis may not best apply to strongly…
format: application/pdf
format: text/html
creator: Domenic C. D’Amore
creator: Megan Harmon
creator: Stephanie K. Drumheller
creator: Jason J. Testin
subject: Ecology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.6485
publisher: PeerJ Inc.
rights: © 2019 D’Amore et al.
abstract: Heterodonty in Crocodylia and closely related taxa has not been defined quantitatively, as the teeth rarely have been measured. This has resulted in a range of qualitative descriptors, with little consensus on the condition of dental morphology in the clade. The purpose of this study is to present a method for the quantification of both size- and shape-heterodonty in members of Crocodylia. Data were collected from dry skeletal and fossil specimens of 34 crown crocodylians and one crocodyliform, resulting in 21 species total. Digital photographs were taken of each tooth and the skull, and the margins of both were converted into landmarks and semilandmarks. We expressed heterodonty through Foote’s morphological disparity, and a principal components analysis quantified shape variance. All specimens sampled were heterodont to varying degrees, with the majority of the shape variance represented by a ‘caniniform’ to ‘molariform’ transition. Heterodonty varied significantly between positions; size undulated whereas shape was significantly linear from mesial to distal. Size and shape appeared to be primarily decoupled. Skull shape correlated significantly with tooth shape. High size-heterodonty often correlated with relatively large caniniform teeth, reflecting a prioritization of securing prey. Large, highly molariform, distal teeth may be a consequence of high-frequency durophagy combined with prey size. The slender-snouted skull shape correlated with a caniniform arcade with low heterodonty. This was reminiscent of other underwater-feeding tetrapods, as they often focus on small prey that requires minimal processing. Several extinct taxa were very molariform, which was associated with low heterodonty. The terrestrial peirosaurid shared similarities with large modern crocodylian taxa, but may have processed prey differently. Disparity measures can be inflated or deflated if certain teeth are absent from the tooth row, and regression analysis may not best apply to strongly…
bibliographic citation: D’Amore et al. (2019) Quantitative heterodonty in Crocodylia: assessing size and shape across modern and extinct taxa. PeerJ 7:e6485 https://doi.org/10.7717/peerj.6485
date submitted: 2018-07-23
date accepted: 2019-01-19
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: D’Amore
  given name: Domenic C.
author list: Agent
  family name: Harmon
  given name: Megan
author list: Agent
  family name: Drumheller
  given name: Stephanie K.
author list: Agent
  family name: Testin
  given name: Jason J.
doi: 10.7717/peerj.6485
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: ©2019 D’Amore et al.
attribution name: D’Amore et al.

A population-based study on prevalence and risk factors of gastroesophageal reflux disease in the Tibet Autonomous Region, China
type: item
type: AcademicArticle
description: Objective To investigate the prevalence and risk factors of gastroesophageal reflux disease (GERD) in the Tibet Autonomous Region, China. Methods In this cross-sectional study, a stratified random sampling method was used for collecting samples in the Tibet Autonomous Region. A total of 10,000 individuals were selected from October 2016 to June 2017. A previously-published, validated questionnaire including six items related to the symptoms of GERD was used for evaluating GERD. In addition, basic demographic data, lifestyle, dietary habits, medical history and family history of GERD were investigated to identify risk factors of GERD. Results A total of 5,680 completed questionnaires were collected and analyzed. The prevalence of GERD in this area was 10.8%. Age (30–40 years vs. under 18 years, odds ratio (OR): 3.025; 40–50 years vs. under 18 years, OR: 4.484), education level (high school vs. primary, OR: 0.698; university vs. primary, OR: 2.804), ethnic group (Han vs. Tibetan, OR: 0.230; others vs. Tibetan, OR: 0.304), altitude of residence (4.0–4.5 km vs. 2.5–3.0 km, OR: 2.469), length of residence (<5 years vs. ≥5 years, OR: 2.218), Tibetan sweet tea (yes vs. no, OR: 2.158), Tibetan barley wine (yes vs. no, OR: 1.271), Tibetan dried meat (yes vs. no, OR: 1.278) and staying up late (yes vs. no, OR: 1.223) were significantly (all P < 0.05) and independently associated with GERD. Conclusions The prevalence of GERD is high in the Tibet Autonomous Region, China. Geographic conditions, ethnic group and lifestyle are risk factors for GERD.
format: application/pdf
format: text/html
creator: Haoxiang Zhang
creator: Wenwen Gao
creator: Lei Wang
creator: Suzhen
creator: Yanming Gao
creator: Baoli Liu
creator: Hao Zhou
creator: Dianchun Fang
subject: Epidemiology
subject: Gastroenterology and Hepatology
subject: Internal Medicine
description: doi:10.7717/peerj.6491
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Objective To investigate the prevalence and risk factors of gastroesophageal reflux disease (GERD) in the Tibet Autonomous Region, China. Methods In this cross-sectional study, a stratified random sampling method was used for collecting samples in the Tibet Autonomous Region. A total of 10,000 individuals were selected from October 2016 to June 2017. A previously-published, validated questionnaire including six items related to the symptoms of GERD was used for evaluating GERD. In addition, basic demographic data, lifestyle, dietary habits, medical history and family history of GERD were investigated to identify risk factors of GERD. Results A total of 5,680 completed questionnaires were collected and analyzed. The prevalence of GERD in this area was 10.8%. Age (30–40 years vs. under 18 years, odds ratio (OR): 3.025; 40–50 years vs. under 18 years, OR: 4.484), education level (high school vs. primary, OR: 0.698; university vs. primary, OR: 2.804), ethnic group (Han vs. Tibetan, OR: 0.230; others vs. Tibetan, OR: 0.304), altitude of residence (4.0–4.5 km vs. 2.5–3.0 km, OR: 2.469), length of residence (<5 years vs. ≥5 years, OR: 2.218), Tibetan sweet tea (yes vs. no, OR: 2.158), Tibetan barley wine (yes vs. no, OR: 1.271), Tibetan dried meat (yes vs. no, OR: 1.278) and staying up late (yes vs. no, OR: 1.223) were significantly (all P < 0.05) and independently associated with GERD. Conclusions The prevalence of GERD is high in the Tibet Autonomous Region, China. Geographic conditions, ethnic group and lifestyle are risk factors for GERD.
bibliographic citation: Zhang et al. (2019) A population-based study on prevalence and risk factors of gastroesophageal reflux disease in the Tibet Autonomous Region, China. PeerJ 7:e6491 https://doi.org/10.7717/peerj.6491
date submitted: 2018-10-11
date accepted: 2019-01-21
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haoxiang
author list: Agent
  family name: Gao
  given name: Wenwen
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Suzhen
author list: Agent
  family name: Gao
  given name: Yanming
author list: Agent
  family name: Liu
  given name: Baoli
author list: Agent
  family name: Zhou
  given name: Hao
author list: Agent
  family name: Fang
  given name: Dianchun
doi: 10.7717/peerj.6491
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Effects of root phenotypic changes on the deep rooting of Populus euphratica seedlings under drought stresses
type: item
type: AcademicArticle
description: Background Deep roots are critical for the survival of Populus euphratica seedlings on the floodplains of arid regions where they easily suffer drought stress. Drought typically suppresses root growth, but P. euphratica seedlings can adjust phenotypically in terms of root-shoot allocation and root architecture and morphology, thus promoting deep rooting. However, the root phenotypic changes undertaken by P. euphratica seedlings as a deep rooting strategy under drought conditions remain unknown. Methods We quantified deep rooting capacity by the relative root depth (RRD), which represents the ratio of taproot length to plant biomass and is controlled by root mass fraction (RMF), taproot mass fraction (TRMF), and specific taproot length (STRL). We recorded phenotypic changes in one-year-old P. euphratica seedlings under control, moderate and severe drought stress treatments and assessed the effects of RMF, TRMF, and STRL on RRD. Results Drought significantly decreased absolute root depth but substantially increased RRD via exerting positive effects on TRMF, RMF, and STRL. Under moderate drought, TRMF contributed 55%, RMF 27%, and STRL 18% to RRD variation. Under severe drought, the contribution of RMF to RRD variation increased to 37%, which was similar to the 41% for TRMF. The contribution of STRL slightly increased to 22%. Conclusion These results suggest that the adjustments in root architecture and root-shoot allocation were predominantly responsible for deep rooting in P. euphratica seedlings under drought conditions, while morphological changes played a minor role. Moreover, P. euphratica seedlings rely mostly on adjusting their root architecture to maintain root depth under moderate drought conditions, whereas root-shoot allocation responds more strongly under severe drought conditions, to the point where it plays a role as important as root architecture does on deep rooting.
format: application/pdf
format: text/html
creator: Zi-qi Ye
creator: Jian-ming Wang
creator: Wen-juan Wang
creator: Tian-han Zhang
creator: Jing-wen Li
subject: Ecology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.6513
publisher: PeerJ Inc.
rights: © 2019 Ye et al.
abstract: Background Deep roots are critical for the survival of Populus euphratica seedlings on the floodplains of arid regions where they easily suffer drought stress. Drought typically suppresses root growth, but P. euphratica seedlings can adjust phenotypically in terms of root-shoot allocation and root architecture and morphology, thus promoting deep rooting. However, the root phenotypic changes undertaken by P. euphratica seedlings as a deep rooting strategy under drought conditions remain unknown. Methods We quantified deep rooting capacity by the relative root depth (RRD), which represents the ratio of taproot length to plant biomass and is controlled by root mass fraction (RMF), taproot mass fraction (TRMF), and specific taproot length (STRL). We recorded phenotypic changes in one-year-old P. euphratica seedlings under control, moderate and severe drought stress treatments and assessed the effects of RMF, TRMF, and STRL on RRD. Results Drought significantly decreased absolute root depth but substantially increased RRD via exerting positive effects on TRMF, RMF, and STRL. Under moderate drought, TRMF contributed 55%, RMF 27%, and STRL 18% to RRD variation. Under severe drought, the contribution of RMF to RRD variation increased to 37%, which was similar to the 41% for TRMF. The contribution of STRL slightly increased to 22%. Conclusion These results suggest that the adjustments in root architecture and root-shoot allocation were predominantly responsible for deep rooting in P. euphratica seedlings under drought conditions, while morphological changes played a minor role. Moreover, P. euphratica seedlings rely mostly on adjusting their root architecture to maintain root depth under moderate drought conditions, whereas root-shoot allocation responds more strongly under severe drought conditions, to the point where it plays a role as important as root architecture does on deep rooting.
bibliographic citation: Ye et al. (2019) Effects of root phenotypic changes on the deep rooting of Populus euphratica seedlings under drought stresses. PeerJ 7:e6513 https://doi.org/10.7717/peerj.6513
date submitted: 2018-08-23
date accepted: 2019-01-20
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Zi-qi
author list: Agent
  family name: Wang
  given name: Jian-ming
author list: Agent
  family name: Wang
  given name: Wen-juan
author list: Agent
  family name: Zhang
  given name: Tian-han
author list: Agent
  family name: Li
  given name: Jing-wen
doi: 10.7717/peerj.6513
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 Ye et al.
attribution name: Ye et al.

TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11
type: item
type: AcademicArticle
description: Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11.
format: application/pdf
format: text/html
creator: Pedro Seoane
creator: Silvana T. Tapia-Paniagua
creator: Rocío Bautista
creator: Elena Alcaide
creator: Consuelo Esteve
creator: Eduardo Martínez-Manzanares
creator: M. Carmen Balebona
creator: M. Gonzalo Claros
creator: Miguel A. Moriñigo
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.6526
publisher: PeerJ Inc.
rights: © 2019 Seoane et al.
abstract: Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 of Shewanella putrefaciens and genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed by PCR using Pdp11-specific primers. Functional inspection of the 15 genes allowed us to hypothesize that Pdp11 underwent genome rearrangements spurred by plasmids and mobile elements. As a result, Pdp11 presents specific proteins for gut colonization, bile salt resistance and gut pathogen adhesion inhibition, which can explain some probiotic features of Pdp11.
bibliographic citation: Seoane et al. (2019) TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens strain Pdp11. PeerJ 7:e6526 https://doi.org/10.7717/peerj.6526
date submitted: 2018-12-20
date accepted: 2019-01-26
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Seoane
  given name: Pedro
author list: Agent
  family name: Tapia-Paniagua
  given name: Silvana T.
author list: Agent
  family name: Bautista
  given name: Rocío
author list: Agent
  family name: Alcaide
  given name: Elena
author list: Agent
  family name: Esteve
  given name: Consuelo
author list: Agent
  family name: Martínez-Manzanares
  given name: Eduardo
author list: Agent
  family name: Balebona
  given name: M. Carmen
author list: Agent
  family name: Claros
  given name: M. Gonzalo
author list: Agent
  family name: Moriñigo
  given name: Miguel A.
doi: 10.7717/peerj.6526
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 Seoane et al.
attribution name: Seoane et al.

Winter temperature predicts prolonged diapause in pine processionary moth species across their geographic range
type: item
type: AcademicArticle
description: Prolonged diapause occurs in a number of insects and is interpreted as a way to evade adverse conditions. The winter pine processionary moths (Thaumetopoea pityocampa and Th. wilkinsoni) are important pests of pines and cedars in the Mediterranean region. They are typically univoltine, with larvae feeding across the winter, pupating in spring in the soil and emerging as adults in summer. Pupae may, however, enter a prolonged diapause with adults emerging one or more years later. We tested the effect of variation in winter temperature on the incidence of prolonged diapause, using a total of 64 individual datasets related to insect cohorts over the period 1964–2015 for 36 sites in seven countries, covering most of the geographic range of both species. We found high variation in prolonged diapause incidence over their ranges. At both lower and upper ends of the thermal range in winter, prolonged diapause tended to be higher than at intermediate temperatures. Prolonged diapause may represent a risk-spreading strategy to mitigate climate uncertainty, although it may increase individual mortality because of a longer exposure to mortality factors such as predation, parasitism, diseases or energy depletion. Climate change, and in particular the increase of winter temperature, may reduce the incidence of prolonged diapause in colder regions whereas it may increase it in warmer ones, with consequences for population dynamics.
format: application/pdf
format: text/html
creator: Md H.R. Salman
creator: Carmelo P. Bonsignore
creator: Ahmed El Alaoui El Fels
creator: Folco Giomi
creator: José A. Hodar
creator: Mathieu Laparie
creator: Lorenzo Marini
creator: Cécile Merel
creator: Myron P. Zalucki
creator: Mohamed Zamoum
creator: Andrea Battisti
subject: Biogeography
subject: Entomology
subject: Forestry
description: doi:10.7717/peerj.6530
publisher: PeerJ Inc.
rights: © 2019 Salman et al.
abstract: Prolonged diapause occurs in a number of insects and is interpreted as a way to evade adverse conditions. The winter pine processionary moths (Thaumetopoea pityocampa and Th. wilkinsoni) are important pests of pines and cedars in the Mediterranean region. They are typically univoltine, with larvae feeding across the winter, pupating in spring in the soil and emerging as adults in summer. Pupae may, however, enter a prolonged diapause with adults emerging one or more years later. We tested the effect of variation in winter temperature on the incidence of prolonged diapause, using a total of 64 individual datasets related to insect cohorts over the period 1964–2015 for 36 sites in seven countries, covering most of the geographic range of both species. We found high variation in prolonged diapause incidence over their ranges. At both lower and upper ends of the thermal range in winter, prolonged diapause tended to be higher than at intermediate temperatures. Prolonged diapause may represent a risk-spreading strategy to mitigate climate uncertainty, although it may increase individual mortality because of a longer exposure to mortality factors such as predation, parasitism, diseases or energy depletion. Climate change, and in particular the increase of winter temperature, may reduce the incidence of prolonged diapause in colder regions whereas it may increase it in warmer ones, with consequences for population dynamics.
bibliographic citation: Salman et al. (2019) Winter temperature predicts prolonged diapause in pine processionary moth species across their geographic range. PeerJ 7:e6530 https://doi.org/10.7717/peerj.6530
date submitted: 2018-08-13
date accepted: 2019-01-28
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salman
  given name: Md H.R.
author list: Agent
  family name: Bonsignore
  given name: Carmelo P.
author list: Agent
  family name: El Alaoui El Fels
  given name: Ahmed
author list: Agent
  family name: Giomi
  given name: Folco
author list: Agent
  family name: Hodar
  given name: José A.
author list: Agent
  family name: Laparie
  given name: Mathieu
author list: Agent
  family name: Marini
  given name: Lorenzo
author list: Agent
  family name: Merel
  given name: Cécile
author list: Agent
  family name: Zalucki
  given name: Myron P.
author list: Agent
  family name: Zamoum
  given name: Mohamed
author list: Agent
  family name: Battisti
  given name: Andrea
doi: 10.7717/peerj.6530
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: ©2019 Salman et al.
attribution name: Salman et al.

Recruitment of cognitive control regions during effortful self-control is associated with altered brain activity in control and reward systems in dieters during subsequent exposure to food commercials
type: item
type: AcademicArticle
description: Engaging in effortful self-control can sometimes impair people’s ability to resist subsequent temptations. Existing research has shown that when chronic dieters’ self-regulatory capacity is challenged by prior exertion of effort, they demonstrate disinhibited eating and altered patterns of brain activity when exposed to food cues. However, the relationship between brain activity during self-control exertion and subsequent food cue exposure remains unclear. In the present study, we investigated whether individual differences in recruitment of cognitive control regions during a difficult response inhibition task are associated with a failure to regulate neural responses to rewarding food cues in a subsequent task in a cohort of 27 female dieters. During self-control exertion, participants recruited regions commonly associated with inhibitory control, including dorsolateral prefrontal cortex (DLPFC). Those dieters with higher DLPFC activity during the initial self-control task showed an altered balance of food cue elicited activity in regions associated with reward and self-control, namely: greater reward-related activity and less recruitment of the frontoparietal control network. These findings suggest that some dieters may be more susceptible to the effects of self-control exertion than others and, whether due to limited capacity or changes in motivation, these dieters subsequently fail to engage control regions that may otherwise modulate activity associated with craving and reward.
format: application/pdf
format: text/html
creator: Richard B. Lopez
creator: Andrea L. Courtney
creator: Dylan D. Wagner
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6550
publisher: PeerJ Inc.
rights: © 2019 Lopez et al.
abstract: Engaging in effortful self-control can sometimes impair people’s ability to resist subsequent temptations. Existing research has shown that when chronic dieters’ self-regulatory capacity is challenged by prior exertion of effort, they demonstrate disinhibited eating and altered patterns of brain activity when exposed to food cues. However, the relationship between brain activity during self-control exertion and subsequent food cue exposure remains unclear. In the present study, we investigated whether individual differences in recruitment of cognitive control regions during a difficult response inhibition task are associated with a failure to regulate neural responses to rewarding food cues in a subsequent task in a cohort of 27 female dieters. During self-control exertion, participants recruited regions commonly associated with inhibitory control, including dorsolateral prefrontal cortex (DLPFC). Those dieters with higher DLPFC activity during the initial self-control task showed an altered balance of food cue elicited activity in regions associated with reward and self-control, namely: greater reward-related activity and less recruitment of the frontoparietal control network. These findings suggest that some dieters may be more susceptible to the effects of self-control exertion than others and, whether due to limited capacity or changes in motivation, these dieters subsequently fail to engage control regions that may otherwise modulate activity associated with craving and reward.
bibliographic citation: Lopez et al. (2019) Recruitment of cognitive control regions during effortful self-control is associated with altered brain activity in control and reward systems in dieters during subsequent exposure to food commercials. PeerJ 7:e6550 https://doi.org/10.7717/peerj.6550
date submitted: 2018-10-19
date accepted: 2019-01-31
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lopez
  given name: Richard B.
author list: Agent
  family name: Courtney
  given name: Andrea L.
author list: Agent
  family name: Wagner
  given name: Dylan D.
doi: 10.7717/peerj.6550
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: ©2019 Lopez et al.
attribution name: Lopez et al.

Repeated ethanol exposure increases anxiety-like behaviour in zebrafish during withdrawal
type: item
type: AcademicArticle
description: Zebrafish (Danio rerio) are quickly becoming an important model organism in behavioural neuroscience and drug addiction research. Conditioned place preference studies show that drugs of abuse produce responses in zebrafish that are similar to mammalian animal models. Repeated administration of ethanol in zebrafish results in withdrawal-induced behavioural responses that vary with dose and exposure duration, requiring additional investigation. Here, we examine the effects of ethanol withdrawal on anxiety-like behaviours in adult zebrafish after a 21-day ethanol dosing schedule at either 0.4% or 0.8%. Anxiety-like behaviour was measured with the novel object approach test; this test involves placing a fish in a circular arena with a novel object in the centre and observing the amount of exploration of the object. We found increased anxiety-like behaviour during ethanol withdrawal. This study adds to the growing body of literature that validates the zebrafish as a model organism in the field of behavioural neuroscience and addiction.
format: application/pdf
format: text/html
creator: Jeffrey T. Krook
creator: Erika Duperreault
creator: Dustin Newton
creator: Matthew S. Ross
creator: Trevor J. Hamilton
subject: Animal Behavior
subject: Neuroscience
description: doi:10.7717/peerj.6551
publisher: PeerJ Inc.
rights: © 2019 Krook et al.
abstract: Zebrafish (Danio rerio) are quickly becoming an important model organism in behavioural neuroscience and drug addiction research. Conditioned place preference studies show that drugs of abuse produce responses in zebrafish that are similar to mammalian animal models. Repeated administration of ethanol in zebrafish results in withdrawal-induced behavioural responses that vary with dose and exposure duration, requiring additional investigation. Here, we examine the effects of ethanol withdrawal on anxiety-like behaviours in adult zebrafish after a 21-day ethanol dosing schedule at either 0.4% or 0.8%. Anxiety-like behaviour was measured with the novel object approach test; this test involves placing a fish in a circular arena with a novel object in the centre and observing the amount of exploration of the object. We found increased anxiety-like behaviour during ethanol withdrawal. This study adds to the growing body of literature that validates the zebrafish as a model organism in the field of behavioural neuroscience and addiction.
bibliographic citation: Krook et al. (2019) Repeated ethanol exposure increases anxiety-like behaviour in zebrafish during withdrawal. PeerJ 7:e6551 https://doi.org/10.7717/peerj.6551
date submitted: 2018-08-30
date accepted: 2019-02-01
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krook
  given name: Jeffrey T.
author list: Agent
  family name: Duperreault
  given name: Erika
author list: Agent
  family name: Newton
  given name: Dustin
author list: Agent
  family name: Ross
  given name: Matthew S.
author list: Agent
  family name: Hamilton
  given name: Trevor J.
doi: 10.7717/peerj.6551
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: © 2019 Krook et al.
attribution name: Krook et al.

A novel and enigmatic two-holed shell aperture in a new species of suspension-feeding worm-snail (Vermetidae)
type: item
type: AcademicArticle
description: Shell aperture modifications are well known in terrestrial and aquatic gastropods, with apertural lip thickening and tooth development common in species with terminal (determinate) shell growth. In contrast, secondary shell openings are rare in snails and are largely limited to slit shells, keyhole limpets, and abalone of the Vetigastropoda. When such features occur in other groups, they are noteworthy and raise interesting questions concerning the functional/adaptive significance of these shell modifications. Here we report on one such modification in a newly described species of vermetid snail. Members of the worm-snail family Vermetidae are sessile, suspension-feeding caenogastropods found in warm temperate to tropical marine environments worldwide. As juveniles, vermetids permanently cement their shells to hard substrata and subsequently produce irregularly coiled polychaete-like shell tubes with indeterminate growth and typically a simple circular shell aperture. In one previously studied group (genus Cupolaconcha), the aperture can be covered by a shell dome with a central slit that retains its widest opening in the center of the aperture. Vermetid specimens collected in the barrier reefs of Belize and the Florida Keys show an extreme aperture modification previously unknown in Gastropoda, in which the shell opening is covered by an apertural dome that leaves two equal-sized circular holes, each corresponding to the inflow and outflow water exchange currents of the animal’s mantle cavity. The function of this perforated apertural dome is unknown, and it is in some ways antithetical to the suspension feeding habit of these snails. Further field and laboratory-based studies will be needed to clarify the functional significance and trade-offs of this unique morphology. The new taxon, which is not closely related to the previously described dome-building clade Cupolaconcha, is described and named as Vermetus biperforatus Bieler, Collins, Golding & Rawlings n. sp.
format: application/pdf
format: text/html
creator: Rüdiger Bieler
creator: Timothy M. Collins
creator: Rosemary Golding
creator: Timothy A. Rawlings
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6569
publisher: PeerJ Inc.
rights: © 2019 Bieler et al.
abstract: Shell aperture modifications are well known in terrestrial and aquatic gastropods, with apertural lip thickening and tooth development common in species with terminal (determinate) shell growth. In contrast, secondary shell openings are rare in snails and are largely limited to slit shells, keyhole limpets, and abalone of the Vetigastropoda. When such features occur in other groups, they are noteworthy and raise interesting questions concerning the functional/adaptive significance of these shell modifications. Here we report on one such modification in a newly described species of vermetid snail. Members of the worm-snail family Vermetidae are sessile, suspension-feeding caenogastropods found in warm temperate to tropical marine environments worldwide. As juveniles, vermetids permanently cement their shells to hard substrata and subsequently produce irregularly coiled polychaete-like shell tubes with indeterminate growth and typically a simple circular shell aperture. In one previously studied group (genus Cupolaconcha), the aperture can be covered by a shell dome with a central slit that retains its widest opening in the center of the aperture. Vermetid specimens collected in the barrier reefs of Belize and the Florida Keys show an extreme aperture modification previously unknown in Gastropoda, in which the shell opening is covered by an apertural dome that leaves two equal-sized circular holes, each corresponding to the inflow and outflow water exchange currents of the animal’s mantle cavity. The function of this perforated apertural dome is unknown, and it is in some ways antithetical to the suspension feeding habit of these snails. Further field and laboratory-based studies will be needed to clarify the functional significance and trade-offs of this unique morphology. The new taxon, which is not closely related to the previously described dome-building clade Cupolaconcha, is described and named as Vermetus biperforatus Bieler, Collins, Golding & Rawlings n. sp.
bibliographic citation: Bieler et al. (2019) A novel and enigmatic two-holed shell aperture in a new species of suspension-feeding worm-snail (Vermetidae). PeerJ 7:e6569 https://doi.org/10.7717/peerj.6569
date submitted: 2019-01-03
date accepted: 2019-02-05
issued: 2019-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bieler
  given name: Rüdiger
author list: Agent
  family name: Collins
  given name: Timothy M.
author list: Agent
  family name: Golding
  given name: Rosemary
author list: Agent
  family name: Rawlings
  given name: Timothy A.
doi: 10.7717/peerj.6569
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-28
copyright: ©2019 Bieler et al.
attribution name: Bieler et al.

Chemical composition, antioxidant and hepatoprotective activities of methanol extracts from leaves of Terminalia bellirica and Terminalia sericea (Combretaceae)
type: item
type: AcademicArticle
description: Background Plants belonging to the genus Terminalia such as Terminalia bellirica and Terminalia sericea are used traditionally to treat several diseases and health disorders. Up to this date, the roots of Terminalia sericea and the fruits of Terminalia bellirica are the mostly studied plant parts. The phytochemical composition and the biological activities of the leaves of both species are not well identified so far. Methods The secondary metabolites of Terminalia bellirica and Terminalia sericea leaves were identified using HPLC-PDA-MS/MS. The antioxidant activities of the leaves extracts were determined by DPPH and FRAP assays. The hepatoprotective potential was evaluated in rats with D-galactosamine induced liver damage. The effect of the extracts on the expression of the anti-apoptotic marker Bcl-2 was measured in an immunohistochemical study. The most abundant compounds identified in the studied extracts were docked into Bcl-2: Bim (BH3) interaction surface using molecular operating environment software. Results A total of 85 secondary metabolites were identified in the leaf extracts of both species. Ellagitannins such as corilagin, chebulagic acid, galloylpunicalagin, and digalloyl-hexahydroxydiphenoyl-hexoside were found to be the major components in Terminalia bellirica whereas flavonoid glycosides including quercetin rutinoside and quercetin galloyl-glucoside were highly abundant in Terminalia sericea. The studied extracts exhibited pronounced antioxidant activities, moderate anti-apoptotic and hepatoprotective potential. In silico docking experiments revealed that the compounds abundant in the extracts were able to bind to Bcl-2: Bim (BH3) interaction surface with an appreciable binding free energy. Discussion The antioxidant and hepatoprotective activities exhibited by the studied extracts might be attributed to the high content of the polyphenols. The anti-apoptotic activity could be due to the interference with the apoptotic pathway mediated by Bcl-2: B…
format: application/pdf
format: text/html
creator: Mansour Sobeh
creator: Mona F. Mahmoud
creator: Rehab A. Hasan
creator: Mohamed A.O. Abdelfattah
creator: Samir Osman
creator: Harun-or Rashid
creator: Assem M. El-Shazly
creator: Michael Wink
subject: Biochemistry
subject: Plant Science
subject: Pharmacology
description: doi:10.7717/peerj.6322
publisher: PeerJ Inc.
rights: © 2019 Sobeh et al.
abstract: Background Plants belonging to the genus Terminalia such as Terminalia bellirica and Terminalia sericea are used traditionally to treat several diseases and health disorders. Up to this date, the roots of Terminalia sericea and the fruits of Terminalia bellirica are the mostly studied plant parts. The phytochemical composition and the biological activities of the leaves of both species are not well identified so far. Methods The secondary metabolites of Terminalia bellirica and Terminalia sericea leaves were identified using HPLC-PDA-MS/MS. The antioxidant activities of the leaves extracts were determined by DPPH and FRAP assays. The hepatoprotective potential was evaluated in rats with D-galactosamine induced liver damage. The effect of the extracts on the expression of the anti-apoptotic marker Bcl-2 was measured in an immunohistochemical study. The most abundant compounds identified in the studied extracts were docked into Bcl-2: Bim (BH3) interaction surface using molecular operating environment software. Results A total of 85 secondary metabolites were identified in the leaf extracts of both species. Ellagitannins such as corilagin, chebulagic acid, galloylpunicalagin, and digalloyl-hexahydroxydiphenoyl-hexoside were found to be the major components in Terminalia bellirica whereas flavonoid glycosides including quercetin rutinoside and quercetin galloyl-glucoside were highly abundant in Terminalia sericea. The studied extracts exhibited pronounced antioxidant activities, moderate anti-apoptotic and hepatoprotective potential. In silico docking experiments revealed that the compounds abundant in the extracts were able to bind to Bcl-2: Bim (BH3) interaction surface with an appreciable binding free energy. Discussion The antioxidant and hepatoprotective activities exhibited by the studied extracts might be attributed to the high content of the polyphenols. The anti-apoptotic activity could be due to the interference with the apoptotic pathway mediated by Bcl-2: B…
bibliographic citation: Sobeh et al. (2019) Chemical composition, antioxidant and hepatoprotective activities of methanol extracts from leaves of Terminalia bellirica and Terminalia sericea (Combretaceae). PeerJ 7:e6322 https://doi.org/10.7717/peerj.6322
date submitted: 2018-10-03
date accepted: 2018-12-20
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sobeh
  given name: Mansour
author list: Agent
  family name: Mahmoud
  given name: Mona F.
author list: Agent
  family name: Hasan
  given name: Rehab A.
author list: Agent
  family name: Abdelfattah
  given name: Mohamed A.O.
author list: Agent
  family name: Osman
  given name: Samir
author list: Agent
  family name: Rashid
  given name: Harun-or
author list: Agent
  family name: El-Shazly
  given name: Assem M.
author list: Agent
  family name: Wink
  given name: Michael
doi: 10.7717/peerj.6322
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: © 2019 Sobeh et al.
attribution name: Sobeh et al.

The nectar report: quantitative review of nectar sugar concentrations offered by bee visited flowers in agricultural and non-agricultural landscapes
type: item
type: AcademicArticle
description: There is growing concern that some bee populations are in decline, potentially threatening pollination security in agricultural and non-agricultural landscapes. Among the numerous causes associated with this trend, nutritional stress resulting from a mismatch between bee nutritional needs and plant community provisioning has been suggested as one potential driver. To ease nutritional stress on bee populations in agricultural habitats, agri-environmental protection schemes aim to provide alternative nutritional resources for bee populations during times of need. However, such efforts have focused mainly on quantity (providing flowering plants) and timing (during flower-scarce periods), while largely ignoring the quality of the offered flower resources. In a first step to start addressing this information gap, we have used literature data to compile a comprehensive geographically explicit dataset on nectar quality (i.e., total sugar concentration), offered to bees both within fields (crop and weed species) as well as outside fields (wild species) around the globe. Social bees are particularly sensitive to nectar sugar concentrations, which directly impact calorie influx into the colony and consequently their fitness making it an important resource quality marker. We find that the total nectar sugar concentrations in general do not differ between the three plant communities studied. In contrast we find increased variability in nectar quality in the wild plant community compared to crop and weed community, which is likely explained by the increased phylogenetic diversity in this category of plants. In a second step we explore the influence of local habitat on nectar quality and its variability utilizing a detailed sunflower (Helianthus annuus L.) data set and find that geography has a small, but significant influence on these parameters. In a third step we identify crop groups (genera), which provide sub-optimal nectar resources for bees and suggest high quality alterna…
format: application/pdf
format: text/html
creator: Tobias Pamminger
creator: Roland Becker
creator: Sophie Himmelreich
creator: Christof W. Schneider
creator: Matthias Bergtold
subject: Agricultural Science
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6329
publisher: PeerJ Inc.
rights: © 2019 Pamminger et al.
abstract: There is growing concern that some bee populations are in decline, potentially threatening pollination security in agricultural and non-agricultural landscapes. Among the numerous causes associated with this trend, nutritional stress resulting from a mismatch between bee nutritional needs and plant community provisioning has been suggested as one potential driver. To ease nutritional stress on bee populations in agricultural habitats, agri-environmental protection schemes aim to provide alternative nutritional resources for bee populations during times of need. However, such efforts have focused mainly on quantity (providing flowering plants) and timing (during flower-scarce periods), while largely ignoring the quality of the offered flower resources. In a first step to start addressing this information gap, we have used literature data to compile a comprehensive geographically explicit dataset on nectar quality (i.e., total sugar concentration), offered to bees both within fields (crop and weed species) as well as outside fields (wild species) around the globe. Social bees are particularly sensitive to nectar sugar concentrations, which directly impact calorie influx into the colony and consequently their fitness making it an important resource quality marker. We find that the total nectar sugar concentrations in general do not differ between the three plant communities studied. In contrast we find increased variability in nectar quality in the wild plant community compared to crop and weed community, which is likely explained by the increased phylogenetic diversity in this category of plants. In a second step we explore the influence of local habitat on nectar quality and its variability utilizing a detailed sunflower (Helianthus annuus L.) data set and find that geography has a small, but significant influence on these parameters. In a third step we identify crop groups (genera), which provide sub-optimal nectar resources for bees and suggest high quality alterna…
bibliographic citation: Pamminger et al. (2019) The nectar report: quantitative review of nectar sugar concentrations offered by bee visited flowers in agricultural and non-agricultural landscapes. PeerJ 7:e6329 https://doi.org/10.7717/peerj.6329
date submitted: 2018-10-15
date accepted: 2018-12-21
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pamminger
  given name: Tobias
author list: Agent
  family name: Becker
  given name: Roland
author list: Agent
  family name: Himmelreich
  given name: Sophie
author list: Agent
  family name: Schneider
  given name: Christof W.
author list: Agent
  family name: Bergtold
  given name: Matthias
doi: 10.7717/peerj.6329
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: ©2019 Pamminger et al.
attribution name: Pamminger et al.

Identification of a novel potassium channel (GiK) as a potential drug target in Giardia lamblia: Computational descriptions of binding sites
type: item
type: AcademicArticle
description: Background The protozoan Giardia lamblia is the causal agent of giardiasis, one of the main diarrheal infections worldwide. Drug resistance to common antigiardial agents and incidence of treatment failures have increased in recent years. Therefore, the search for new molecular targets for drugs against Giardia infection is essential. In protozoa, ionic channels have roles in their life cycle, growth, and stress response. Thus, they are promising targets for drug design. The strategy of ligand-protein docking has demonstrated a great potential in the discovery of new targets and structure-based drug design studies. Methods In this work, we identify and characterize a new potassium channel, GiK, in the genome of Giardia lamblia. Characterization was performed in silico. Because its crystallographic structure remains unresolved, homology modeling was used to construct the three-dimensional model for the pore domain of GiK. The docking virtual screening approach was employed to determine whether GiK is a good target for potassium channel blockers. Results The GiK sequence showed 24–50% identity and 50–90% positivity with 21 different types of potassium channels. The quality assessment and validation parameters indicated the reliability of the modeled structure of GiK. We identified 110 potassium channel blockers exhibiting high affinity toward GiK. A total of 39 of these drugs bind in three specific regions. Discussion The GiK pore signature sequence is related to the small conductance calcium-activated potassium channels (SKCa). The predicted binding of 110 potassium blockers to GiK makes this protein an attractive target for biological testing to evaluate its role in the life cycle of Giardia lamblia and potential candidate for the design of novel antigiardial drugs.
format: application/pdf
format: text/html
creator: Lissethe Palomo-Ligas
creator: Filiberto Gutiérrez-Gutiérrez
creator: Verónica Yadira Ochoa-Maganda
creator: Rafael Cortés-Zárate
creator: Claudia Lisette Charles-Niño
creator: Araceli Castillo-Romero
subject: Bioinformatics
subject: Computational Biology
subject: Parasitology
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.6430
publisher: PeerJ Inc.
rights: © 2019 Palomo-Ligas et al.
abstract: Background The protozoan Giardia lamblia is the causal agent of giardiasis, one of the main diarrheal infections worldwide. Drug resistance to common antigiardial agents and incidence of treatment failures have increased in recent years. Therefore, the search for new molecular targets for drugs against Giardia infection is essential. In protozoa, ionic channels have roles in their life cycle, growth, and stress response. Thus, they are promising targets for drug design. The strategy of ligand-protein docking has demonstrated a great potential in the discovery of new targets and structure-based drug design studies. Methods In this work, we identify and characterize a new potassium channel, GiK, in the genome of Giardia lamblia. Characterization was performed in silico. Because its crystallographic structure remains unresolved, homology modeling was used to construct the three-dimensional model for the pore domain of GiK. The docking virtual screening approach was employed to determine whether GiK is a good target for potassium channel blockers. Results The GiK sequence showed 24–50% identity and 50–90% positivity with 21 different types of potassium channels. The quality assessment and validation parameters indicated the reliability of the modeled structure of GiK. We identified 110 potassium channel blockers exhibiting high affinity toward GiK. A total of 39 of these drugs bind in three specific regions. Discussion The GiK pore signature sequence is related to the small conductance calcium-activated potassium channels (SKCa). The predicted binding of 110 potassium blockers to GiK makes this protein an attractive target for biological testing to evaluate its role in the life cycle of Giardia lamblia and potential candidate for the design of novel antigiardial drugs.
bibliographic citation: Palomo-Ligas et al. (2019) Identification of a novel potassium channel (GiK) as a potential drug target in Giardia lamblia: Computational descriptions of binding sites. PeerJ 7:e6430 https://doi.org/10.7717/peerj.6430
date submitted: 2018-07-13
date accepted: 2019-01-10
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palomo-Ligas
  given name: Lissethe
author list: Agent
  family name: Gutiérrez-Gutiérrez
  given name: Filiberto
author list: Agent
  family name: Ochoa-Maganda
  given name: Verónica Yadira
author list: Agent
  family name: Cortés-Zárate
  given name: Rafael
author list: Agent
  family name: Charles-Niño
  given name: Claudia Lisette
author list: Agent
  family name: Castillo-Romero
  given name: Araceli
doi: 10.7717/peerj.6430
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: © 2019 Palomo-Ligas et al.
attribution name: Palomo-Ligas et al.

Trends in fragmentation and connectivity of Paspalum quadrifarium grasslands in the Buenos Aires province, Argentina
type: item
type: AcademicArticle
description: Background Despite its wide distribution worldwide, only 4.6% of temperate grasslands are included within systems of protected areas. In Argentina, this situation is even more alarming: only 1.05% is protected. The study area (central area of the southern Salado River basin) has a large extent of grasslands of Paspalum quadrifarium (Pq) which has been target since the middle of the last century of a variety of agricultural management practices including fire burning for cattle grazing. Methods Five binary images of presence-absence data of Pq from a 42-year range (1974–2016) derived from a land cover change study were used as base data. Morphological Spatial Pattern Analysis (MSPA), Morphological Change Detection (MCD) and Network Connectivity Analysis (NCA) were performed to the data using Guidos Toolbox (GTB) for the estimation of habitat and connectivity dynamics of the Pq patches (fragments). Results A loss of the coverage area and habitat nuclei of this grassland was observed during the study period, with some temporal oscillation but no recovery to initial states. Additional drastic reduction in connectivity was also evident in resulting maps. The number of large Pq grassland fragments (>50 ha) decreased at beginning of the study period. Also, fragmentation measured as number of components (patches) was higher at the end of the study period. The Pq pajonal nuclei had their minimum representativeness in 2000, and recovered slightly in area in 2011, but with a significant percentage increase of smaller patches (=islets) and linear elements as bridges and branches. Large corridors (mainly edge of roads) could be observed at the end of the study period, while the total connectivity of the landscape pattern drops continuously. Statistics of links shows mean values decreasing from 1974 to 2016. On the other hand, maximum values of links decreased up to 19% in 2011, and recovered to a 54% of their original value in 2016. Discussion Pq fragmentation and habitat reduct…
format: application/pdf
format: text/html
creator: Marcelo L. Gandini
creator: Bruno D. Lara
creator: Laura B. Moreno
creator: Maria A. Cañibano
creator: Patricia A. Gandini
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6450
publisher: PeerJ Inc.
rights: © 2019 Gandini et al.
abstract: Background Despite its wide distribution worldwide, only 4.6% of temperate grasslands are included within systems of protected areas. In Argentina, this situation is even more alarming: only 1.05% is protected. The study area (central area of the southern Salado River basin) has a large extent of grasslands of Paspalum quadrifarium (Pq) which has been target since the middle of the last century of a variety of agricultural management practices including fire burning for cattle grazing. Methods Five binary images of presence-absence data of Pq from a 42-year range (1974–2016) derived from a land cover change study were used as base data. Morphological Spatial Pattern Analysis (MSPA), Morphological Change Detection (MCD) and Network Connectivity Analysis (NCA) were performed to the data using Guidos Toolbox (GTB) for the estimation of habitat and connectivity dynamics of the Pq patches (fragments). Results A loss of the coverage area and habitat nuclei of this grassland was observed during the study period, with some temporal oscillation but no recovery to initial states. Additional drastic reduction in connectivity was also evident in resulting maps. The number of large Pq grassland fragments (>50 ha) decreased at beginning of the study period. Also, fragmentation measured as number of components (patches) was higher at the end of the study period. The Pq pajonal nuclei had their minimum representativeness in 2000, and recovered slightly in area in 2011, but with a significant percentage increase of smaller patches (=islets) and linear elements as bridges and branches. Large corridors (mainly edge of roads) could be observed at the end of the study period, while the total connectivity of the landscape pattern drops continuously. Statistics of links shows mean values decreasing from 1974 to 2016. On the other hand, maximum values of links decreased up to 19% in 2011, and recovered to a 54% of their original value in 2016. Discussion Pq fragmentation and habitat reduct…
bibliographic citation: Gandini et al. (2019) Trends in fragmentation and connectivity of Paspalum quadrifarium grasslands in the Buenos Aires province, Argentina. PeerJ 7:e6450 https://doi.org/10.7717/peerj.6450
date submitted: 2018-10-08
date accepted: 2019-01-14
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gandini
  given name: Marcelo L.
author list: Agent
  family name: Lara
  given name: Bruno D.
author list: Agent
  family name: Moreno
  given name: Laura B.
author list: Agent
  family name: Cañibano
  given name: Maria A.
author list: Agent
  family name: Gandini
  given name: Patricia A.
doi: 10.7717/peerj.6450
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: ©2019 Gandini et al.
attribution name: Gandini et al.

Considerations for studying transmission of antimicrobial resistant enteric bacteria between wild birds and the environment on intensive dairy and beef cattle operations
type: item
type: AcademicArticle
description: Background Wild birds using livestock facilities for food and shelter may contribute to dissemination of enteric pathogens or antimicrobial resistant bacteria. However, drivers of microbial exchange among wildlife and livestock are not well characterized. Predisposition for acquiring and retaining environmental bacteria may vary among species because of physiologic or behavioral differences, complicating selection of a bacterial model that can accurately characterize microbial connections among hosts of interest. This study compares the prevalence and antibiotic resistance phenotypes of two potential model bacterial organisms isolated from wild birds and their environments. Methods We compared prevalence and resistance profiles of Escherichia coli and Enterococcus species isolated from environmental swabs and bird feces on a residential control site, a confinement dairy, a pasture-based beef farm, and a confinement beef farm. Results Bird feces at all sites had low-to-moderate prevalence of Escherichia coli (range: 17–47%), despite potential for exposure on farms (range: 63–97%). Few Escherichia coli were isolated from the control environment. Enterococcus faecalis was dominant in birds at both beef farms (62% and 81% of Enterococcus isolates) and low-to-moderately prevalent at the dairy and control sites (29% and 23% of isolates, respectively). Antimicrobial resistance prevalence was higher in farm samples compared to those from the residential control, but distribution of resistant isolates varied between the bacterial genera. Birds on all farms carried resistant Enterococcus at similar rates to that of the environment, but resistance was less common in bird-associated Escherichia coli despite presence of resistant isolates in the farm environment. Discussion Bacterial species studied may affect how readily bacterial exchange among populations is detected. Selection of microbial models must carefully consider both the questions being posed and how findings might i…
format: application/pdf
format: text/html
creator: Kristin Tormoehlen
creator: Yvette J. Johnson-Walker
creator: Emily W. Lankau
creator: Maung San Myint
creator: John A. Herrmann
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.6460
publisher: PeerJ Inc.
rights: © 2019 Tormoehlen et al.
abstract: Background Wild birds using livestock facilities for food and shelter may contribute to dissemination of enteric pathogens or antimicrobial resistant bacteria. However, drivers of microbial exchange among wildlife and livestock are not well characterized. Predisposition for acquiring and retaining environmental bacteria may vary among species because of physiologic or behavioral differences, complicating selection of a bacterial model that can accurately characterize microbial connections among hosts of interest. This study compares the prevalence and antibiotic resistance phenotypes of two potential model bacterial organisms isolated from wild birds and their environments. Methods We compared prevalence and resistance profiles of Escherichia coli and Enterococcus species isolated from environmental swabs and bird feces on a residential control site, a confinement dairy, a pasture-based beef farm, and a confinement beef farm. Results Bird feces at all sites had low-to-moderate prevalence of Escherichia coli (range: 17–47%), despite potential for exposure on farms (range: 63–97%). Few Escherichia coli were isolated from the control environment. Enterococcus faecalis was dominant in birds at both beef farms (62% and 81% of Enterococcus isolates) and low-to-moderately prevalent at the dairy and control sites (29% and 23% of isolates, respectively). Antimicrobial resistance prevalence was higher in farm samples compared to those from the residential control, but distribution of resistant isolates varied between the bacterial genera. Birds on all farms carried resistant Enterococcus at similar rates to that of the environment, but resistance was less common in bird-associated Escherichia coli despite presence of resistant isolates in the farm environment. Discussion Bacterial species studied may affect how readily bacterial exchange among populations is detected. Selection of microbial models must carefully consider both the questions being posed and how findings might i…
bibliographic citation: Tormoehlen et al. (2019) Considerations for studying transmission of antimicrobial resistant enteric bacteria between wild birds and the environment on intensive dairy and beef cattle operations. PeerJ 7:e6460 https://doi.org/10.7717/peerj.6460
date submitted: 2018-09-04
date accepted: 2019-01-15
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tormoehlen
  given name: Kristin
author list: Agent
  family name: Johnson-Walker
  given name: Yvette J.
author list: Agent
  family name: Lankau
  given name: Emily W.
author list: Agent
  family name: Myint
  given name: Maung San
author list: Agent
  family name: Herrmann
  given name: John A.
doi: 10.7717/peerj.6460
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: © 2019 Tormoehlen et al.
attribution name: Tormoehlen et al.

Phylogeny and circumscription of Dasyphyllum (Asteraceae: Barnadesioideae) based on molecular data with the recognition of a new genus, Archidasyphyllum
type: item
type: AcademicArticle
description: Dasyphyllum Kunth is the most diverse genus of the South American subfamily Barnadesioideae (Asteraceae), comprising 33 species that occur in tropical Andes, Atlantic Forest, Caatinga, Cerrado, and Chaco. Based on distribution, variation in anther apical appendages, and leaf venation pattern, it has traditionally been divided into two subgenera, namely, Archidasyphyllum and Dasyphyllum. Further, based on involucre size and capitula arrangement, two sections have been recognized within subgenus Dasyphyllum: Macrocephala and Microcephala (=Dasyphyllum). Here, we report a phylogenetic analysis performed to test the monophyly of Dasyphyllum and its infrageneric classification based on molecular data from three non-coding regions (trnL-trnF, psbA-trnH, and ITS), using a broad taxonomic sampling of Dasyphyllum and representatives of all nine genera of Barnadesioideae. Moreover, we used a phylogenetic framework to investigate the evolution of the morphological characters traditionally used to recognize its infrageneric groups. Our results show that neither Dasyphyllum nor its infrageneric classification are currently monophyletic. Based on phylogenetic, morphological, and biogeographical evidence, we propose a new circumscription for Dasyphyllum, elevating subgenus Archidasyphyllum to generic rank and doing away with the infrageneric classification. Ancestral states reconstruction shows that the ancestor of Dasyphyllum probably had acrodromous leaf venation, bifid anther apical appendages, involucres up to 18 mm in length, and capitula arranged in synflorescence.
format: application/pdf
format: text/html
creator: Paola de Lima Ferreira
creator: Mariana Machado Saavedra
creator: Milton Groppo
subject: Biodiversity
subject: Evolutionary Studies
subject: Molecular Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6475
publisher: PeerJ Inc.
rights: © 2019 Ferreira et al.
abstract: Dasyphyllum Kunth is the most diverse genus of the South American subfamily Barnadesioideae (Asteraceae), comprising 33 species that occur in tropical Andes, Atlantic Forest, Caatinga, Cerrado, and Chaco. Based on distribution, variation in anther apical appendages, and leaf venation pattern, it has traditionally been divided into two subgenera, namely, Archidasyphyllum and Dasyphyllum. Further, based on involucre size and capitula arrangement, two sections have been recognized within subgenus Dasyphyllum: Macrocephala and Microcephala (=Dasyphyllum). Here, we report a phylogenetic analysis performed to test the monophyly of Dasyphyllum and its infrageneric classification based on molecular data from three non-coding regions (trnL-trnF, psbA-trnH, and ITS), using a broad taxonomic sampling of Dasyphyllum and representatives of all nine genera of Barnadesioideae. Moreover, we used a phylogenetic framework to investigate the evolution of the morphological characters traditionally used to recognize its infrageneric groups. Our results show that neither Dasyphyllum nor its infrageneric classification are currently monophyletic. Based on phylogenetic, morphological, and biogeographical evidence, we propose a new circumscription for Dasyphyllum, elevating subgenus Archidasyphyllum to generic rank and doing away with the infrageneric classification. Ancestral states reconstruction shows that the ancestor of Dasyphyllum probably had acrodromous leaf venation, bifid anther apical appendages, involucres up to 18 mm in length, and capitula arranged in synflorescence.
bibliographic citation: Ferreira et al. (2019) Phylogeny and circumscription of Dasyphyllum (Asteraceae: Barnadesioideae) based on molecular data with the recognition of a new genus, Archidasyphyllum. PeerJ 7:e6475 https://doi.org/10.7717/peerj.6475
date submitted: 2018-10-11
date accepted: 2019-01-17
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ferreira
  given name: Paola de Lima
author list: Agent
  family name: Saavedra
  given name: Mariana Machado
author list: Agent
  family name: Groppo
  given name: Milton
doi: 10.7717/peerj.6475
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: © 2019 Ferreira et al.
attribution name: Ferreira et al.

Change of soil microbial community under long-term fertilization in a reclaimed sandy agricultural ecosystem
type: item
type: AcademicArticle
description: The importance of soil microbial flora in agro-ecosystems is well known, but there is limited understanding of the effects of long-term fertilization on soil microbial community succession in different farming management practices. Here, we report the responses of soil microbial community structure, abundance and activity to chemical (CF) and organic fertilization (OF) treatments in a sandy agricultural system of wheat-maize rotation over a 17-year period. Illumina MiSeq sequencing showed that the microbial community diversity and richness showed no significant changes in bacteria but decreased in fungi under both CF and OF treatments. The dominant species showing significant differences between fertilization regimes were Actinobacteria, Acidobacteria and Ascomycota at the phylum level, as well as some unclassified genera of other phyla at the genus level. As expected, soil organic matter content, nutrient element concentrations and bacterial abundance were enhanced by both types of fertilization, especially in OF, but fungal abundance was inhibited by OF. Redundancy analysis revealed that soil enzyme activities were closely related to both bacterial and fungal communities, and the soil nutrient, texture and pH value together determined the community structures. Bacterial abundance might be the primary driver of crop yield, and soil enzyme activities may reflect crop yield. Our results suggest a relatively permanent response of soil microbial communities to the long-term fertilization regimes in a reclaimed sandy agro-ecosystem from a mobile dune, and indicate that the appropriate dosage of chemical fertilizers is beneficial to sandy soil sustainability.
format: application/pdf
format: text/html
creator: Zengru Wang
creator: Yubing Liu
creator: Lina Zhao
creator: Wenli Zhang
creator: Lichao Liu
subject: Microbiology
description: doi:10.7717/peerj.6497
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: The importance of soil microbial flora in agro-ecosystems is well known, but there is limited understanding of the effects of long-term fertilization on soil microbial community succession in different farming management practices. Here, we report the responses of soil microbial community structure, abundance and activity to chemical (CF) and organic fertilization (OF) treatments in a sandy agricultural system of wheat-maize rotation over a 17-year period. Illumina MiSeq sequencing showed that the microbial community diversity and richness showed no significant changes in bacteria but decreased in fungi under both CF and OF treatments. The dominant species showing significant differences between fertilization regimes were Actinobacteria, Acidobacteria and Ascomycota at the phylum level, as well as some unclassified genera of other phyla at the genus level. As expected, soil organic matter content, nutrient element concentrations and bacterial abundance were enhanced by both types of fertilization, especially in OF, but fungal abundance was inhibited by OF. Redundancy analysis revealed that soil enzyme activities were closely related to both bacterial and fungal communities, and the soil nutrient, texture and pH value together determined the community structures. Bacterial abundance might be the primary driver of crop yield, and soil enzyme activities may reflect crop yield. Our results suggest a relatively permanent response of soil microbial communities to the long-term fertilization regimes in a reclaimed sandy agro-ecosystem from a mobile dune, and indicate that the appropriate dosage of chemical fertilizers is beneficial to sandy soil sustainability.
bibliographic citation: Wang et al. (2019) Change of soil microbial community under long-term fertilization in a reclaimed sandy agricultural ecosystem. PeerJ 7:e6497 https://doi.org/10.7717/peerj.6497
date submitted: 2018-11-06
date accepted: 2019-01-21
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zengru
author list: Agent
  family name: Liu
  given name: Yubing
author list: Agent
  family name: Zhao
  given name: Lina
author list: Agent
  family name: Zhang
  given name: Wenli
author list: Agent
  family name: Liu
  given name: Lichao
doi: 10.7717/peerj.6497
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: ©2019 Wang et al.
attribution name: Wang et al.

TRPV1 protects renal ischemia-reperfusion injury in diet-induced obese mice by enhancing CGRP release and increasing renal blood flow
type: item
type: AcademicArticle
description: Background Obesity is a major risk factor for end-stage renal disease. Using transient receptor potential vanilloid 1 knockout (TRPV1−/−) mice, we tested the hypothesis that TRPV1 protects against obesity-induced exacerbation of renal ischemia-reperfusion (I/R) injury. Methods TRPV1−/− and wild-type (WT) mice were fed a chow or Western diet (WD) for 22–23 weeks. After that, mice were subjected to renal I/R injury, and renal cortical blood flow (CBF) and medullary blood flow (MBF) were measured. Results The Western diet significantly increased body weight and fasting blood glucose levels in both TRPV1−/− and WT mice. WD-induced impairment of glucose tolerance was worsened in TRPV1−/− mice compared with WT mice. WD intake prolonged the time required to reach peak reperfusion in the cortex and medulla (both P < 0.05), decreased the recovery rate of CBF (P < 0.05) and MBF (P < 0.05), and increased blood urea nitrogen, plasma creatinine, and urinary 8-isoprostane levels after I/R in both mouse strains, with greater effects in TRPV1−/− mice (all P < 0.05). Renal I/R increased calcitonin gene-related peptide (CGRP) release in WT but not in TRPV1−/− mice, and WD attenuated CGRP release in WT mice. Moreover, blockade of CGRP receptors impaired renal regional blood flow and renal function in renal I/R injured WT mice. Conclusion These results indicate that TRPV1 plays a protective role in WD-induced exacerbation of renal I/R injury probably through enhancing CGRP release and increasing renal blood flow.
format: application/pdf
format: text/html
creator: Beihua Zhong
creator: Shuangtao Ma
creator: Donna H. Wang
subject: Anatomy and Physiology
subject: Cardiology
subject: Diabetes and Endocrinology
subject: Nephrology
subject: Pharmacology
description: doi:10.7717/peerj.6505
publisher: PeerJ Inc.
rights: © 2019 Zhong et al.
abstract: Background Obesity is a major risk factor for end-stage renal disease. Using transient receptor potential vanilloid 1 knockout (TRPV1−/−) mice, we tested the hypothesis that TRPV1 protects against obesity-induced exacerbation of renal ischemia-reperfusion (I/R) injury. Methods TRPV1−/− and wild-type (WT) mice were fed a chow or Western diet (WD) for 22–23 weeks. After that, mice were subjected to renal I/R injury, and renal cortical blood flow (CBF) and medullary blood flow (MBF) were measured. Results The Western diet significantly increased body weight and fasting blood glucose levels in both TRPV1−/− and WT mice. WD-induced impairment of glucose tolerance was worsened in TRPV1−/− mice compared with WT mice. WD intake prolonged the time required to reach peak reperfusion in the cortex and medulla (both P < 0.05), decreased the recovery rate of CBF (P < 0.05) and MBF (P < 0.05), and increased blood urea nitrogen, plasma creatinine, and urinary 8-isoprostane levels after I/R in both mouse strains, with greater effects in TRPV1−/− mice (all P < 0.05). Renal I/R increased calcitonin gene-related peptide (CGRP) release in WT but not in TRPV1−/− mice, and WD attenuated CGRP release in WT mice. Moreover, blockade of CGRP receptors impaired renal regional blood flow and renal function in renal I/R injured WT mice. Conclusion These results indicate that TRPV1 plays a protective role in WD-induced exacerbation of renal I/R injury probably through enhancing CGRP release and increasing renal blood flow.
bibliographic citation: Zhong et al. (2019) TRPV1 protects renal ischemia-reperfusion injury in diet-induced obese mice by enhancing CGRP release and increasing renal blood flow. PeerJ 7:e6505 https://doi.org/10.7717/peerj.6505
date submitted: 2018-07-18
date accepted: 2019-01-23
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Beihua
author list: Agent
  family name: Ma
  given name: Shuangtao
author list: Agent
  family name: Wang
  given name: Donna H.
doi: 10.7717/peerj.6505
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: © 2019 Zhong et al.
attribution name: Zhong et al.

Revision of the Afro-Madagascan genus Costularia (Schoeneae, Cyperaceae): infrageneric relationships and species delimitation
type: item
type: AcademicArticle
description: A recent molecular phylogenetic study revealed four distinct evolutionary lineages in the genus Costularia s.l. (Schoeneae, Cyperaceae, Poales). Two lineages are part of the Oreobolus clade of tribe Schoeneae: the first being a much-reduced genus Costularia s.s., and the second a lineage endemic to New Caledonia for which a new genus Chamaedendron was erected. The other two lineages were shown to be part of the Tricostularia clade of tribe Schoeneae. Based on morphological and molecular data, the genus Costularia is here redelimited to represent a monophyletic entity including 15 species, which is restricted in distribution to southeastern Africa (Malawi, Mozambique, South Africa, Swaziland, Zimbabwe), Madagascar, the Mascarenes (La Réunion, Mauritius), and the Seychelles (Mahé). Molecular phylogenetic data based on two nuclear markers (ETS, ITS) and a chloroplast marker (trnL-F) resolve the studied taxa as monophyletic where multiple accessions could be included (except for Costularia laxa and Costularia purpurea, which are now considered conspecific), and indicate that the genus dispersed once to Africa, twice to the Mascarenes, and once to the Seychelles. Two endemic species from Madagascar are here described and illustrated as new to science, as is one additional species endemic to La Réunion. Two taxa previously accepted as varieties of Costularia pantopoda are here recognised at species level (Costularia baronii and Costularia robusta). We provide a taxonomic revision including an identification key, species descriptions and illustrations, distribution maps and assessments of conservation status for all species.
format: application/pdf
format: text/html
creator: Isabel Larridon
creator: Linah Rabarivola
creator: Martin Xanthos
creator: A. Muthama Muasya
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6528
publisher: PeerJ Inc.
rights: © 2019 Larridon et al.
abstract: A recent molecular phylogenetic study revealed four distinct evolutionary lineages in the genus Costularia s.l. (Schoeneae, Cyperaceae, Poales). Two lineages are part of the Oreobolus clade of tribe Schoeneae: the first being a much-reduced genus Costularia s.s., and the second a lineage endemic to New Caledonia for which a new genus Chamaedendron was erected. The other two lineages were shown to be part of the Tricostularia clade of tribe Schoeneae. Based on morphological and molecular data, the genus Costularia is here redelimited to represent a monophyletic entity including 15 species, which is restricted in distribution to southeastern Africa (Malawi, Mozambique, South Africa, Swaziland, Zimbabwe), Madagascar, the Mascarenes (La Réunion, Mauritius), and the Seychelles (Mahé). Molecular phylogenetic data based on two nuclear markers (ETS, ITS) and a chloroplast marker (trnL-F) resolve the studied taxa as monophyletic where multiple accessions could be included (except for Costularia laxa and Costularia purpurea, which are now considered conspecific), and indicate that the genus dispersed once to Africa, twice to the Mascarenes, and once to the Seychelles. Two endemic species from Madagascar are here described and illustrated as new to science, as is one additional species endemic to La Réunion. Two taxa previously accepted as varieties of Costularia pantopoda are here recognised at species level (Costularia baronii and Costularia robusta). We provide a taxonomic revision including an identification key, species descriptions and illustrations, distribution maps and assessments of conservation status for all species.
bibliographic citation: Larridon et al. (2019) Revision of the Afro-Madagascan genus Costularia (Schoeneae, Cyperaceae): infrageneric relationships and species delimitation. PeerJ 7:e6528 https://doi.org/10.7717/peerj.6528
date submitted: 2018-11-30
date accepted: 2019-01-28
issued: 2019-02-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Larridon
  given name: Isabel
author list: Agent
  family name: Rabarivola
  given name: Linah
author list: Agent
  family name: Xanthos
  given name: Martin
author list: Agent
  family name: Muasya
  given name: A. Muthama
doi: 10.7717/peerj.6528
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-27
copyright: © 2019 Larridon et al.
attribution name: Larridon et al.

Validation of reference genes for gene expression studies in tartary buckwheat (Fagopyrum tataricum Gaertn.) using quantitative real-time PCR
type: item
type: AcademicArticle
description: Quantitative real-time reverse transcriptase polymerase chain reaction is a sensitive technique for quantifying gene expression levels. By implementing three distinct algorithms (geNorm, normFinder and BestKeeper), we have validated the stability of the expression of seven candidate reference genes in tartary buckwheat, including FtSAND, FtCACS, FtExpressed1, FtGAPDH, FtActin, FtEF-1a and FtH3. In this study, the results indicated that FtCACS and FtSAND were the best reference genes for ‘abiotic cotyledons’, FtExpressed1 and FtEF-1α were the best reference genes for aluminium treatment, FtCACS and FtExpressed1 performed the best for the immature seed stage, FtCACS was best for the abiotic treatment, and FtH3 appeared to be the most suitable reference gene for the abiotic treatment in hypocotyls and all samples in this study. In contrast, FtActin and FtGAPDH are unsuitable genes. Our findings offer additional stable reference genes for gene expression research on tartary buckwheat at the immature seed stage and under abiotic treatment.
format: application/pdf
format: text/html
creator: Chenglei Li
creator: Haixia Zhao
creator: Maofei Li
creator: Panfeng Yao
creator: Qingqing Li
creator: Xuerong Zhao
creator: Anhu Wang
creator: Hui Chen
creator: Zizhong Tang
creator: Tongliang Bu
creator: Qi Wu
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.6522
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Quantitative real-time reverse transcriptase polymerase chain reaction is a sensitive technique for quantifying gene expression levels. By implementing three distinct algorithms (geNorm, normFinder and BestKeeper), we have validated the stability of the expression of seven candidate reference genes in tartary buckwheat, including FtSAND, FtCACS, FtExpressed1, FtGAPDH, FtActin, FtEF-1a and FtH3. In this study, the results indicated that FtCACS and FtSAND were the best reference genes for ‘abiotic cotyledons’, FtExpressed1 and FtEF-1α were the best reference genes for aluminium treatment, FtCACS and FtExpressed1 performed the best for the immature seed stage, FtCACS was best for the abiotic treatment, and FtH3 appeared to be the most suitable reference gene for the abiotic treatment in hypocotyls and all samples in this study. In contrast, FtActin and FtGAPDH are unsuitable genes. Our findings offer additional stable reference genes for gene expression research on tartary buckwheat at the immature seed stage and under abiotic treatment.
bibliographic citation: Li et al. (2019) Validation of reference genes for gene expression studies in tartary buckwheat (Fagopyrum tataricum Gaertn.) using quantitative real-time PCR. PeerJ 7:e6522 https://doi.org/10.7717/peerj.6522
date submitted: 2018-11-19
date accepted: 2019-01-27
issued: 2019-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Chenglei
author list: Agent
  family name: Zhao
  given name: Haixia
author list: Agent
  family name: Li
  given name: Maofei
author list: Agent
  family name: Yao
  given name: Panfeng
author list: Agent
  family name: Li
  given name: Qingqing
author list: Agent
  family name: Zhao
  given name: Xuerong
author list: Agent
  family name: Wang
  given name: Anhu
author list: Agent
  family name: Chen
  given name: Hui
author list: Agent
  family name: Tang
  given name: Zizhong
author list: Agent
  family name: Bu
  given name: Tongliang
author list: Agent
  family name: Wu
  given name: Qi
doi: 10.7717/peerj.6522
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-26
copyright: © 2019 Li et al.
attribution name: Li et al.

A new glassfrog (Centrolenidae) from the Chocó-Andean Río Manduriacu Reserve, Ecuador, endangered by mining
type: item
type: AcademicArticle
description: We describe a new glassfrog from Río Manduriacu Reserve, Imbabura Province, on the Pacific slopes of the Ecuadorian Andes. The new species can be distinguished from most other glassfrogs by having numerous yellow spots on the dorsum and lacking membranes among fingers. Both morphological and molecular data support the placement of the species in the genus Nymphargus. We present a new mitochondrial phylogeny of Nymphargus and discuss the speciation patterns of this genus; most importantly, recent speciation events seem to result from the effect of the linearity of the Andes. Finally, although the new species occurs within a private reserve, it is seriously endangered by mining activities; thus, following IUCN criteria, we consider the new species as Critically Endangered.
format: application/pdf
format: text/html
creator: Juan M. Guayasamin
creator: Diego F. Cisneros-Heredia
creator: José Vieira
creator: Sebastián Kohn
creator: Gabriela Gavilanes
creator: Ryan L. Lynch
creator: Paul S. Hamilton
creator: Ross J. Maynard
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6400
publisher: PeerJ Inc.
rights: © 2019 Guayasamin et al.
abstract: We describe a new glassfrog from Río Manduriacu Reserve, Imbabura Province, on the Pacific slopes of the Ecuadorian Andes. The new species can be distinguished from most other glassfrogs by having numerous yellow spots on the dorsum and lacking membranes among fingers. Both morphological and molecular data support the placement of the species in the genus Nymphargus. We present a new mitochondrial phylogeny of Nymphargus and discuss the speciation patterns of this genus; most importantly, recent speciation events seem to result from the effect of the linearity of the Andes. Finally, although the new species occurs within a private reserve, it is seriously endangered by mining activities; thus, following IUCN criteria, we consider the new species as Critically Endangered.
bibliographic citation: Guayasamin et al. (2019) A new glassfrog (Centrolenidae) from the Chocó-Andean Río Manduriacu Reserve, Ecuador, endangered by mining. PeerJ 7:e6400 https://doi.org/10.7717/peerj.6400
date submitted: 2018-10-02
date accepted: 2019-01-06
issued: 2019-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guayasamin
  given name: Juan M.
author list: Agent
  family name: Cisneros-Heredia
  given name: Diego F.
author list: Agent
  family name: Vieira
  given name: José
author list: Agent
  family name: Kohn
  given name: Sebastián
author list: Agent
  family name: Gavilanes
  given name: Gabriela
author list: Agent
  family name: Lynch
  given name: Ryan L.
author list: Agent
  family name: Hamilton
  given name: Paul S.
author list: Agent
  family name: Maynard
  given name: Ross J.
doi: 10.7717/peerj.6400
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-26
copyright: © 2019 Guayasamin et al.
attribution name: Guayasamin et al.

Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures in Sulfolobus acidocaldarius
type: item
type: AcademicArticle
description: In Archaea and Bacteria, gene expression is tightly regulated in response to environmental stimuli. In the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius nutrient limitation induces expression of the archaellum, the archaeal motility structure. This expression is orchestrated by a complex hierarchical network of positive and negative regulators—the archaellum regulatory network (arn). The membrane-bound one-component system ArnR and its paralog ArnR1 were recently described as main activators of archaellum expression in S. acidocaldarius. They regulate gene expression of the archaellum operon by targeting the promoter of flaB, encoding the archaellum filament protein. Here we describe a strategy for the isolation and biochemical characterization of these two archaellum regulators. Both regulators are capable of forming oligomers and are phosphorylated by the Ser/Thr kinase ArnC. Apart from binding to pflaB, ArnR but not ArnR1 bound to promoter sequences of aapF and upsX, which encode components of the archaeal adhesive pilus and UV-inducible pili system, demonstrating a regulatory connection between different surface appendages of S. acidocaldarius.
format: application/pdf
format: text/html
creator: Lisa Franziska Bischof
creator: Maria Florencia Haurat
creator: Sonja-Verena Albers
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6459
publisher: PeerJ Inc.
rights: © 2019 Bischof et al.
abstract: In Archaea and Bacteria, gene expression is tightly regulated in response to environmental stimuli. In the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius nutrient limitation induces expression of the archaellum, the archaeal motility structure. This expression is orchestrated by a complex hierarchical network of positive and negative regulators—the archaellum regulatory network (arn). The membrane-bound one-component system ArnR and its paralog ArnR1 were recently described as main activators of archaellum expression in S. acidocaldarius. They regulate gene expression of the archaellum operon by targeting the promoter of flaB, encoding the archaellum filament protein. Here we describe a strategy for the isolation and biochemical characterization of these two archaellum regulators. Both regulators are capable of forming oligomers and are phosphorylated by the Ser/Thr kinase ArnC. Apart from binding to pflaB, ArnR but not ArnR1 bound to promoter sequences of aapF and upsX, which encode components of the archaeal adhesive pilus and UV-inducible pili system, demonstrating a regulatory connection between different surface appendages of S. acidocaldarius.
bibliographic citation: Bischof et al. (2019) Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures in Sulfolobus acidocaldarius. PeerJ 7:e6459 https://doi.org/10.7717/peerj.6459
date submitted: 2018-11-09
date accepted: 2019-01-15
issued: 2019-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bischof
  given name: Lisa Franziska
author list: Agent
  family name: Haurat
  given name: Maria Florencia
author list: Agent
  family name: Albers
  given name: Sonja-Verena
doi: 10.7717/peerj.6459
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-26
copyright: © 2019 Bischof et al.
attribution name: Bischof et al.

Effects of stigmata maydis on the methicillin resistant Staphylococus aureus biofilm formation
type: item
type: AcademicArticle
description: Background Mastitis is an inflammatory reaction of the mammary gland tissue, which causes huge losses to dairy farms throughout the world. Staphylococcus aureus is the most frequent agent associated with this disease. Staphylococcus aureus isolates, which have the ability to form biofilms, usually lead to chronic mastitis in dairy cows. Moreover, methicillin resistance of the bacteria further complicates the treatment of this disease. Stigmata maydis (corn silk), a traditional Chinese medicine, possess many biological activities. Methods In this study, we performed antibacterial activity assays, biofilm formation assays and real-time reverse transcription PCR experiments to investigate the effect of stigmata maydis (corn silk) on biofilm formation and vancomycin susceptibility of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from dairy cows with mastitis. Results In this study, the aqueous extracts of stigmata maydis inhibited the biofilm formation ability of MRSA strains and increased the vancomycin susceptibility of the strains under biofilm-cultured conditions. Conclusion This study proves that the aqueous extracts of stigmata maydis inhibit the biofilm formation ability of MRSA strains and increase the vancomycin susceptibility of the MRSA strains under biofilm-cultured conditions.
format: application/pdf
format: text/html
creator: Fei Shang
creator: Long Li
creator: Lumin Yu
creator: Jingtian Ni
creator: Xiaolin Chen
creator: Ting Xue
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6461
publisher: PeerJ Inc.
rights: © 2019 Shang et al.
abstract: Background Mastitis is an inflammatory reaction of the mammary gland tissue, which causes huge losses to dairy farms throughout the world. Staphylococcus aureus is the most frequent agent associated with this disease. Staphylococcus aureus isolates, which have the ability to form biofilms, usually lead to chronic mastitis in dairy cows. Moreover, methicillin resistance of the bacteria further complicates the treatment of this disease. Stigmata maydis (corn silk), a traditional Chinese medicine, possess many biological activities. Methods In this study, we performed antibacterial activity assays, biofilm formation assays and real-time reverse transcription PCR experiments to investigate the effect of stigmata maydis (corn silk) on biofilm formation and vancomycin susceptibility of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from dairy cows with mastitis. Results In this study, the aqueous extracts of stigmata maydis inhibited the biofilm formation ability of MRSA strains and increased the vancomycin susceptibility of the strains under biofilm-cultured conditions. Conclusion This study proves that the aqueous extracts of stigmata maydis inhibit the biofilm formation ability of MRSA strains and increase the vancomycin susceptibility of the MRSA strains under biofilm-cultured conditions.
bibliographic citation: Shang et al. (2019) Effects of stigmata maydis on the methicillin resistant Staphylococus aureus biofilm formation. PeerJ 7:e6461 https://doi.org/10.7717/peerj.6461
date submitted: 2018-08-31
date accepted: 2019-01-15
issued: 2019-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shang
  given name: Fei
author list: Agent
  family name: Li
  given name: Long
author list: Agent
  family name: Yu
  given name: Lumin
author list: Agent
  family name: Ni
  given name: Jingtian
author list: Agent
  family name: Chen
  given name: Xiaolin
author list: Agent
  family name: Xue
  given name: Ting
doi: 10.7717/peerj.6461
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-26
copyright: © 2019 Shang et al.
attribution name: Shang et al.

Optimizing plant density and nitrogen application to manipulate tiller growth and increase grain yield and nitrogen-use efficiency in winter wheat
type: item
type: AcademicArticle
description: The growth of wheat tillers and plant nitrogen-use efficiency (NUE) will gradually deteriorate in response to high plant density and over-application of N. Therefore, in this study, a 2-year field study was conducted with three levels of plant densities (75 ×104plants ha−1, D1; 300 ×104plants ha−1, D2; 525 ×104plants ha−1, D3) and three levels of N application rates (120 kg N ha−1, N1; 240 kg N ha−1, N2; 360 kg N ha−1, N3) to determine how to optimize plant density and N application to regulate tiller growth and to assess the contribution of such measures to enhancing grain yield (GY) and NUE. The results indicated that an increase in plant density significantly increased the number of superior tillers and the number of spikes per m2(SN), resulting in a higher GY and higher partial factor productivity of applied N (PFPN). However, there was no significant difference in GY and PFPN between plant densities D2 and D3. Increasing the N application rate significantly increased the vascular bundle number (NVB) and area (AVB), however, excess N application (N3) did not significantly improve these parameters. N application significantly increased GY, whereas there was a significant decrease in PFPN in response to an increase in N application rate. The two years results suggested that increasing the plant density (from 75 ×104plants ha−1to 336 ×104plants ha−1) in conjunction with the application of 290 kg N ha−1N will maximize GY, and also increase PFPN(39.7 kg kg−1), compared with the application of 360 kg N ha−1N. Therefore, an appropriate combination of increased planting density with reduced N application could regulate tiller number and favor the superior tiller group, to produce wheat populations with enhanced yield and NUE.
format: application/pdf
format: text/html
creator: Dongqing Yang
creator: Tie Cai
creator: Yongli Luo
creator: Zhenlin Wang
subject: Agricultural Science
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.6484
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: The growth of wheat tillers and plant nitrogen-use efficiency (NUE) will gradually deteriorate in response to high plant density and over-application of N. Therefore, in this study, a 2-year field study was conducted with three levels of plant densities (75 ×104plants ha−1, D1; 300 ×104plants ha−1, D2; 525 ×104plants ha−1, D3) and three levels of N application rates (120 kg N ha−1, N1; 240 kg N ha−1, N2; 360 kg N ha−1, N3) to determine how to optimize plant density and N application to regulate tiller growth and to assess the contribution of such measures to enhancing grain yield (GY) and NUE. The results indicated that an increase in plant density significantly increased the number of superior tillers and the number of spikes per m2(SN), resulting in a higher GY and higher partial factor productivity of applied N (PFPN). However, there was no significant difference in GY and PFPN between plant densities D2 and D3. Increasing the N application rate significantly increased the vascular bundle number (NVB) and area (AVB), however, excess N application (N3) did not significantly improve these parameters. N application significantly increased GY, whereas there was a significant decrease in PFPN in response to an increase in N application rate. The two years results suggested that increasing the plant density (from 75 ×104plants ha−1to 336 ×104plants ha−1) in conjunction with the application of 290 kg N ha−1N will maximize GY, and also increase PFPN(39.7 kg kg−1), compared with the application of 360 kg N ha−1N. Therefore, an appropriate combination of increased planting density with reduced N application could regulate tiller number and favor the superior tiller group, to produce wheat populations with enhanced yield and NUE.
bibliographic citation: Yang et al. (2019) Optimizing plant density and nitrogen application to manipulate tiller growth and increase grain yield and nitrogen-use efficiency in winter wheat. PeerJ 7:e6484 https://doi.org/10.7717/peerj.6484
date submitted: 2018-08-28
date accepted: 2019-01-20
issued: 2019-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Dongqing
author list: Agent
  family name: Cai
  given name: Tie
author list: Agent
  family name: Luo
  given name: Yongli
author list: Agent
  family name: Wang
  given name: Zhenlin
doi: 10.7717/peerj.6484
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-26
copyright: ©2019 Yang et al.
attribution name: Yang et al.

Heat stress compromises epithelial integrity in the coral, Acropora hyacinthus
type: item
type: AcademicArticle
description: It is well understood that heat stress causes bleaching in corals. Much work has focused on the way heat stress disrupts corals’ symbiotic relationship with endosymbiotic algal dinoflagellate, Symbiodiniaceae, a process called bleaching. However, the damage to the coral tissue that occurs during the bleaching process and, importantly, the factors that contribute to subsequent recovery, are not well understood. I hypothesize that the host tissue damage created by heat stress initiates cascades of wound healing factors that maintain epithelial integrity. These factors may be found to contribute to the coral’s potential capacity to recover. In this study, I present evidence that heat stress causes damage to the coral host tissue and that collagen is present in the gastrodermis of heat-stressed corals. I found that, during the early stages of bleaching, an important transcription factor for wound healing, Grainyhead, is expressed throughout the gastrodermis, where the cellular and tissue rearrangements occur. Lastly, using phylogenetics, I found that cnidarian Grainyhead proteins evolved three distinct groups and that evolution of this protein family likely happened within each taxonomic group. These findings have important implications for our study of coral resiliency in the face of climate change.
format: application/pdf
format: text/html
creator: Nikki Traylor-Knowles
subject: Marine Biology
subject: Histology
description: doi:10.7717/peerj.6510
publisher: PeerJ Inc.
rights: © 2019 Traylor-Knowles
abstract: It is well understood that heat stress causes bleaching in corals. Much work has focused on the way heat stress disrupts corals’ symbiotic relationship with endosymbiotic algal dinoflagellate, Symbiodiniaceae, a process called bleaching. However, the damage to the coral tissue that occurs during the bleaching process and, importantly, the factors that contribute to subsequent recovery, are not well understood. I hypothesize that the host tissue damage created by heat stress initiates cascades of wound healing factors that maintain epithelial integrity. These factors may be found to contribute to the coral’s potential capacity to recover. In this study, I present evidence that heat stress causes damage to the coral host tissue and that collagen is present in the gastrodermis of heat-stressed corals. I found that, during the early stages of bleaching, an important transcription factor for wound healing, Grainyhead, is expressed throughout the gastrodermis, where the cellular and tissue rearrangements occur. Lastly, using phylogenetics, I found that cnidarian Grainyhead proteins evolved three distinct groups and that evolution of this protein family likely happened within each taxonomic group. These findings have important implications for our study of coral resiliency in the face of climate change.
bibliographic citation: Traylor-Knowles (2019) Heat stress compromises epithelial integrity in the coral, Acropora hyacinthus. PeerJ 7:e6510 https://doi.org/10.7717/peerj.6510
date submitted: 2018-08-17
date accepted: 2019-01-23
issued: 2019-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Traylor-Knowles
  given name: Nikki
doi: 10.7717/peerj.6510
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-26
copyright: ©2019 Traylor-Knowles
attribution name: Traylor-Knowles

Psychological flexibility and attitudes toward evidence-based interventions by amyotrophic lateral sclerosis patients
type: item
type: AcademicArticle
description: Objective Declining a percutaneous endoscopic gastrostomy (PEG) or non-invasive ventilation (NIV) by people with amyotrophic lateral sclerosis (ALS) is often contrary to advice provided by health-care-professionals guided by evidence-based principles. This study proposes relational frame theory (RFT) to offer a viable explanation of this phenomenon. Design A total of 35 people (14 female, 21 male) aged between 34 and 73 years, with ALS, participated in this cross-sectional research. Main outcome measures This research examined the predictive power and interaction effect of psychological flexibility (the fundamental construct of RFT) and psychological well-being on attitudes toward intervention options. Results Participants with high psychological flexibility reported lower depression, anxiety, and stress, and higher quality of life. In addition, psychological flexibility was predictive of a participant’s understanding and acceptance of a PEG as an intervention option. Psychological flexibility was not found to be a significant predictor of understanding and acceptance of NIV. Conclusion Although the criterion measure had not been piloted or validated outside of the current study and asks about expected rather than actual acceptance, findings suggest that applied RFT may be helpful for clients with ALS.
format: application/pdf
format: text/html
creator: James R. Pearlman
creator: Einar B. Thorsteinsson
subject: Drugs and Devices
subject: Evidence Based Medicine
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6527
publisher: PeerJ Inc.
rights: © 2019 Pearlman and Thorsteinsson
abstract: Objective Declining a percutaneous endoscopic gastrostomy (PEG) or non-invasive ventilation (NIV) by people with amyotrophic lateral sclerosis (ALS) is often contrary to advice provided by health-care-professionals guided by evidence-based principles. This study proposes relational frame theory (RFT) to offer a viable explanation of this phenomenon. Design A total of 35 people (14 female, 21 male) aged between 34 and 73 years, with ALS, participated in this cross-sectional research. Main outcome measures This research examined the predictive power and interaction effect of psychological flexibility (the fundamental construct of RFT) and psychological well-being on attitudes toward intervention options. Results Participants with high psychological flexibility reported lower depression, anxiety, and stress, and higher quality of life. In addition, psychological flexibility was predictive of a participant’s understanding and acceptance of a PEG as an intervention option. Psychological flexibility was not found to be a significant predictor of understanding and acceptance of NIV. Conclusion Although the criterion measure had not been piloted or validated outside of the current study and asks about expected rather than actual acceptance, findings suggest that applied RFT may be helpful for clients with ALS.
bibliographic citation: Pearlman et al. (2019) Psychological flexibility and attitudes toward evidence-based interventions by amyotrophic lateral sclerosis patients. PeerJ 7:e6527 https://doi.org/10.7717/peerj.6527
date submitted: 2018-06-29
date accepted: 2019-01-25
issued: 2019-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pearlman
  given name: James R.
author list: Agent
  family name: Thorsteinsson
  given name: Einar B.
doi: 10.7717/peerj.6527
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-26
copyright: © 2019 Pearlman and Thorsteinsson
attribution name: Pearlman and Thorsteinsson

Genetic diversity of Simao pine in China revealed by SRAP markers
type: item
type: AcademicArticle
description: Background Simao pine (Pinus kesiya Royle ex Gordon var. langbianensis (A. Chev.) Gaussen) is one of the most important tree species in the production of timber and resin in China. However, the genetic diversity of the natural populations has not been assessed to date. In this study, sequence related amplified polymorphism (SRAP) markers were used to investigate the genetic composition of natural Simao pine populations. Method The SRAP markers were applied and their efficiency was compared using various statistical multivariate methods, including analysis molecular of variance (AMOVA), the unweighted pair group method with arithmetic mean (UPGMA), and Principal coordinate analysis (PCoA). Results The 11 populations revealed a high level of genetic diversity (PPB = 95.45%, H = 0.4567, I = 0.6484) at the species level. A moderately low level of genetic differentiation (Gst = 0.1701), and a slightly high level of gene flow (Nm = 2.4403) were observed among populations using AMOVA. Eleven populations of Simao pine were gathered into four distinct clusters based on molecular data, and the results of UPGMA and PCoA also illustrated that assignment of populations is not completely consistent with geographic origin. The Mantel test revealed there was no significant correlation between geographic and genetic distance (r = 0.241, p = 0.090). Discussion The SRAP markers were very effective in the assessment of genetic diversity in Simao pine. Simao pine populations display high levels of genetic diversity and low or moderate levels of genetic differentiation due to frequent gene exchange among populations. The low genetic differentiation among populations implied that conservation efforts should aim to preserve all remaining natural populations of this species. The information derived from this study is useful when identifying populations and categorizing their population origins, making possible the design of long term management program such as genetic improvement by selecti…
format: application/pdf
format: text/html
creator: Dawei Wang
creator: Bingqi Shen
creator: Hede Gong
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6529
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Simao pine (Pinus kesiya Royle ex Gordon var. langbianensis (A. Chev.) Gaussen) is one of the most important tree species in the production of timber and resin in China. However, the genetic diversity of the natural populations has not been assessed to date. In this study, sequence related amplified polymorphism (SRAP) markers were used to investigate the genetic composition of natural Simao pine populations. Method The SRAP markers were applied and their efficiency was compared using various statistical multivariate methods, including analysis molecular of variance (AMOVA), the unweighted pair group method with arithmetic mean (UPGMA), and Principal coordinate analysis (PCoA). Results The 11 populations revealed a high level of genetic diversity (PPB = 95.45%, H = 0.4567, I = 0.6484) at the species level. A moderately low level of genetic differentiation (Gst = 0.1701), and a slightly high level of gene flow (Nm = 2.4403) were observed among populations using AMOVA. Eleven populations of Simao pine were gathered into four distinct clusters based on molecular data, and the results of UPGMA and PCoA also illustrated that assignment of populations is not completely consistent with geographic origin. The Mantel test revealed there was no significant correlation between geographic and genetic distance (r = 0.241, p = 0.090). Discussion The SRAP markers were very effective in the assessment of genetic diversity in Simao pine. Simao pine populations display high levels of genetic diversity and low or moderate levels of genetic differentiation due to frequent gene exchange among populations. The low genetic differentiation among populations implied that conservation efforts should aim to preserve all remaining natural populations of this species. The information derived from this study is useful when identifying populations and categorizing their population origins, making possible the design of long term management program such as genetic improvement by selecti…
bibliographic citation: Wang et al. (2019) Genetic diversity of Simao pine in China revealed by SRAP markers. PeerJ 7:e6529 https://doi.org/10.7717/peerj.6529
date submitted: 2018-09-07
date accepted: 2019-01-28
issued: 2019-02-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Dawei
author list: Agent
  family name: Shen
  given name: Bingqi
author list: Agent
  family name: Gong
  given name: Hede
doi: 10.7717/peerj.6529
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-26
copyright: ©2019 Wang et al.
attribution name: Wang et al.

Oxidative stress and the presence of bacteria increase gene expression of the antimicrobial peptide aclasin, a fungal CSαβ defensin in Aspergillus clavatus
type: item
type: AcademicArticle
description: Background Antimicrobial peptides (AMPs) represent a broad class of naturally occurring antimicrobial compounds. Plants, invertebrates and fungi produce various AMPs as, for example, defensins. Most of these defensins are characterised by the presence of a cysteine-stabilised α-helical and β-sheet (CSαβ) motif. The changes in gene expression of a fungal CSαβ defensin by stress conditions were investigated in Aspergillus clavatus. A. clavatus produces the CSαβ defensin Aclasin, which is encoded by the aclasin gene. Methods Aclasin expression was evaluated in submerged mycelium cultures under heat shock, osmotic stress, oxidative stress and the presence of bacteria by quantitative real-time PCR. Results Aclasin expression increased two fold under oxidative stress conditions and in the presence of viable and heat-killed Bacillus megaterium. Under heat shock and osmotic stress, aclasin expression decreased. Discussion The results suggest that oxidative stress and the presence of bacteria might regulate fungal defensin expression. Moreover, fungi might recognise microorganisms as plants and animals do.
format: application/pdf
format: text/html
creator: Gabriela Contreras
creator: Nessa Wang
creator: Holger Schäfer
creator: Michael Wink
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.6290
publisher: PeerJ Inc.
rights: © 2019 Contreras et al.
abstract: Background Antimicrobial peptides (AMPs) represent a broad class of naturally occurring antimicrobial compounds. Plants, invertebrates and fungi produce various AMPs as, for example, defensins. Most of these defensins are characterised by the presence of a cysteine-stabilised α-helical and β-sheet (CSαβ) motif. The changes in gene expression of a fungal CSαβ defensin by stress conditions were investigated in Aspergillus clavatus. A. clavatus produces the CSαβ defensin Aclasin, which is encoded by the aclasin gene. Methods Aclasin expression was evaluated in submerged mycelium cultures under heat shock, osmotic stress, oxidative stress and the presence of bacteria by quantitative real-time PCR. Results Aclasin expression increased two fold under oxidative stress conditions and in the presence of viable and heat-killed Bacillus megaterium. Under heat shock and osmotic stress, aclasin expression decreased. Discussion The results suggest that oxidative stress and the presence of bacteria might regulate fungal defensin expression. Moreover, fungi might recognise microorganisms as plants and animals do.
bibliographic citation: Contreras et al. (2019) Oxidative stress and the presence of bacteria increase gene expression of the antimicrobial peptide aclasin, a fungal CSαβ defensin in Aspergillus clavatus. PeerJ 7:e6290 https://doi.org/10.7717/peerj.6290
date submitted: 2018-10-11
date accepted: 2018-12-15
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Contreras
  given name: Gabriela
author list: Agent
  family name: Wang
  given name: Nessa
author list: Agent
  family name: Schäfer
  given name: Holger
author list: Agent
  family name: Wink
  given name: Michael
doi: 10.7717/peerj.6290
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Contreras et al.
attribution name: Contreras et al.

Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis
type: item
type: AcademicArticle
description: Background The elderly population is at risk of osteoarthritis (OA), a common, multifactorial, degenerative joint disease. Environmental, genetic, and epigenetic (such as DNA hydroxymethylation) factors may be involved in the etiology, development, and pathogenesis of OA. Here, comprehensive bioinformatic analyses were used to identify aberrantly hydroxymethylated differentially expressed genes and pathways in osteoarthritis to determine the underlying molecular mechanisms of osteoarthritis and susceptibility-related genes for osteoarthritis inheritance. Methods Gene expression microarray data, mRNA expression profile data, and a whole genome 5hmC dataset were obtained from the Gene Expression Omnibus repository. Differentially expressed genes with abnormal hydroxymethylation were identified by MATCH function. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the genes differentially expressed in OA were performed using Metascape and the KOBAS online tool, respectively. The protein–protein interaction network was built using STRING and visualized in Cytoscape, and the modular analysis of the network was performed using the Molecular Complex Detection app. Results In total, 104 hyperhydroxymethylated highly expressed genes and 14 hypohydroxymethylated genes with low expression were identified. Gene ontology analyses indicated that the biological functions of hyperhydroxymethylated highly expressed genes included skeletal system development, ossification, and bone development; KEGG pathway analysis showed enrichment in protein digestion and absorption, extracellular matrix–receptor interaction, and focal adhesion. The top 10 hub genes in the protein–protein interaction network were COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL6A1, COL8A1, COL11A1, and COL24A1. All the aforementioned results are consistent with changes observed in OA. Conclusion After comprehensive bioinformatics analysis, we found aberrantly hydroxym…
format: application/pdf
format: text/html
creator: Yang Fang
creator: Pingping Wang
creator: Lin Xia
creator: Suwen Bai
creator: Yonggang Shen
creator: Qing Li
creator: Yang Wang
creator: Jinhang Zhu
creator: Juan Du
creator: Bing Shen
subject: Bioinformatics
subject: Genetics
subject: Orthopedics
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6425
publisher: PeerJ Inc.
rights: © 2019 Fang et al.
abstract: Background The elderly population is at risk of osteoarthritis (OA), a common, multifactorial, degenerative joint disease. Environmental, genetic, and epigenetic (such as DNA hydroxymethylation) factors may be involved in the etiology, development, and pathogenesis of OA. Here, comprehensive bioinformatic analyses were used to identify aberrantly hydroxymethylated differentially expressed genes and pathways in osteoarthritis to determine the underlying molecular mechanisms of osteoarthritis and susceptibility-related genes for osteoarthritis inheritance. Methods Gene expression microarray data, mRNA expression profile data, and a whole genome 5hmC dataset were obtained from the Gene Expression Omnibus repository. Differentially expressed genes with abnormal hydroxymethylation were identified by MATCH function. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of the genes differentially expressed in OA were performed using Metascape and the KOBAS online tool, respectively. The protein–protein interaction network was built using STRING and visualized in Cytoscape, and the modular analysis of the network was performed using the Molecular Complex Detection app. Results In total, 104 hyperhydroxymethylated highly expressed genes and 14 hypohydroxymethylated genes with low expression were identified. Gene ontology analyses indicated that the biological functions of hyperhydroxymethylated highly expressed genes included skeletal system development, ossification, and bone development; KEGG pathway analysis showed enrichment in protein digestion and absorption, extracellular matrix–receptor interaction, and focal adhesion. The top 10 hub genes in the protein–protein interaction network were COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL6A1, COL8A1, COL11A1, and COL24A1. All the aforementioned results are consistent with changes observed in OA. Conclusion After comprehensive bioinformatics analysis, we found aberrantly hydroxym…
bibliographic citation: Fang et al. (2019) Aberrantly hydroxymethylated differentially expressed genes and the associated protein pathways in osteoarthritis. PeerJ 7:e6425 https://doi.org/10.7717/peerj.6425
date submitted: 2018-10-11
date accepted: 2019-01-10
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Yang
author list: Agent
  family name: Wang
  given name: Pingping
author list: Agent
  family name: Xia
  given name: Lin
author list: Agent
  family name: Bai
  given name: Suwen
author list: Agent
  family name: Shen
  given name: Yonggang
author list: Agent
  family name: Li
  given name: Qing
author list: Agent
  family name: Wang
  given name: Yang
author list: Agent
  family name: Zhu
  given name: Jinhang
author list: Agent
  family name: Du
  given name: Juan
author list: Agent
  family name: Shen
  given name: Bing
doi: 10.7717/peerj.6425
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: ©2019 Fang et al.
attribution name: Fang et al.

Some methods to improve the utility of conditioned Latin hypercube sampling
type: item
type: AcademicArticle
description: The conditioned Latin hypercube sampling (cLHS) algorithm is popularly used for planning field sampling surveys in order to understand the spatial behavior of natural phenomena such as soils. This technical note collates, summarizes, and extends existing solutions to problems that field scientists face when using cLHS. These problems include optimizing the sample size, re-locating sites when an original site is deemed inaccessible, and how to account for existing sample data, so that under-sampled areas can be prioritized for sampling. These solutions, which we also share as individual R scripts, will facilitate much wider application of what has been a very useful sampling algorithm for scientific investigation of soil spatial variation.
format: application/pdf
format: text/html
creator: Brendan P. Malone
creator: Budiman Minansy
creator: Colby Brungard
subject: Agricultural Science
subject: Soil Science
subject: Statistics
subject: Data Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6451
publisher: PeerJ Inc.
rights: © 2019 Malone et al.
abstract: The conditioned Latin hypercube sampling (cLHS) algorithm is popularly used for planning field sampling surveys in order to understand the spatial behavior of natural phenomena such as soils. This technical note collates, summarizes, and extends existing solutions to problems that field scientists face when using cLHS. These problems include optimizing the sample size, re-locating sites when an original site is deemed inaccessible, and how to account for existing sample data, so that under-sampled areas can be prioritized for sampling. These solutions, which we also share as individual R scripts, will facilitate much wider application of what has been a very useful sampling algorithm for scientific investigation of soil spatial variation.
bibliographic citation: Malone et al. (2019) Some methods to improve the utility of conditioned Latin hypercube sampling. PeerJ 7:e6451 https://doi.org/10.7717/peerj.6451
date submitted: 2018-10-02
date accepted: 2019-01-15
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malone
  given name: Brendan P.
author list: Agent
  family name: Minansy
  given name: Budiman
author list: Agent
  family name: Brungard
  given name: Colby
doi: 10.7717/peerj.6451
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Malone et al.
attribution name: Malone et al.

A simulation framework for evaluating multi-stage sampling designs in populations with spatially structured traits
type: item
type: AcademicArticle
description: Selecting an appropriate and efficient sampling strategy in biological surveys is a major concern in ecological research, particularly when the population abundance and individual traits of the sampled population are highly structured over space. Multi-stage sampling designs typically present sampling sites as primary units. However, to collect trait data, such as age or maturity, only a sub-sample of individuals collected in the sampling site is retained. Therefore, not only the sampling design, but also the sub-sampling strategy can have a major impact on important population estimates, commonly used as reference points for management and conservation. We developed a simulation framework to evaluate sub-sampling strategies from multi-stage biological surveys. Specifically, we compare quantitatively precision and bias of the population estimates obtained using two common but contrasting sub-sampling strategies: the random and the stratified designs. The sub-sampling strategy evaluation was applied to age data collection of a virtual fish population that has the same statistical and biological characteristics of the Eastern Bering Sea population of Pacific cod. The simulation scheme allowed us to incorporate contributions of several sources of error and to analyze the sensitivity of the different strategies in the population estimates. We found that, on average across all scenarios tested, the main differences between sub-sampling designs arise from the inability of the stratified design to reproduce spatial patterns of the individual traits. However, differences between the sub-sampling strategies in other population estimates may be small, particularly when large sub-sample sizes are used. On isolated scenarios (representative of specific environmental or demographic conditions), the random sub-sampling provided better precision in all population estimates analyzed. The sensitivity analysis revealed the important contribution of spatial autocorrelation in the erro…
format: application/pdf
format: text/html
creator: Patricia Puerta
creator: Lorenzo Ciannelli
creator: Bethany Johnson
subject: Aquaculture, Fisheries and Fish Science
subject: Computational Biology
subject: Ecology
subject: Biological Oceanography
subject: Population Biology
description: doi:10.7717/peerj.6471
publisher: PeerJ Inc.
rights: © 2019 Puerta et al.
abstract: Selecting an appropriate and efficient sampling strategy in biological surveys is a major concern in ecological research, particularly when the population abundance and individual traits of the sampled population are highly structured over space. Multi-stage sampling designs typically present sampling sites as primary units. However, to collect trait data, such as age or maturity, only a sub-sample of individuals collected in the sampling site is retained. Therefore, not only the sampling design, but also the sub-sampling strategy can have a major impact on important population estimates, commonly used as reference points for management and conservation. We developed a simulation framework to evaluate sub-sampling strategies from multi-stage biological surveys. Specifically, we compare quantitatively precision and bias of the population estimates obtained using two common but contrasting sub-sampling strategies: the random and the stratified designs. The sub-sampling strategy evaluation was applied to age data collection of a virtual fish population that has the same statistical and biological characteristics of the Eastern Bering Sea population of Pacific cod. The simulation scheme allowed us to incorporate contributions of several sources of error and to analyze the sensitivity of the different strategies in the population estimates. We found that, on average across all scenarios tested, the main differences between sub-sampling designs arise from the inability of the stratified design to reproduce spatial patterns of the individual traits. However, differences between the sub-sampling strategies in other population estimates may be small, particularly when large sub-sample sizes are used. On isolated scenarios (representative of specific environmental or demographic conditions), the random sub-sampling provided better precision in all population estimates analyzed. The sensitivity analysis revealed the important contribution of spatial autocorrelation in the erro…
bibliographic citation: Puerta et al. (2019) A simulation framework for evaluating multi-stage sampling designs in populations with spatially structured traits. PeerJ 7:e6471 https://doi.org/10.7717/peerj.6471
date submitted: 2018-08-26
date accepted: 2019-01-16
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Puerta
  given name: Patricia
author list: Agent
  family name: Ciannelli
  given name: Lorenzo
author list: Agent
  family name: Johnson
  given name: Bethany
doi: 10.7717/peerj.6471
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Puerta et al.
attribution name: Puerta et al.

Association between maternal pre-delivery body mass index and offspring overweight/obesity at 1 and 2 years of age among residents of a suburb in Taiwan
type: item
type: AcademicArticle
description: Background Overweight and obesity among children can cause metabolic syndrome in adulthood and are a significant public health issue. Some studies suggest that maternal pre-pregnancy body mass index (BMI) and excessive gestational weight gain during pregnancy are associated with overweight and obesity in offspring. However, it is difficult to collect information on accurate pre-pregnancy BMI and pregnancy weight gain for women living in areas where medical resources are scarce. Maternal pre-delivery BMI might be predictive of the risk of overweight and obesity among offspring of pregnant mothers living in suburban areas. Methods We retrospectively collected data on term neonates with appropriate weights for their gestational age born between April 2013 and October 2015. We excluded neonates with major congenital anomalies or diseases and incomplete data. Mothers with systemic diseases or drug abuse were also excluded. Offspring body weights and heights at 1- and 2-years-old were recorded. Maternal pre-delivery BMI was divided into following groups: <25, 25–29.9, and ≧30 kg/m2. Results We included 261 mother-child pairs in this study. The BMIs of the offspring differed significantly among the three maternal pre-delivery BMI groups at the age of 2 years (15.18 ± 1.04, 15.83 ± 1.28, and 16.29 ± 1.61 kg/m2, p < 0.001, respectively). After adjusting for potential cofounders possibly affecting weight using multivariate linear regression, the children’s BMIs (adjusted 95% CI: 0.71 [0.31–1.11]; p = 0.001) and BMI percentiles (adjusted 95% CI 15.80 [7.32–24.28]; p < 0.001) at the age of 2 years were significantly higher in those born to mothers with pre-delivery BMIs of 25–29.9 kg/m2 compared to mothers with pre-delivery BMIs <25 kg/m2. Maternal pre-delivery BMI ≧30 kg/m2 was significantly associated with increased BMIs (adjusted 95% CI: 1.17 [0.72–1.63]; p < 0.001) and BMI percentiles (adjusted 95% CI: 23.48 [13.87–33.09]; p < 0.001) in their children. A maternal pre-delive…
format: application/pdf
format: text/html
creator: Hsien-Kuan Liu
creator: Chien-Yi Wu
creator: Yung-Ning Yang
creator: Pei-Ling Wu
creator: Zong-Rong He
creator: San-Nan Yang
creator: Shu-Leei Tey
subject: Global Health
subject: Gynecology and Obstetrics
subject: Pediatrics
subject: Public Health
subject: Women's Health
description: doi:10.7717/peerj.6473
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Background Overweight and obesity among children can cause metabolic syndrome in adulthood and are a significant public health issue. Some studies suggest that maternal pre-pregnancy body mass index (BMI) and excessive gestational weight gain during pregnancy are associated with overweight and obesity in offspring. However, it is difficult to collect information on accurate pre-pregnancy BMI and pregnancy weight gain for women living in areas where medical resources are scarce. Maternal pre-delivery BMI might be predictive of the risk of overweight and obesity among offspring of pregnant mothers living in suburban areas. Methods We retrospectively collected data on term neonates with appropriate weights for their gestational age born between April 2013 and October 2015. We excluded neonates with major congenital anomalies or diseases and incomplete data. Mothers with systemic diseases or drug abuse were also excluded. Offspring body weights and heights at 1- and 2-years-old were recorded. Maternal pre-delivery BMI was divided into following groups: <25, 25–29.9, and ≧30 kg/m2. Results We included 261 mother-child pairs in this study. The BMIs of the offspring differed significantly among the three maternal pre-delivery BMI groups at the age of 2 years (15.18 ± 1.04, 15.83 ± 1.28, and 16.29 ± 1.61 kg/m2, p < 0.001, respectively). After adjusting for potential cofounders possibly affecting weight using multivariate linear regression, the children’s BMIs (adjusted 95% CI: 0.71 [0.31–1.11]; p = 0.001) and BMI percentiles (adjusted 95% CI 15.80 [7.32–24.28]; p < 0.001) at the age of 2 years were significantly higher in those born to mothers with pre-delivery BMIs of 25–29.9 kg/m2 compared to mothers with pre-delivery BMIs <25 kg/m2. Maternal pre-delivery BMI ≧30 kg/m2 was significantly associated with increased BMIs (adjusted 95% CI: 1.17 [0.72–1.63]; p < 0.001) and BMI percentiles (adjusted 95% CI: 23.48 [13.87–33.09]; p < 0.001) in their children. A maternal pre-delive…
bibliographic citation: Liu et al. (2019) Association between maternal pre-delivery body mass index and offspring overweight/obesity at 1 and 2 years of age among residents of a suburb in Taiwan. PeerJ 7:e6473 https://doi.org/10.7717/peerj.6473
date submitted: 2018-06-08
date accepted: 2019-01-18
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hsien-Kuan
author list: Agent
  family name: Wu
  given name: Chien-Yi
author list: Agent
  family name: Yang
  given name: Yung-Ning
author list: Agent
  family name: Wu
  given name: Pei-Ling
author list: Agent
  family name: He
  given name: Zong-Rong
author list: Agent
  family name: Yang
  given name: San-Nan
author list: Agent
  family name: Tey
  given name: Shu-Leei
doi: 10.7717/peerj.6473
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Integrative taxonomic reassessment of Odontophrynus populations in Argentina and phylogenetic relationships within Odontophrynidae (Anura)
type: item
type: AcademicArticle
description: Amphibians are the most vulnerable vertebrates to biodiversity loss mediated by habitat destruction, climate change and diseases. Informed conservation management requires improving the taxonomy of anurans to assess reliably the species’ geographic range. The genus Odontophrynus that is geographically refined to Argentina, Bolivia, Brazil, Uruguay and Paraguay includes currently 12 nominal species with many populations of uncertain taxonomic assignment and subsequently unclear geographic ranges. In this study, we applied integrative taxonomic methods combining molecular (mitochondrial 16S gene), allozyme, morphological and bioacoustic data to delimit species of the genus Odontophrynus sampled from throughout Argentina where most species occur. The combined evidence demonstrates one case of cryptic diversity and another of overestimation of species richness. The populations referred to as O. americanus comprise at least three species. In contrast, O. achalensis and O. barrioi represent junior synonyms of the phenotypically plastic species O. occidentalis. We conclude that each of the four species occurring in Argentina inhabits medium to large areas. The Red List classification is currently “Least Concern”. We also propose a phylogenetic hypothesis for the genus and associated genera Macrogenioglottus and Proceratophrys (Odontophrynidae).
format: application/pdf
format: text/html
creator: Adolfo Ludovico Martino
creator: Jonas Maximilian Dehling
creator: Ulrich Sinsch
subject: Biodiversity
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6480
publisher: PeerJ Inc.
rights: © 2019 Martino et al.
abstract: Amphibians are the most vulnerable vertebrates to biodiversity loss mediated by habitat destruction, climate change and diseases. Informed conservation management requires improving the taxonomy of anurans to assess reliably the species’ geographic range. The genus Odontophrynus that is geographically refined to Argentina, Bolivia, Brazil, Uruguay and Paraguay includes currently 12 nominal species with many populations of uncertain taxonomic assignment and subsequently unclear geographic ranges. In this study, we applied integrative taxonomic methods combining molecular (mitochondrial 16S gene), allozyme, morphological and bioacoustic data to delimit species of the genus Odontophrynus sampled from throughout Argentina where most species occur. The combined evidence demonstrates one case of cryptic diversity and another of overestimation of species richness. The populations referred to as O. americanus comprise at least three species. In contrast, O. achalensis and O. barrioi represent junior synonyms of the phenotypically plastic species O. occidentalis. We conclude that each of the four species occurring in Argentina inhabits medium to large areas. The Red List classification is currently “Least Concern”. We also propose a phylogenetic hypothesis for the genus and associated genera Macrogenioglottus and Proceratophrys (Odontophrynidae).
bibliographic citation: Martino et al. (2019) Integrative taxonomic reassessment of Odontophrynus populations in Argentina and phylogenetic relationships within Odontophrynidae (Anura). PeerJ 7:e6480 https://doi.org/10.7717/peerj.6480
date submitted: 2018-10-08
date accepted: 2019-01-20
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martino
  given name: Adolfo Ludovico
author list: Agent
  family name: Dehling
  given name: Jonas Maximilian
author list: Agent
  family name: Sinsch
  given name: Ulrich
doi: 10.7717/peerj.6480
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Martino et al.
attribution name: Martino et al.

Evaluating the utility of camera traps in field studies of predation
type: item
type: AcademicArticle
description: Artificial prey techniques—wherein synthetic replicas of real organisms are placed in natural habitats—are widely used to study predation in the field. We investigated the extent to which videography could provide additional information to such studies. As a part of studies on aposematism and mimicry of coral snakes (Micrurus) and their mimics, observational data from 109 artificial snake prey were collected from video-recording camera traps in three locations in the Americas (terra firme forest, Tiputini Biodiversity Station, Ecuador; premontane wet forest, Nahá Reserve, Mexico; longleaf pine forest, Southeastern Coastal Plain, North Carolina, USA). During 1,536 camera days, a total of 268 observations of 20 putative snake predator species were recorded in the vicinity of artificial prey. Predators were observed to detect artificial prey 52 times, but only 21 attacks were recorded. Mammals were the most commonly recorded group of predators near replicas (243) and were responsible for most detections (48) and attacks (20). There was no difference between avian or mammalian predators in their probability of detecting replicas nor in their probability of attacking replicas after detecting them. Bite and beak marks left on clay replicas registered a higher ratio of avian:mammalian attacks than videos registered. Approximately 61.5% of artificial prey monitored with cameras remained undetected by predators throughout the duration of the experiments. Observational data collected from videos could provide more robust inferences on the relative fitness of different prey phenotypes, predator behavior, and the relative contribution of different predator species to selection on prey. However, we estimate that the level of predator activity necessary for the benefit of additional information that videos provide to be worth their financial costs is achieved in fewer than 20% of published artificial prey studies. Although we suggest future predation studies employing artificial …
format: application/pdf
format: text/html
creator: Christopher K. Akcali
creator: Hibraim Adán Pérez-Mendoza
creator: David Salazar-Valenzuela
creator: David W. Kikuchi
creator: Juan M. Guayasamin
creator: David W. Pfennig
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6487
publisher: PeerJ Inc.
rights: © 2019 Akcali et al.
abstract: Artificial prey techniques—wherein synthetic replicas of real organisms are placed in natural habitats—are widely used to study predation in the field. We investigated the extent to which videography could provide additional information to such studies. As a part of studies on aposematism and mimicry of coral snakes (Micrurus) and their mimics, observational data from 109 artificial snake prey were collected from video-recording camera traps in three locations in the Americas (terra firme forest, Tiputini Biodiversity Station, Ecuador; premontane wet forest, Nahá Reserve, Mexico; longleaf pine forest, Southeastern Coastal Plain, North Carolina, USA). During 1,536 camera days, a total of 268 observations of 20 putative snake predator species were recorded in the vicinity of artificial prey. Predators were observed to detect artificial prey 52 times, but only 21 attacks were recorded. Mammals were the most commonly recorded group of predators near replicas (243) and were responsible for most detections (48) and attacks (20). There was no difference between avian or mammalian predators in their probability of detecting replicas nor in their probability of attacking replicas after detecting them. Bite and beak marks left on clay replicas registered a higher ratio of avian:mammalian attacks than videos registered. Approximately 61.5% of artificial prey monitored with cameras remained undetected by predators throughout the duration of the experiments. Observational data collected from videos could provide more robust inferences on the relative fitness of different prey phenotypes, predator behavior, and the relative contribution of different predator species to selection on prey. However, we estimate that the level of predator activity necessary for the benefit of additional information that videos provide to be worth their financial costs is achieved in fewer than 20% of published artificial prey studies. Although we suggest future predation studies employing artificial …
bibliographic citation: Akcali et al. (2019) Evaluating the utility of camera traps in field studies of predation. PeerJ 7:e6487 https://doi.org/10.7717/peerj.6487
date submitted: 2018-09-13
date accepted: 2019-01-19
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Akcali
  given name: Christopher K.
author list: Agent
  family name: Adán Pérez-Mendoza
  given name: Hibraim
author list: Agent
  family name: Salazar-Valenzuela
  given name: David
author list: Agent
  family name: Kikuchi
  given name: David W.
author list: Agent
  family name: Guayasamin
  given name: Juan M.
author list: Agent
  family name: Pfennig
  given name: David W.
doi: 10.7717/peerj.6487
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Akcali et al.
attribution name: Akcali et al.

Success of concrete and crab traps in facilitating Eastern oyster recruitment and reef development
type: item
type: AcademicArticle
description: Background Abundance of the commercially and ecologically important Eastern oyster, Crassostrea virginica, has declined across the US Eastern and Gulf coasts in recent decades, spurring substantial efforts to restore oyster reefs. These efforts are widely constrained by the availability, cost, and suitability of substrates to support oyster settlement and reef establishment. In particular, oyster shell is often the preferred substrate but is relatively scarce and increasingly expensive. Thus, there is a need for alternative oyster restoration materials that are cost-effective, abundant, and durable. Methods We tested the viability of two low-cost substrates—concrete and recycled blue crab (Callinectes sapidus) traps—in facilitating oyster recovery in a replicated 22-month field experiment at historically productive but now degraded intertidal oyster grounds on northwestern Florida’s Nature Coast. Throughout the trial, we monitored areal oyster cover on each substrate; at the end of the trial, we measured the densities of oysters by size class (spat, juvenile, and market-size) and the biomass and volume of each reef. Results Oysters colonized the concrete structures more quickly than the crab traps, as evidenced by significantly higher oyster cover during the first year of the experiment. By the end of the experiment, the concrete structures hosted higher densities of spat and juveniles, while the density of market-size oysters was relatively low and similar between treatments. The open structure of the crab traps led to the development of larger-volume reefs, while oyster biomass per unit area was similar between treatments. In addition, substrates positioned at lower elevations (relative to mean sea level) supported higher oyster abundance, size, and biomass than those less frequently inundated at higher elevations. Discussion Together, these findings indicate that both concrete and crab traps are viable substrates for oyster reef restoration, especially when place…
format: application/pdf
format: text/html
creator: Emma E. Johnson
creator: Miles D. Medina
creator: Ada C. Bersoza Hernandez
creator: Gregory A. Kusel
creator: Audrey N. Batzer
creator: Christine Angelini
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.6488
publisher: PeerJ Inc.
rights: © 2019 Johnson et al.
abstract: Background Abundance of the commercially and ecologically important Eastern oyster, Crassostrea virginica, has declined across the US Eastern and Gulf coasts in recent decades, spurring substantial efforts to restore oyster reefs. These efforts are widely constrained by the availability, cost, and suitability of substrates to support oyster settlement and reef establishment. In particular, oyster shell is often the preferred substrate but is relatively scarce and increasingly expensive. Thus, there is a need for alternative oyster restoration materials that are cost-effective, abundant, and durable. Methods We tested the viability of two low-cost substrates—concrete and recycled blue crab (Callinectes sapidus) traps—in facilitating oyster recovery in a replicated 22-month field experiment at historically productive but now degraded intertidal oyster grounds on northwestern Florida’s Nature Coast. Throughout the trial, we monitored areal oyster cover on each substrate; at the end of the trial, we measured the densities of oysters by size class (spat, juvenile, and market-size) and the biomass and volume of each reef. Results Oysters colonized the concrete structures more quickly than the crab traps, as evidenced by significantly higher oyster cover during the first year of the experiment. By the end of the experiment, the concrete structures hosted higher densities of spat and juveniles, while the density of market-size oysters was relatively low and similar between treatments. The open structure of the crab traps led to the development of larger-volume reefs, while oyster biomass per unit area was similar between treatments. In addition, substrates positioned at lower elevations (relative to mean sea level) supported higher oyster abundance, size, and biomass than those less frequently inundated at higher elevations. Discussion Together, these findings indicate that both concrete and crab traps are viable substrates for oyster reef restoration, especially when place…
bibliographic citation: Johnson et al. (2019) Success of concrete and crab traps in facilitating Eastern oyster recruitment and reef development. PeerJ 7:e6488 https://doi.org/10.7717/peerj.6488
date submitted: 2018-08-02
date accepted: 2019-01-19
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johnson
  given name: Emma E.
author list: Agent
  family name: Medina
  given name: Miles D.
author list: Agent
  family name: Bersoza Hernandez
  given name: Ada C.
author list: Agent
  family name: Kusel
  given name: Gregory A.
author list: Agent
  family name: Batzer
  given name: Audrey N.
author list: Agent
  family name: Angelini
  given name: Christine
doi: 10.7717/peerj.6488
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Johnson et al.
attribution name: Johnson et al.

Tumor mutational profile of triple negative breast cancer patients in Thailand revealed distinctive genetic alteration in chromatin remodeling gene
type: item
type: AcademicArticle
description: Background Triple negative breast cancer (TNBC) is a breast cancer subtype characterized by absence of both hormonal receptors and human epithelial growth factor receptor 2 (HER2). TNBC accounts for 15–20% of breast cancer. TNBC is associated with more aggressive disease and worse clinical outcome. Though the underlying mechanism of TNBC is currently unclear, the heterogeneity of clinical characteristics in various population may relate to the difference in tumor mutational profile. There were studies on TNBC gene mutations in various ethnic groups but the tumor genome data on Thai TNBC patients is currently unknown. This study aims to investigate mutational profile of Thai TNBC. Methods The patients were Thai individuals who were diagnosed with primary breast carcinoma between 2014 and 2017. All surgically removed primary tumor tissues were carefully examined by pathologists and archived as formalin-fixed paraffin-embedded tumor. TNBC was defined by absence of hormonal receptors and HER2 by immunohistochemistry. Genomic DNA was extracted, enriched and sequenced of all exomes on the Illumina HiSeq. Genomic data were then processed through bioinformatics platform to identify genomic alterations and tumor mutational burden. Results A total of 116 TNBC patients were recruited. Genomic analysis of TNBC samples identified 81,460 variants, of which 5,906 variants were in cancer-associated genes. The result showed that Thai TNBC has higher tumor mutation burden than previously reported data. The most frequently mutated cancer-associated gene was TP53 similar to other TNBC cohorts. Meanwhile KMT2C was found to be more commonly mutated in Thai TNBC than previous studies. Mutational profile of Thai TNBC patients also revealed difference in many frequently mutated genes when compared to other Western TNBC cohorts. Conclusion This result supported that TNBC breast cancer patients from various ethnic background showed diverse genome alteration pattern. Although TP53 is the most …
format: application/pdf
format: text/html
creator: Suvimol Niyomnaitham
creator: Napa Parinyanitikul
creator: Ekkapong Roothumnong
creator: Worapoj Jinda
creator: Norasate Samarnthai
creator: Taywin Atikankul
creator: Bhoom Suktitipat
creator: Wanna Thongnoppakhun
creator: Chanin Limwongse
creator: Manop Pithukpakorn
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Oncology
subject: Pathology
description: doi:10.7717/peerj.6501
publisher: PeerJ Inc.
rights: © 2019 Niyomnaitham et al.
abstract: Background Triple negative breast cancer (TNBC) is a breast cancer subtype characterized by absence of both hormonal receptors and human epithelial growth factor receptor 2 (HER2). TNBC accounts for 15–20% of breast cancer. TNBC is associated with more aggressive disease and worse clinical outcome. Though the underlying mechanism of TNBC is currently unclear, the heterogeneity of clinical characteristics in various population may relate to the difference in tumor mutational profile. There were studies on TNBC gene mutations in various ethnic groups but the tumor genome data on Thai TNBC patients is currently unknown. This study aims to investigate mutational profile of Thai TNBC. Methods The patients were Thai individuals who were diagnosed with primary breast carcinoma between 2014 and 2017. All surgically removed primary tumor tissues were carefully examined by pathologists and archived as formalin-fixed paraffin-embedded tumor. TNBC was defined by absence of hormonal receptors and HER2 by immunohistochemistry. Genomic DNA was extracted, enriched and sequenced of all exomes on the Illumina HiSeq. Genomic data were then processed through bioinformatics platform to identify genomic alterations and tumor mutational burden. Results A total of 116 TNBC patients were recruited. Genomic analysis of TNBC samples identified 81,460 variants, of which 5,906 variants were in cancer-associated genes. The result showed that Thai TNBC has higher tumor mutation burden than previously reported data. The most frequently mutated cancer-associated gene was TP53 similar to other TNBC cohorts. Meanwhile KMT2C was found to be more commonly mutated in Thai TNBC than previous studies. Mutational profile of Thai TNBC patients also revealed difference in many frequently mutated genes when compared to other Western TNBC cohorts. Conclusion This result supported that TNBC breast cancer patients from various ethnic background showed diverse genome alteration pattern. Although TP53 is the most …
bibliographic citation: Niyomnaitham et al. (2019) Tumor mutational profile of triple negative breast cancer patients in Thailand revealed distinctive genetic alteration in chromatin remodeling gene. PeerJ 7:e6501 https://doi.org/10.7717/peerj.6501
date submitted: 2018-12-15
date accepted: 2019-01-22
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niyomnaitham
  given name: Suvimol
author list: Agent
  family name: Parinyanitikul
  given name: Napa
author list: Agent
  family name: Roothumnong
  given name: Ekkapong
author list: Agent
  family name: Jinda
  given name: Worapoj
author list: Agent
  family name: Samarnthai
  given name: Norasate
author list: Agent
  family name: Atikankul
  given name: Taywin
author list: Agent
  family name: Suktitipat
  given name: Bhoom
author list: Agent
  family name: Thongnoppakhun
  given name: Wanna
author list: Agent
  family name: Limwongse
  given name: Chanin
author list: Agent
  family name: Pithukpakorn
  given name: Manop
doi: 10.7717/peerj.6501
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Niyomnaitham et al.
attribution name: Niyomnaitham et al.

Effects of narrow linear clearings on movement and habitat use in a boreal forest mammal community during winter
type: item
type: AcademicArticle
description: Linear clearings for human activities cause internal fragmentation of otherwise intact native forest, with many potential impacts on wildlife. Across a boreal forest region of some 4,000 km2, we investigated how movements and habitat use of ecologically different mammal species are affected by narrow (about eight m) seismic line (SL) clearings associated with fossil fuel extraction, which form extensive networks many kilometers long. We conducted nine repeat snow track surveys during three winters at 14 pairs of one-kilometer transects, each comprising one transect along the SL and a second running perpendicular into adjacent forest. Data for 13 individually-analyzed mammal taxa (species or sets of closely related species) and five mammal groups, categorized based on body size-diet combinations, showed that movements across transects were either unaffected by SL clearings (relative to continuous forest) or restricted only slightly. However, these clearings were favored for linear travel by most species and body size-diet groups (excepting small mammals). The strength of this preference varied in a manner consistent with species’ differing needs to move long distances (associated with their energetic requirements): large predators > large herbivores > mid-sized predators > mid-sized herbivores > small mammals. In terms of overall habitat use, large-bodied predators (e.g., wolves and coyotes) strongly selected SL clearings over forest, medium-sized predators (e.g., mustelids) and medium-sized herbivores (e.g., hares and squirrels) preferred forest, and neither large herbivores nor small mammals had a clear habitat preference. Consequently, there was a net shift in both species and trophic composition within the SL, in favor of large predators and away from medium-sized predators and herbivores. Given the high regional SL density (1.9 km/km2) such shifts are likely to have complex ecological consequences, of currently unknown magnitude.
format: application/pdf
format: text/html
creator: Colin A. Pattison
creator: Carla P. Catterall
subject: Animal Behavior
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Biosphere Interactions
description: doi:10.7717/peerj.6504
publisher: PeerJ Inc.
rights: © 2019 Pattison and Catterall
abstract: Linear clearings for human activities cause internal fragmentation of otherwise intact native forest, with many potential impacts on wildlife. Across a boreal forest region of some 4,000 km2, we investigated how movements and habitat use of ecologically different mammal species are affected by narrow (about eight m) seismic line (SL) clearings associated with fossil fuel extraction, which form extensive networks many kilometers long. We conducted nine repeat snow track surveys during three winters at 14 pairs of one-kilometer transects, each comprising one transect along the SL and a second running perpendicular into adjacent forest. Data for 13 individually-analyzed mammal taxa (species or sets of closely related species) and five mammal groups, categorized based on body size-diet combinations, showed that movements across transects were either unaffected by SL clearings (relative to continuous forest) or restricted only slightly. However, these clearings were favored for linear travel by most species and body size-diet groups (excepting small mammals). The strength of this preference varied in a manner consistent with species’ differing needs to move long distances (associated with their energetic requirements): large predators > large herbivores > mid-sized predators > mid-sized herbivores > small mammals. In terms of overall habitat use, large-bodied predators (e.g., wolves and coyotes) strongly selected SL clearings over forest, medium-sized predators (e.g., mustelids) and medium-sized herbivores (e.g., hares and squirrels) preferred forest, and neither large herbivores nor small mammals had a clear habitat preference. Consequently, there was a net shift in both species and trophic composition within the SL, in favor of large predators and away from medium-sized predators and herbivores. Given the high regional SL density (1.9 km/km2) such shifts are likely to have complex ecological consequences, of currently unknown magnitude.
bibliographic citation: Pattison et al. (2019) Effects of narrow linear clearings on movement and habitat use in a boreal forest mammal community during winter. PeerJ 7:e6504 https://doi.org/10.7717/peerj.6504
date submitted: 2017-03-16
date accepted: 2019-01-22
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pattison
  given name: Colin A.
author list: Agent
  family name: Catterall
  given name: Carla P.
doi: 10.7717/peerj.6504
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Pattison and Catterall
attribution name: Pattison and Catterall

Emergence of visible light optical properties of L-phenylalanine aggregates
type: item
type: AcademicArticle
description: The ability of phenylalanine to form fibrillar nanostructures was demonstrated on multiple occasions, and such an oligomerization reaction could be the cause of cytotoxicity in patients with phenylketonuria. These findings were supported by claims that L-phenylalanine (Phe) fibrils have amyloid properties and can be detected using thioflavin T fluorescence assay. However, a part of Phe aggregation studies reported the opposite data, suggesting no amyloid structures to be formed. Due to the contradicting reports, the amyloid nature of Phe aggregates remains uncertain. In this work we tested Phe aggregation under conditions where amyloid formation was previously reported. We show the emergence of Phe aggregates with visible light optical properties that overlap with the spectra of dyes used in amyloid fibril assays, which could lead to false-positive identifications.
format: application/pdf
format: text/html
creator: Mantas Ziaunys
creator: Vytautas Smirnovas
subject: Biochemistry
subject: Biophysics
description: doi:10.7717/peerj.6518
publisher: PeerJ Inc.
rights: © 2019 Ziaunys and Smirnovas
abstract: The ability of phenylalanine to form fibrillar nanostructures was demonstrated on multiple occasions, and such an oligomerization reaction could be the cause of cytotoxicity in patients with phenylketonuria. These findings were supported by claims that L-phenylalanine (Phe) fibrils have amyloid properties and can be detected using thioflavin T fluorescence assay. However, a part of Phe aggregation studies reported the opposite data, suggesting no amyloid structures to be formed. Due to the contradicting reports, the amyloid nature of Phe aggregates remains uncertain. In this work we tested Phe aggregation under conditions where amyloid formation was previously reported. We show the emergence of Phe aggregates with visible light optical properties that overlap with the spectra of dyes used in amyloid fibril assays, which could lead to false-positive identifications.
bibliographic citation: Ziaunys et al. (2019) Emergence of visible light optical properties of L-phenylalanine aggregates. PeerJ 7:e6518 https://doi.org/10.7717/peerj.6518
date submitted: 2018-11-07
date accepted: 2019-01-26
issued: 2019-02-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ziaunys
  given name: Mantas
author list: Agent
  family name: Smirnovas
  given name: Vytautas
doi: 10.7717/peerj.6518
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-25
copyright: © 2019 Ziaunys and Smirnovas
attribution name: Ziaunys and Smirnovas

The impact on life cycle carbon footprint of converting from disposable to reusable sharps containers in a large US hospital geographically distant from manufacturing and processing facilities
type: item
type: AcademicArticle
description: Background Sustainable purchasing can reduce greenhouse gas (GHG) emissions at healthcare facilities (HCF). A previous study found that converting from disposable to reusable sharps containers (DSC, RSC) reduced sharps waste stream GHG by 84% but found transport distances impacted significantly on GHG outcomes and recommended further studies where transport distances are large. This case-study examines the impact on GHG of nation-wide transport distances when a large US health system converted from DSC to RSC. Methods The study’s scope was to examine life cycle GHG emissions during 12 months of facility-wide use of DSC and RSC at Loma Linda University Health (LLUH). The facility is an 1100-bed US, 5-hospital system where: the source of polymer was distant from the RSC manufacturing plant; both manufacturing plants were over 3,000 km from the HCF; and the RSC processing plant was considerably further from the HCF than was the DSC disposal plant. Using a “cradle to grave” life cycle GHG tool we calculated the annual GHG emissions of CO2, CH4 and N2O expressed in metric tonnes of carbon dioxide equivalents (MTCO2eq) for each container system. Primary energy input data was used wherever possible and region-specific energy-impact conversions were used to calculate GHG of each unit process over a 12-month period. The scope included Manufacture, Transport, Washing, and Treatment & disposal. GHG emissions from all unit process within these four life cycle stages were summed to estimate each container-system’s carbon footprint. Emission totals were workload-normalized and analysed using CHI2test with P ≤ 0.05 and rate ratios at 95% CL. Results Converting to RSC, LLUH reduced its annual GHG by 162.4 MTCO2eq (−65.3%; p < 0.001; RR 2.27–3.71), and annually eliminated 50.2 tonnes of plastic DSC and 8.1 tonnes of cardboard from the sharps waste stream. Of the plastic eliminated, 31.8 tonnes were diverted from landfill and 18.4 from incineration. Discussion Unlike GHG reduction st…
format: application/pdf
format: text/html
creator: Brett McPherson
creator: Mihray Sharip
creator: Terry Grimmond
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.6204
publisher: PeerJ Inc.
rights: © 2019 McPherson et al.
abstract: Background Sustainable purchasing can reduce greenhouse gas (GHG) emissions at healthcare facilities (HCF). A previous study found that converting from disposable to reusable sharps containers (DSC, RSC) reduced sharps waste stream GHG by 84% but found transport distances impacted significantly on GHG outcomes and recommended further studies where transport distances are large. This case-study examines the impact on GHG of nation-wide transport distances when a large US health system converted from DSC to RSC. Methods The study’s scope was to examine life cycle GHG emissions during 12 months of facility-wide use of DSC and RSC at Loma Linda University Health (LLUH). The facility is an 1100-bed US, 5-hospital system where: the source of polymer was distant from the RSC manufacturing plant; both manufacturing plants were over 3,000 km from the HCF; and the RSC processing plant was considerably further from the HCF than was the DSC disposal plant. Using a “cradle to grave” life cycle GHG tool we calculated the annual GHG emissions of CO2, CH4 and N2O expressed in metric tonnes of carbon dioxide equivalents (MTCO2eq) for each container system. Primary energy input data was used wherever possible and region-specific energy-impact conversions were used to calculate GHG of each unit process over a 12-month period. The scope included Manufacture, Transport, Washing, and Treatment & disposal. GHG emissions from all unit process within these four life cycle stages were summed to estimate each container-system’s carbon footprint. Emission totals were workload-normalized and analysed using CHI2test with P ≤ 0.05 and rate ratios at 95% CL. Results Converting to RSC, LLUH reduced its annual GHG by 162.4 MTCO2eq (−65.3%; p < 0.001; RR 2.27–3.71), and annually eliminated 50.2 tonnes of plastic DSC and 8.1 tonnes of cardboard from the sharps waste stream. Of the plastic eliminated, 31.8 tonnes were diverted from landfill and 18.4 from incineration. Discussion Unlike GHG reduction st…
bibliographic citation: McPherson et al. (2019) The impact on life cycle carbon footprint of converting from disposable to reusable sharps containers in a large US hospital geographically distant from manufacturing and processing facilities. PeerJ 7:e6204 https://doi.org/10.7717/peerj.6204
date submitted: 2018-02-12
date accepted: 2018-12-03
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McPherson
  given name: Brett
author list: Agent
  family name: Sharip
  given name: Mihray
author list: Agent
  family name: Grimmond
  given name: Terry
doi: 10.7717/peerj.6204
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: ©2019 McPherson et al.
attribution name: McPherson et al.

A second HD mating type sublocus of Flammulina velutipes is at least di-allelic and active: new primers for identification of HD-a and HD-b subloci
type: item
type: AcademicArticle
description: Background Sexual development in Flammulina velutipes is controlled by two different mating type loci (HD and PR). The HD locus contains homeodomain (Hd) genes on two separate HD subloci: HD-a and HD-b. While the functionality of the HD-b sublocus has been largely confirmed, the status and content of the HD-a sublocus has remained unclear. Methods To examine the function of the HD-a sublocus, genome sequences of a series of F. velutipes strains were analyzed and tested through series of amplification by specific primer sets. Furthermore, activity of di-allelic HD-a locus was confirmed by crossing strains with different combinations of HD-a and HD-b subloci. Results Sublocus HD-b contained a large variety of fixed Hd1/Hd2 gene pairs, while the HD-a sublocus either contained a conserved Hd2 gene or, a newly discovered Hd1 gene that was also conserved. Identification of whole HD loci, that is, the contents of HD-a and HD-b subloci in a strain, revealed that strains with similar HD-b subloci could still form normal dikaryons if the two genes at the HD-a sublocus differed. At least di-allelic HD-a sublocus, is thus indicated to be actively involved in mating type compatibility. Conclusions HD-a sublocus is active and di-allelic. Using the new information on the HD subloci, primers sets were developed that specifically amplify HD-a or HD-b subloci in the majority of F. velutipes strains. In this way, unknown HD mating types of F. velutipes can now be quickly identified, and HD mating type compatibility conferred by HD-a or HD-b can be confirmed by PCR.
format: application/pdf
format: text/html
creator: Wei Wang
creator: Irum Mukhtar
creator: Tiansheng Chou
creator: Siyuan Jiang
creator: Xinrui Liu
creator: Arend F. van Peer
creator: Baogui Xie
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.6292
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Sexual development in Flammulina velutipes is controlled by two different mating type loci (HD and PR). The HD locus contains homeodomain (Hd) genes on two separate HD subloci: HD-a and HD-b. While the functionality of the HD-b sublocus has been largely confirmed, the status and content of the HD-a sublocus has remained unclear. Methods To examine the function of the HD-a sublocus, genome sequences of a series of F. velutipes strains were analyzed and tested through series of amplification by specific primer sets. Furthermore, activity of di-allelic HD-a locus was confirmed by crossing strains with different combinations of HD-a and HD-b subloci. Results Sublocus HD-b contained a large variety of fixed Hd1/Hd2 gene pairs, while the HD-a sublocus either contained a conserved Hd2 gene or, a newly discovered Hd1 gene that was also conserved. Identification of whole HD loci, that is, the contents of HD-a and HD-b subloci in a strain, revealed that strains with similar HD-b subloci could still form normal dikaryons if the two genes at the HD-a sublocus differed. At least di-allelic HD-a sublocus, is thus indicated to be actively involved in mating type compatibility. Conclusions HD-a sublocus is active and di-allelic. Using the new information on the HD subloci, primers sets were developed that specifically amplify HD-a or HD-b subloci in the majority of F. velutipes strains. In this way, unknown HD mating types of F. velutipes can now be quickly identified, and HD mating type compatibility conferred by HD-a or HD-b can be confirmed by PCR.
bibliographic citation: Wang et al. (2019) A second HD mating type sublocus of Flammulina velutipes is at least di-allelic and active: new primers for identification of HD-a and HD-b subloci. PeerJ 7:e6292 https://doi.org/10.7717/peerj.6292
date submitted: 2018-08-17
date accepted: 2018-12-17
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Mukhtar
  given name: Irum
author list: Agent
  family name: Chou
  given name: Tiansheng
author list: Agent
  family name: Jiang
  given name: Siyuan
author list: Agent
  family name: Liu
  given name: Xinrui
author list: Agent
  family name: van Peer
  given name: Arend F.
author list: Agent
  family name: Xie
  given name: Baogui
doi: 10.7717/peerj.6292
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Grazing exclosures solely are not the best methods for sustaining alpine grasslands
type: item
type: AcademicArticle
description: Background Grazing is widely regarded as a critical factor affecting the vegetation structure, productivity and nutritional value of natural grasslands. To protect and restore degraded grasslands, non-grazed exclosures are considered as a valuable tool. However, it is not clear whether long term non-grazed exclosures of grazers can improve the condition and nutritional value of vegetation and soil properties. Methods We have compared the impact of long-term non-grazed and continuous grazed management strategy on vegetation structure, nutritional values and soil properties of alpine meadow of the Qinghai-Tibet Plateau by field investigation (11–13 years) and indoor analysis during 2015–2017. Results Our results showed that long-term non-grazed exclosures clearly increased the aboveground biomass and coverage of plant functional types. Long-term non-grazed exclosures improved the development of all vegetation types, except NG (GG, grass species type; SG, sedge species type; LG, leguminous species type; FG, forbs species type and NG, noxious species type). Long-term non-grazed exclosures significantly improved all six measured soil properties (TN, total nitrogen; TP, total phosphorus; TK, total potassium; AN, available nitrogen; AP, available phosphorus and AK, available potassium) in 0–10 cm soil layer, considerable effect on the improvement of all measured soil properties, except TK in 10–20 cm soil layer and all measured soil properties, except TN and TK in 20–30 cm soil layer were observed. However, long-term non-grazed exclosures significantly decreased biodiversity indicators i.e., species richness, Shannon diversity index and Evenness index of vegetation. A substantial decrease in the density, biodiversity and nutritional values (CP (crude protein), IVTD (in vitro ture digestibility) and NDF (neutral detergent fiber)) of all vegetation types, except NG were recorded. While a downward trend in aboveground biomass and all measured soil properties except TP and TK …
format: application/pdf
format: text/html
creator: Xixi Yao
creator: Jianping Wu
creator: Xuyin Gong
creator: Xia Lang
creator: Cailian Wang
subject: Ecology
description: doi:10.7717/peerj.6462
publisher: PeerJ Inc.
rights: © 2019 Yao et al.
abstract: Background Grazing is widely regarded as a critical factor affecting the vegetation structure, productivity and nutritional value of natural grasslands. To protect and restore degraded grasslands, non-grazed exclosures are considered as a valuable tool. However, it is not clear whether long term non-grazed exclosures of grazers can improve the condition and nutritional value of vegetation and soil properties. Methods We have compared the impact of long-term non-grazed and continuous grazed management strategy on vegetation structure, nutritional values and soil properties of alpine meadow of the Qinghai-Tibet Plateau by field investigation (11–13 years) and indoor analysis during 2015–2017. Results Our results showed that long-term non-grazed exclosures clearly increased the aboveground biomass and coverage of plant functional types. Long-term non-grazed exclosures improved the development of all vegetation types, except NG (GG, grass species type; SG, sedge species type; LG, leguminous species type; FG, forbs species type and NG, noxious species type). Long-term non-grazed exclosures significantly improved all six measured soil properties (TN, total nitrogen; TP, total phosphorus; TK, total potassium; AN, available nitrogen; AP, available phosphorus and AK, available potassium) in 0–10 cm soil layer, considerable effect on the improvement of all measured soil properties, except TK in 10–20 cm soil layer and all measured soil properties, except TN and TK in 20–30 cm soil layer were observed. However, long-term non-grazed exclosures significantly decreased biodiversity indicators i.e., species richness, Shannon diversity index and Evenness index of vegetation. A substantial decrease in the density, biodiversity and nutritional values (CP (crude protein), IVTD (in vitro ture digestibility) and NDF (neutral detergent fiber)) of all vegetation types, except NG were recorded. While a downward trend in aboveground biomass and all measured soil properties except TP and TK …
bibliographic citation: Yao et al. (2019) Grazing exclosures solely are not the best methods for sustaining alpine grasslands. PeerJ 7:e6462 https://doi.org/10.7717/peerj.6462
date submitted: 2018-10-23
date accepted: 2019-01-16
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Xixi
author list: Agent
  family name: Wu
  given name: Jianping
author list: Agent
  family name: Gong
  given name: Xuyin
author list: Agent
  family name: Lang
  given name: Xia
author list: Agent
  family name: Wang
  given name: Cailian
doi: 10.7717/peerj.6462
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: ©2019 Yao et al.
attribution name: Yao et al.

The tetrapod fauna of the upper Permian Naobaogou Formation of China: 3. Jiufengia jiai gen. et sp. nov., a large akidnognathid therocephalian
type: item
type: AcademicArticle
description: Recent field trips to Member III of the Naobaogou Formation, Nei Mongol, China yielded new fossil discoveries, increasing our knowledge of the late Permian continental fauna from China. We present here a new large therocephalian, Jiufengia jiai gen. et sp. nov., represented by a partial skull with mandibles and part of the postcranial skeleton. This is the second therocephalian recovered from the Naobaogou faunal association and, in turn, the second akidnognathid from this unit and from China. The new taxon shows clear differences from Shiguaignathus wangi, the akidnogathid previously reported from the Naobaogou Formation: the presence of four upper postcanines, of a large suborbital vacuity, and the flat ventral surface of the vomer, lacking a ventromedian crest. Updating a previous phylogeny of therocephalians, we recover the new species as a basal member of Akidnognathidae, above a basal polytomy including the other two Laurasian akidnognathids, Shiguaignathus and Annatherapsidus, adding support to the hypothesis that this group originated in Laurasia.
format: application/pdf
format: text/html
creator: Jun Liu
creator: Fernando Abdala
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6463
publisher: PeerJ Inc.
rights: © 2019 Liu and Abdala
abstract: Recent field trips to Member III of the Naobaogou Formation, Nei Mongol, China yielded new fossil discoveries, increasing our knowledge of the late Permian continental fauna from China. We present here a new large therocephalian, Jiufengia jiai gen. et sp. nov., represented by a partial skull with mandibles and part of the postcranial skeleton. This is the second therocephalian recovered from the Naobaogou faunal association and, in turn, the second akidnognathid from this unit and from China. The new taxon shows clear differences from Shiguaignathus wangi, the akidnogathid previously reported from the Naobaogou Formation: the presence of four upper postcanines, of a large suborbital vacuity, and the flat ventral surface of the vomer, lacking a ventromedian crest. Updating a previous phylogeny of therocephalians, we recover the new species as a basal member of Akidnognathidae, above a basal polytomy including the other two Laurasian akidnognathids, Shiguaignathus and Annatherapsidus, adding support to the hypothesis that this group originated in Laurasia.
bibliographic citation: Liu et al. (2019) The tetrapod fauna of the upper Permian Naobaogou Formation of China: 3. Jiufengia jiai gen. et sp. nov., a large akidnognathid therocephalian. PeerJ 7:e6463 https://doi.org/10.7717/peerj.6463
date submitted: 2018-09-11
date accepted: 2019-01-15
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Jun
author list: Agent
  family name: Abdala
  given name: Fernando
doi: 10.7717/peerj.6463
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: © 2019 Liu and Abdala
attribution name: Liu and Abdala

Epidemiology and spatial distribution of bluetongue virus in Xinjiang, China
type: item
type: AcademicArticle
description: Bluetongue (BT) is a non-contagious disease affecting domestic and wild ruminants. Outbreaks of BT can cause serious economic losses. To investigate the distribution characteristics of bluetongue virus (BTV), two large-scale censuses of BTV prevalence in Xinjiang, China were collected. Spatial autocorrelation analysis, including global spatial autocorrelation and local spatial autocorrelation, was performed. Risk areas for BTV occurrence in Xinjiang were detected using the presence-only maximum entropy model. The global spatial autocorrelation of BTV distribution in Xinjiang in 2012 showed a random pattern. In contrast, the spatial distribution of BTV from 2014 to 2015 was significantly clustered. The hotspot areas for BTV infection included Balikun County (p < 0.05), Yiwu County (p < 0.05) and Hami City (p < 0.05) in 2012. These three regions were also hotspot areas during 2014 and 2015. Sheep distribution (25.6% contribution), precipitation seasonality (22.1% contribution) and mean diurnal range (16.2% contribution) were identified as the most important predictors for BTV occurrence in Xinjiang. This study demonstrated the presence of high-risk areas for BTV infection in Xinjiang, which can serve as a tool to aid in the development of preventative countermeasures of BT outbreaks.
format: application/pdf
format: text/html
creator: Jun Ma
creator: Xiang Gao
creator: Boyang Liu
creator: Hao Chen
creator: Jianhua Xiao
creator: Hongbin Wang
subject: Agricultural Science
subject: Microbiology
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.6514
publisher: PeerJ Inc.
rights: © 2019 Ma et al.
abstract: Bluetongue (BT) is a non-contagious disease affecting domestic and wild ruminants. Outbreaks of BT can cause serious economic losses. To investigate the distribution characteristics of bluetongue virus (BTV), two large-scale censuses of BTV prevalence in Xinjiang, China were collected. Spatial autocorrelation analysis, including global spatial autocorrelation and local spatial autocorrelation, was performed. Risk areas for BTV occurrence in Xinjiang were detected using the presence-only maximum entropy model. The global spatial autocorrelation of BTV distribution in Xinjiang in 2012 showed a random pattern. In contrast, the spatial distribution of BTV from 2014 to 2015 was significantly clustered. The hotspot areas for BTV infection included Balikun County (p < 0.05), Yiwu County (p < 0.05) and Hami City (p < 0.05) in 2012. These three regions were also hotspot areas during 2014 and 2015. Sheep distribution (25.6% contribution), precipitation seasonality (22.1% contribution) and mean diurnal range (16.2% contribution) were identified as the most important predictors for BTV occurrence in Xinjiang. This study demonstrated the presence of high-risk areas for BTV infection in Xinjiang, which can serve as a tool to aid in the development of preventative countermeasures of BT outbreaks.
bibliographic citation: Ma et al. (2019) Epidemiology and spatial distribution of bluetongue virus in Xinjiang, China. PeerJ 7:e6514 https://doi.org/10.7717/peerj.6514
date submitted: 2018-10-08
date accepted: 2019-01-25
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Jun
author list: Agent
  family name: Gao
  given name: Xiang
author list: Agent
  family name: Liu
  given name: Boyang
author list: Agent
  family name: Chen
  given name: Hao
author list: Agent
  family name: Xiao
  given name: Jianhua
author list: Agent
  family name: Wang
  given name: Hongbin
doi: 10.7717/peerj.6514
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: © 2019 Ma et al.
attribution name: Ma et al.

Experimental investigation on the effects of website aesthetics on user performance in different virtual tasks
type: item
type: AcademicArticle
description: In Human-Computer Interaction research, the positive effect of aesthetics on users’ subjective impressions and reactions is well-accepted. However, results regarding the influence of interface aesthetics on a user’s individual performance as an objective outcome are very mixed, yet of urgent interest due to the proceeding of digitalization. In this web-based experiment (N = 331), the effect of interface aesthetics on individual performance considering three different types of tasks (search, creative, and transfer tasks) is investigated. The tasks were presented on an either aesthetic or unaesthetic website, which differed significantly in subjective aesthetics. Goal orientation (learning versus performance goals) was included as a possible moderator variable, which was manipulated by using different task instructions. Both aesthetics and goal orientation were a between-subject factor, leading to a 2 × 2 between subject design. Manipulation checks were highly significant. Yet the results show neither significant main effects of aesthetics and goal orientation on performance regarding both accuracy and response times in each of the three tasks, nor significant interaction effects. Nevertheless, from a practical perspective aesthetics still should be considered due to its positive effects on subjective perceptions of users, even as no substantial effects on user performance occurred in the present experiment.
format: application/pdf
format: text/html
creator: Meinald T. Thielsch
creator: Russell Haines
creator: Leonie Flacke
subject: Human–Computer Interaction
subject: World Wide Web and Web Science
description: doi:10.7717/peerj.6516
publisher: PeerJ Inc.
rights: © 2019 Thielsch et al.
abstract: In Human-Computer Interaction research, the positive effect of aesthetics on users’ subjective impressions and reactions is well-accepted. However, results regarding the influence of interface aesthetics on a user’s individual performance as an objective outcome are very mixed, yet of urgent interest due to the proceeding of digitalization. In this web-based experiment (N = 331), the effect of interface aesthetics on individual performance considering three different types of tasks (search, creative, and transfer tasks) is investigated. The tasks were presented on an either aesthetic or unaesthetic website, which differed significantly in subjective aesthetics. Goal orientation (learning versus performance goals) was included as a possible moderator variable, which was manipulated by using different task instructions. Both aesthetics and goal orientation were a between-subject factor, leading to a 2 × 2 between subject design. Manipulation checks were highly significant. Yet the results show neither significant main effects of aesthetics and goal orientation on performance regarding both accuracy and response times in each of the three tasks, nor significant interaction effects. Nevertheless, from a practical perspective aesthetics still should be considered due to its positive effects on subjective perceptions of users, even as no substantial effects on user performance occurred in the present experiment.
bibliographic citation: Thielsch et al. (2019) Experimental investigation on the effects of website aesthetics on user performance in different virtual tasks. PeerJ 7:e6516 https://doi.org/10.7717/peerj.6516
date submitted: 2018-03-07
date accepted: 2019-01-25
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thielsch
  given name: Meinald T.
author list: Agent
  family name: Haines
  given name: Russell
author list: Agent
  family name: Flacke
  given name: Leonie
doi: 10.7717/peerj.6516
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: ©2019 Thielsch et al.
attribution name: Thielsch et al.

From data compilation to model validation: a comprehensive analysis of a full deep-sea ecosystem model of the Chatham Rise
type: item
type: AcademicArticle
description: The Chatham Rise is a highly productive deep-sea ecosystem that supports numerous substantial commercial fisheries, and is a likely candidate for an ecosystem based approach to fisheries management in New Zealand. We present the first end-to-end ecosystem model of the Chatham Rise, which is also to the best of our knowledge, the first end-to-end ecosystem model of any deep-sea ecosystem. We describe the process of data compilation through to model validation and analyse the importance of knowledge gaps with respect to model dynamics and results. The model produces very similar results to fisheries stock assessment models for key fisheries species, and the population dynamics and system interactions are realistic. Confidence intervals based on bootstrapping oceanographic variables are produced. The model components that have knowledge gaps and are most likely to influence model results were oceanographic variables, and the aggregate species groups ‘seabird’ and ‘cetacean other’. We recommend applications of the model, such as forecasting biomasses under various fishing regimes, include alternatives that vary these components.
format: application/pdf
format: text/html
creator: Vidette L. McGregor
creator: Peter L. Horn
creator: Elizabeth A. Fulton
creator: Matthew R. Dunn
subject: Fisheries and Fish Science
subject: Ecology
subject: Ecosystem Science
subject: Mathematical Biology
subject: Population Biology
description: doi:10.7717/peerj.6517
publisher: PeerJ Inc.
rights: © 2019 McGregor et al.
abstract: The Chatham Rise is a highly productive deep-sea ecosystem that supports numerous substantial commercial fisheries, and is a likely candidate for an ecosystem based approach to fisheries management in New Zealand. We present the first end-to-end ecosystem model of the Chatham Rise, which is also to the best of our knowledge, the first end-to-end ecosystem model of any deep-sea ecosystem. We describe the process of data compilation through to model validation and analyse the importance of knowledge gaps with respect to model dynamics and results. The model produces very similar results to fisheries stock assessment models for key fisheries species, and the population dynamics and system interactions are realistic. Confidence intervals based on bootstrapping oceanographic variables are produced. The model components that have knowledge gaps and are most likely to influence model results were oceanographic variables, and the aggregate species groups ‘seabird’ and ‘cetacean other’. We recommend applications of the model, such as forecasting biomasses under various fishing regimes, include alternatives that vary these components.
bibliographic citation: McGregor et al. (2019) From data compilation to model validation: a comprehensive analysis of a full deep-sea ecosystem model of the Chatham Rise. PeerJ 7:e6517 https://doi.org/10.7717/peerj.6517
date submitted: 2018-08-14
date accepted: 2019-01-25
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McGregor
  given name: Vidette L.
author list: Agent
  family name: Horn
  given name: Peter L.
author list: Agent
  family name: Fulton
  given name: Elizabeth A.
author list: Agent
  family name: Dunn
  given name: Matthew R.
doi: 10.7717/peerj.6517
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: © 2019 McGregor et al.
attribution name: McGregor et al.

Tracking down the lizards from Gravenhorst's collection at the University of Wrocław: type specimens of Callopistes maculatus Gravenhorst, 1838 and three Liolaemus species rediscovered
type: item
type: AcademicArticle
description: Johann Ludwig Christian Gravenhorst’s herpetological collection at the Museum of Natural History, University of Wrocław included numerous important specimens of amphibians and reptiles. The majority, if not the entirety, of this collection has long been thought to be lost. However, we were able to rediscover some type specimens of lizards. The rediscovered specimens include the holotypes of Liolaemus conspersus and L. hieroglyphicus, one syntype of Callopistes maculatus (here designated as the lectotype) and two syntypes of L. lineatus (one of which is herein designated as the lectotype). Reexamination of these specimens indicates that previous synonymies proposed for L. conspersus and two syntypes of L. hieroglyphicus are problematic; furthermore, more complex taxonomic work is needed to resolve this issue. Two rediscovered syntypes of L. lineatus differ in several scalation traits and are possibly not conspecific. The type specimens of several other species of lizards from Gravenhorst’s collection (Liolaemus marmoratus, L. unicolor and two other syntypes of L. lineatus, Leiocephalus schreibersii and Chalcides viridanus) were not found and are probably lost.
format: application/pdf
format: text/html
creator: Bartosz Borczyk
creator: Tomasz Skawiński
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6525
publisher: PeerJ Inc.
rights: © 2019 Borczyk and Skawiński
abstract: Johann Ludwig Christian Gravenhorst’s herpetological collection at the Museum of Natural History, University of Wrocław included numerous important specimens of amphibians and reptiles. The majority, if not the entirety, of this collection has long been thought to be lost. However, we were able to rediscover some type specimens of lizards. The rediscovered specimens include the holotypes of Liolaemus conspersus and L. hieroglyphicus, one syntype of Callopistes maculatus (here designated as the lectotype) and two syntypes of L. lineatus (one of which is herein designated as the lectotype). Reexamination of these specimens indicates that previous synonymies proposed for L. conspersus and two syntypes of L. hieroglyphicus are problematic; furthermore, more complex taxonomic work is needed to resolve this issue. Two rediscovered syntypes of L. lineatus differ in several scalation traits and are possibly not conspecific. The type specimens of several other species of lizards from Gravenhorst’s collection (Liolaemus marmoratus, L. unicolor and two other syntypes of L. lineatus, Leiocephalus schreibersii and Chalcides viridanus) were not found and are probably lost.
bibliographic citation: Borczyk et al. (2019) Tracking down the lizards from Gravenhorst's collection at the University of Wrocław: type specimens of Callopistes maculatus Gravenhorst, 1838 and three Liolaemus species rediscovered. PeerJ 7:e6525 https://doi.org/10.7717/peerj.6525
date submitted: 2018-10-10
date accepted: 2019-01-26
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Borczyk
  given name: Bartosz
author list: Agent
  family name: Skawiński
  given name: Tomasz
doi: 10.7717/peerj.6525
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: © 2019 Borczyk and Skawiński
attribution name: Borczyk and Skawiński

The response of sulfur dioxygenase to sulfide in the body wall of Urechis unincinctus
type: item
type: AcademicArticle
description: Background In some sedimentary environments, such as coastal intertidal and subtidal mudflats, sulfide levels can reach millimolar concentrations (2–5 mM) and can be toxic to marine species. Interestingly, some organisms have evolved biochemical strategies to overcome and tolerate high sulfide conditions, such as the echiuran worm, Urechis unicinctus. Mitochondrial sulfide oxidation is important for detoxification, in which sulfur dioxygenase (SDO) plays an indispensable role. Meanwhile, the body wall of the surface of the worm is in direct contact with sulfide. In our study, we chose the body wall to explore the SDO response to sulfide. Methods Two sulfide treatment groups (50 µM and 150 µM) and a control group (natural seawater) were used. The worms, U. unicinctus, were collected from the intertidal flat of Yantai, China, and temporarily reared in aerated seawater for three days without feeding. Finally, sixty worms with similar length and mass were evenly assigned to the three groups. The worms were sampled at 0, 6, 24, 48 and 72 h after initiation of sulfide exposure. The body walls were excised, frozen in liquid nitrogen and stored at −80 °C for RNA and protein extraction. Real-time quantitative RT-PCR, enzyme-linked immunosorbent assay and specific activity detection were used to explore the SDO response to sulfide in the body wall. Results The body wall of U. unicinctus consists of a rugal epidermis, connective tissue, outer circular muscle and middle longitudinal muscle. SDO protein is mainly located in the epidermis. When exposed to 50 µM sulfide, SDO mRNA and protein contents almost remained stable, but SDO activity increased significantly after 6 h (P < 0.05). However, in the 150 µM sulfide treatment group, SDO mRNA and protein contents and activity all increased with sulfide exposure time; significant increases all began to occur at 48 h (P < 0.05). Discussion All the results indicated that SDO activity can be enhanced by sulfide in two regulation mechan…
format: application/pdf
format: text/html
creator: Litao Zhang
creator: Zhifeng Zhang
subject: Marine Biology
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.6544
publisher: PeerJ Inc.
rights: © 2019 Zhang and Zhang
abstract: Background In some sedimentary environments, such as coastal intertidal and subtidal mudflats, sulfide levels can reach millimolar concentrations (2–5 mM) and can be toxic to marine species. Interestingly, some organisms have evolved biochemical strategies to overcome and tolerate high sulfide conditions, such as the echiuran worm, Urechis unicinctus. Mitochondrial sulfide oxidation is important for detoxification, in which sulfur dioxygenase (SDO) plays an indispensable role. Meanwhile, the body wall of the surface of the worm is in direct contact with sulfide. In our study, we chose the body wall to explore the SDO response to sulfide. Methods Two sulfide treatment groups (50 µM and 150 µM) and a control group (natural seawater) were used. The worms, U. unicinctus, were collected from the intertidal flat of Yantai, China, and temporarily reared in aerated seawater for three days without feeding. Finally, sixty worms with similar length and mass were evenly assigned to the three groups. The worms were sampled at 0, 6, 24, 48 and 72 h after initiation of sulfide exposure. The body walls were excised, frozen in liquid nitrogen and stored at −80 °C for RNA and protein extraction. Real-time quantitative RT-PCR, enzyme-linked immunosorbent assay and specific activity detection were used to explore the SDO response to sulfide in the body wall. Results The body wall of U. unicinctus consists of a rugal epidermis, connective tissue, outer circular muscle and middle longitudinal muscle. SDO protein is mainly located in the epidermis. When exposed to 50 µM sulfide, SDO mRNA and protein contents almost remained stable, but SDO activity increased significantly after 6 h (P < 0.05). However, in the 150 µM sulfide treatment group, SDO mRNA and protein contents and activity all increased with sulfide exposure time; significant increases all began to occur at 48 h (P < 0.05). Discussion All the results indicated that SDO activity can be enhanced by sulfide in two regulation mechan…
bibliographic citation: Zhang et al. (2019) The response of sulfur dioxygenase to sulfide in the body wall of Urechis unincinctus. PeerJ 7:e6544 https://doi.org/10.7717/peerj.6544
date submitted: 2018-09-18
date accepted: 2019-01-26
issued: 2019-02-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Litao
author list: Agent
  family name: Zhang
  given name: Zhifeng
doi: 10.7717/peerj.6544
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-22
copyright: ©2019 Zhang and Zhang
attribution name: Zhang and Zhang

Diversity, spatial distribution and activity of fungi in freshwater ecosystems
type: item
type: AcademicArticle
description: High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.
format: application/pdf
format: text/html
creator: Cécile Lepère
creator: Isabelle Domaizon
creator: Jean-Francois Humbert
creator: Ludwig Jardillier
creator: Mylène Hugoni
creator: Didier Debroas
subject: Biodiversity
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.6247
publisher: PeerJ Inc.
rights: © 2019 Lepère et al.
abstract: High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.
bibliographic citation: Lepère et al. (2019) Diversity, spatial distribution and activity of fungi in freshwater ecosystems. PeerJ 7:e6247 https://doi.org/10.7717/peerj.6247
date submitted: 2018-09-07
date accepted: 2018-11-30
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lepère
  given name: Cécile
author list: Agent
  family name: Domaizon
  given name: Isabelle
author list: Agent
  family name: Humbert
  given name: Jean-Francois
author list: Agent
  family name: Jardillier
  given name: Ludwig
author list: Agent
  family name: Hugoni
  given name: Mylène
author list: Agent
  family name: Debroas
  given name: Didier
doi: 10.7717/peerj.6247
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: ©2019 Lepère et al.
attribution name: Lepère et al.

What does a Pacman eat? Macrophagy and necrophagy in a generalist predator (Ceratophrys stolzmanni)
type: item
type: AcademicArticle
description: We describe for the first time the feeding ecology of the Pacific horned frog (Ceratophrys stolzmanni), as inferred through gastrointestinal tract content analysis and behavioural observations in its natural habitat. Ingested prey in adults ranged from mites and various insects to frogs and snakes. Prey items predominantly consisted of gastropods, non-formicid hymenopterans, and centipedes. We found no relationship between the size of the predator and the prey ingested, in terms of prey size, volume or number of items ingested. Additional direct observations indicate that all post-metamorphic stages are voracious, preying on vertebrates and engaging in anurophagy, cannibalism, and even necrophagy. Our study sheds light on the feeding habits of one of the least known species of horned frog.
format: application/pdf
format: text/html
creator: Diana Székely
creator: Fernando P. Gaona
creator: Paul Székely
creator: Dan Cogălniceanu
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.6406
publisher: PeerJ Inc.
rights: © 2019 Székely et al.
abstract: We describe for the first time the feeding ecology of the Pacific horned frog (Ceratophrys stolzmanni), as inferred through gastrointestinal tract content analysis and behavioural observations in its natural habitat. Ingested prey in adults ranged from mites and various insects to frogs and snakes. Prey items predominantly consisted of gastropods, non-formicid hymenopterans, and centipedes. We found no relationship between the size of the predator and the prey ingested, in terms of prey size, volume or number of items ingested. Additional direct observations indicate that all post-metamorphic stages are voracious, preying on vertebrates and engaging in anurophagy, cannibalism, and even necrophagy. Our study sheds light on the feeding habits of one of the least known species of horned frog.
bibliographic citation: Székely et al. (2019) What does a Pacman eat? Macrophagy and necrophagy in a generalist predator (Ceratophrys stolzmanni). PeerJ 7:e6406 https://doi.org/10.7717/peerj.6406
date submitted: 2018-09-14
date accepted: 2019-01-08
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Székely
  given name: Diana
author list: Agent
  family name: Gaona
  given name: Fernando P.
author list: Agent
  family name: Székely
  given name: Paul
author list: Agent
  family name: Cogălniceanu
  given name: Dan
doi: 10.7717/peerj.6406
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: © 2019 Székely et al.
attribution name: Székely et al.

Lower rotational inertia and larger leg muscles indicate more rapid turns in tyrannosaurids than in other large theropods
type: item
type: AcademicArticle
description: Synopsis Tyrannosaurid dinosaurs had large preserved leg muscle attachments and low rotational inertia relative to their body mass, indicating that they could turn more quickly than other large theropods. Methods To compare turning capability in theropods, we regressed agility estimates against body mass, incorporating superellipse-based modeled mass, centers of mass, and rotational inertia (mass moment of inertia). Muscle force relative to body mass is a direct correlate of agility in humans, and torque gives potential angular acceleration. Agility scores therefore include rotational inertia values divided by proxies for (1) muscle force (ilium area and estimates of m. caudofemoralis longus cross-section), and (2) musculoskeletal torque. Phylogenetic ANCOVA (phylANCOVA) allow assessment of differences in agility between tyrannosaurids and non-tyrannosaurid theropods (accounting for both ontogeny and phylogeny). We applied conditional error probabilities a(p) to stringently test the null hypothesis of equal agility. Results Tyrannosaurids consistently have agility index magnitudes twice those of allosauroids and some other theropods of equivalent mass, turning the body with both legs planted or pivoting over a stance leg. PhylANCOVA demonstrates definitively greater agilities in tyrannosaurids, and phylogeny explains nearly all covariance. Mass property results are consistent with those of other studies based on skeletal mounts, and between different figure-based methods (our main mathematical slicing procedures, lofted 3D computer models, and simplified graphical double integration). Implications The capacity for relatively rapid turns in tyrannosaurids is ecologically intriguing in light of their monopolization of large (>400 kg), toothed dinosaurian predator niches in their habitats.
format: application/pdf
format: text/html
creator: Eric Snively
creator: Haley O’Brien
creator: Donald M. Henderson
creator: Heinrich Mallison
creator: Lara A. Surring
creator: Michael E. Burns
creator: Thomas R. Holtz
creator: Anthony P. Russell
creator: Lawrence M. Witmer
creator: Philip J. Currie
creator: Scott A. Hartman
creator: John R. Cotton
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.6432
publisher: PeerJ Inc.
rights: © 2019 Snively et al.
abstract: Synopsis Tyrannosaurid dinosaurs had large preserved leg muscle attachments and low rotational inertia relative to their body mass, indicating that they could turn more quickly than other large theropods. Methods To compare turning capability in theropods, we regressed agility estimates against body mass, incorporating superellipse-based modeled mass, centers of mass, and rotational inertia (mass moment of inertia). Muscle force relative to body mass is a direct correlate of agility in humans, and torque gives potential angular acceleration. Agility scores therefore include rotational inertia values divided by proxies for (1) muscle force (ilium area and estimates of m. caudofemoralis longus cross-section), and (2) musculoskeletal torque. Phylogenetic ANCOVA (phylANCOVA) allow assessment of differences in agility between tyrannosaurids and non-tyrannosaurid theropods (accounting for both ontogeny and phylogeny). We applied conditional error probabilities a(p) to stringently test the null hypothesis of equal agility. Results Tyrannosaurids consistently have agility index magnitudes twice those of allosauroids and some other theropods of equivalent mass, turning the body with both legs planted or pivoting over a stance leg. PhylANCOVA demonstrates definitively greater agilities in tyrannosaurids, and phylogeny explains nearly all covariance. Mass property results are consistent with those of other studies based on skeletal mounts, and between different figure-based methods (our main mathematical slicing procedures, lofted 3D computer models, and simplified graphical double integration). Implications The capacity for relatively rapid turns in tyrannosaurids is ecologically intriguing in light of their monopolization of large (>400 kg), toothed dinosaurian predator niches in their habitats.
bibliographic citation: Snively et al. (2019) Lower rotational inertia and larger leg muscles indicate more rapid turns in tyrannosaurids than in other large theropods. PeerJ 7:e6432 https://doi.org/10.7717/peerj.6432
date submitted: 2016-09-06
date accepted: 2019-01-10
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Snively
  given name: Eric
author list: Agent
  family name: O’Brien
  given name: Haley
author list: Agent
  family name: Henderson
  given name: Donald M.
author list: Agent
  family name: Mallison
  given name: Heinrich
author list: Agent
  family name: Surring
  given name: Lara A.
author list: Agent
  family name: Burns
  given name: Michael E.
author list: Agent
  family name: Holtz
  given name: Thomas R.
author list: Agent
  family name: Russell
  given name: Anthony P.
author list: Agent
  family name: Witmer
  given name: Lawrence M.
author list: Agent
  family name: Currie
  given name: Philip J.
author list: Agent
  family name: Hartman
  given name: Scott A.
author list: Agent
  family name: Cotton
  given name: John R.
doi: 10.7717/peerj.6432
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: © 2019 Snively et al.
attribution name: Snively et al.

Comparative study on the composition of four different varieties of garlic
type: item
type: AcademicArticle
description: Garlic is used as a medicinal seasoning worldwide. The aim of this work was to compare four varieties of garlic: ‘Taicangbaipi’, ‘Ershuizao’, ‘Hongqixing’, and ‘Single-clove’; among them, ‘Ershuizao’ and ‘Hongqixing’ are unique to the Sichuan Province of China. Firstly, soluble sugar, starch, and the protein content of the garlic were analysed. There was more soluble sugar in ‘Single-clove’, total starch in ‘Hongqixing’, and protein content in ‘Ershuizao’ relative to the other three varieties, respectively. Gas chromatography–mass spectrometry analysis showed that ‘Ershuizao’ and ‘Hongqixing’ contained high levels of 5-hydroxymethylfurfural, which has antitumor, antioxidant, and cytoprotective effects. Indeed, the extracts from these two types of garlic were more effective at inhibiting tumour growth than that from the others. Moreover, the sulphide content and antimicrobial effects of ‘Ershuizao’ and ‘Hongqixing’ garlic were also higher than those of the other two types of garlic. In addition, changes observed in the membrane permeability and protein leakage suggest that the antimicrobial activity of the ‘Ershuizao’ and ‘Hongqixing’ extracts may be due to the destruction of the structural integrity of the cell membranes, leading to cell death.
format: application/pdf
format: text/html
creator: Cun Chen
creator: Jing Cai
creator: Song-qing Liu
creator: Guo-liang Qiu
creator: Xiao-gang Wu
creator: Wei Zhang
creator: Cheng Chen
creator: Wei-liang Qi
creator: Yong Wu
creator: Zhi-bin Liu
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
subject: Nutrition
description: doi:10.7717/peerj.6442
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Garlic is used as a medicinal seasoning worldwide. The aim of this work was to compare four varieties of garlic: ‘Taicangbaipi’, ‘Ershuizao’, ‘Hongqixing’, and ‘Single-clove’; among them, ‘Ershuizao’ and ‘Hongqixing’ are unique to the Sichuan Province of China. Firstly, soluble sugar, starch, and the protein content of the garlic were analysed. There was more soluble sugar in ‘Single-clove’, total starch in ‘Hongqixing’, and protein content in ‘Ershuizao’ relative to the other three varieties, respectively. Gas chromatography–mass spectrometry analysis showed that ‘Ershuizao’ and ‘Hongqixing’ contained high levels of 5-hydroxymethylfurfural, which has antitumor, antioxidant, and cytoprotective effects. Indeed, the extracts from these two types of garlic were more effective at inhibiting tumour growth than that from the others. Moreover, the sulphide content and antimicrobial effects of ‘Ershuizao’ and ‘Hongqixing’ garlic were also higher than those of the other two types of garlic. In addition, changes observed in the membrane permeability and protein leakage suggest that the antimicrobial activity of the ‘Ershuizao’ and ‘Hongqixing’ extracts may be due to the destruction of the structural integrity of the cell membranes, leading to cell death.
bibliographic citation: Chen et al. (2019) Comparative study on the composition of four different varieties of garlic. PeerJ 7:e6442 https://doi.org/10.7717/peerj.6442
date submitted: 2018-10-02
date accepted: 2019-01-13
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Cun
author list: Agent
  family name: Cai
  given name: Jing
author list: Agent
  family name: Liu
  given name: Song-qing
author list: Agent
  family name: Qiu
  given name: Guo-liang
author list: Agent
  family name: Wu
  given name: Xiao-gang
author list: Agent
  family name: Zhang
  given name: Wei
author list: Agent
  family name: Chen
  given name: Cheng
author list: Agent
  family name: Qi
  given name: Wei-liang
author list: Agent
  family name: Wu
  given name: Yong
author list: Agent
  family name: Liu
  given name: Zhi-bin
doi: 10.7717/peerj.6442
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: © 2019 Chen et al.
attribution name: Chen et al.

The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont
type: item
type: AcademicArticle
description: Background It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into at least four groups (A–D), with the A group infecting a range of arthropods, the B group infecting nematode worms, the C group infecting Culicoides biting midges, and the D group associated with the marine copepod Nitocra spinipes. To date, genome sequence has only been available for strains from groups A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A and B group, and the importance of Culicoides biting midge hosts as arbovirus vectors. Methods We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens. Results The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins do not support Cardinium from arthropod hosts as a monophyletic group, with nematode Cardinium strains nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g., ankyrin domain containing genes), and one set—characterized by DUF1703 domains—not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, 24 of which shared a common ancestor in the C group. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin. Discussion These data indicate strains of Cardinium within nematodes cluster within Cardinium stra…
format: application/pdf
format: text/html
creator: Stefanos Siozios
creator: Jack Pilgrim
creator: Alistair C. Darby
creator: Matthew Baylis
creator: Gregory D.D. Hurst
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6448
publisher: PeerJ Inc.
rights: © 2019 Siozios et al.
abstract: Background It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into at least four groups (A–D), with the A group infecting a range of arthropods, the B group infecting nematode worms, the C group infecting Culicoides biting midges, and the D group associated with the marine copepod Nitocra spinipes. To date, genome sequence has only been available for strains from groups A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A and B group, and the importance of Culicoides biting midge hosts as arbovirus vectors. Methods We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens. Results The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins do not support Cardinium from arthropod hosts as a monophyletic group, with nematode Cardinium strains nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g., ankyrin domain containing genes), and one set—characterized by DUF1703 domains—not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, 24 of which shared a common ancestor in the C group. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin. Discussion These data indicate strains of Cardinium within nematodes cluster within Cardinium stra…
bibliographic citation: Siozios et al. (2019) The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont. PeerJ 7:e6448 https://doi.org/10.7717/peerj.6448
date submitted: 2018-09-19
date accepted: 2019-01-15
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Siozios
  given name: Stefanos
author list: Agent
  family name: Pilgrim
  given name: Jack
author list: Agent
  family name: Darby
  given name: Alistair C.
author list: Agent
  family name: Baylis
  given name: Matthew
author list: Agent
  family name: Hurst
  given name: Gregory D.D.
doi: 10.7717/peerj.6448
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: © 2019 Siozios et al.
attribution name: Siozios et al.

Distribution and status of living colonies of Acropora spp. in the reef crests of a protected marine area of the Caribbean (Jardines de la Reina National Park, Cuba)
type: item
type: AcademicArticle
description: The reef crests of the Jardines de la Reina National Park (JRNP) are largely formed by Acropora palmata, but colonies of A. cervicornis and the hybrid A. prolifera are also present. This study shows spatial distribution of colonies, thickets and live fragments of these species in the fore reefs. Snorkeling was used to perform the direct observations. The maximum diameter of 4,399 colonies of A. palmata was measured and the health of 3,546 colonies was evaluated. The same was done to 168 colonies of A. cervicornis and 104 colonies of A. prolifera. The influence of the location and marine currents on a number of living colonies of A. palmata was analyzed. For such purpose, reef crests were divided into segments of 500 m. The marine park was divided into two sectors: East and West. The Caballones Channel was used as the reference dividing line. The park was also divided into five reserve zones. We counted 7,276 live colonies of Acropora spp. 1.4% was A. prolifera, 3.5% A. cervicornis and 95.1% A. palmata. There were 104 thickets of A. palmata, ranging from eight to 12 colonies, and 3,495 fragments; 0.6% was A. cervicornis and the rest A. palmata (99.4%). In the East sector, 263 colonies (3.8% of the total), six thickets (5.8%) and 32 fragments (1%) of A. palmate were recorded. In the same sector, there were 11 fragments (50%) of A.cervicornis and two (2%) colonies of A. prolifera. Health of A. palmata was evaluated as good and not so good in the study area. Health of A. cervicornis was critical and health of A. prolifera was good in all five reserve zones. There was a significant increase in the number of colonies from east to west (Χ2 = 11.5, gl = 3.0, p = 0.009). This corroborates the existence of an important abundance differences between the eastern and the western region of the JRNP. A negative relationship was observed between the number of colonies and the distance from the channel (Χ2 = 65.0, df = 3.0, p < 0.001). The influence of the channel, for the live colo…
format: application/pdf
format: text/html
creator: Leslie Hernández-Fernández
creator: Roberto González de Zayas
creator: Yunier M. Olivera
creator: Fabián Pina Amargós
creator: Claudia Bustamante López
creator: Lisadys B. Dulce Sotolongo
creator: Fernando Bretos
creator: Tamara Figueredo Martín
creator: Dayli Lladó Cabrera
creator: Francisco Salmón Moret
subject: Ecology
description: doi:10.7717/peerj.6470
publisher: PeerJ Inc.
rights: © 2019 Hernández-Fernández et al.
abstract: The reef crests of the Jardines de la Reina National Park (JRNP) are largely formed by Acropora palmata, but colonies of A. cervicornis and the hybrid A. prolifera are also present. This study shows spatial distribution of colonies, thickets and live fragments of these species in the fore reefs. Snorkeling was used to perform the direct observations. The maximum diameter of 4,399 colonies of A. palmata was measured and the health of 3,546 colonies was evaluated. The same was done to 168 colonies of A. cervicornis and 104 colonies of A. prolifera. The influence of the location and marine currents on a number of living colonies of A. palmata was analyzed. For such purpose, reef crests were divided into segments of 500 m. The marine park was divided into two sectors: East and West. The Caballones Channel was used as the reference dividing line. The park was also divided into five reserve zones. We counted 7,276 live colonies of Acropora spp. 1.4% was A. prolifera, 3.5% A. cervicornis and 95.1% A. palmata. There were 104 thickets of A. palmata, ranging from eight to 12 colonies, and 3,495 fragments; 0.6% was A. cervicornis and the rest A. palmata (99.4%). In the East sector, 263 colonies (3.8% of the total), six thickets (5.8%) and 32 fragments (1%) of A. palmate were recorded. In the same sector, there were 11 fragments (50%) of A.cervicornis and two (2%) colonies of A. prolifera. Health of A. palmata was evaluated as good and not so good in the study area. Health of A. cervicornis was critical and health of A. prolifera was good in all five reserve zones. There was a significant increase in the number of colonies from east to west (Χ2 = 11.5, gl = 3.0, p = 0.009). This corroborates the existence of an important abundance differences between the eastern and the western region of the JRNP. A negative relationship was observed between the number of colonies and the distance from the channel (Χ2 = 65.0, df = 3.0, p < 0.001). The influence of the channel, for the live colo…
bibliographic citation: Hernández-Fernández et al. (2019) Distribution and status of living colonies of Acropora spp. in the reef crests of a protected marine area of the Caribbean (Jardines de la Reina National Park, Cuba). PeerJ 7:e6470 https://doi.org/10.7717/peerj.6470
date submitted: 2018-08-26
date accepted: 2019-01-15
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Fernández
  given name: Leslie
author list: Agent
  family name: González de Zayas
  given name: Roberto
author list: Agent
  family name: Olivera
  given name: Yunier M.
author list: Agent
  family name: Pina Amargós
  given name: Fabián
author list: Agent
  family name: Bustamante López
  given name: Claudia
author list: Agent
  family name: Dulce Sotolongo
  given name: Lisadys B.
author list: Agent
  family name: Bretos
  given name: Fernando
author list: Agent
  family name: Figueredo Martín
  given name: Tamara
author list: Agent
  family name: Lladó Cabrera
  given name: Dayli
author list: Agent
  family name: Salmón Moret
  given name: Francisco
doi: 10.7717/peerj.6470
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: © 2019 Hernández-Fernández et al.
attribution name: Hernández-Fernández et al.

Seasonal variations of the ichthyoplankton assemblage in the Yangtze Estuary and its relationship with environmental factors
type: item
type: AcademicArticle
description: Seasonal variations of the ichthyoplankton assemblage and its relationship with the environment were analyzed based on four seasonal surveys during 2012. Historical data was collected to be compared with results from previous years in order to indicate the seasonal and inter-annual variation of the ichthyoplankton assemblage in the Yangtze Estuary and the adjacent waters. A total of 3,688 individuals belonging to 5 orders, 9 families, and 15 species were collected. No samples were collected in the winter cruise. In 2012, all samples were separated into four ecotypes, which is comparable with the historical data from previous years. The Engraulis japonicus was the most abundant species of all teleost fishes. The E. japonicus was captured in every season and contributed the most to the abundance of ichthyoplankton, which was greater than that of previous years. This result may be due to the periodic fluctuations of E. japonicus or from the displacement of spawning grounds offshore for environmental reasons. The diversity indices of the assemblage were significantly different among seasons, with the number and abundance of the species peaking in the spring, while richness, evenness and diversity indices peaked in the autumn. The species richness of the ichthyoplankton varied from 0.74 to 1.62, the Pielou evenness index varied from 0.10 to 0.49 and the Shannon–Wiener index varied from 0.19 to 1.04. The results of CCA analysis showed that the major factors affecting the ichthyoplankton assemblage differed throughout the seasons. Chla was the key factor affecting the ichthyoplankton in 2012. These seasonal and inter-annual variations likely resulted from migrations associated with fish spawning as well as the environment. Compared with data from previous studies, the relationship between the assemblage structure of ichthyoplankton and corresponding environmental variables have undergone a decline.
format: application/pdf
format: text/html
creator: Hui Zhang
creator: Weiwei Xian
creator: Shude Liu
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.6482
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Seasonal variations of the ichthyoplankton assemblage and its relationship with the environment were analyzed based on four seasonal surveys during 2012. Historical data was collected to be compared with results from previous years in order to indicate the seasonal and inter-annual variation of the ichthyoplankton assemblage in the Yangtze Estuary and the adjacent waters. A total of 3,688 individuals belonging to 5 orders, 9 families, and 15 species were collected. No samples were collected in the winter cruise. In 2012, all samples were separated into four ecotypes, which is comparable with the historical data from previous years. The Engraulis japonicus was the most abundant species of all teleost fishes. The E. japonicus was captured in every season and contributed the most to the abundance of ichthyoplankton, which was greater than that of previous years. This result may be due to the periodic fluctuations of E. japonicus or from the displacement of spawning grounds offshore for environmental reasons. The diversity indices of the assemblage were significantly different among seasons, with the number and abundance of the species peaking in the spring, while richness, evenness and diversity indices peaked in the autumn. The species richness of the ichthyoplankton varied from 0.74 to 1.62, the Pielou evenness index varied from 0.10 to 0.49 and the Shannon–Wiener index varied from 0.19 to 1.04. The results of CCA analysis showed that the major factors affecting the ichthyoplankton assemblage differed throughout the seasons. Chla was the key factor affecting the ichthyoplankton in 2012. These seasonal and inter-annual variations likely resulted from migrations associated with fish spawning as well as the environment. Compared with data from previous studies, the relationship between the assemblage structure of ichthyoplankton and corresponding environmental variables have undergone a decline.
bibliographic citation: Zhang et al. (2019) Seasonal variations of the ichthyoplankton assemblage in the Yangtze Estuary and its relationship with environmental factors. PeerJ 7:e6482 https://doi.org/10.7717/peerj.6482
date submitted: 2018-09-12
date accepted: 2019-01-18
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hui
author list: Agent
  family name: Xian
  given name: Weiwei
author list: Agent
  family name: Liu
  given name: Shude
doi: 10.7717/peerj.6482
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Dual mechanism of TRKB activation by anandamide through CB1 and TRPV1 receptors
type: item
type: AcademicArticle
description: Background Administration of anandamide (AEA) or 2-arachidonoylglycerol (2AG) induces CB1 coupling and activation of TRKB receptors, regulating the neuronal migration and maturation in the developing cortex. However, at higher concentrations AEA also engages vanilloid receptor TRPV1, usually with opposed consequences on behavior. Methods and Results Using primary cell cultures from the cortex of rat embryos (E18) we determined the effects of AEA on phosphorylated TRKB (pTRK). We observed that AEA (at 100 and 200 nM) induced a significant increase in pTRK levels. Such effect of AEA at 100 nM was blocked by pretreatment with the CB1 antagonist AM251 (200 nM) and, at the higher concentration of 200 nM by the TRPV1 antagonist capsazepine (200 nM), but mildly attenuated by AM251. Interestingly, the effect of AEA or capsaicin (a TRPV1 agonist, also at 200 nM) on pTRK was blocked by TRKB.Fc (a soluble form of TRKB able to bind BDNF) or capsazepine, suggesting a mechanism dependent on BDNF release. Using the marble-burying test (MBT) in mice, we observed that the local administration of ACEA (a CB1 agonist) into the prelimbic region of prefrontal cortex (PL-PFC) was sufficient to reduce the burying behavior, while capsaicin or BDNF exerted the opposite effect, increasing the number of buried marbles. In addition, both ACEA and capsaicin effects were blocked by previous administration of k252a (an antagonist of TRK receptors) into PL-PFC. The effect of systemically injected CB1 agonist WIN55,212-2 was blocked by previous administration of k252a. We also observed a partial colocalization of CB1/TRPV1/TRKB in the PL-PFC, and the localization of TRPV1 in CaMK2+ cells. Conclusion Taken together, our data indicate that anandamide engages a coordinated activation of TRKB, via CB1 and TRPV1. Thus, acting upon CB1 and TRPV1, AEA could regulate the TRKB-dependent plasticity in both pre- and postsynaptic compartments.
format: application/pdf
format: text/html
creator: Cassiano R.A.F. Diniz
creator: Caroline Biojone
creator: Samia R.L. Joca
creator: Tomi Rantamäki
creator: Eero Castrén
creator: Francisco S. Guimarães
creator: Plinio C. Casarotto
subject: Animal Behavior
subject: Neuroscience
subject: Pharmacology
description: doi:10.7717/peerj.6493
publisher: PeerJ Inc.
rights: © 2019 Diniz et al.
abstract: Background Administration of anandamide (AEA) or 2-arachidonoylglycerol (2AG) induces CB1 coupling and activation of TRKB receptors, regulating the neuronal migration and maturation in the developing cortex. However, at higher concentrations AEA also engages vanilloid receptor TRPV1, usually with opposed consequences on behavior. Methods and Results Using primary cell cultures from the cortex of rat embryos (E18) we determined the effects of AEA on phosphorylated TRKB (pTRK). We observed that AEA (at 100 and 200 nM) induced a significant increase in pTRK levels. Such effect of AEA at 100 nM was blocked by pretreatment with the CB1 antagonist AM251 (200 nM) and, at the higher concentration of 200 nM by the TRPV1 antagonist capsazepine (200 nM), but mildly attenuated by AM251. Interestingly, the effect of AEA or capsaicin (a TRPV1 agonist, also at 200 nM) on pTRK was blocked by TRKB.Fc (a soluble form of TRKB able to bind BDNF) or capsazepine, suggesting a mechanism dependent on BDNF release. Using the marble-burying test (MBT) in mice, we observed that the local administration of ACEA (a CB1 agonist) into the prelimbic region of prefrontal cortex (PL-PFC) was sufficient to reduce the burying behavior, while capsaicin or BDNF exerted the opposite effect, increasing the number of buried marbles. In addition, both ACEA and capsaicin effects were blocked by previous administration of k252a (an antagonist of TRK receptors) into PL-PFC. The effect of systemically injected CB1 agonist WIN55,212-2 was blocked by previous administration of k252a. We also observed a partial colocalization of CB1/TRPV1/TRKB in the PL-PFC, and the localization of TRPV1 in CaMK2+ cells. Conclusion Taken together, our data indicate that anandamide engages a coordinated activation of TRKB, via CB1 and TRPV1. Thus, acting upon CB1 and TRPV1, AEA could regulate the TRKB-dependent plasticity in both pre- and postsynaptic compartments.
bibliographic citation: Diniz et al. (2019) Dual mechanism of TRKB activation by anandamide through CB1 and TRPV1 receptors. PeerJ 7:e6493 https://doi.org/10.7717/peerj.6493
date submitted: 2018-10-04
date accepted: 2019-01-21
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Diniz
  given name: Cassiano R.A.F.
author list: Agent
  family name: Biojone
  given name: Caroline
author list: Agent
  family name: Joca
  given name: Samia R.L.
author list: Agent
  family name: Rantamäki
  given name: Tomi
author list: Agent
  family name: Castrén
  given name: Eero
author list: Agent
  family name: Guimarães
  given name: Francisco S.
author list: Agent
  family name: Casarotto
  given name: Plinio C.
doi: 10.7717/peerj.6493
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: ©2019 Diniz et al.
attribution name: Diniz et al.

Subjective wellbeing at different spatial scales for individuals satisfied and dissatisfied with life
type: item
type: AcademicArticle
description: Indicators that attempt to gauge wellbeing have been created and used at multiple spatial scales around the world. The most commonly used indicators are at the national level to enable international comparisons. When analyzing subjective life satisfaction (LS), an aspect of wellbeing, at multiple spatial scales in Australia, variables (drawn from environmental, social, and economic domains) that are significantly correlated to LS at smaller scales become less significant at larger sub-national scales. The reverse is seen for other variables, which become more significant at larger scales. Regression analysis over multiple scales on three groups (1) all individuals within the sample, (2) individuals with self-reported LS as dissatisfied (LS ≤ 5), and (3) individuals self-reporting LS as satisfied (LS > 5), show that variables critical for LS differ between subgroups of the sample as well as by spatial scale. Wellbeing measures need to be created at multiple scales appropriate to the purpose of the indicator. Concurrently, policies need to address the factors that are important to wellbeing at those respective scales, segments, and values of the population.
format: application/pdf
format: text/html
creator: Ida Kubiszewski
creator: Nabeeh Zakariyya
creator: Diane Jarvis
subject: Science Policy
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.6502
publisher: PeerJ Inc.
rights: © 2019 Kubiszewski et al.
abstract: Indicators that attempt to gauge wellbeing have been created and used at multiple spatial scales around the world. The most commonly used indicators are at the national level to enable international comparisons. When analyzing subjective life satisfaction (LS), an aspect of wellbeing, at multiple spatial scales in Australia, variables (drawn from environmental, social, and economic domains) that are significantly correlated to LS at smaller scales become less significant at larger sub-national scales. The reverse is seen for other variables, which become more significant at larger scales. Regression analysis over multiple scales on three groups (1) all individuals within the sample, (2) individuals with self-reported LS as dissatisfied (LS ≤ 5), and (3) individuals self-reporting LS as satisfied (LS > 5), show that variables critical for LS differ between subgroups of the sample as well as by spatial scale. Wellbeing measures need to be created at multiple scales appropriate to the purpose of the indicator. Concurrently, policies need to address the factors that are important to wellbeing at those respective scales, segments, and values of the population.
bibliographic citation: Kubiszewski et al. (2019) Subjective wellbeing at different spatial scales for individuals satisfied and dissatisfied with life. PeerJ 7:e6502 https://doi.org/10.7717/peerj.6502
date submitted: 2018-09-21
date accepted: 2019-01-22
issued: 2019-02-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kubiszewski
  given name: Ida
author list: Agent
  family name: Zakariyya
  given name: Nabeeh
author list: Agent
  family name: Jarvis
  given name: Diane
doi: 10.7717/peerj.6502
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-21
copyright: © 2019 Kubiszewski et al.
attribution name: Kubiszewski et al.

Carbon and nitrogen isotopic composition of commercial dog food in Brazil
type: item
type: AcademicArticle
description: Background Brazil is a low- to medium-income country and has the second largest pet food market in the world with 8% of world pet food consumption. The lowest-income social class spends around 17% of their domestic budget on pet food and other items related to pets. Consumers are frequently misled by advertising as there is no precise information about the main sources of protein, carbohydrates and fat in the labels, and the Brazilian pet food industry can legally claim that their products contain certain items like salmon or beef even if they use just a flavoring compound. Methods The stable isotope methodology compares the stable isotope ratios of carbon (13C/12C) and nitrogen (15N/14N) between source and product. The 13C/12C ratio of a specific product (e.g., dog food) reveals the proportions of C4 (maize) and C3 (soybean, rice and wheat) plants in that product and the 15N/14N ratio reveals the proportion of the compounds derived from animals. With this isotopic data, we used MixSIAR, a Bayesian stable isotope-mixing model, to estimate the proportion of maize, grains, poultry and beef in dog food. Results The δ13C values of dry dog food ranged from −24.2‰ to −12.8‰, with an average (± standard-deviation) of −17.1‰ ± 2.8‰. The δ13C values of wet pet food ranged from −25.4‰ to −16.9‰, with an average (± standard-deviation) of −21.2‰ ± 2.4‰, which was significantly lower (p < 0.01). The δ15N values of the dry and wet food ranged from 1.7‰ to 4.2‰, and from 0.5‰ to 5.5‰, respectively. The average δ15N values of dry food (2.9‰ ± 0.5‰) was not higher than the wet food (2.6‰ ± 1.3‰) (p > 0.01). The output of the MixSIAR showed a low proportion of bovine products in dry dog food samples. On the other hand, poultry was obviously the dominant ingredient present in most of the samples. Maize was the second dominant ingredient. Wet and dry dog food showed similar isotopic analysis results. The only difference was a lower proportion of maize and higher proportion of grains in…
format: application/pdf
format: text/html
creator: Leonardo de Aro Galera
creator: Adibe Luiz Abdalla Filho
creator: Luiza Santos Reis
creator: Janaina Leite de Souza
creator: Yeleine Almoza Hernandez
creator: Luiz Antonio Martinelli
subject: Agricultural Science
subject: Food Science and Technology
subject: Veterinary Medicine
description: doi:10.7717/peerj.5828
publisher: PeerJ Inc.
rights: © 2019 Galera et al.
abstract: Background Brazil is a low- to medium-income country and has the second largest pet food market in the world with 8% of world pet food consumption. The lowest-income social class spends around 17% of their domestic budget on pet food and other items related to pets. Consumers are frequently misled by advertising as there is no precise information about the main sources of protein, carbohydrates and fat in the labels, and the Brazilian pet food industry can legally claim that their products contain certain items like salmon or beef even if they use just a flavoring compound. Methods The stable isotope methodology compares the stable isotope ratios of carbon (13C/12C) and nitrogen (15N/14N) between source and product. The 13C/12C ratio of a specific product (e.g., dog food) reveals the proportions of C4 (maize) and C3 (soybean, rice and wheat) plants in that product and the 15N/14N ratio reveals the proportion of the compounds derived from animals. With this isotopic data, we used MixSIAR, a Bayesian stable isotope-mixing model, to estimate the proportion of maize, grains, poultry and beef in dog food. Results The δ13C values of dry dog food ranged from −24.2‰ to −12.8‰, with an average (± standard-deviation) of −17.1‰ ± 2.8‰. The δ13C values of wet pet food ranged from −25.4‰ to −16.9‰, with an average (± standard-deviation) of −21.2‰ ± 2.4‰, which was significantly lower (p < 0.01). The δ15N values of the dry and wet food ranged from 1.7‰ to 4.2‰, and from 0.5‰ to 5.5‰, respectively. The average δ15N values of dry food (2.9‰ ± 0.5‰) was not higher than the wet food (2.6‰ ± 1.3‰) (p > 0.01). The output of the MixSIAR showed a low proportion of bovine products in dry dog food samples. On the other hand, poultry was obviously the dominant ingredient present in most of the samples. Maize was the second dominant ingredient. Wet and dry dog food showed similar isotopic analysis results. The only difference was a lower proportion of maize and higher proportion of grains in…
bibliographic citation: Galera et al. (2019) Carbon and nitrogen isotopic composition of commercial dog food in Brazil. PeerJ 7:e5828 https://doi.org/10.7717/peerj.5828
date submitted: 2018-07-09
date accepted: 2018-09-24
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Galera
  given name: Leonardo de Aro
author list: Agent
  family name: Abdalla Filho
  given name: Adibe Luiz
author list: Agent
  family name: Reis
  given name: Luiza Santos
author list: Agent
  family name: Souza
  given name: Janaina Leite de
author list: Agent
  family name: Hernandez
  given name: Yeleine Almoza
author list: Agent
  family name: Martinelli
  given name: Luiz Antonio
doi: 10.7717/peerj.5828
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: © 2019 Galera et al.
attribution name: Galera et al.

Genome organization and molecular characterization of the three Formica exsecta viruses—FeV1, FeV2 and FeV4
type: item
type: AcademicArticle
description: We present the genome organization and molecular characterization of the three Formica exsecta viruses, along with ORF predictions, and functional annotation of genes. The Formica exsecta virus-4 (FeV4; GenBank ID: MF287670) is a newly discovered negative-sense single-stranded RNA virus representing the first identified member of order Mononegavirales in ants, whereas the Formica exsecta virus-1 (FeV1; GenBank ID: KF500001), and the Formica exsecta virus-2 (FeV2; GenBank ID: KF500002) are positive single-stranded RNA viruses initially identified (but not characterized) in our earlier study. The new virus FeV4 was found by re-analyzing data from a study published earlier. The Formica exsecta virus-4 genome is 9,866 bp in size, with an overall G + C content of 44.92%, and containing five predicted open reading frames (ORFs). Our bioinformatics analysis indicates that gaps are absent and the ORFs are complete, which based on our comparative genomics analysis suggests that the genomes are complete. Following the characterization, we validate virus infection for FeV1, FeV2 and FeV4 for the first time in field-collected worker ants. Some colonies were infected by multiple viruses, and the viruses were observed to infect all castes, and multiple life stages of workers and queens. Finally, highly similar viruses were expressed in adult workers and queens of six other Formica species: F. fusca, F. pressilabris, F. pratensis, F. aquilonia, F. truncorum and F. cinerea. This research indicates that viruses can be shared between ant species, but further studies on viral transmission are needed to understand viral infection pathways.
format: application/pdf
format: text/html
creator: Kishor Dhaygude
creator: Helena Johansson
creator: Jonna Kulmuni
creator: Liselotte Sundström
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.6216
publisher: PeerJ Inc.
rights: © 2019 Dhaygude et al.
abstract: We present the genome organization and molecular characterization of the three Formica exsecta viruses, along with ORF predictions, and functional annotation of genes. The Formica exsecta virus-4 (FeV4; GenBank ID: MF287670) is a newly discovered negative-sense single-stranded RNA virus representing the first identified member of order Mononegavirales in ants, whereas the Formica exsecta virus-1 (FeV1; GenBank ID: KF500001), and the Formica exsecta virus-2 (FeV2; GenBank ID: KF500002) are positive single-stranded RNA viruses initially identified (but not characterized) in our earlier study. The new virus FeV4 was found by re-analyzing data from a study published earlier. The Formica exsecta virus-4 genome is 9,866 bp in size, with an overall G + C content of 44.92%, and containing five predicted open reading frames (ORFs). Our bioinformatics analysis indicates that gaps are absent and the ORFs are complete, which based on our comparative genomics analysis suggests that the genomes are complete. Following the characterization, we validate virus infection for FeV1, FeV2 and FeV4 for the first time in field-collected worker ants. Some colonies were infected by multiple viruses, and the viruses were observed to infect all castes, and multiple life stages of workers and queens. Finally, highly similar viruses were expressed in adult workers and queens of six other Formica species: F. fusca, F. pressilabris, F. pratensis, F. aquilonia, F. truncorum and F. cinerea. This research indicates that viruses can be shared between ant species, but further studies on viral transmission are needed to understand viral infection pathways.
bibliographic citation: Dhaygude et al. (2019) Genome organization and molecular characterization of the three Formica exsecta viruses—FeV1, FeV2 and FeV4. PeerJ 6:e6216 https://doi.org/10.7717/peerj.6216
date submitted: 2018-07-09
date accepted: 2018-12-05
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dhaygude
  given name: Kishor
author list: Agent
  family name: Johansson
  given name: Helena
author list: Agent
  family name: Kulmuni
  given name: Jonna
author list: Agent
  family name: Sundström
  given name: Liselotte
doi: 10.7717/peerj.6216
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: ©2019 Dhaygude et al.
attribution name: Dhaygude et al.

Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses
type: item
type: AcademicArticle
description: Species of the genus Populus, which is widely distributed in the northern hemisphere from subtropical to boreal forests, are among the most commercially exploited groups of forest trees. In this study, the complete chloroplast genomes of five Populus species (Populus cathayana, P. kangdingensis, P. pseudoglauca, P. schneideri, and P. xiangchengensis) were compared. The chloroplast genomes of the five Populus species are very similar. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,513, and 156,465 bp, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. The GC content was 36.7% for all plastomes. We analyzed nucleotide substitutions, small inversions, simple sequence repeats and long repeats in the chloroplast genomes and found nine divergence hotspots (ccsA+ccsA-ndhD, ndhC-trnV, psbZ-trnfM, trnG-atpA, trnL-ndhJ, trnR-trnN, ycf4-cemA, ycf1, and trnR-trnN), which could be useful molecular genetic markers for future population genetic and phylogenetic studies. We also observed that two genes (rpoC2 and rbcL) were subject to positive selection. Phylogenetic analysis based on whole cp genomes showed that P. schneideri had a close relationship with P. kangdingensis and P. pseudoglauca, while P. xiangchengensis was a sister to P. cathayana.
format: application/pdf
format: text/html
creator: Dan Zong
creator: Anpei Zhou
creator: Yao Zhang
creator: Xinlian Zou
creator: Dan Li
creator: Anan Duan
creator: Chengzhong He
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.6386
publisher: PeerJ Inc.
rights: © 2019 Zong et al.
abstract: Species of the genus Populus, which is widely distributed in the northern hemisphere from subtropical to boreal forests, are among the most commercially exploited groups of forest trees. In this study, the complete chloroplast genomes of five Populus species (Populus cathayana, P. kangdingensis, P. pseudoglauca, P. schneideri, and P. xiangchengensis) were compared. The chloroplast genomes of the five Populus species are very similar. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,513, and 156,465 bp, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes and eight rRNA genes. Seven genes were duplicated in the protein-coding genes, whereas 11 genes were duplicated in the RNA genes. The GC content was 36.7% for all plastomes. We analyzed nucleotide substitutions, small inversions, simple sequence repeats and long repeats in the chloroplast genomes and found nine divergence hotspots (ccsA+ccsA-ndhD, ndhC-trnV, psbZ-trnfM, trnG-atpA, trnL-ndhJ, trnR-trnN, ycf4-cemA, ycf1, and trnR-trnN), which could be useful molecular genetic markers for future population genetic and phylogenetic studies. We also observed that two genes (rpoC2 and rbcL) were subject to positive selection. Phylogenetic analysis based on whole cp genomes showed that P. schneideri had a close relationship with P. kangdingensis and P. pseudoglauca, while P. xiangchengensis was a sister to P. cathayana.
bibliographic citation: Zong et al. (2019) Characterization of the complete chloroplast genomes of five Populus species from the western Sichuan plateau, southwest China: comparative and phylogenetic analyses. PeerJ 7:e6386 https://doi.org/10.7717/peerj.6386
date submitted: 2018-11-05
date accepted: 2019-01-02
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zong
  given name: Dan
author list: Agent
  family name: Zhou
  given name: Anpei
author list: Agent
  family name: Zhang
  given name: Yao
author list: Agent
  family name: Zou
  given name: Xinlian
author list: Agent
  family name: Li
  given name: Dan
author list: Agent
  family name: Duan
  given name: Anan
author list: Agent
  family name: He
  given name: Chengzhong
doi: 10.7717/peerj.6386
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: © 2019 Zong et al.
attribution name: Zong et al.

Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach
type: item
type: AcademicArticle
description: Despite years of research, we are still unraveling crucial stages of gene expression regulation in cancer. On the basis of major biological hallmarks, we hypothesized that there must be a uniform gene expression pattern and regulation across cancer types. Among non-coding genes, long non-coding RNAs (lncRNAs) are emerging as key gene regulators playing powerful roles in cancer. Using TCGA RNAseq data, we analyzed coding (mRNA) and non-coding (lncRNA) gene expression across 15 and 9 common cancer types, respectively. 70 significantly differentially expressed genes common to all 15 cancer types were enlisted. Correlating with protein expression levels from Human Protein Atlas, we observed 34 positively correlated gene sets which are enriched in gene expression, transcription from RNA Pol-II, regulation of transcription and mitotic cell cycle biological processes. Further, 24 lncRNAs were among common significantly differentially expressed non-coding genes. Using guilt-by-association method, we predicted lncRNAs to be involved in same biological processes. Combining RNA-RNA interaction prediction and transcription regulatory networks, we identified E2F1, FOXM1 and PVT1 regulatory path as recurring pan-cancer regulatory entity. PVT1 is predicted to interact with SYNE1 at 3′-UTR; DNAJC9, RNPS1 at 5′-UTR and ATXN2L, ALAD, FOXM1 and IRAK1 at CDS sites. The key findings are that through E2F1, FOXM1 and PVT1 regulatory axis and possible interactions with different coding genes, PVT1 may be playing a prominent role in pan-cancer development and progression.
format: application/pdf
format: text/html
creator: Asanigari Saleembhasha
creator: Seema Mishra
subject: Computational Biology
subject: Genomics
subject: Oncology
description: doi:10.7717/peerj.6388
publisher: PeerJ Inc.
rights: © 2019 Saleembhasha and Mishra
abstract: Despite years of research, we are still unraveling crucial stages of gene expression regulation in cancer. On the basis of major biological hallmarks, we hypothesized that there must be a uniform gene expression pattern and regulation across cancer types. Among non-coding genes, long non-coding RNAs (lncRNAs) are emerging as key gene regulators playing powerful roles in cancer. Using TCGA RNAseq data, we analyzed coding (mRNA) and non-coding (lncRNA) gene expression across 15 and 9 common cancer types, respectively. 70 significantly differentially expressed genes common to all 15 cancer types were enlisted. Correlating with protein expression levels from Human Protein Atlas, we observed 34 positively correlated gene sets which are enriched in gene expression, transcription from RNA Pol-II, regulation of transcription and mitotic cell cycle biological processes. Further, 24 lncRNAs were among common significantly differentially expressed non-coding genes. Using guilt-by-association method, we predicted lncRNAs to be involved in same biological processes. Combining RNA-RNA interaction prediction and transcription regulatory networks, we identified E2F1, FOXM1 and PVT1 regulatory path as recurring pan-cancer regulatory entity. PVT1 is predicted to interact with SYNE1 at 3′-UTR; DNAJC9, RNPS1 at 5′-UTR and ATXN2L, ALAD, FOXM1 and IRAK1 at CDS sites. The key findings are that through E2F1, FOXM1 and PVT1 regulatory axis and possible interactions with different coding genes, PVT1 may be playing a prominent role in pan-cancer development and progression.
bibliographic citation: Saleembhasha et al. (2019) Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach. PeerJ 7:e6388 https://doi.org/10.7717/peerj.6388
date submitted: 2018-06-18
date accepted: 2019-01-04
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saleembhasha
  given name: Asanigari
author list: Agent
  family name: Mishra
  given name: Seema
doi: 10.7717/peerj.6388
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: ©2019 Saleembhasha and Mishra
attribution name: Saleembhasha and Mishra

Fecal microbiota transplantation research output from 2004 to 2017: a bibliometric analysis
type: item
type: AcademicArticle
description: Background Fecal microbiota transplantation (FMT) is an emerging therapy against Clostridium difficile infection (CDI) and inflammatory bowel disease (IBD). Although the therapy has gained prominence, there has been no bibliometric analysis of FMT. Methods Studies published from 2004 to 2017 were extracted from the Science Citation Index Expanded. Bibliometric analysis was used to evaluate the number or cooperation network of publications, countries, citations, references, journals, authors, institutions and keywords. Results A total of 796 items were included, showing an increasing trend annually. Publications mainly came from 10 countries, led by the US (n = 363). In the top 100 articles ranked by the number of citations (range 47–1,158), American Journal of Gastroenterology (2017 IF = 10.231) took the top spot. The co-citation network had 7 co-citation clusters headed by ‘recurrent Clostridium difficile infection’. The top 7 keywords with the strongest citation bursts had three parts, ‘microbiota’, ‘ diarrhea ’, and ‘case series’. All keywords were divided into four domains, ‘disease’, ‘nosogenesis’, ‘trial’, and ‘therapy’. Conclusions This study shows the research performance of FMT from 2004 to 2017 and helps investigators master the trend of FMT, which is also an ongoing hotspot of research.
format: application/pdf
format: text/html
creator: Yan Li
creator: Ziyuan Zou
creator: Xiaohui Bian
creator: Yushan Huang
creator: Yanru Wang
creator: Chen Yang
creator: Jian Zhao
creator: Lang Xie
subject: Gastroenterology and Hepatology
subject: Global Health
subject: Statistics
description: doi:10.7717/peerj.6411
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Background Fecal microbiota transplantation (FMT) is an emerging therapy against Clostridium difficile infection (CDI) and inflammatory bowel disease (IBD). Although the therapy has gained prominence, there has been no bibliometric analysis of FMT. Methods Studies published from 2004 to 2017 were extracted from the Science Citation Index Expanded. Bibliometric analysis was used to evaluate the number or cooperation network of publications, countries, citations, references, journals, authors, institutions and keywords. Results A total of 796 items were included, showing an increasing trend annually. Publications mainly came from 10 countries, led by the US (n = 363). In the top 100 articles ranked by the number of citations (range 47–1,158), American Journal of Gastroenterology (2017 IF = 10.231) took the top spot. The co-citation network had 7 co-citation clusters headed by ‘recurrent Clostridium difficile infection’. The top 7 keywords with the strongest citation bursts had three parts, ‘microbiota’, ‘ diarrhea ’, and ‘case series’. All keywords were divided into four domains, ‘disease’, ‘nosogenesis’, ‘trial’, and ‘therapy’. Conclusions This study shows the research performance of FMT from 2004 to 2017 and helps investigators master the trend of FMT, which is also an ongoing hotspot of research.
bibliographic citation: Li et al. (2019) Fecal microbiota transplantation research output from 2004 to 2017: a bibliometric analysis. PeerJ 7:e6411 https://doi.org/10.7717/peerj.6411
date submitted: 2018-10-02
date accepted: 2019-01-01
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yan
author list: Agent
  family name: Zou
  given name: Ziyuan
author list: Agent
  family name: Bian
  given name: Xiaohui
author list: Agent
  family name: Huang
  given name: Yushan
author list: Agent
  family name: Wang
  given name: Yanru
author list: Agent
  family name: Yang
  given name: Chen
author list: Agent
  family name: Zhao
  given name: Jian
author list: Agent
  family name: Xie
  given name: Lang
doi: 10.7717/peerj.6411
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: ©2019 Li et al.
attribution name: Li et al.

Variation in pelvic shape and size in Eastern European males: a computed tomography comparative study
type: item
type: AcademicArticle
description: Background The significantly accelerated development of human society in the last millennium has brought about changes in human behavior and body mass that may have influenced human bone morphology. Our objective was to analyze the variation in pelvic shape and size in males from modern and medieval populations. Methods We obtained 22 pelvic girdles of adult males from a medieval cemetery located in Cedynia, Poland. The control group comprised 31 contemporary male pelves from individuals inhabiting the same region. The analyzed parameters were: interspinous distance (ISD), intercristal distance (ICD), intertuberous distance (ITD), anatomic conjugate of the pelvis, height of the pelvis (HP), iliac opening angle (IOA), iliac tilt angle (ITA), and ISD/ITD/HP ratio. Geometric morphometrics was used to analyze differences in shape in the pelves. All analyses were carried out on three-dimensional CT reconstructions of pelves. Results ISD, ICD, and IOA were significantly greater in modern pelves than in those from Cedynia, but no significant differences were seen between the two groups in ITD, anatomical conjugate, HP, or ITA. ISD/ITD/HP ratios were significantly lower in the Cedynia group. Geometric morphometrics revealed significant differences in pelvic shape between the analyzed groups. Discussion The pelves of modern males are larger, wider, and flatter than those of medieval males. Changes in the set of daily activities that produce mechanical loading and estimated body mass may constitute the main factors explaining pelvic variability. However, differences in ontogenesis should also be taken into consideration, especially since growth in past populations is often found to be reduced relative to modern populations.
format: application/pdf
format: text/html
creator: Bartosz Musielak
creator: Anna Maria Kubicka
creator: Michał Rychlik
creator: Jarosław Czubak
creator: Adam Czwojdziński
creator: Andrzej Grzegorzewski
creator: Marek Jóźwiak
subject: Anthropology
subject: Anatomy and Physiology
subject: Kinesiology
subject: Orthopedics
description: doi:10.7717/peerj.6433
publisher: PeerJ Inc.
rights: © 2019 Musielak et al.
abstract: Background The significantly accelerated development of human society in the last millennium has brought about changes in human behavior and body mass that may have influenced human bone morphology. Our objective was to analyze the variation in pelvic shape and size in males from modern and medieval populations. Methods We obtained 22 pelvic girdles of adult males from a medieval cemetery located in Cedynia, Poland. The control group comprised 31 contemporary male pelves from individuals inhabiting the same region. The analyzed parameters were: interspinous distance (ISD), intercristal distance (ICD), intertuberous distance (ITD), anatomic conjugate of the pelvis, height of the pelvis (HP), iliac opening angle (IOA), iliac tilt angle (ITA), and ISD/ITD/HP ratio. Geometric morphometrics was used to analyze differences in shape in the pelves. All analyses were carried out on three-dimensional CT reconstructions of pelves. Results ISD, ICD, and IOA were significantly greater in modern pelves than in those from Cedynia, but no significant differences were seen between the two groups in ITD, anatomical conjugate, HP, or ITA. ISD/ITD/HP ratios were significantly lower in the Cedynia group. Geometric morphometrics revealed significant differences in pelvic shape between the analyzed groups. Discussion The pelves of modern males are larger, wider, and flatter than those of medieval males. Changes in the set of daily activities that produce mechanical loading and estimated body mass may constitute the main factors explaining pelvic variability. However, differences in ontogenesis should also be taken into consideration, especially since growth in past populations is often found to be reduced relative to modern populations.
bibliographic citation: Musielak et al. (2019) Variation in pelvic shape and size in Eastern European males: a computed tomography comparative study. PeerJ 7:e6433 https://doi.org/10.7717/peerj.6433
date submitted: 2018-08-27
date accepted: 2019-01-10
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Musielak
  given name: Bartosz
author list: Agent
  family name: Kubicka
  given name: Anna Maria
author list: Agent
  family name: Rychlik
  given name: Michał
author list: Agent
  family name: Czubak
  given name: Jarosław
author list: Agent
  family name: Czwojdziński
  given name: Adam
author list: Agent
  family name: Grzegorzewski
  given name: Andrzej
author list: Agent
  family name: Jóźwiak
  given name: Marek
doi: 10.7717/peerj.6433
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: ©2019 Musielak et al.
attribution name: Musielak et al.

Enhancing fitness, enjoyment, and physical self-efficacy in primary school children: a DEDIPAC naturalistic study
type: item
type: AcademicArticle
description: Background Physical activity (PA) (e.g., sport, physical education) promotes the psychophysical development of children, enhances health and wellbeing, offers opportunities for enjoyable experiences, and increases self-efficacy. Methods In the DEDIPAC framework, we conducted a naturalistic, cross-sectional study to evaluate the effects of a school-based, long-term intervention on fitness (i.e., cardiovascular endurance, muscular strength, flexibility, speed, and finger dexterity), body mass index (BMI), PA levels, sedentary levels, enjoyment, and physical self-efficacy in primary school children. A group of Italian children (41 boys and 39 girls, aged 10–11 years) involved in the project—named “Più Sport @ Scuola” (PS@S)—was compared with a group of children (41 boys and 39 girls) of the same age not involved in the project. Results After a four-year long attendance to the PS@S project, participants reported higher scores of cardiovascular endurance, muscular strength, enjoyment, and physical self-efficacy compared to children not involved in the project. Correlation analysis results showed that muscular strength scores correlated positively with BMI, PA levels, and enjoyment. Flexibility of the upper body was positively related to physical self-efficacy, and negatively related to speed and BMI. Conclusions Findings suggest that the PS@S project enhanced fitness level, enjoyment, and physical self-efficacy of children.
format: application/pdf
format: text/html
creator: Francesca Vitali
creator: Claudio Robazza
creator: Laura Bortoli
creator: Luciano Bertinato
creator: Federico Schena
creator: Massimo Lanza
subject: Kinesiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.6436
publisher: PeerJ Inc.
rights: © 2019 Vitali et al.
abstract: Background Physical activity (PA) (e.g., sport, physical education) promotes the psychophysical development of children, enhances health and wellbeing, offers opportunities for enjoyable experiences, and increases self-efficacy. Methods In the DEDIPAC framework, we conducted a naturalistic, cross-sectional study to evaluate the effects of a school-based, long-term intervention on fitness (i.e., cardiovascular endurance, muscular strength, flexibility, speed, and finger dexterity), body mass index (BMI), PA levels, sedentary levels, enjoyment, and physical self-efficacy in primary school children. A group of Italian children (41 boys and 39 girls, aged 10–11 years) involved in the project—named “Più Sport @ Scuola” (PS@S)—was compared with a group of children (41 boys and 39 girls) of the same age not involved in the project. Results After a four-year long attendance to the PS@S project, participants reported higher scores of cardiovascular endurance, muscular strength, enjoyment, and physical self-efficacy compared to children not involved in the project. Correlation analysis results showed that muscular strength scores correlated positively with BMI, PA levels, and enjoyment. Flexibility of the upper body was positively related to physical self-efficacy, and negatively related to speed and BMI. Conclusions Findings suggest that the PS@S project enhanced fitness level, enjoyment, and physical self-efficacy of children.
bibliographic citation: Vitali et al. (2019) Enhancing fitness, enjoyment, and physical self-efficacy in primary school children: a DEDIPAC naturalistic study. PeerJ 7:e6436 https://doi.org/10.7717/peerj.6436
date submitted: 2018-09-18
date accepted: 2019-01-11
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vitali
  given name: Francesca
author list: Agent
  family name: Robazza
  given name: Claudio
author list: Agent
  family name: Bortoli
  given name: Laura
author list: Agent
  family name: Bertinato
  given name: Luciano
author list: Agent
  family name: Schena
  given name: Federico
author list: Agent
  family name: Lanza
  given name: Massimo
doi: 10.7717/peerj.6436
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: ©2019 Vitali et al.
attribution name: Vitali et al.

A community-level investigation following a yellow fever virus outbreak in South Omo Zone, South-West Ethiopia
type: item
type: AcademicArticle
description: Background Despite the availability of a highly effective vaccine, yellow fever virus (YFV) remains an important public health problem across Africa and South America due to its high case-fatality rate. This study investigated the historical epidemiology and contemporary entomological and social determinants of a YFV outbreak in South Omo Zone (SOZ), Ethiopia. Methods A YFV outbreak occurred in SOZ, Ethiopia in 2012–2014. Historical epidemiological data were retrieved from the SOZ Health Department and analyzed. Entomological sampling was undertaken in 2017, including mosquito species identification and molecular screening for arboviruses to understand mosquito habitat distribution, and finally current knowledge, attitudes and preventative practices within the affected communities were assessed. Results From October 2012 to March 2014, 165 suspected cases and 62 deaths were reported, principally in rural areas of South Ari region (83.6%). The majority of patients were 15–44 years old (75.8%) and most case deaths were males (76%). Between June and August 2017, 688 containers were sampled across 180 households to identify key breeding sites for Aedes mosquitoes. Ensete ventricosum (“false banana”) and clay pots outside the home were the most productive natural and artificial breeding sites, respectively. Entomological risk indices classified most sites as “high risk” for future outbreaks under current World Health Organization criteria. Adult mosquitoes in houses were identified as members of the Aedes simpsoni complex but no YFV or other arboviruses were detected by PCR. The majority of community members had heard of YFV, however few activities were undertaken to actively reduce mosquito breeding sites. Discussion Study results highlight the potential role vector control could play in mitigating local disease transmission and emphasize the urgent need to strengthen disease surveillance systems and in-country laboratory capacity to facilitate more rapid responses to f…
format: application/pdf
format: text/html
creator: Ranya Mulchandani
creator: Fekadu Massebo
creator: Fekadu Bocho
creator: Claire L. Jeffries
creator: Thomas Walker
creator: Louisa A. Messenger
subject: Entomology
subject: Virology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.6466
publisher: PeerJ Inc.
rights: © 2019 Mulchandani et al.
abstract: Background Despite the availability of a highly effective vaccine, yellow fever virus (YFV) remains an important public health problem across Africa and South America due to its high case-fatality rate. This study investigated the historical epidemiology and contemporary entomological and social determinants of a YFV outbreak in South Omo Zone (SOZ), Ethiopia. Methods A YFV outbreak occurred in SOZ, Ethiopia in 2012–2014. Historical epidemiological data were retrieved from the SOZ Health Department and analyzed. Entomological sampling was undertaken in 2017, including mosquito species identification and molecular screening for arboviruses to understand mosquito habitat distribution, and finally current knowledge, attitudes and preventative practices within the affected communities were assessed. Results From October 2012 to March 2014, 165 suspected cases and 62 deaths were reported, principally in rural areas of South Ari region (83.6%). The majority of patients were 15–44 years old (75.8%) and most case deaths were males (76%). Between June and August 2017, 688 containers were sampled across 180 households to identify key breeding sites for Aedes mosquitoes. Ensete ventricosum (“false banana”) and clay pots outside the home were the most productive natural and artificial breeding sites, respectively. Entomological risk indices classified most sites as “high risk” for future outbreaks under current World Health Organization criteria. Adult mosquitoes in houses were identified as members of the Aedes simpsoni complex but no YFV or other arboviruses were detected by PCR. The majority of community members had heard of YFV, however few activities were undertaken to actively reduce mosquito breeding sites. Discussion Study results highlight the potential role vector control could play in mitigating local disease transmission and emphasize the urgent need to strengthen disease surveillance systems and in-country laboratory capacity to facilitate more rapid responses to f…
bibliographic citation: Mulchandani et al. (2019) A community-level investigation following a yellow fever virus outbreak in South Omo Zone, South-West Ethiopia. PeerJ 7:e6466 https://doi.org/10.7717/peerj.6466
date submitted: 2018-11-13
date accepted: 2019-01-17
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mulchandani
  given name: Ranya
author list: Agent
  family name: Massebo
  given name: Fekadu
author list: Agent
  family name: Bocho
  given name: Fekadu
author list: Agent
  family name: Jeffries
  given name: Claire L.
author list: Agent
  family name: Walker
  given name: Thomas
author list: Agent
  family name: Messenger
  given name: Louisa A.
doi: 10.7717/peerj.6466
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: © 2019 Mulchandani et al.
attribution name: Mulchandani et al.

Yeasts producing zeatin
type: item
type: AcademicArticle
description: The present paper describes the first screening study of the ability of natural yeast strains to synthesize in culture the plant-related cytokine hormone zeatin, which was carried out using HPLC-MS/MS. A collection of 76 wild strains of 36 yeast species (23 genera) isolated from a variety of natural substrates was tested for the production of zeatin using HPLC-MS/MS. Zeatin was detected in more than a half (55%) of studied strains and was more frequently observed among basidiomycetous than ascomycetous species. The amount of zeatin accumulated during the experiment varied among species and strains. Highest zeatin values were recorded for basidiomycete Sporobolomyces roseus and ascomycete Taphrina sp. that produced up to 8,850.0 ng and 5,166.4 ng of zeatin per g of dry biomass, respectively. On average, the ability to produce zeatin was more pronounced among species isolated from the arctic-alpine zone than among strains from tropical and temperate climates. Our study also demonstrated that epiphytic strains and pigmented yeast species, typically for phyllosphere, are able to more often produce a plant hormone zeatin than other yeasts.
format: application/pdf
format: text/html
creator: Rostislav A. Streletskii
creator: Aleksey V. Kachalkin
creator: Anna M. Glushakova
creator: Andrey M. Yurkov
creator: Vladimir V. Demin
subject: Biochemistry
subject: Mycology
description: doi:10.7717/peerj.6474
publisher: PeerJ Inc.
rights: © 2019 Streletskii et al.
abstract: The present paper describes the first screening study of the ability of natural yeast strains to synthesize in culture the plant-related cytokine hormone zeatin, which was carried out using HPLC-MS/MS. A collection of 76 wild strains of 36 yeast species (23 genera) isolated from a variety of natural substrates was tested for the production of zeatin using HPLC-MS/MS. Zeatin was detected in more than a half (55%) of studied strains and was more frequently observed among basidiomycetous than ascomycetous species. The amount of zeatin accumulated during the experiment varied among species and strains. Highest zeatin values were recorded for basidiomycete Sporobolomyces roseus and ascomycete Taphrina sp. that produced up to 8,850.0 ng and 5,166.4 ng of zeatin per g of dry biomass, respectively. On average, the ability to produce zeatin was more pronounced among species isolated from the arctic-alpine zone than among strains from tropical and temperate climates. Our study also demonstrated that epiphytic strains and pigmented yeast species, typically for phyllosphere, are able to more often produce a plant hormone zeatin than other yeasts.
bibliographic citation: Streletskii et al. (2019) Yeasts producing zeatin. PeerJ 7:e6474 https://doi.org/10.7717/peerj.6474
date submitted: 2018-09-06
date accepted: 2019-01-15
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Streletskii
  given name: Rostislav A.
author list: Agent
  family name: Kachalkin
  given name: Aleksey V.
author list: Agent
  family name: Glushakova
  given name: Anna M.
author list: Agent
  family name: Yurkov
  given name: Andrey M.
author list: Agent
  family name: Demin
  given name: Vladimir V.
doi: 10.7717/peerj.6474
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: © 2019 Streletskii et al.
attribution name: Streletskii et al.

Alternative reproductive strategies in black-winged territorial males of Paraphlebia zoe (Odonata, Thaumatoneuridae)
type: item
type: AcademicArticle
description: Alternative reproductive strategies are commonly associated with male dimorphism. In Paraphlebia zoe, a species of damselfly whose males are dimorphic in wing coloration, black-and-white-winged (BW) males defend territories, while hyaline-winged (HW) males usually play the role of satellites. We found that several BW males can sometimes share a territory, and we hypothesized that within this morph there are two alternative tactics: submissive and dominant. We conducted an experiment to test whether dominant and submissive roles are plastic or stable and fixed on each individual. To this end, we manipulated black and white spots of BW males in four treatments: (i) painting over white and black spots without changing their size, (ii) erasing the white spot using black painting, (iii) increasing the black spot and moving the white spot maintaining its size and (iv) control males. Additionally, we investigated the correlation between some phenotypic variables (wing asymmetry, survival and recapture probabilities) and male behaviour (in terms of quality of the territory). We found that the two behavioural roles (submissive and dominant) were not affected by the manipulative experiments, therefore suggesting that they are stable and fixed. Additionally, we found a positive correlation between body size and survival in both sexes, and a positive effect of territory quality and lifespan on mating success. Moreover, the largest and youngest BW males were the most symmetrical. We conclude that Paraphlebia zoe holds high behavioural diversity, with two types of strategies in BW males, dominant and submissive. The occurrence of this intra-morph behavioural diversity might depend on demographic factors such as population density and/or the relative frequency of the different morphs.
format: application/pdf
format: text/html
creator: Anais Rivas-Torres
creator: Rosa Ana Sánchez-Guillén
creator: Adolfo Cordero-Rivera
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.6489
publisher: PeerJ Inc.
rights: © 2019 Rivas-Torres et al.
abstract: Alternative reproductive strategies are commonly associated with male dimorphism. In Paraphlebia zoe, a species of damselfly whose males are dimorphic in wing coloration, black-and-white-winged (BW) males defend territories, while hyaline-winged (HW) males usually play the role of satellites. We found that several BW males can sometimes share a territory, and we hypothesized that within this morph there are two alternative tactics: submissive and dominant. We conducted an experiment to test whether dominant and submissive roles are plastic or stable and fixed on each individual. To this end, we manipulated black and white spots of BW males in four treatments: (i) painting over white and black spots without changing their size, (ii) erasing the white spot using black painting, (iii) increasing the black spot and moving the white spot maintaining its size and (iv) control males. Additionally, we investigated the correlation between some phenotypic variables (wing asymmetry, survival and recapture probabilities) and male behaviour (in terms of quality of the territory). We found that the two behavioural roles (submissive and dominant) were not affected by the manipulative experiments, therefore suggesting that they are stable and fixed. Additionally, we found a positive correlation between body size and survival in both sexes, and a positive effect of territory quality and lifespan on mating success. Moreover, the largest and youngest BW males were the most symmetrical. We conclude that Paraphlebia zoe holds high behavioural diversity, with two types of strategies in BW males, dominant and submissive. The occurrence of this intra-morph behavioural diversity might depend on demographic factors such as population density and/or the relative frequency of the different morphs.
bibliographic citation: Rivas-Torres et al. (2019) Alternative reproductive strategies in black-winged territorial males of Paraphlebia zoe (Odonata, Thaumatoneuridae). PeerJ 7:e6489 https://doi.org/10.7717/peerj.6489
date submitted: 2018-09-07
date accepted: 2019-01-19
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rivas-Torres
  given name: Anais
author list: Agent
  family name: Sánchez-Guillén
  given name: Rosa Ana
author list: Agent
  family name: Cordero-Rivera
  given name: Adolfo
doi: 10.7717/peerj.6489
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: ©2019 Rivas-Torres et al.
attribution name: Rivas-Torres et al.

Incidence of gestational trophoblastic disease in South Korea: a longitudinal, population-based study
type: item
type: AcademicArticle
description: Introduction We investigated the rate and longitudinal trends of gestational trophoblastic disease (GTD) incidence in the Republic of Korea between 2009 and 2015 using population-based data. Materials and Methods Data of patients diagnosed with GTD from 2009 to 2015 were obtained from the Health Insurance Review and Assessment Service/National Inpatient Sample (HIRA-NIS) in the Republic of Korea. The HIRA annually provides the HIRA-NIS, a collection of clinical data from over one million people. For each year, the HIRA-NIS extracted records of 13% of patients admitted at any one time during the year and 1% of all remaining patients using the weighted sample method. Results Medical records of 370,117 women with at least one pregnancy (GTD, ectopic pregnancy, abortion, or delivery) were extracted from a total of 4,476,495 records. Of these, 372 episodes of GTD were identified in women with a mean age of 35.4 ± 0.7 years. The incidence rate of GTD was 130 ± 10 cases per 100,000 pregnancies, which was classified as hydatidiform mole (HM), invasive mole, or malignant neoplasm of the placenta with incidence rates of 110 ± 10, 20 ± 0, or 10 ± 0 cases per 100,000 pregnancies, respectively. Incidence of GTD was lowest among women in their late 20 s and early 30 s. Occurrences of HM accounted for 80.3% all GTD cases. Weighted logistic analysis indicated that while age significantly affected the incidence of GTD (odds ratio (OR): 2.46; 95% confidence interval (CI) [1.79–3.37]; P < 0.001), socioeconomic status did not (OR: 1.94; 95% CI [1.0–3.79]; P = 0.05). Conclusions In the Republic of Korea, we observed overall incidence rates of GTD and HM of 1.3 and 1.1 per 1,000 pregnancies, respectively, which are similar to those reported in recent Western population-based studies. We also noted that annual incidence rates of GTD stabilized from 2009 to 2015.
format: application/pdf
format: text/html
creator: Jin-Sung Yuk
creator: Jong Chul Baek
creator: Ji Eun Park
creator: Hyen Chul Jo
creator: Ji Kwon Park
creator: In Ae Cho
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Women's Health
description: doi:10.7717/peerj.6490
publisher: PeerJ Inc.
rights: © 2019 Yuk et al.
abstract: Introduction We investigated the rate and longitudinal trends of gestational trophoblastic disease (GTD) incidence in the Republic of Korea between 2009 and 2015 using population-based data. Materials and Methods Data of patients diagnosed with GTD from 2009 to 2015 were obtained from the Health Insurance Review and Assessment Service/National Inpatient Sample (HIRA-NIS) in the Republic of Korea. The HIRA annually provides the HIRA-NIS, a collection of clinical data from over one million people. For each year, the HIRA-NIS extracted records of 13% of patients admitted at any one time during the year and 1% of all remaining patients using the weighted sample method. Results Medical records of 370,117 women with at least one pregnancy (GTD, ectopic pregnancy, abortion, or delivery) were extracted from a total of 4,476,495 records. Of these, 372 episodes of GTD were identified in women with a mean age of 35.4 ± 0.7 years. The incidence rate of GTD was 130 ± 10 cases per 100,000 pregnancies, which was classified as hydatidiform mole (HM), invasive mole, or malignant neoplasm of the placenta with incidence rates of 110 ± 10, 20 ± 0, or 10 ± 0 cases per 100,000 pregnancies, respectively. Incidence of GTD was lowest among women in their late 20 s and early 30 s. Occurrences of HM accounted for 80.3% all GTD cases. Weighted logistic analysis indicated that while age significantly affected the incidence of GTD (odds ratio (OR): 2.46; 95% confidence interval (CI) [1.79–3.37]; P < 0.001), socioeconomic status did not (OR: 1.94; 95% CI [1.0–3.79]; P = 0.05). Conclusions In the Republic of Korea, we observed overall incidence rates of GTD and HM of 1.3 and 1.1 per 1,000 pregnancies, respectively, which are similar to those reported in recent Western population-based studies. We also noted that annual incidence rates of GTD stabilized from 2009 to 2015.
bibliographic citation: Yuk et al. (2019) Incidence of gestational trophoblastic disease in South Korea: a longitudinal, population-based study. PeerJ 7:e6490 https://doi.org/10.7717/peerj.6490
date submitted: 2018-09-20
date accepted: 2019-01-19
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuk
  given name: Jin-Sung
author list: Agent
  family name: Baek
  given name: Jong Chul
author list: Agent
  family name: Park
  given name: Ji Eun
author list: Agent
  family name: Jo
  given name: Hyen Chul
author list: Agent
  family name: Park
  given name: Ji Kwon
author list: Agent
  family name: Cho
  given name: In Ae
doi: 10.7717/peerj.6490
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: © 2019 Yuk et al.
attribution name: Yuk et al.

Estivation-responsive microRNAs in a hypometabolic terrestrial snail
type: item
type: AcademicArticle
description: When faced with extreme environmental conditions, the milk snail (Otala lactea) enters a state of dormancy known as estivation. This is characterized by a strong reduction in metabolic rate to <30% of normal resting rate that is facilitated by various behavioural, physiological, and molecular mechanisms. Herein, we investigated the regulation of microRNA in the induction of estivation. Changes in the expression levels of 75 highly conserved microRNAs were analysed in snail foot muscle, of which 26 were significantly upregulated during estivation compared with controls. These estivation-responsive microRNAs were linked to cell functions that are crucial for long-term survival in a hypometabolic state including anti-apoptosis, cell-cycle arrest, and maintenance of muscle functionality. Several of the microRNA responses by snail foot muscle also characterize hypometabolism in other species and support the existence of a conserved suite of miRNA responses that regulate environmental stress responsive metabolic rate depression across phylogeny.
format: application/pdf
format: text/html
creator: Myriam P. Hoyeck
creator: Hanane Hadj-Moussa
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.6515
publisher: PeerJ Inc.
rights: © 2019 Hoyeck et al.
abstract: When faced with extreme environmental conditions, the milk snail (Otala lactea) enters a state of dormancy known as estivation. This is characterized by a strong reduction in metabolic rate to <30% of normal resting rate that is facilitated by various behavioural, physiological, and molecular mechanisms. Herein, we investigated the regulation of microRNA in the induction of estivation. Changes in the expression levels of 75 highly conserved microRNAs were analysed in snail foot muscle, of which 26 were significantly upregulated during estivation compared with controls. These estivation-responsive microRNAs were linked to cell functions that are crucial for long-term survival in a hypometabolic state including anti-apoptosis, cell-cycle arrest, and maintenance of muscle functionality. Several of the microRNA responses by snail foot muscle also characterize hypometabolism in other species and support the existence of a conserved suite of miRNA responses that regulate environmental stress responsive metabolic rate depression across phylogeny.
bibliographic citation: Hoyeck et al. (2019) Estivation-responsive microRNAs in a hypometabolic terrestrial snail. PeerJ 7:e6515 https://doi.org/10.7717/peerj.6515
date submitted: 2018-12-06
date accepted: 2019-01-25
issued: 2019-02-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoyeck
  given name: Myriam P.
author list: Agent
  family name: Hadj-Moussa
  given name: Hanane
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.6515
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-20
copyright: ©2019 Hoyeck et al.
attribution name: Hoyeck et al.

Fiber fractions, multielemental and isotopic composition of a tropical C4 grass grown under elevated atmospheric carbon dioxide
type: item
type: AcademicArticle
description: Background Brazil has the largest commercial herd of ruminants with approximately 211 million head, representing 15% of world’s beef production, in an area of 170 million hectares of grasslands, mostly cultivated with Brachiaria spp. Although nutrient reduction due to increased atmospheric carbon dioxide (CO2) concentration has already been verified in important crops, studies evaluating its effects on fiber fractions and elemental composition of this grass genus are still scarce. Therefore, a better understanding of the effects of elevated CO2 on forage quality can elucidate the interaction between forage and livestock production and possible adaptations for a climate change scenario. The objective of this study was to evaluate the effects of contrasting atmospheric CO2 concentrations on biomass production, morphological characteristics, fiber fractions, and elemental composition of Brachiaria decumbens (cv. Basilisk). Methods A total of 12 octagonal rings with 10 m diameter were distributed in a seven-ha coffee plantation and inside each of them, two plots of 0.25 m2 were seeded with B. decumbens (cv. Basilisk) in a free air carbon dioxide enrichment facility. Six rings were kept under natural conditions (≈390 μmol mol−1 CO2; Control) and other six under pure CO2 flux to achieve a higher concentration (≈550 μmol mol−1 CO2; Elevated CO2). After 30 months under contrasting atmospheric CO2 concentration, grass samples were collected, and then splitted into two portions: in the first, whole forage was kept intact and in the second portion, the leaf, true stem, inflorescence and senescence fractions were manually separated to determine their proportions (%). All samples were then analyzed to determine the fiber fractions (NDF, hemicellulose, ADF, cellulose, and Lignin), carbon (C), nitrogen (N), potassium (K), calcium (Ca), sulfur (S), phosphorus (P), iron (Fe), and manganese (Mn) contents and N isotopic composition. Results Elevated atmospheric CO2 concentration did n…
format: application/pdf
format: text/html
creator: Adibe L. Abdalla Filho
creator: Geovani T. Costa Junior
creator: Paulo M.T. Lima
creator: Amin Soltangheisi
creator: Adibe L. Abdalla
creator: Raquel Ghini
creator: Marisa C. Piccolo
subject: Agricultural Science
subject: Climate Change Biology
description: doi:10.7717/peerj.5932
publisher: PeerJ Inc.
rights: © 2019 Abdalla Filho et al.
abstract: Background Brazil has the largest commercial herd of ruminants with approximately 211 million head, representing 15% of world’s beef production, in an area of 170 million hectares of grasslands, mostly cultivated with Brachiaria spp. Although nutrient reduction due to increased atmospheric carbon dioxide (CO2) concentration has already been verified in important crops, studies evaluating its effects on fiber fractions and elemental composition of this grass genus are still scarce. Therefore, a better understanding of the effects of elevated CO2 on forage quality can elucidate the interaction between forage and livestock production and possible adaptations for a climate change scenario. The objective of this study was to evaluate the effects of contrasting atmospheric CO2 concentrations on biomass production, morphological characteristics, fiber fractions, and elemental composition of Brachiaria decumbens (cv. Basilisk). Methods A total of 12 octagonal rings with 10 m diameter were distributed in a seven-ha coffee plantation and inside each of them, two plots of 0.25 m2 were seeded with B. decumbens (cv. Basilisk) in a free air carbon dioxide enrichment facility. Six rings were kept under natural conditions (≈390 μmol mol−1 CO2; Control) and other six under pure CO2 flux to achieve a higher concentration (≈550 μmol mol−1 CO2; Elevated CO2). After 30 months under contrasting atmospheric CO2 concentration, grass samples were collected, and then splitted into two portions: in the first, whole forage was kept intact and in the second portion, the leaf, true stem, inflorescence and senescence fractions were manually separated to determine their proportions (%). All samples were then analyzed to determine the fiber fractions (NDF, hemicellulose, ADF, cellulose, and Lignin), carbon (C), nitrogen (N), potassium (K), calcium (Ca), sulfur (S), phosphorus (P), iron (Fe), and manganese (Mn) contents and N isotopic composition. Results Elevated atmospheric CO2 concentration did n…
bibliographic citation: Abdalla Filho et al. (2019) Fiber fractions, multielemental and isotopic composition of a tropical C4 grass grown under elevated atmospheric carbon dioxide. PeerJ 7:e5932 https://doi.org/10.7717/peerj.5932
date submitted: 2018-06-14
date accepted: 2018-10-15
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdalla Filho
  given name: Adibe L.
author list: Agent
  family name: Costa Junior
  given name: Geovani T.
author list: Agent
  family name: Lima
  given name: Paulo M.T.
author list: Agent
  family name: Soltangheisi
  given name: Amin
author list: Agent
  family name: Abdalla
  given name: Adibe L.
author list: Agent
  family name: Ghini
  given name: Raquel
author list: Agent
  family name: Piccolo
  given name: Marisa C.
doi: 10.7717/peerj.5932
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Abdalla Filho et al.
attribution name: Abdalla Filho et al.

Pollen metabarcoding reveals broad and species-specific resource use by urban bees
type: item
type: AcademicArticle
description: Bee populations are currently undergoing severe global declines driven by the interactive effects of a number of factors. Ongoing urbanisation has the potential to exacerbate bee declines, unless steps are taken to ensure appropriate floral resources are available. Sown wildflower strips are one way in which floral resources can be provided to urban bees. However, the use of these strips by pollinators in urban environments remains little studied. Here, we employ pollen metabarcoding of the rbcL gene to compare the foraging patterns of different bee species observed using urban sown wildflower strips in July 2016, with a goal of identifying which plant species are most important for bees. We also demonstrate the use of a non-destructive method of pollen collection. Bees were found to forage on a wide variety of plant genera and families, including a diverse range of plants from outside the wildflower plots, suggesting that foragers visiting sown wildflower strips also utilize other urban habitats. Particular plants within the wildflower strips dominated metabarcoding data, particularly Papaver rhoeas and Phacelia tanacetifolia. Overall, we demonstrate that pollinators observed in sown wildflower strips use certain sown foodplants as part of a larger urban matrix.
format: application/pdf
format: text/html
creator: Caitlin Potter
creator: Natasha de Vere
creator: Laura E. Jones
creator: Col R. Ford
creator: Matthew J. Hegarty
creator: Kathy H. Hodder
creator: Anita Diaz
creator: Elizabeth L. Franklin
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Genetics
description: doi:10.7717/peerj.5999
publisher: PeerJ Inc.
rights: © 2019 Potter et al.
abstract: Bee populations are currently undergoing severe global declines driven by the interactive effects of a number of factors. Ongoing urbanisation has the potential to exacerbate bee declines, unless steps are taken to ensure appropriate floral resources are available. Sown wildflower strips are one way in which floral resources can be provided to urban bees. However, the use of these strips by pollinators in urban environments remains little studied. Here, we employ pollen metabarcoding of the rbcL gene to compare the foraging patterns of different bee species observed using urban sown wildflower strips in July 2016, with a goal of identifying which plant species are most important for bees. We also demonstrate the use of a non-destructive method of pollen collection. Bees were found to forage on a wide variety of plant genera and families, including a diverse range of plants from outside the wildflower plots, suggesting that foragers visiting sown wildflower strips also utilize other urban habitats. Particular plants within the wildflower strips dominated metabarcoding data, particularly Papaver rhoeas and Phacelia tanacetifolia. Overall, we demonstrate that pollinators observed in sown wildflower strips use certain sown foodplants as part of a larger urban matrix.
bibliographic citation: Potter et al. (2019) Pollen metabarcoding reveals broad and species-specific resource use by urban bees. PeerJ 7:e5999 https://doi.org/10.7717/peerj.5999
date submitted: 2018-08-03
date accepted: 2018-10-25
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Potter
  given name: Caitlin
author list: Agent
  family name: de Vere
  given name: Natasha
author list: Agent
  family name: Jones
  given name: Laura E.
author list: Agent
  family name: Ford
  given name: Col R.
author list: Agent
  family name: Hegarty
  given name: Matthew J.
author list: Agent
  family name: Hodder
  given name: Kathy H.
author list: Agent
  family name: Diaz
  given name: Anita
author list: Agent
  family name: Franklin
  given name: Elizabeth L.
doi: 10.7717/peerj.5999
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Potter et al.
attribution name: Potter et al.

Association between education and health outcomes among adults with disabilities: evidence from Shanghai, China
type: item
type: AcademicArticle
description: Background Adults with disabilities often have worse health outcomes than do their peers without disabilities. While education is a key determinant of health, there is little research available on the health disparities across education levels among adults with disabilities in developing countries. We therefore examined the association between health outcomes and education among adults with disabilities in Shanghai, China. Methods We used the health examination records of 42,715 adults with disabilities in Shanghai in 2014. Five health outcomes, including two diseases (fatty liver and hemorrhoids) and three risk factors (overweight [body mass index ≥ 24]), high blood glucose, and high blood lipid), were evaluated. Descriptive statistics and Pearson’s chi-square test were used to assess differences in participants’ demographic and disability characteristics. Pearson’s chi-square test and Fisher’s exact test were conducted to compare the prevalence of each health outcome among the different education levels. Finally, logistic regression analyses were conducted to explore the association between education and health outcomes after adjusting for sociodemographic characteristics. Results People with an elementary school or lower degree had the highest prevalence of overweight (52.1%) and high blood glucose (20.8%), but the lowest prevalence of hemorrhoids (18.6%) and fatty liver (38.9%). We observed significant differences in the association between education and health outcomes across disability types. For example, in physically disabled adults, higher education was related to higher odds of hemorrhoids (p < 0.001); however, there were no significant disparities in hemorrhoids across the education levels among adults with intellectual disabilities. Discussion Compared with people without disabilities, adults with disabilities in Shanghai have relatively poor health. The association between education and health outcomes differed according to the health condition and disa…
format: application/pdf
format: text/html
creator: Tong Ge
creator: Qi Zhang
creator: Jun Lu
creator: Gang Chen
creator: Mei Sun
creator: Xiaohong Li
subject: Global Health
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.6382
publisher: PeerJ Inc.
rights: © 2019 Ge et al.
abstract: Background Adults with disabilities often have worse health outcomes than do their peers without disabilities. While education is a key determinant of health, there is little research available on the health disparities across education levels among adults with disabilities in developing countries. We therefore examined the association between health outcomes and education among adults with disabilities in Shanghai, China. Methods We used the health examination records of 42,715 adults with disabilities in Shanghai in 2014. Five health outcomes, including two diseases (fatty liver and hemorrhoids) and three risk factors (overweight [body mass index ≥ 24]), high blood glucose, and high blood lipid), were evaluated. Descriptive statistics and Pearson’s chi-square test were used to assess differences in participants’ demographic and disability characteristics. Pearson’s chi-square test and Fisher’s exact test were conducted to compare the prevalence of each health outcome among the different education levels. Finally, logistic regression analyses were conducted to explore the association between education and health outcomes after adjusting for sociodemographic characteristics. Results People with an elementary school or lower degree had the highest prevalence of overweight (52.1%) and high blood glucose (20.8%), but the lowest prevalence of hemorrhoids (18.6%) and fatty liver (38.9%). We observed significant differences in the association between education and health outcomes across disability types. For example, in physically disabled adults, higher education was related to higher odds of hemorrhoids (p < 0.001); however, there were no significant disparities in hemorrhoids across the education levels among adults with intellectual disabilities. Discussion Compared with people without disabilities, adults with disabilities in Shanghai have relatively poor health. The association between education and health outcomes differed according to the health condition and disa…
bibliographic citation: Ge et al. (2019) Association between education and health outcomes among adults with disabilities: evidence from Shanghai, China. PeerJ 7:e6382 https://doi.org/10.7717/peerj.6382
date submitted: 2018-09-18
date accepted: 2019-01-01
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ge
  given name: Tong
author list: Agent
  family name: Zhang
  given name: Qi
author list: Agent
  family name: Lu
  given name: Jun
author list: Agent
  family name: Chen
  given name: Gang
author list: Agent
  family name: Sun
  given name: Mei
author list: Agent
  family name: Li
  given name: Xiaohong
doi: 10.7717/peerj.6382
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: ©2019 Ge et al.
attribution name: Ge et al.

Mulberry EIL3 confers salt and drought tolerances and modulates ethylene biosynthetic gene expression
type: item
type: AcademicArticle
description: Ethylene regulates plant abiotic stress responses and tolerances, and ethylene-insensitive3 (EIN3)/EIN3-like (EIL) proteins are the key components of ethylene signal transduction. Although the functions of EIN3/EIL proteins in response to abiotic stresses have been investigated in model plants, little is known in non-model plants, including mulberry (Morus L.), which is an economically important perennial woody plant. We functionally characterized a gene encoding an EIN3-like protein from mulberry, designated as MnEIL3. A quantitative real-time PCR analysis demonstrated that the expression of MnEIL3 could be induced in roots and shoot by salt and drought stresses. Arabidopsis overexpressing MnEIL3 exhibited an enhanced tolerance to salt and drought stresses. MnEIL3 overexpression in Arabidopsis significantly upregulated the transcript abundances of ethylene biosynthetic genes. Furthermore, MnEIL3 enhanced the activities of the MnACO1 and MnACS1 promoters, which respond to salt and drought stresses. Thus, MnEIL3 may play important roles in tolerance to abiotic stresses and the expression of ethylene biosynthetic genes.
format: application/pdf
format: text/html
creator: Changying Liu
creator: Jun Li
creator: Panpan Zhu
creator: Jian Yu
creator: Jiamin Hou
creator: Chuanhong Wang
creator: Dingpei Long
creator: Maode Yu
creator: Aichun Zhao
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6391
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Ethylene regulates plant abiotic stress responses and tolerances, and ethylene-insensitive3 (EIN3)/EIN3-like (EIL) proteins are the key components of ethylene signal transduction. Although the functions of EIN3/EIL proteins in response to abiotic stresses have been investigated in model plants, little is known in non-model plants, including mulberry (Morus L.), which is an economically important perennial woody plant. We functionally characterized a gene encoding an EIN3-like protein from mulberry, designated as MnEIL3. A quantitative real-time PCR analysis demonstrated that the expression of MnEIL3 could be induced in roots and shoot by salt and drought stresses. Arabidopsis overexpressing MnEIL3 exhibited an enhanced tolerance to salt and drought stresses. MnEIL3 overexpression in Arabidopsis significantly upregulated the transcript abundances of ethylene biosynthetic genes. Furthermore, MnEIL3 enhanced the activities of the MnACO1 and MnACS1 promoters, which respond to salt and drought stresses. Thus, MnEIL3 may play important roles in tolerance to abiotic stresses and the expression of ethylene biosynthetic genes.
bibliographic citation: Liu et al. (2019) Mulberry EIL3 confers salt and drought tolerances and modulates ethylene biosynthetic gene expression. PeerJ 7:e6391 https://doi.org/10.7717/peerj.6391
date submitted: 2018-10-15
date accepted: 2019-01-02
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Changying
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Zhu
  given name: Panpan
author list: Agent
  family name: Yu
  given name: Jian
author list: Agent
  family name: Hou
  given name: Jiamin
author list: Agent
  family name: Wang
  given name: Chuanhong
author list: Agent
  family name: Long
  given name: Dingpei
author list: Agent
  family name: Yu
  given name: Maode
author list: Agent
  family name: Zhao
  given name: Aichun
doi: 10.7717/peerj.6391
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Sexual dimorphism in the Chinese endemic species Pachyhynobius shangchengensis Fei, Qu and Wu, 1983 (Urodela: Hynobiidae)
type: item
type: AcademicArticle
description: Sexual dimorphism (SD) is a widespread phenomenon in most vertebrate species and is exhibited in a myriad of ways. In amphibians, sexual size dimorphism, in which females are larger than males, is the most common type, and sexual shape dimorphism varies among species. Different selection forces (sexual selection, fecundity selection, and ecological selection) that act differently upon the sexes form the consequence of SD. Thus, studies of SD provide information about the general intersexual divergence of the same species and allow insights into the impact of selective forces on the sexes. In this study, we analyzed morphometric data of the Shangcheng stout salamander, Pachyhynobius shangchengensis, an endemic and poorly known Chinese salamander, to examine sexual dimorphism in size and shape. The morphometric data included 15 characteristics of 68 females and 55 males which were analyzed using univariate and multivariate methods. A significant difference was found between the sexes in terms of both body size (snout-vent length) and some body shapes (e.g., head length and width, tail length and width, distance between limbs, and limb length and width) in this salamander. The longer snout-vent length in males may be attributed to sexual selection, longer and wider head in males may contribute to male-male competition, longer and wider tail in males may be attributed to energy storage and reproductive success, the larger distance between limbs in females is likely due to a fecundity advantage, and longer and more robust limbs in males may be related to reproductive or competitive behaviors. These results demonstrated that sexual dimorphism of different morphological traits is the consequence of different selection forces that act differently upon the sexes.
format: application/pdf
format: text/html
creator: Jianli Xiong
creator: Baowei Zhang
creator: Qiangqiang Liu
creator: Tao Pan
creator: Jianping Gou
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6408
publisher: PeerJ Inc.
rights: © 2019 Xiong et al.
abstract: Sexual dimorphism (SD) is a widespread phenomenon in most vertebrate species and is exhibited in a myriad of ways. In amphibians, sexual size dimorphism, in which females are larger than males, is the most common type, and sexual shape dimorphism varies among species. Different selection forces (sexual selection, fecundity selection, and ecological selection) that act differently upon the sexes form the consequence of SD. Thus, studies of SD provide information about the general intersexual divergence of the same species and allow insights into the impact of selective forces on the sexes. In this study, we analyzed morphometric data of the Shangcheng stout salamander, Pachyhynobius shangchengensis, an endemic and poorly known Chinese salamander, to examine sexual dimorphism in size and shape. The morphometric data included 15 characteristics of 68 females and 55 males which were analyzed using univariate and multivariate methods. A significant difference was found between the sexes in terms of both body size (snout-vent length) and some body shapes (e.g., head length and width, tail length and width, distance between limbs, and limb length and width) in this salamander. The longer snout-vent length in males may be attributed to sexual selection, longer and wider head in males may contribute to male-male competition, longer and wider tail in males may be attributed to energy storage and reproductive success, the larger distance between limbs in females is likely due to a fecundity advantage, and longer and more robust limbs in males may be related to reproductive or competitive behaviors. These results demonstrated that sexual dimorphism of different morphological traits is the consequence of different selection forces that act differently upon the sexes.
bibliographic citation: Xiong et al. (2019) Sexual dimorphism in the Chinese endemic species Pachyhynobius shangchengensis Fei, Qu and Wu, 1983 (Urodela: Hynobiidae). PeerJ 7:e6408 https://doi.org/10.7717/peerj.6408
date submitted: 2018-07-13
date accepted: 2019-01-04
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiong
  given name: Jianli
author list: Agent
  family name: Zhang
  given name: Baowei
author list: Agent
  family name: Liu
  given name: Qiangqiang
author list: Agent
  family name: Pan
  given name: Tao
author list: Agent
  family name: Gou
  given name: Jianping
doi: 10.7717/peerj.6408
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: ©2019 Xiong et al.
attribution name: Xiong et al.

Sulfated polysaccharides from Phaeodactylum tricornutum: isolation, structural characteristics, and inhibiting HepG2 growth activity in vitro
type: item
type: AcademicArticle
description: Microalgae, eukaryotic unicellular plants, are increasing in demand due to their use as nutraceutical and food supplements. They consisted different kinds of biologically active components such as polysaccharides. On the other hand, cancer is the leading cause of death globally. At present, there is no efficient method to cure it. Therefore, in this work, we extracted polysaccharides from Phaeodactylum tricornutum (PTP), characterized the chemical composition and structure, and investigated its anticancer activity on HepG2 cells. The results showed that PTP was a sulfated polysaccharide with a high Mw of 4,810 kDa, and xylose, fucose, glucose and galactose were the main monosaccharides. PTP has significant anticancer activity in a dose-dependent manner (up to 60.37% at 250 ug/mL) according to MTT assays. Furthermore, cycle analysis was carried out to explain its anticancer activity. The results showed that it exhibited anticancer effect mainly through the induction of apoptosis without affecting the cycle and mitosis of HepG2 cells. This might make it a potential drug for anticancer treatment in the future.
format: application/pdf
format: text/html
creator: Shengfeng Yang
creator: Haitao Wan
creator: Rui Wang
creator: Daijun Hao
subject: Biochemistry
subject: Evidence Based Medicine
subject: Oncology
description: doi:10.7717/peerj.6409
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Microalgae, eukaryotic unicellular plants, are increasing in demand due to their use as nutraceutical and food supplements. They consisted different kinds of biologically active components such as polysaccharides. On the other hand, cancer is the leading cause of death globally. At present, there is no efficient method to cure it. Therefore, in this work, we extracted polysaccharides from Phaeodactylum tricornutum (PTP), characterized the chemical composition and structure, and investigated its anticancer activity on HepG2 cells. The results showed that PTP was a sulfated polysaccharide with a high Mw of 4,810 kDa, and xylose, fucose, glucose and galactose were the main monosaccharides. PTP has significant anticancer activity in a dose-dependent manner (up to 60.37% at 250 ug/mL) according to MTT assays. Furthermore, cycle analysis was carried out to explain its anticancer activity. The results showed that it exhibited anticancer effect mainly through the induction of apoptosis without affecting the cycle and mitosis of HepG2 cells. This might make it a potential drug for anticancer treatment in the future.
bibliographic citation: Yang et al. (2019) Sulfated polysaccharides from Phaeodactylum tricornutum: isolation, structural characteristics, and inhibiting HepG2 growth activity in vitro. PeerJ 7:e6409 https://doi.org/10.7717/peerj.6409
date submitted: 2018-09-13
date accepted: 2019-01-08
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Shengfeng
author list: Agent
  family name: Wan
  given name: Haitao
author list: Agent
  family name: Wang
  given name: Rui
author list: Agent
  family name: Hao
  given name: Daijun
doi: 10.7717/peerj.6409
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Yang et al.
attribution name: Yang et al.

Expression analysis of four pseudo-response regulator (PRR) genes in Chrysanthemum morifolium under different photoperiods
type: item
type: AcademicArticle
description: Genes encoding pseudo-response regulator (PRR) proteins play significant roles in plant circadian clocks. In this study, four genes related to flowering time were isolated from Chrysanthemum morifolium. Phylogenetic analysis showed that they are highly homologous to the counterparts of PRRs of Helianthus annuus and named as CmPRR2, CmPRR7, CmPRR37, and CmPRR73. Conserved motifs prediction indicated that most of the closely related members in the phylogenetic tree share common protein sequence motifs, suggesting functional similarities among the PRR proteins within the same subtree. In order to explore functions of the genes, we selected two Chrysanthemum varieties for comparison; that is, a short-day sensitive Zijiao and a short-day insensitive Aoyunbaixue. Compared to Aoyunbaixue, Zijiao needs 13 more days to complete the flower bud differentiation. Evidence from spatio-temporal gene expression patterns demonstrated that the CmPRRs are highly expressed in flower and stem tissues, with a growing trend across the Chrysanthemum developmental process. In addition, we also characterized the CmPRRs expression patterns and found that CmPRRs can maintain their circadian oscillation features to some extent under different photoperiod treatment conditions. These lines of evidence indicated that the four CmPRRs undergo circadian oscillation and possibly play roles in regulating the flowering time of C. morifolium.
format: application/pdf
format: text/html
creator: Shengji Wang
creator: Chunlai Zhang
creator: Jing Zhao
creator: Renhua Li
creator: Jinhui Lv
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6420
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Genes encoding pseudo-response regulator (PRR) proteins play significant roles in plant circadian clocks. In this study, four genes related to flowering time were isolated from Chrysanthemum morifolium. Phylogenetic analysis showed that they are highly homologous to the counterparts of PRRs of Helianthus annuus and named as CmPRR2, CmPRR7, CmPRR37, and CmPRR73. Conserved motifs prediction indicated that most of the closely related members in the phylogenetic tree share common protein sequence motifs, suggesting functional similarities among the PRR proteins within the same subtree. In order to explore functions of the genes, we selected two Chrysanthemum varieties for comparison; that is, a short-day sensitive Zijiao and a short-day insensitive Aoyunbaixue. Compared to Aoyunbaixue, Zijiao needs 13 more days to complete the flower bud differentiation. Evidence from spatio-temporal gene expression patterns demonstrated that the CmPRRs are highly expressed in flower and stem tissues, with a growing trend across the Chrysanthemum developmental process. In addition, we also characterized the CmPRRs expression patterns and found that CmPRRs can maintain their circadian oscillation features to some extent under different photoperiod treatment conditions. These lines of evidence indicated that the four CmPRRs undergo circadian oscillation and possibly play roles in regulating the flowering time of C. morifolium.
bibliographic citation: Wang et al. (2019) Expression analysis of four pseudo-response regulator (PRR) genes in Chrysanthemum morifolium under different photoperiods. PeerJ 7:e6420 https://doi.org/10.7717/peerj.6420
date submitted: 2018-09-25
date accepted: 2019-01-05
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Shengji
author list: Agent
  family name: Zhang
  given name: Chunlai
author list: Agent
  family name: Zhao
  given name: Jing
author list: Agent
  family name: Li
  given name: Renhua
author list: Agent
  family name: Lv
  given name: Jinhui
doi: 10.7717/peerj.6420
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Wang et al.
attribution name: Wang et al.

Maternal inheritance of F1 hybrid morphology and colony shape in the coral genus Acropora
type: item
type: AcademicArticle
description: Background The coral genus Acropora contains more than 150 species with very high morphological diversity. This high diversity may have been caused by repeated hybridization via mass spawning. However, we have little information whether hybrids are formed in these corals. Identifying morphological differences between hybrids and their parental species would provide an opportunity to find wild hybrids in the field and to understand how colony shapes of Acropora have become highly diversified throughout evolutionary history. In the two morphologically distinctive coral species Acropora florida and A. intermedia in the Indo-Pacific, their gametes show high rates of bi-directional intercrossing in vitro, and thus these two species are ideal species to investigate the morphological traits of the hybrids. Methods We examined morphological characters of F1 hybrids from A. florida to A. intermedia, which were produced from in vitro crossing experiments. To compare morphological differences, we grew juveniles and mature colonies of reciprocal F1 hybrids (FLOint: A. florida eggs × A. intermedia sperm, and INTflo: A. intermedia eggs × A. florida sperm) and of the parental species (purebreds of A. intermedia and A. florida). We analyzed skeletal morphology such as colony size, branch length, and branching number, and compared them with those of a putative F1 hybrid between A. florida and A. intermedia found in the field. We also confirmed the molecular phylogenetic position of F1 hybrids, parental species, and a putative F1 hybrid using the mitochondrial non-coding region. Results Our morphological analysis revealed that branching number of the F1 hybrids was intermediate relative to the parental species. Moreover, the FLOint hybrids were morphologically more closely related to the maternal species A. florida, and the INTflo hybrids were to A. intermedia. Molecular data showed that A. florida and A. intermedia were clearly divided into two clades, and that F1 hybrids grouped in…
format: application/pdf
format: text/html
creator: Hironobu Fukami
creator: Kenji Iwao
creator: Naoki H. Kumagai
creator: Masaya Morita
creator: Naoko Isomura
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.6429
publisher: PeerJ Inc.
rights: © 2019 Fukami et al.
abstract: Background The coral genus Acropora contains more than 150 species with very high morphological diversity. This high diversity may have been caused by repeated hybridization via mass spawning. However, we have little information whether hybrids are formed in these corals. Identifying morphological differences between hybrids and their parental species would provide an opportunity to find wild hybrids in the field and to understand how colony shapes of Acropora have become highly diversified throughout evolutionary history. In the two morphologically distinctive coral species Acropora florida and A. intermedia in the Indo-Pacific, their gametes show high rates of bi-directional intercrossing in vitro, and thus these two species are ideal species to investigate the morphological traits of the hybrids. Methods We examined morphological characters of F1 hybrids from A. florida to A. intermedia, which were produced from in vitro crossing experiments. To compare morphological differences, we grew juveniles and mature colonies of reciprocal F1 hybrids (FLOint: A. florida eggs × A. intermedia sperm, and INTflo: A. intermedia eggs × A. florida sperm) and of the parental species (purebreds of A. intermedia and A. florida). We analyzed skeletal morphology such as colony size, branch length, and branching number, and compared them with those of a putative F1 hybrid between A. florida and A. intermedia found in the field. We also confirmed the molecular phylogenetic position of F1 hybrids, parental species, and a putative F1 hybrid using the mitochondrial non-coding region. Results Our morphological analysis revealed that branching number of the F1 hybrids was intermediate relative to the parental species. Moreover, the FLOint hybrids were morphologically more closely related to the maternal species A. florida, and the INTflo hybrids were to A. intermedia. Molecular data showed that A. florida and A. intermedia were clearly divided into two clades, and that F1 hybrids grouped in…
bibliographic citation: Fukami et al. (2019) Maternal inheritance of F1 hybrid morphology and colony shape in the coral genus Acropora. PeerJ 7:e6429 https://doi.org/10.7717/peerj.6429
date submitted: 2018-10-24
date accepted: 2019-01-10
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fukami
  given name: Hironobu
author list: Agent
  family name: Iwao
  given name: Kenji
author list: Agent
  family name: Kumagai
  given name: Naoki H.
author list: Agent
  family name: Morita
  given name: Masaya
author list: Agent
  family name: Isomura
  given name: Naoko
doi: 10.7717/peerj.6429
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Fukami et al.
attribution name: Fukami et al.

The anatomy and phylogenetic position of the erythrosuchid archosauriform Guchengosuchus shiguaiensis from the earliest Middle Triassic of China
type: item
type: AcademicArticle
description: Erythrosuchidae is a clade of early archosauriform reptiles, which were apex predators in many late Early and Middle Triassic ecosystems, following the Permo-Triassic mass extinction. Erythrosuchids had a worldwide distribution, with well-preserved fossil material known from South Africa, European Russia, and China. We here redescribe the anatomy and revise the taxonomy of Guchengosuchus shiguaiensis, which is one of the stratigraphically oldest erythrosuchids and is known from a single partial skeleton from the lowermost Middle Triassic (lower Anisian) lower Ermaying Formation of Shaanxi Province, China. We provide a new differential diagnosis for Guchengosuchus shiguaiensis, and identify a series of autapomorphies relating to the morphologies of the skull roof and vertebrae. Incorporating updated anatomical information for Guchengosuchus into the most comprehensive morphological phylogenetic analysis available for early archosauromorphs recovers it as an early branching member of Erythrosuchidae, outside of the clade formed by Garjainia, Erythrosuchus, Chalishevia, and Shansisuchus. Fugusuchus hejiapanensis, from the uppermost Lower Triassic to lower Middle Triassic Heshanggou Formation of China, is recovered as the earliest branching member of Erythrosuchidae.
format: application/pdf
format: text/html
creator: Richard J. Butler
creator: Martín D. Ezcurra
creator: Jun Liu
creator: Roland B. Sookias
creator: Corwin Sullivan
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6435
publisher: PeerJ Inc.
rights: © 2019 Butler et al.
abstract: Erythrosuchidae is a clade of early archosauriform reptiles, which were apex predators in many late Early and Middle Triassic ecosystems, following the Permo-Triassic mass extinction. Erythrosuchids had a worldwide distribution, with well-preserved fossil material known from South Africa, European Russia, and China. We here redescribe the anatomy and revise the taxonomy of Guchengosuchus shiguaiensis, which is one of the stratigraphically oldest erythrosuchids and is known from a single partial skeleton from the lowermost Middle Triassic (lower Anisian) lower Ermaying Formation of Shaanxi Province, China. We provide a new differential diagnosis for Guchengosuchus shiguaiensis, and identify a series of autapomorphies relating to the morphologies of the skull roof and vertebrae. Incorporating updated anatomical information for Guchengosuchus into the most comprehensive morphological phylogenetic analysis available for early archosauromorphs recovers it as an early branching member of Erythrosuchidae, outside of the clade formed by Garjainia, Erythrosuchus, Chalishevia, and Shansisuchus. Fugusuchus hejiapanensis, from the uppermost Lower Triassic to lower Middle Triassic Heshanggou Formation of China, is recovered as the earliest branching member of Erythrosuchidae.
bibliographic citation: Butler et al. (2019) The anatomy and phylogenetic position of the erythrosuchid archosauriform Guchengosuchus shiguaiensis from the earliest Middle Triassic of China. PeerJ 7:e6435 https://doi.org/10.7717/peerj.6435
date submitted: 2018-10-09
date accepted: 2019-01-10
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Butler
  given name: Richard J.
author list: Agent
  family name: Ezcurra
  given name: Martín D.
author list: Agent
  family name: Liu
  given name: Jun
author list: Agent
  family name: Sookias
  given name: Roland B.
author list: Agent
  family name: Sullivan
  given name: Corwin
doi: 10.7717/peerj.6435
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Butler et al.
attribution name: Butler et al.

Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis
type: item
type: AcademicArticle
description: The interactions between rhizosphere microorganisms and plants are important for the health and development of crops. Analysis of plant rhizosphere bacterial compositions, particularly of those with resistance to biotic/abiotic stresses, may improve their applications in sustainable agriculture. Large-scale rhizosphere samplings in the field are usually required; however, such samples, cannot be immediately frozen. We found that the storage of samples at room temperature for 2 days leads to a considerable reduction in the operational taxonomic unit (OTU) number and the indices of bacterial alpha-diversity of rhizosphere communities. In this study, in order to overcome these problems, we established a method using guanidine thiocyanate (GTC) solution for the preservation of rhizosphere samples after their collection. This method allowed the maintenance of the samples for at least 1 day at room temperature prior to their cryopreservation and was shown to be compatible with conventional DNA isolation protocols. Illumina sequencing of V3 and V4 hypervariable regions of the 16S rRNA gene was used to assess the feasibility and reliability of this method, and no significant differences were observed in the number of OTUs and in the Chao and Shannon indices between samples stored at −70 °C and those stored in GTC solution. Moreover, the representation of Pseudomonas spp. in samples stored in GTC solution was not significantly different from that in samples stored at −70 °C, as determined by real-time quantitative polymerase chain reaction (p > 0.05). Both types of samples were shown to cluster together according to principal coordinate analysis. Furthermore, GTC solution did not affect the bacterial taxon profiles at different storage periods compared with those observed when storing the samples below −70 °C. Even incubation of thawed samples (frozen at −70 °C) for 15 min at room temperature induced minor changes in the bacterial composition. Taken together, our results dem…
format: application/pdf
format: text/html
creator: Xiaoxiao Sun
creator: Meiling Wang
creator: Lin Guo
creator: Changlong Shu
creator: Jie Zhang
creator: Lili Geng
subject: Agricultural Science
subject: Biotechnology
subject: Ecology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6440
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: The interactions between rhizosphere microorganisms and plants are important for the health and development of crops. Analysis of plant rhizosphere bacterial compositions, particularly of those with resistance to biotic/abiotic stresses, may improve their applications in sustainable agriculture. Large-scale rhizosphere samplings in the field are usually required; however, such samples, cannot be immediately frozen. We found that the storage of samples at room temperature for 2 days leads to a considerable reduction in the operational taxonomic unit (OTU) number and the indices of bacterial alpha-diversity of rhizosphere communities. In this study, in order to overcome these problems, we established a method using guanidine thiocyanate (GTC) solution for the preservation of rhizosphere samples after their collection. This method allowed the maintenance of the samples for at least 1 day at room temperature prior to their cryopreservation and was shown to be compatible with conventional DNA isolation protocols. Illumina sequencing of V3 and V4 hypervariable regions of the 16S rRNA gene was used to assess the feasibility and reliability of this method, and no significant differences were observed in the number of OTUs and in the Chao and Shannon indices between samples stored at −70 °C and those stored in GTC solution. Moreover, the representation of Pseudomonas spp. in samples stored in GTC solution was not significantly different from that in samples stored at −70 °C, as determined by real-time quantitative polymerase chain reaction (p > 0.05). Both types of samples were shown to cluster together according to principal coordinate analysis. Furthermore, GTC solution did not affect the bacterial taxon profiles at different storage periods compared with those observed when storing the samples below −70 °C. Even incubation of thawed samples (frozen at −70 °C) for 15 min at room temperature induced minor changes in the bacterial composition. Taken together, our results dem…
bibliographic citation: Sun et al. (2019) Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis. PeerJ 7:e6440 https://doi.org/10.7717/peerj.6440
date submitted: 2018-07-18
date accepted: 2019-01-13
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xiaoxiao
author list: Agent
  family name: Wang
  given name: Meiling
author list: Agent
  family name: Guo
  given name: Lin
author list: Agent
  family name: Shu
  given name: Changlong
author list: Agent
  family name: Zhang
  given name: Jie
author list: Agent
  family name: Geng
  given name: Lili
doi: 10.7717/peerj.6440
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Sun et al.
attribution name: Sun et al.

Breastfeeding in the time of Zika: a systematic literature review
type: item
type: AcademicArticle
description: Background The disease Zika is considered as emergent. The infection can be acquired through different routes: a bite from the Aedes mosquito, sexual contact, from mother to child during pregnancy and by blood transfusion. The possibility of Zika transmission through human lactation has been considered. Zika is a disease of great concern for public health because it has been associated with neonatal and postnatal microcephaly, among other birth defects. Objectives To review published evidence of the probable transmission of Zika through human lactation. Data sources Electronic databases: Cochrane Central Register of Controlled Trials, EBSCO, Gale, Science Direct, Scopus, US National Library of Medicine (PubMed) and Web of Science. World Health Organization and Centers for Disease Control and Prevention web pages. Study eligibility criteria To be eligible, studies of any design had to provide primary data of human breast milk as a potential fluid for the transmission of Zika, or primary or secondary follow-up data of infants with at least one previous published study that complied with the first criterion of eligibility. Participants Studies about women with suspected, probable or confirmed Zika during pregnancy, or the postnatal period and beyond. Studies about infants who breastfeed directly from the breast or where fed with the expressed breast milk of the suspected, probable or confirmed women with Zika. Results This study only chose data from research papers; no patients were taken directly by the authors. A total of 1,146 were screened and nine studies were included in the qualitative synthesis, from which a total of 10 cases were identified, with documented follow-up in three of these cases. Through the timing of maternal Zika infection, five cases were classified as prenatal (time before delivery), one as immediate postnatal (period from 0 to 4 days after birth); no cases were classified as medium postnatal (period from 5 days to 8 weeks after birth); two wer…
format: application/pdf
format: text/html
creator: Clara Luz Sampieri
creator: Hilda Montero
subject: Virology
subject: Pediatrics
subject: Women’s Health
description: doi:10.7717/peerj.6452
publisher: PeerJ Inc.
rights: © 2019 Sampieri and Montero
abstract: Background The disease Zika is considered as emergent. The infection can be acquired through different routes: a bite from the Aedes mosquito, sexual contact, from mother to child during pregnancy and by blood transfusion. The possibility of Zika transmission through human lactation has been considered. Zika is a disease of great concern for public health because it has been associated with neonatal and postnatal microcephaly, among other birth defects. Objectives To review published evidence of the probable transmission of Zika through human lactation. Data sources Electronic databases: Cochrane Central Register of Controlled Trials, EBSCO, Gale, Science Direct, Scopus, US National Library of Medicine (PubMed) and Web of Science. World Health Organization and Centers for Disease Control and Prevention web pages. Study eligibility criteria To be eligible, studies of any design had to provide primary data of human breast milk as a potential fluid for the transmission of Zika, or primary or secondary follow-up data of infants with at least one previous published study that complied with the first criterion of eligibility. Participants Studies about women with suspected, probable or confirmed Zika during pregnancy, or the postnatal period and beyond. Studies about infants who breastfeed directly from the breast or where fed with the expressed breast milk of the suspected, probable or confirmed women with Zika. Results This study only chose data from research papers; no patients were taken directly by the authors. A total of 1,146 were screened and nine studies were included in the qualitative synthesis, from which a total of 10 cases were identified, with documented follow-up in three of these cases. Through the timing of maternal Zika infection, five cases were classified as prenatal (time before delivery), one as immediate postnatal (period from 0 to 4 days after birth); no cases were classified as medium postnatal (period from 5 days to 8 weeks after birth); two wer…
bibliographic citation: Sampieri et al. (2019) Breastfeeding in the time of Zika: a systematic literature review. PeerJ 7:e6452 https://doi.org/10.7717/peerj.6452
date submitted: 2018-09-21
date accepted: 2019-01-15
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sampieri
  given name: Clara Luz
author list: Agent
  family name: Montero
  given name: Hilda
doi: 10.7717/peerj.6452
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: ©2019 Sampieri and Montero
attribution name: Sampieri and Montero

Impact of agricultural farms on the environment of the Puck Commune: Integrated agriculture calculator—CalcGosPuck
type: item
type: AcademicArticle
description: Background Leaching of nutrients from agricultural areas is the main cause of water pollution and eutrophication of the Baltic Sea. A variety of remedial actions to reduce nitrogen and phosphorus losses from agricultural holdings and cultivated fields have been taken in the past. However, knowledge about the risk of nutrient leaching has not yet reached many farmers operating in the water catchment area of the Baltic Sea. Methods The nutrient balance method known as “At the farm gate” involves calculating separate balances for nitrogen (N), phosphorus (P) and potassium (K). After estimating all the components of the nutrient balance, the total balance for NPK is calculated and the data obtained is expressed as the ratio of total change (surplus) to the area of arable land on a farm. In addition, the nutrient usage efficiency on a farm is also calculated. An opinion poll was conducted in 2017 on 3.6% (n = 31) of the farms located in commune of Puck. The total area of the farms including arable and grass land ranged from 5 to 130 ha with an average of 45.82 ha. The arable land was on average 30.79 ha ranging from 4.45 to 130 ha while the grassland averaged 12.77 ha and ranged from 0 to 53 ha. Results The average consumption of mineral fertilizer in the sample population of farms was 114.9 kg N, 9.3 kg P, and 22.9 kg K·ha−1of agricultural land (AL), respectively. N balance in the sample farms being ranged from −23.3 to 254.5 kg N·ha−1AL while nutrient use efficiency ranged from 0.40% to 231.3%. In comparison, P surplus in the sample farms was 5.0 kg P·ha−1AL with the P use efficiency of 0.4–266.5%. Discussion Mean N fertilizer consumption in the tested farms was higher than the average usage across Poland and in the Pomeranian Voivodeship. However, mean consumption of potassium fertilizers was lower than mentioned averages. Mean P fertilizer consumption was higher than in the Pomeranian Voivodeship, but lower compared to the entire country. Generally, on the basis of d…
format: application/pdf
format: text/html
creator: Lidia Dzierzbicka-Glowacka
creator: Stefan Pietrzak
creator: Dawid Dybowski
creator: Michał Białoskórski
creator: Tadeusz Marcinkowski
creator: Ludmiła Rossa
creator: Marek Urbaniak
creator: Zuzanna Majewska
creator: Dominika Juszkowska
creator: Piotr Nawalany
creator: Grażyna Pazikowska-Sapota
creator: Bożena Kamińska
creator: Bartłomiej Selke
creator: Paweł Korthals
creator: Tadeusz Puszkarczuk
subject: Agricultural Science
subject: Computational Science
subject: Environmental Impacts
description: doi:10.7717/peerj.6478
publisher: PeerJ Inc.
rights: © 2019 Dzierzbicka-Glowacka et al.
abstract: Background Leaching of nutrients from agricultural areas is the main cause of water pollution and eutrophication of the Baltic Sea. A variety of remedial actions to reduce nitrogen and phosphorus losses from agricultural holdings and cultivated fields have been taken in the past. However, knowledge about the risk of nutrient leaching has not yet reached many farmers operating in the water catchment area of the Baltic Sea. Methods The nutrient balance method known as “At the farm gate” involves calculating separate balances for nitrogen (N), phosphorus (P) and potassium (K). After estimating all the components of the nutrient balance, the total balance for NPK is calculated and the data obtained is expressed as the ratio of total change (surplus) to the area of arable land on a farm. In addition, the nutrient usage efficiency on a farm is also calculated. An opinion poll was conducted in 2017 on 3.6% (n = 31) of the farms located in commune of Puck. The total area of the farms including arable and grass land ranged from 5 to 130 ha with an average of 45.82 ha. The arable land was on average 30.79 ha ranging from 4.45 to 130 ha while the grassland averaged 12.77 ha and ranged from 0 to 53 ha. Results The average consumption of mineral fertilizer in the sample population of farms was 114.9 kg N, 9.3 kg P, and 22.9 kg K·ha−1of agricultural land (AL), respectively. N balance in the sample farms being ranged from −23.3 to 254.5 kg N·ha−1AL while nutrient use efficiency ranged from 0.40% to 231.3%. In comparison, P surplus in the sample farms was 5.0 kg P·ha−1AL with the P use efficiency of 0.4–266.5%. Discussion Mean N fertilizer consumption in the tested farms was higher than the average usage across Poland and in the Pomeranian Voivodeship. However, mean consumption of potassium fertilizers was lower than mentioned averages. Mean P fertilizer consumption was higher than in the Pomeranian Voivodeship, but lower compared to the entire country. Generally, on the basis of d…
bibliographic citation: Dzierzbicka-Glowacka et al. (2019) Impact of agricultural farms on the environment of the Puck Commune: Integrated agriculture calculator—CalcGosPuck. PeerJ 7:e6478 https://doi.org/10.7717/peerj.6478
date submitted: 2018-09-10
date accepted: 2019-01-19
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dzierzbicka-Glowacka
  given name: Lidia
author list: Agent
  family name: Pietrzak
  given name: Stefan
author list: Agent
  family name: Dybowski
  given name: Dawid
author list: Agent
  family name: Białoskórski
  given name: Michał
author list: Agent
  family name: Marcinkowski
  given name: Tadeusz
author list: Agent
  family name: Rossa
  given name: Ludmiła
author list: Agent
  family name: Urbaniak
  given name: Marek
author list: Agent
  family name: Majewska
  given name: Zuzanna
author list: Agent
  family name: Juszkowska
  given name: Dominika
author list: Agent
  family name: Nawalany
  given name: Piotr
author list: Agent
  family name: Pazikowska-Sapota
  given name: Grażyna
author list: Agent
  family name: Kamińska
  given name: Bożena
author list: Agent
  family name: Selke
  given name: Bartłomiej
author list: Agent
  family name: Korthals
  given name: Paweł
author list: Agent
  family name: Puszkarczuk
  given name: Tadeusz
doi: 10.7717/peerj.6478
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Dzierzbicka-Glowacka et al.
attribution name: Dzierzbicka-Glowacka et al.

Hybrid identification for Glycine max and Glycine soja with SSR markers and analysis of salt tolerance
type: item
type: AcademicArticle
description: Glycine max cultivars Lee68, Nannong 1138-2, and Nannong 8831 were used as the female parents, and hybrid lines (F5) 4,111, 4,076 (N23674 × BB52), 3,060 (Lee68 × N23227), and 185 (Jackson × BB52) that selected for salt tolerance generation by generation from the cross combination of G. max and G. soja were used as the male parents, 11 (A–K) backcrosses or three-way crosses were designed and 213 single hybrids were harvested. The optimized soybean simple sequence repeat (SSR)–polymerase chain reaction (PCR) system was used to analyze the SSR polymorphism of above parental lines and get the parental co-dominant SSR markers for hybrid identification, and in which 30 true hybrids were gained. The true hybrids (G1, G3, G9, G12, G13, G16) of G cross combination were chosen as the representative for the salt tolerance test, and the results showed that, as exposed to salt stress, the seedlings of G9 line displayed higher salt tolerant coefficient, relative growth rate, and dry matter accumulation, when compared with their female parent Nannong 1138-2, and even performed equally strong salt tolerance as the male parent 3,060. It provides a feasible method of the combination of molecular SSR markers and simple physiological parameters to identify the true hybrids of G. max and G. soja, and to innovate the salt-tolerant soybean germplasms.
format: application/pdf
format: text/html
creator: Fayuan Li
creator: Xun Liu
creator: Shengyan Wu
creator: Qingyun Luo
creator: Bingjun Yu
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6483
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Glycine max cultivars Lee68, Nannong 1138-2, and Nannong 8831 were used as the female parents, and hybrid lines (F5) 4,111, 4,076 (N23674 × BB52), 3,060 (Lee68 × N23227), and 185 (Jackson × BB52) that selected for salt tolerance generation by generation from the cross combination of G. max and G. soja were used as the male parents, 11 (A–K) backcrosses or three-way crosses were designed and 213 single hybrids were harvested. The optimized soybean simple sequence repeat (SSR)–polymerase chain reaction (PCR) system was used to analyze the SSR polymorphism of above parental lines and get the parental co-dominant SSR markers for hybrid identification, and in which 30 true hybrids were gained. The true hybrids (G1, G3, G9, G12, G13, G16) of G cross combination were chosen as the representative for the salt tolerance test, and the results showed that, as exposed to salt stress, the seedlings of G9 line displayed higher salt tolerant coefficient, relative growth rate, and dry matter accumulation, when compared with their female parent Nannong 1138-2, and even performed equally strong salt tolerance as the male parent 3,060. It provides a feasible method of the combination of molecular SSR markers and simple physiological parameters to identify the true hybrids of G. max and G. soja, and to innovate the salt-tolerant soybean germplasms.
bibliographic citation: Li et al. (2019) Hybrid identification for Glycine max and Glycine soja with SSR markers and analysis of salt tolerance. PeerJ 7:e6483 https://doi.org/10.7717/peerj.6483
date submitted: 2018-10-08
date accepted: 2019-01-19
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Fayuan
author list: Agent
  family name: Liu
  given name: Xun
author list: Agent
  family name: Wu
  given name: Shengyan
author list: Agent
  family name: Luo
  given name: Qingyun
author list: Agent
  family name: Yu
  given name: Bingjun
doi: 10.7717/peerj.6483
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Li et al.
attribution name: Li et al.

Phytochemical content and antioxidant activity in aqueous extracts of Cyclocarya paliurus leaves collected from different populations
type: item
type: AcademicArticle
description: Cyclocarya paliurus (Batal) Iljinskaja is a multiple function tree species, but its main utilization is for the harvesting of its leaves as materials for tea production and recently as ingredients for the food industry. In this study aqueous extracts of C. paliurus leaves collected from 21 natural populations were evaluated for their phytochemical content and antioxidant activity. The content of water-soluble polysaccharide, total flavonoid and total polyphenol varied from 66.05 to 153.32 mg/g, 9.01 to 19.65 mg/g and 20.80 to 52.69 mg/g, respectively. Quercetin-3-O-glucuronide, aemferol-3-O-glucuronide and 3-O-caffeoylquinic acid were the major phenolic components in aqueous extracts of C. paliurus leaves. Both redundancy analysis and Pearson's correlation analysis indicated that water-soluble polysaccharide, total polyphenol, total flavonoid, quercetin-3-O-glucuronide, 3-O-caffeoylquinic acid and 4-O-caffeoylquinic acid were significantly correlated with antioxidant activity, but total polyphenol showed the greatest contribution to antioxidant capacity. The antioxidant activity of the 21 populations was classified into six distinct groups based on the squared Euclidean distance. These results would provide a theoretical basis for obtaining the greatest yield of targeted antioxidant phytochemicals of C. paliurus leaves for tea and food ingredient production.
format: application/pdf
format: text/html
creator: Mingming Zhou
creator: Yuan Lin
creator: Shengzuo Fang
creator: Yang Liu
creator: Xulan Shang
subject: Biochemistry
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.6492
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Cyclocarya paliurus (Batal) Iljinskaja is a multiple function tree species, but its main utilization is for the harvesting of its leaves as materials for tea production and recently as ingredients for the food industry. In this study aqueous extracts of C. paliurus leaves collected from 21 natural populations were evaluated for their phytochemical content and antioxidant activity. The content of water-soluble polysaccharide, total flavonoid and total polyphenol varied from 66.05 to 153.32 mg/g, 9.01 to 19.65 mg/g and 20.80 to 52.69 mg/g, respectively. Quercetin-3-O-glucuronide, aemferol-3-O-glucuronide and 3-O-caffeoylquinic acid were the major phenolic components in aqueous extracts of C. paliurus leaves. Both redundancy analysis and Pearson's correlation analysis indicated that water-soluble polysaccharide, total polyphenol, total flavonoid, quercetin-3-O-glucuronide, 3-O-caffeoylquinic acid and 4-O-caffeoylquinic acid were significantly correlated with antioxidant activity, but total polyphenol showed the greatest contribution to antioxidant capacity. The antioxidant activity of the 21 populations was classified into six distinct groups based on the squared Euclidean distance. These results would provide a theoretical basis for obtaining the greatest yield of targeted antioxidant phytochemicals of C. paliurus leaves for tea and food ingredient production.
bibliographic citation: Zhou et al. (2019) Phytochemical content and antioxidant activity in aqueous extracts of Cyclocarya paliurus leaves collected from different populations. PeerJ 7:e6492 https://doi.org/10.7717/peerj.6492
date submitted: 2018-10-22
date accepted: 2019-01-18
issued: 2019-02-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Mingming
author list: Agent
  family name: Lin
  given name: Yuan
author list: Agent
  family name: Fang
  given name: Shengzuo
author list: Agent
  family name: Liu
  given name: Yang
author list: Agent
  family name: Shang
  given name: Xulan
doi: 10.7717/peerj.6492
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-19
copyright: © 2019 Zhou et al.
attribution name: Zhou et al.

A new testudinoid turtle from the middle to late Eocene of Vietnam
type: item
type: AcademicArticle
description: Background Testudinoidea is a major clade of turtles that has colonized different ecological environments across the globe throughout the Tertiary. Aquatic testudinoids have a particularly rich fossil record in the Tertiary of the northern hemisphere, but little is known about the evolutionary history of the group, as the phylogenetic relationships of most fossils have not been established with confidence, in part due to high levels of homoplasy and polymorphism. Methods We here focus on describing a sample of 30 testudinoid shells, belonging to a single population that was collected from lake sediments from the middle to late Eocene (35–39 Ma) Na Duong Formation in Vietnam. The phylogenetic placement of this new material is investigated by integrating it and 11 other species of putative geoemydids from the Eocene and Oligocene to a recently published matrix of geoemydid turtles, that embraces the use of polymorphic characters, and then running a total-evidence analysis. Results The new material is highly polymorphic, but can be inferred with confidence to be a new taxon, Banhxeochelys trani gen. et sp. nov. It shares morphological similarities with other southeastern Asian testudinoids, Isometremys lacuna and Guangdongemys pingi, but is placed phylogenetically at the base of Pan-Testuguria when fossils are included in the analysis, or as a stem geoemydid when other fossils are deactivated from the matrix. The vast majority of other putative fossil geoemydids are placed at the base of Pan-Testuguria as well. Discussion The phylogenetic placement of fossil testudinoids used in the analysis is discussed individually and each species compared to Banhxeochelys trani gen. et sp. nov. The high levels of polymorphism observed in the new taxon is discussed in terms of ontogenetic and random variability. This is the first time that a large sample of fossil testudinoids has its morphological variation described in detail.
format: application/pdf
format: text/html
creator: Rafaella C. Garbin
creator: Madelaine Böhme
creator: Walter G. Joyce
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6280
publisher: PeerJ Inc.
rights: © 2019 Garbin et al.
abstract: Background Testudinoidea is a major clade of turtles that has colonized different ecological environments across the globe throughout the Tertiary. Aquatic testudinoids have a particularly rich fossil record in the Tertiary of the northern hemisphere, but little is known about the evolutionary history of the group, as the phylogenetic relationships of most fossils have not been established with confidence, in part due to high levels of homoplasy and polymorphism. Methods We here focus on describing a sample of 30 testudinoid shells, belonging to a single population that was collected from lake sediments from the middle to late Eocene (35–39 Ma) Na Duong Formation in Vietnam. The phylogenetic placement of this new material is investigated by integrating it and 11 other species of putative geoemydids from the Eocene and Oligocene to a recently published matrix of geoemydid turtles, that embraces the use of polymorphic characters, and then running a total-evidence analysis. Results The new material is highly polymorphic, but can be inferred with confidence to be a new taxon, Banhxeochelys trani gen. et sp. nov. It shares morphological similarities with other southeastern Asian testudinoids, Isometremys lacuna and Guangdongemys pingi, but is placed phylogenetically at the base of Pan-Testuguria when fossils are included in the analysis, or as a stem geoemydid when other fossils are deactivated from the matrix. The vast majority of other putative fossil geoemydids are placed at the base of Pan-Testuguria as well. Discussion The phylogenetic placement of fossil testudinoids used in the analysis is discussed individually and each species compared to Banhxeochelys trani gen. et sp. nov. The high levels of polymorphism observed in the new taxon is discussed in terms of ontogenetic and random variability. This is the first time that a large sample of fossil testudinoids has its morphological variation described in detail.
bibliographic citation: Garbin et al. (2019) A new testudinoid turtle from the middle to late Eocene of Vietnam. PeerJ 7:e6280 https://doi.org/10.7717/peerj.6280
date submitted: 2018-09-07
date accepted: 2018-12-12
issued: 2019-02-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garbin
  given name: Rafaella C.
author list: Agent
  family name: Böhme
  given name: Madelaine
author list: Agent
  family name: Joyce
  given name: Walter G.
doi: 10.7717/peerj.6280
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-18
copyright: © 2019 Garbin et al.
attribution name: Garbin et al.

Diverse microbial communities hosted by the model carnivorous pitcher plant Sarracenia purpurea: analysis of both bacterial and eukaryotic composition across distinct host plant populations
type: item
type: AcademicArticle
description: Background The pitcher plant Sarracenia purpurea supplements nutrient acquisition through carnivory, capturing insect prey which are digested by a food web community of eukaryotes and bacteria. While the food web invertebrates are well studied, and some recent studies have characterized bacteria, detailed genetic analysis of eukaryotic diversity is lacking. This study aimed to compare eukaryotic and bacterial composition and diversity of pitcher communities within and between populations of host plants in nearby but distinct wetland habitats, and to characterize microbial functions across populations and in comparison with another freshwater community. Methods Pitcher fluid was sampled from the two wetlands, Cedarburg and Sapa Bogs, community DNA was extracted, and 16S and 18S rRNA amplicons were sequenced and data processed for community-level comparisons. Results and Conclusions Bacterial diversity in the small pitcher volume rivaled that of larger aquatic communities. Between pitcher plant populations, several bacterial families (Kiloniellaceae, Acetobacteraceae, Xanthobacteraceae, Sanguibacteraceae, Oligoflexaceae, Nitrosomonadaceae, Chromatiaceae, Saprospiraceae) were significantly higher in one population. However, although predicted pitcher bacterial functions were distinct from other freshwater communities, especially for some amino acid metabolism, functions were similar across all the pitchers in the two populations. This suggests some functional redundancy among bacterial taxa, and that functions converge to achieve similar food web processes. The sequencing identified a previously under-appreciated high diversity of ciliates, Acari mites, fungi and flagellates in pitcher communities; the most abundant sequences from eukaryotic taxa were Oligohymenophorea ciliates, millipedes and Ichthyosporea flagellates. Two thirds of taxa were identified as food web inhabitants and less than one third as prey organisms. Although eukaryotic composition was not significa…
format: application/pdf
format: text/html
creator: Jacob J. Grothjan
creator: Erica B. Young
subject: Biodiversity
subject: Microbiology
subject: Plant Science
subject: Freshwater Biology
description: doi:10.7717/peerj.6392
publisher: PeerJ Inc.
rights: © 2019 Grothjan and Young
abstract: Background The pitcher plant Sarracenia purpurea supplements nutrient acquisition through carnivory, capturing insect prey which are digested by a food web community of eukaryotes and bacteria. While the food web invertebrates are well studied, and some recent studies have characterized bacteria, detailed genetic analysis of eukaryotic diversity is lacking. This study aimed to compare eukaryotic and bacterial composition and diversity of pitcher communities within and between populations of host plants in nearby but distinct wetland habitats, and to characterize microbial functions across populations and in comparison with another freshwater community. Methods Pitcher fluid was sampled from the two wetlands, Cedarburg and Sapa Bogs, community DNA was extracted, and 16S and 18S rRNA amplicons were sequenced and data processed for community-level comparisons. Results and Conclusions Bacterial diversity in the small pitcher volume rivaled that of larger aquatic communities. Between pitcher plant populations, several bacterial families (Kiloniellaceae, Acetobacteraceae, Xanthobacteraceae, Sanguibacteraceae, Oligoflexaceae, Nitrosomonadaceae, Chromatiaceae, Saprospiraceae) were significantly higher in one population. However, although predicted pitcher bacterial functions were distinct from other freshwater communities, especially for some amino acid metabolism, functions were similar across all the pitchers in the two populations. This suggests some functional redundancy among bacterial taxa, and that functions converge to achieve similar food web processes. The sequencing identified a previously under-appreciated high diversity of ciliates, Acari mites, fungi and flagellates in pitcher communities; the most abundant sequences from eukaryotic taxa were Oligohymenophorea ciliates, millipedes and Ichthyosporea flagellates. Two thirds of taxa were identified as food web inhabitants and less than one third as prey organisms. Although eukaryotic composition was not significa…
bibliographic citation: Grothjan et al. (2019) Diverse microbial communities hosted by the model carnivorous pitcher plant Sarracenia purpurea: analysis of both bacterial and eukaryotic composition across distinct host plant populations. PeerJ 7:e6392 https://doi.org/10.7717/peerj.6392
date submitted: 2018-10-22
date accepted: 2019-01-04
issued: 2019-02-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grothjan
  given name: Jacob J.
author list: Agent
  family name: Young
  given name: Erica B.
doi: 10.7717/peerj.6392
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-18
copyright: ©2019 Grothjan and Young
attribution name: Grothjan and Young

Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers
type: item
type: AcademicArticle
description: Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.
format: application/pdf
format: text/html
creator: Lei Hao
creator: Guosheng Zhang
creator: Dongye Lu
creator: Jianjun Hu
creator: Huixia Jia
subject: Plant Science
description: doi:10.7717/peerj.6419
publisher: PeerJ Inc.
rights: © 2019 Hao et al.
abstract: Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.
bibliographic citation: Hao et al. (2019) Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers. PeerJ 7:e6419 https://doi.org/10.7717/peerj.6419
date submitted: 2018-08-24
date accepted: 2019-01-04
issued: 2019-02-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Lei
author list: Agent
  family name: Zhang
  given name: Guosheng
author list: Agent
  family name: Lu
  given name: Dongye
author list: Agent
  family name: Hu
  given name: Jianjun
author list: Agent
  family name: Jia
  given name: Huixia
doi: 10.7717/peerj.6419
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-18
copyright: © 2019 Hao et al.
attribution name: Hao et al.

Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes
type: item
type: AcademicArticle
description: Background Our aim was to explore how the ectomycorrhizae of an indigenous tree,Quercus acutissima, with a commercial truffle, Chinese black truffle (Tuber indicum), affects the host plant physiology and shapes the associated microbial communities in the surrounding environment during the early stage of symbiosis. Methods To achieve this, changes in root morphology and microscopic characteristics, plant physiology indices, and the rhizosphere soil properties were investigated when six-month-old ectomycorrhizae were synthesized. Meanwhile, next-generation sequencing technology was used to analyze the bacterial and fungal communities in the root endosphere and rhizosphere soil inoculated with T. indicum or not. Results The results showed that colonization by T. indicum significantly improved the activity of superoxide dismutase in roots but significantly decreased the root activity. The biomass, leaf chlorophyll content and root peroxidase activity did not obviously differ. Ectomycorrhization of Q. acutissima with T. indicum affected the characteristics of the rhizosphere soil, improving the content of organic matter, total nitrogen, total phosphorus and available nitrogen. The bacterial and fungal community composition in the root endosphere and rhizosphere soil was altered by T. indicum colonization, as was the community richness and diversity. The dominant bacteria in all the samples were Proteobacteria and Actinobacteria, and the dominant fungi were Eukaryota_norank, Ascomycota, and Mucoromycota. Some bacterial communities, such as Streptomyces, SM1A02, and Rhizomicrobium were more abundant in the ectomycorrhizae or ectomycorrhizosphere soil. Tuber was the second-most abundant fungal genus, and Fusarium was present at lower amounts in the inoculated samples. Discussion Overall, the symbiotic relationship between Q. acutissima and T. indicum had an obvious effect on host plant physiology, soil properties, and microbial community composition in the root endosphere a…
format: application/pdf
format: text/html
creator: Xiaoping Zhang
creator: Lei Ye
creator: Zongjing Kang
creator: Jie Zou
creator: Xiaolin Li
subject: Agricultural Science
subject: Biodiversity
subject: Biotechnology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.6421
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Our aim was to explore how the ectomycorrhizae of an indigenous tree,Quercus acutissima, with a commercial truffle, Chinese black truffle (Tuber indicum), affects the host plant physiology and shapes the associated microbial communities in the surrounding environment during the early stage of symbiosis. Methods To achieve this, changes in root morphology and microscopic characteristics, plant physiology indices, and the rhizosphere soil properties were investigated when six-month-old ectomycorrhizae were synthesized. Meanwhile, next-generation sequencing technology was used to analyze the bacterial and fungal communities in the root endosphere and rhizosphere soil inoculated with T. indicum or not. Results The results showed that colonization by T. indicum significantly improved the activity of superoxide dismutase in roots but significantly decreased the root activity. The biomass, leaf chlorophyll content and root peroxidase activity did not obviously differ. Ectomycorrhization of Q. acutissima with T. indicum affected the characteristics of the rhizosphere soil, improving the content of organic matter, total nitrogen, total phosphorus and available nitrogen. The bacterial and fungal community composition in the root endosphere and rhizosphere soil was altered by T. indicum colonization, as was the community richness and diversity. The dominant bacteria in all the samples were Proteobacteria and Actinobacteria, and the dominant fungi were Eukaryota_norank, Ascomycota, and Mucoromycota. Some bacterial communities, such as Streptomyces, SM1A02, and Rhizomicrobium were more abundant in the ectomycorrhizae or ectomycorrhizosphere soil. Tuber was the second-most abundant fungal genus, and Fusarium was present at lower amounts in the inoculated samples. Discussion Overall, the symbiotic relationship between Q. acutissima and T. indicum had an obvious effect on host plant physiology, soil properties, and microbial community composition in the root endosphere a…
bibliographic citation: Zhang et al. (2019) Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes. PeerJ 7:e6421 https://doi.org/10.7717/peerj.6421
date submitted: 2018-09-18
date accepted: 2019-01-07
issued: 2019-02-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiaoping
author list: Agent
  family name: Ye
  given name: Lei
author list: Agent
  family name: Kang
  given name: Zongjing
author list: Agent
  family name: Zou
  given name: Jie
author list: Agent
  family name: Zhang
  given name: Xiaoping
author list: Agent
  family name: Li
  given name: Xiaolin
doi: 10.7717/peerj.6421
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-18
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Stress responses upon starvation and exposure to bacteria in the ant Formica exsecta
type: item
type: AcademicArticle
description: Organisms are simultaneously exposed to multiple stresses, which requires regulation of the resistance to each stress. Starvation is one of the most severe stresses organisms encounter, yet nutritional state is also one of the most crucial conditions on which other stress resistances depend. Concomitantly, organisms often deploy lower immune defenses when deprived of resources. This indicates that the investment into starvation resistance and immune defenses is likely to be subject to trade-offs. Here, we investigated the impact of starvation and oral exposure to bacteria on survival and gene expression in the ant Formica exsecta. Of the three bacteria used in this study, only Serratia marcescens increased the mortality of the ants, whereas exposure to Escherichia coli and Pseudomonas entomophila alleviated the effects of starvation. Both exposure to bacteria and starvation induced changes in gene expression, but in different directions depending on the species of bacteria used, as well as on the nutritional state of the ants.
format: application/pdf
format: text/html
creator: Dimitri Stucki
creator: Dalial Freitak
creator: Nick Bos
creator: Liselotte Sundström
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.6428
publisher: PeerJ Inc.
rights: © 2019 Stucki et al.
abstract: Organisms are simultaneously exposed to multiple stresses, which requires regulation of the resistance to each stress. Starvation is one of the most severe stresses organisms encounter, yet nutritional state is also one of the most crucial conditions on which other stress resistances depend. Concomitantly, organisms often deploy lower immune defenses when deprived of resources. This indicates that the investment into starvation resistance and immune defenses is likely to be subject to trade-offs. Here, we investigated the impact of starvation and oral exposure to bacteria on survival and gene expression in the ant Formica exsecta. Of the three bacteria used in this study, only Serratia marcescens increased the mortality of the ants, whereas exposure to Escherichia coli and Pseudomonas entomophila alleviated the effects of starvation. Both exposure to bacteria and starvation induced changes in gene expression, but in different directions depending on the species of bacteria used, as well as on the nutritional state of the ants.
bibliographic citation: Stucki et al. (2019) Stress responses upon starvation and exposure to bacteria in the ant Formica exsecta. PeerJ 7:e6428 https://doi.org/10.7717/peerj.6428
date submitted: 2018-08-15
date accepted: 2019-01-10
issued: 2019-02-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stucki
  given name: Dimitri
author list: Agent
  family name: Freitak
  given name: Dalial
author list: Agent
  family name: Bos
  given name: Nick
author list: Agent
  family name: Sundström
  given name: Liselotte
doi: 10.7717/peerj.6428
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-18
copyright: © 2019 Stucki et al.
attribution name: Stucki et al.

Potential antidiabetic effect of ethanolic and aqueous-ethanolic extracts of Ricinus communis leaves on streptozotocin-induced diabetes in rats
type: item
type: AcademicArticle
description: Recently, herbal drugs and their bioactive compounds have gained popularity in the management of diabetes mellitus (DM), which has become an epidemic disease all over the world and is especially prevalent in the Kingdom of Saudi Arabia (KSA). This study aimed to investigate the antidiabetic effect of ethanolic and aqueous-ethanolic extracts of wild Ricinus communis (R. communis) leaves in streptozotocin (STZ) induced diabetic rats. Diabetic rats were administered orally with the mentioned extracts at doses of 300 and 600 mg/kg/BW for 14 days, and the obtained results of different biochemical parameters were compared with normal control, diabetic control and standard drug glibenclamide (5 mg/kg/BW). The obtained results revealed a remarkable and significantly (P < 0.05) reverse effect of the body weight loss, observed when diabetic rats were treated with ethanol and aqueous-ethanol extracts at 300 mg/kg/BW. Administration of the ethanol extract at 600 mg/kg/BW significantly (P < 0.05) reduced the blood glucose level. A significant increase in the AST, ALT and ALP levels (P < 0.05) was observed in the diabetic control and in the experimental groups with glibenclamide which was also significantly (P < 0.05) lowered after treatment with extracts at special doses. Total proteins, albumin, total bilirubin, direct bilirubin, creatinine and urea were also investigated and compared to the corresponding controls. We showed that administration of R. communis extract generally significantly (P < 0.05) ameliorated the biochemical parameters of diabetic rats. Also, the changes in serum electrolyte profile were assessed and the results demonstrate that administration of extracts at concentration of 600 mg/kg/BW generally inhibits the alteration maintain their levels. The obtained data imply the hypoglycemic effects of this plant, which may be used as a good alternative for managing DM and therefore validating its traditional usage in KSA.
format: application/pdf
format: text/html
creator: Mohamed A.M. Gad-Elkareem
creator: Elkhatim H. Abdelgadir
creator: Ossama M. Badawy
creator: Adel Kadri
subject: Diabetes and Endocrinology
subject: Pharmacology
description: doi:10.7717/peerj.6441
publisher: PeerJ Inc.
rights: © 2019 Gad-Elkareem et al.
abstract: Recently, herbal drugs and their bioactive compounds have gained popularity in the management of diabetes mellitus (DM), which has become an epidemic disease all over the world and is especially prevalent in the Kingdom of Saudi Arabia (KSA). This study aimed to investigate the antidiabetic effect of ethanolic and aqueous-ethanolic extracts of wild Ricinus communis (R. communis) leaves in streptozotocin (STZ) induced diabetic rats. Diabetic rats were administered orally with the mentioned extracts at doses of 300 and 600 mg/kg/BW for 14 days, and the obtained results of different biochemical parameters were compared with normal control, diabetic control and standard drug glibenclamide (5 mg/kg/BW). The obtained results revealed a remarkable and significantly (P < 0.05) reverse effect of the body weight loss, observed when diabetic rats were treated with ethanol and aqueous-ethanol extracts at 300 mg/kg/BW. Administration of the ethanol extract at 600 mg/kg/BW significantly (P < 0.05) reduced the blood glucose level. A significant increase in the AST, ALT and ALP levels (P < 0.05) was observed in the diabetic control and in the experimental groups with glibenclamide which was also significantly (P < 0.05) lowered after treatment with extracts at special doses. Total proteins, albumin, total bilirubin, direct bilirubin, creatinine and urea were also investigated and compared to the corresponding controls. We showed that administration of R. communis extract generally significantly (P < 0.05) ameliorated the biochemical parameters of diabetic rats. Also, the changes in serum electrolyte profile were assessed and the results demonstrate that administration of extracts at concentration of 600 mg/kg/BW generally inhibits the alteration maintain their levels. The obtained data imply the hypoglycemic effects of this plant, which may be used as a good alternative for managing DM and therefore validating its traditional usage in KSA.
bibliographic citation: Gad-Elkareem et al. (2019) Potential antidiabetic effect of ethanolic and aqueous-ethanolic extracts of Ricinus communis leaves on streptozotocin-induced diabetes in rats. PeerJ 7:e6441 https://doi.org/10.7717/peerj.6441
date submitted: 2018-10-16
date accepted: 2019-01-13
issued: 2019-02-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gad-Elkareem
  given name: Mohamed A.M.
author list: Agent
  family name: Abdelgadir
  given name: Elkhatim H.
author list: Agent
  family name: Badawy
  given name: Ossama M.
author list: Agent
  family name: Kadri
  given name: Adel
doi: 10.7717/peerj.6441
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-18
copyright: ©2019 Gad-Elkareem et al.
attribution name: Gad-Elkareem et al.

Tricin levels and expression of flavonoid biosynthetic genes in developing grains of purple and brown pericarp rice
type: item
type: AcademicArticle
description: The methylated flavone tricin has been associated with numerous health benefits, including reductions in intestinal and colon cancers in animal models. Tricin is found in a wide range of plant species and in many different tissues. However, whole cereal grains, such as rice, barley, oats, and wheat, are the only food sources of tricin, which is located in the bran portion of the grain. Variation in tricin levels was found in bran from rice genotypes with light brown, brown, red, and purple pericarp color, with the purple pericarp genotypes having the highest levels of tricin. Here, we analyzed tricin and tricin derivative levels in developing pericarp and embryo samples of a purple pericarp genotype, IAC600, that had high tricin and tricin derivative levels in the bran, and a light brown pericarp genotype, Cocodrie, that had no detectable tricin or tricin derivatives in the bran. Tricin and tricin derivatives were detected in both the pericarp and embryo of IAC600 but only in the embryo of Cocodrie. The purple pericarp rice had higher total levels of free tricin plus tricin derivatives than the light brown pericarp rice. When expressed on a per grain basis, most of the tricin component of IAC600 was in the pericarp. In contrast, Cocodrie had no detectable tricin in the pericarp samples but did have detectable chrysoeriol, a precursor of tricin, in the pericarp samples. We also used RNA-Seq analysis of developing pericarp and embryo samples of the two cultivars to compare the expression of genes involved in the flavonoid biosynthetic pathway. The results presented here suggest that understanding the basis of tricin accumulation in rice pericarp may lead to an approach to increasing tricin levels in whole grain rice. From analysis of gene expression levels in the pericarp samples it appears that regulation of the flavone specific genes is independent of regulation of the anthocyanin biosynthetic genes. It therefore may be feasible to develop brown pericarp rice cultiv…
format: application/pdf
format: text/html
creator: Alexander Poulev
creator: Joseph R. Heckman
creator: Ilya Raskin
creator: Faith C. Belanger
subject: Agricultural Science
subject: Plant Science
subject: Nutrition
description: doi:10.7717/peerj.6477
publisher: PeerJ Inc.
rights: © 2019 Poulev et al.
abstract: The methylated flavone tricin has been associated with numerous health benefits, including reductions in intestinal and colon cancers in animal models. Tricin is found in a wide range of plant species and in many different tissues. However, whole cereal grains, such as rice, barley, oats, and wheat, are the only food sources of tricin, which is located in the bran portion of the grain. Variation in tricin levels was found in bran from rice genotypes with light brown, brown, red, and purple pericarp color, with the purple pericarp genotypes having the highest levels of tricin. Here, we analyzed tricin and tricin derivative levels in developing pericarp and embryo samples of a purple pericarp genotype, IAC600, that had high tricin and tricin derivative levels in the bran, and a light brown pericarp genotype, Cocodrie, that had no detectable tricin or tricin derivatives in the bran. Tricin and tricin derivatives were detected in both the pericarp and embryo of IAC600 but only in the embryo of Cocodrie. The purple pericarp rice had higher total levels of free tricin plus tricin derivatives than the light brown pericarp rice. When expressed on a per grain basis, most of the tricin component of IAC600 was in the pericarp. In contrast, Cocodrie had no detectable tricin in the pericarp samples but did have detectable chrysoeriol, a precursor of tricin, in the pericarp samples. We also used RNA-Seq analysis of developing pericarp and embryo samples of the two cultivars to compare the expression of genes involved in the flavonoid biosynthetic pathway. The results presented here suggest that understanding the basis of tricin accumulation in rice pericarp may lead to an approach to increasing tricin levels in whole grain rice. From analysis of gene expression levels in the pericarp samples it appears that regulation of the flavone specific genes is independent of regulation of the anthocyanin biosynthetic genes. It therefore may be feasible to develop brown pericarp rice cultiv…
bibliographic citation: Poulev et al. (2019) Tricin levels and expression of flavonoid biosynthetic genes in developing grains of purple and brown pericarp rice. PeerJ 7:e6477 https://doi.org/10.7717/peerj.6477
date submitted: 2018-10-12
date accepted: 2019-01-18
issued: 2019-02-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Poulev
  given name: Alexander
author list: Agent
  family name: Heckman
  given name: Joseph R.
author list: Agent
  family name: Raskin
  given name: Ilya
author list: Agent
  family name: Belanger
  given name: Faith C.
doi: 10.7717/peerj.6477
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-18
copyright: © 2019 Poulev et al.
attribution name: Poulev et al.

Dynamic multi-species occupancy models reveal individualistic habitat preferences in a high-altitude grassland bird community
type: item
type: AcademicArticle
description: Moist, high-altitude grasslands of eastern South African harbour rich avian diversity and endemism. This area is also threatened by increasingly intensive agriculture and land conversion for energy production. This conflict is particularly evident at Ingula, an Important Bird and Biodiversity Area located within the least conserved high-altitude grasslands and which is also the site of a new Pumped Storage Scheme. The new management seeks to maximise biodiversity through manipulation of the key habitat variables: grass height and grass cover through burning and grazing to make habitat suitable for birds. However, different species have individual habitat preferences, which further vary through the season. We used a dynamic multi-species occupancy model to examine the seasonal occupancy dynamics of 12 common grassland bird species and their habitat preferences. We estimated monthly occupancy, colonisation and persistence in relation to grass height and grass cover throughout the summer breeding season of 2011/12. For majority of these species, at the beginning of the season occupancy increased with increasing grass height and decreased with increasing grass cover. Persistence and colonisation decreased with increasing grass height and cover. However, the 12 species varied considerably in their responses to grass height and cover. Our results suggest that management should aim to provide plots which vary in grass height and cover to maximise bird diversity. We also conclude that the decreasing occupancy with increasing grass cover and low colonisation with increasing grass height and cover is a results of little grazing on our study site. We further conclude that some of the 12 selected species are good indicators of habitat suitability more generally because they represent a range of habitat needs and are relatively easy to monitor.
format: application/pdf
format: text/html
creator: David H. Maphisa
creator: Hanneline Smit-Robinson
creator: Res Altwegg
subject: Biodiversity
subject: Ecology
subject: Environmental Sciences
subject: Statistics
description: doi:10.7717/peerj.6276
publisher: PeerJ Inc.
rights: © 2019 Maphisa et al.
abstract: Moist, high-altitude grasslands of eastern South African harbour rich avian diversity and endemism. This area is also threatened by increasingly intensive agriculture and land conversion for energy production. This conflict is particularly evident at Ingula, an Important Bird and Biodiversity Area located within the least conserved high-altitude grasslands and which is also the site of a new Pumped Storage Scheme. The new management seeks to maximise biodiversity through manipulation of the key habitat variables: grass height and grass cover through burning and grazing to make habitat suitable for birds. However, different species have individual habitat preferences, which further vary through the season. We used a dynamic multi-species occupancy model to examine the seasonal occupancy dynamics of 12 common grassland bird species and their habitat preferences. We estimated monthly occupancy, colonisation and persistence in relation to grass height and grass cover throughout the summer breeding season of 2011/12. For majority of these species, at the beginning of the season occupancy increased with increasing grass height and decreased with increasing grass cover. Persistence and colonisation decreased with increasing grass height and cover. However, the 12 species varied considerably in their responses to grass height and cover. Our results suggest that management should aim to provide plots which vary in grass height and cover to maximise bird diversity. We also conclude that the decreasing occupancy with increasing grass cover and low colonisation with increasing grass height and cover is a results of little grazing on our study site. We further conclude that some of the 12 selected species are good indicators of habitat suitability more generally because they represent a range of habitat needs and are relatively easy to monitor.
bibliographic citation: Maphisa et al. (2019) Dynamic multi-species occupancy models reveal individualistic habitat preferences in a high-altitude grassland bird community. PeerJ 7:e6276 https://doi.org/10.7717/peerj.6276
date submitted: 2018-05-09
date accepted: 2018-12-12
issued: 2019-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maphisa
  given name: David H.
author list: Agent
  family name: Smit-Robinson
  given name: Hanneline
author list: Agent
  family name: Altwegg
  given name: Res
doi: 10.7717/peerj.6276
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-15
copyright: ©2019 Maphisa et al.
attribution name: Maphisa et al.

Impact of old age on resectable colorectal cancer outcomes
type: item
type: AcademicArticle
description: Objective This study was performed to identify a reasonable cutoff age for defining older patients with colorectal cancer (CRC) and to examine whether old age was related with increased colorectal cancer-specific death (CSD) and poor colorectal cancer-specific survival (CSS). Methods A total of 76,858 eligible patients from the surveillance, epidemiology, and end results (SEER) database were included in this study. The Cox proportional hazard regression model and the Chow test were used to determine a suitable cutoff age for defining the older group. Furthermore, a propensity score matching analysis was performed to adjust for heterogeneity between groups. A competing risk regression model was used to explore the impact of age on CSD and non-colorectal cancer-specific death (non-CSD). Kaplan–Meier survival curves were plotted to compare CSS between groups. Also, a Cox regression model was used to validate the results. External validation was performed on data from 1998 to 2003 retrieved from the SEER database. Results Based on a cutoff age of 70 years, the examined cohort of patients was classified into a younger group (n = 51,915, <70 years of old) and an older group (n = 24,943, ≥70 years of old). Compared with younger patients, older patients were more likely to have fewer lymph nodes sampled and were less likely to receive chemotherapy and radiotherapy. When adjusted for other covariates, age-dependent differences of 5-year CSD and 5-year non-CSD were significant in the younger and older groups (15.84% and 22.42%, P < 0.001; 5.21% and 14.21%, P < 0.001). Also an age of ≥70 years remained associated with worse CSS comparing with younger group (subdistribution hazard ratio, 1.51 95% confidence interval (CI) [1.45–1.57], P < 0.001). The Cox regression model as a sensitivity analysis had a similar result. External validation also supported an age of 70 years as a suitable cutoff, and this older group was associated with having reduced CSS and increased CSD. Conclusi…
format: application/pdf
format: text/html
creator: Jianfei Fu
creator: Hang Ruan
creator: Hongjuan Zheng
creator: Cheng Cai
creator: Shishi Zhou
creator: Qinghua Wang
creator: Wenbin Chen
creator: Wei Fu
creator: Jinlin Du
subject: Gastroenterology and Hepatology
subject: Geriatrics
subject: Oncology
description: doi:10.7717/peerj.6350
publisher: PeerJ Inc.
rights: © 2019 Fu et al.
abstract: Objective This study was performed to identify a reasonable cutoff age for defining older patients with colorectal cancer (CRC) and to examine whether old age was related with increased colorectal cancer-specific death (CSD) and poor colorectal cancer-specific survival (CSS). Methods A total of 76,858 eligible patients from the surveillance, epidemiology, and end results (SEER) database were included in this study. The Cox proportional hazard regression model and the Chow test were used to determine a suitable cutoff age for defining the older group. Furthermore, a propensity score matching analysis was performed to adjust for heterogeneity between groups. A competing risk regression model was used to explore the impact of age on CSD and non-colorectal cancer-specific death (non-CSD). Kaplan–Meier survival curves were plotted to compare CSS between groups. Also, a Cox regression model was used to validate the results. External validation was performed on data from 1998 to 2003 retrieved from the SEER database. Results Based on a cutoff age of 70 years, the examined cohort of patients was classified into a younger group (n = 51,915, <70 years of old) and an older group (n = 24,943, ≥70 years of old). Compared with younger patients, older patients were more likely to have fewer lymph nodes sampled and were less likely to receive chemotherapy and radiotherapy. When adjusted for other covariates, age-dependent differences of 5-year CSD and 5-year non-CSD were significant in the younger and older groups (15.84% and 22.42%, P < 0.001; 5.21% and 14.21%, P < 0.001). Also an age of ≥70 years remained associated with worse CSS comparing with younger group (subdistribution hazard ratio, 1.51 95% confidence interval (CI) [1.45–1.57], P < 0.001). The Cox regression model as a sensitivity analysis had a similar result. External validation also supported an age of 70 years as a suitable cutoff, and this older group was associated with having reduced CSS and increased CSD. Conclusi…
bibliographic citation: Fu et al. (2019) Impact of old age on resectable colorectal cancer outcomes. PeerJ 7:e6350 https://doi.org/10.7717/peerj.6350
date submitted: 2018-08-03
date accepted: 2018-12-27
issued: 2019-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Jianfei
author list: Agent
  family name: Ruan
  given name: Hang
author list: Agent
  family name: Zheng
  given name: Hongjuan
author list: Agent
  family name: Cai
  given name: Cheng
author list: Agent
  family name: Zhou
  given name: Shishi
author list: Agent
  family name: Wang
  given name: Qinghua
author list: Agent
  family name: Chen
  given name: Wenbin
author list: Agent
  family name: Fu
  given name: Wei
author list: Agent
  family name: Du
  given name: Jinlin
doi: 10.7717/peerj.6350
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-15
copyright: © 2019 Fu et al.
attribution name: Fu et al.

Effects of traditional agroecosystems and grazing areas on amphibian diversity in a region of central Mexico
type: item
type: AcademicArticle
description: Habitat loss or degradation due to land cover change is regarded as one of the main drivers of amphibian decline; therefore, it is imperative to assess the effects of land-cover change on this group of vertebrates. In this study, we analyze changes in alpha and beta diversity of amphibian communities found in five land-cover types: mountain cloud forest, tropical evergreen forest, shade coffee, milpa huasteca, and grazing areas; six samples sites were established for each land-cover type, separated at least one km away. The study was conducted in the northwest part of the state of Hidalgo, in a transition zone between the Sierra Madre Oriental and the Gulf of Mexico, which is a region rich in amphibian species. The results indicate that alpha diversity decreases with loss of canopy cover, this being high in mountain cloud forest, tropical evergreen forest, and Shade coffee, and low in milpa huasteca and grazing areas. The land-cover type with the highest species evenness was found in milpa huasteca and the lowest in. The highest beta diversity was observed among tropical evergreen forest and grazing areas. Mountain cloud forest contains both exclusive species and the highest number of species currently regarded as threatened by national and international conservation assessment systems. In order to preserve amphibian diversity in the study area it is vital to protect the last remnants of native vegetation, especially mountain cloud forest, but also including Shade coffee, since the latter habitat harbors amphibian diversity similar to that found in native forests. Finally, implementation of policies that both reduce Grazing areas and increase their productivity is also necessary, since these highly modified areas turn out to be the ones that affect amphibian diversity the most.
format: application/pdf
format: text/html
creator: José Daniel Lara-Tufiño
creator: Luis M. Badillo-Saldaña
creator: Raquel Hernández-Austria
creator: Aurelio Ramírez-Bautista
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.6390
publisher: PeerJ Inc.
rights: © 2019 Lara-Tufiño et al.
abstract: Habitat loss or degradation due to land cover change is regarded as one of the main drivers of amphibian decline; therefore, it is imperative to assess the effects of land-cover change on this group of vertebrates. In this study, we analyze changes in alpha and beta diversity of amphibian communities found in five land-cover types: mountain cloud forest, tropical evergreen forest, shade coffee, milpa huasteca, and grazing areas; six samples sites were established for each land-cover type, separated at least one km away. The study was conducted in the northwest part of the state of Hidalgo, in a transition zone between the Sierra Madre Oriental and the Gulf of Mexico, which is a region rich in amphibian species. The results indicate that alpha diversity decreases with loss of canopy cover, this being high in mountain cloud forest, tropical evergreen forest, and Shade coffee, and low in milpa huasteca and grazing areas. The land-cover type with the highest species evenness was found in milpa huasteca and the lowest in. The highest beta diversity was observed among tropical evergreen forest and grazing areas. Mountain cloud forest contains both exclusive species and the highest number of species currently regarded as threatened by national and international conservation assessment systems. In order to preserve amphibian diversity in the study area it is vital to protect the last remnants of native vegetation, especially mountain cloud forest, but also including Shade coffee, since the latter habitat harbors amphibian diversity similar to that found in native forests. Finally, implementation of policies that both reduce Grazing areas and increase their productivity is also necessary, since these highly modified areas turn out to be the ones that affect amphibian diversity the most.
bibliographic citation: Lara-Tufiño et al. (2019) Effects of traditional agroecosystems and grazing areas on amphibian diversity in a region of central Mexico. PeerJ 7:e6390 https://doi.org/10.7717/peerj.6390
date submitted: 2018-03-22
date accepted: 2019-01-04
issued: 2019-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lara-Tufiño
  given name: José Daniel
author list: Agent
  family name: Badillo-Saldaña
  given name: Luis M.
author list: Agent
  family name: Hernández-Austria
  given name: Raquel
author list: Agent
  family name: Ramírez-Bautista
  given name: Aurelio
doi: 10.7717/peerj.6390
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-15
copyright: © 2019 Lara-Tufiño et al.
attribution name: Lara-Tufiño et al.

Shifting headlines? Size trends of newsworthy fishes
type: item
type: AcademicArticle
description: The shifting baseline syndrome describes a gradual lowering of human cognitive baselines, as each generation accepts a lower standard of resource abundance or size as the new norm. There is strong empirical evidence of declining trends of abundance and body sizes of marine fish species reported from docks and markets. We asked whether these widespread trends in shrinking marine fish are detectable in popular English-language media, or whether news writers, like many marine stakeholders, are captive to shifting baselines. We collected 266 English-language news articles, printed between 1869 and 2015, which featured headlines that used a superlative adjective, such as ‘giant’, ‘huge’, or ‘monster’, to describe an individual fish caught. We combined the reported sizes of the captured fish with information on maximum species-specific recorded sizes to reconstruct trends of relative size (reported size divided by maximum size) of newsworthy fishes over time. We found some evidence of a shifting baseline syndrome in news media over the last 140 years: overall, the relative length of the largest fish worthy of a headline has declined over time. This pattern held for charismatic fish species (e.g. basking sharks, whale sharks, giant mantas), which are now reported in the media at smaller relative lengths than they were near the turn of the 20th century, and for the largest species under high risk of extinction. In contrast, there was no similar trend for pelagic gamefish and oceanic sharks, or for species under lower risk of extinction. While landing any individual of the large-bodied ‘megafish’ may be newsworthy in part because of their large size relative to other fish species, the ‘megafish’ covered in our dataset were small relative to their own species—on average only 56% of the species-specific maximum length. The continued use in the English-language media of superlatives to describe fish that are now a fraction of the maximum size they could reach, or a fraction of …
format: application/pdf
format: text/html
creator: Fiona T. Francis
creator: Brett R. Howard
creator: Adrienne E. Berchtold
creator: Trevor A. Branch
creator: Laís C.T. Chaves
creator: Jillian C. Dunic
creator: Brett Favaro
creator: Kyla M. Jeffrey
creator: Luis Malpica-Cruz
creator: Natalie Maslowski
creator: Jessica A. Schultz
creator: Nicola S. Smith
creator: Isabelle M. Côté
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6395
publisher: PeerJ Inc.
rights: © 2019 Francis et al.
abstract: The shifting baseline syndrome describes a gradual lowering of human cognitive baselines, as each generation accepts a lower standard of resource abundance or size as the new norm. There is strong empirical evidence of declining trends of abundance and body sizes of marine fish species reported from docks and markets. We asked whether these widespread trends in shrinking marine fish are detectable in popular English-language media, or whether news writers, like many marine stakeholders, are captive to shifting baselines. We collected 266 English-language news articles, printed between 1869 and 2015, which featured headlines that used a superlative adjective, such as ‘giant’, ‘huge’, or ‘monster’, to describe an individual fish caught. We combined the reported sizes of the captured fish with information on maximum species-specific recorded sizes to reconstruct trends of relative size (reported size divided by maximum size) of newsworthy fishes over time. We found some evidence of a shifting baseline syndrome in news media over the last 140 years: overall, the relative length of the largest fish worthy of a headline has declined over time. This pattern held for charismatic fish species (e.g. basking sharks, whale sharks, giant mantas), which are now reported in the media at smaller relative lengths than they were near the turn of the 20th century, and for the largest species under high risk of extinction. In contrast, there was no similar trend for pelagic gamefish and oceanic sharks, or for species under lower risk of extinction. While landing any individual of the large-bodied ‘megafish’ may be newsworthy in part because of their large size relative to other fish species, the ‘megafish’ covered in our dataset were small relative to their own species—on average only 56% of the species-specific maximum length. The continued use in the English-language media of superlatives to describe fish that are now a fraction of the maximum size they could reach, or a fraction of …
bibliographic citation: Francis et al. (2019) Shifting headlines? Size trends of newsworthy fishes. PeerJ 7:e6395 https://doi.org/10.7717/peerj.6395
date submitted: 2018-08-14
date accepted: 2019-01-05
issued: 2019-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Francis
  given name: Fiona T.
author list: Agent
  family name: Howard
  given name: Brett R.
author list: Agent
  family name: Berchtold
  given name: Adrienne E.
author list: Agent
  family name: Branch
  given name: Trevor A.
author list: Agent
  family name: Chaves
  given name: Laís C.T.
author list: Agent
  family name: Dunic
  given name: Jillian C.
author list: Agent
  family name: Favaro
  given name: Brett
author list: Agent
  family name: Jeffrey
  given name: Kyla M.
author list: Agent
  family name: Malpica-Cruz
  given name: Luis
author list: Agent
  family name: Maslowski
  given name: Natalie
author list: Agent
  family name: Schultz
  given name: Jessica A.
author list: Agent
  family name: Smith
  given name: Nicola S.
author list: Agent
  family name: Côté
  given name: Isabelle M.
doi: 10.7717/peerj.6395
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-15
copyright: © 2019 Francis et al.
attribution name: Francis et al.

Biodiversity and temporal patterns of macrozoobenthos in a coal mining subsidence area in North China
type: item
type: AcademicArticle
description: Coal resources play a strategic role in the long-term development of China. Large-scale mining has a considerable impact on the landscape, and it is a long-term heritage of industrialization unique to the Anthropocene. We investigated the macrozoobenthos and water in nine mining subsidence wetlands at different developmental stages (3–20 years) in North China. A total of 68 species were found, and the macrozoobenthos community in the newly formed wetlands showed high diversity. We believe that this high diversity is not random; rather, the high diversity was because of the special origin and development of the wetland. We used three time slices from the timeline of the development of the newly formed wetlands and compared them. It was found that the macrozoobenthos community was significantly affected by the change in the subsidence history. We emphasize that coal mining subsidence should not be merely identified as secondary man-made disasters, as they are often secondary habitats with high conservation value, and their conservation potential lies in the fact that these secondary habitats can replace rapidly decreasing natural wetlands.
format: application/pdf
format: text/html
creator: Guanxiong Zhang
creator: Xingzhong Yuan
creator: Kehong Wang
subject: Biodiversity
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.6456
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Coal resources play a strategic role in the long-term development of China. Large-scale mining has a considerable impact on the landscape, and it is a long-term heritage of industrialization unique to the Anthropocene. We investigated the macrozoobenthos and water in nine mining subsidence wetlands at different developmental stages (3–20 years) in North China. A total of 68 species were found, and the macrozoobenthos community in the newly formed wetlands showed high diversity. We believe that this high diversity is not random; rather, the high diversity was because of the special origin and development of the wetland. We used three time slices from the timeline of the development of the newly formed wetlands and compared them. It was found that the macrozoobenthos community was significantly affected by the change in the subsidence history. We emphasize that coal mining subsidence should not be merely identified as secondary man-made disasters, as they are often secondary habitats with high conservation value, and their conservation potential lies in the fact that these secondary habitats can replace rapidly decreasing natural wetlands.
bibliographic citation: Zhang et al. (2019) Biodiversity and temporal patterns of macrozoobenthos in a coal mining subsidence area in North China. PeerJ 7:e6456 https://doi.org/10.7717/peerj.6456
date submitted: 2018-10-15
date accepted: 2019-01-16
issued: 2019-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Guanxiong
author list: Agent
  family name: Yuan
  given name: Xingzhong
author list: Agent
  family name: Wang
  given name: Kehong
doi: 10.7717/peerj.6456
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-15
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Mat thickness associated with Didymosphenia geminata and Cymbella spp. in the southern rivers of Chile
type: item
type: AcademicArticle
description: Didymosphenia geminata is a diatom that can alter aquatic systems. Several investigations have shown as chemical, and hydraulic factors have a great influence on the proliferation of D. geminata, but the study of other microalgae that could be associated with it has been poorly addressed. The objective of this study is to evaluate the relationship between mat thickness, D. geminata and another taxon that produces mucilage, Cymbella, while also considering physical and chemical factors. For this, two samples were taken, one in the spring of 2013 and the other in the autumn of 2014, from eight rivers in central-southern Chile-South America, where the benthic community was characterized, and the thickness of the mat was measured. The results show that the mat thickness on sites with the presence of both taxa is doubled, and while sites with D. geminata presence showed mat peak on autumn, sites with Cymbella spp. presence showed on spring. Also, higher values of mat thickness associated with low cell densities of D. geminata and intermediate cell densities of Cymbella spp. Finally, physicochemical variables that better explain mat thickness are phosphorus and water temperature. An alternation process of mucilage production may explain these results by these taxa strongly related to physicochemical variables. The present study contributes evidence about the relationship between mat thickness D. geminata and other microalgae contribution, and aquatic condition for this development.
format: application/pdf
format: text/html
creator: Daniel Zamorano
creator: Matías Peredo-Parada
creator: Diana J. Lillo
creator: Jorge Parodi
creator: Carolina A. Díaz
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.6481
publisher: PeerJ Inc.
rights: © 2019 Zamorano et al.
abstract: Didymosphenia geminata is a diatom that can alter aquatic systems. Several investigations have shown as chemical, and hydraulic factors have a great influence on the proliferation of D. geminata, but the study of other microalgae that could be associated with it has been poorly addressed. The objective of this study is to evaluate the relationship between mat thickness, D. geminata and another taxon that produces mucilage, Cymbella, while also considering physical and chemical factors. For this, two samples were taken, one in the spring of 2013 and the other in the autumn of 2014, from eight rivers in central-southern Chile-South America, where the benthic community was characterized, and the thickness of the mat was measured. The results show that the mat thickness on sites with the presence of both taxa is doubled, and while sites with D. geminata presence showed mat peak on autumn, sites with Cymbella spp. presence showed on spring. Also, higher values of mat thickness associated with low cell densities of D. geminata and intermediate cell densities of Cymbella spp. Finally, physicochemical variables that better explain mat thickness are phosphorus and water temperature. An alternation process of mucilage production may explain these results by these taxa strongly related to physicochemical variables. The present study contributes evidence about the relationship between mat thickness D. geminata and other microalgae contribution, and aquatic condition for this development.
bibliographic citation: Zamorano et al. (2019) Mat thickness associated with Didymosphenia geminata and Cymbella spp. in the southern rivers of Chile. PeerJ 7:e6481 https://doi.org/10.7717/peerj.6481
date submitted: 2018-05-11
date accepted: 2019-01-20
issued: 2019-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zamorano
  given name: Daniel
author list: Agent
  family name: Peredo-Parada
  given name: Matías
author list: Agent
  family name: Lillo
  given name: Diana J.
author list: Agent
  family name: Parodi
  given name: Jorge
author list: Agent
  family name: Díaz
  given name: Carolina A.
doi: 10.7717/peerj.6481
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-15
copyright: ©2019 Zamorano et al.
attribution name: Zamorano et al.

Protein signatures linking history of miscarriages and metabolic syndrome: a proteomic study among North Indian women
type: item
type: AcademicArticle
description: Background Metabolic syndrome (MeS), a constellation of metabolic adversities, and history of miscarriage make women at a higher risk for cardiovascular diseases (CVDs). However, molecular evidence indicating a link between the two phenotypes (history of miscarriage and MeS) among women would offer an opportunity to predict the risk factor for CVDs at an early stage. Thus, the present retrospective study attempts to identify the proteins signatures (if any) to understand the connection between the history of miscarriage and MeS. Methods Age-matched 80 pre-menopausal women who were not on any medical intervention or drugs were recruited from a Mendelian population of the same gene pool. Recruited women were classified into four groups—(a) Group A—absolute cases with history of miscarriage and MeS, (b) Group B—absolute controls without any history of miscarriage and MeS, (c) Group C—cases with MeS but lack any history of miscarriage, (d) Group D—cases with history of miscarriage but lack MeS. Differentially expressed proteins in plasma samples of women from four groups were identified using 2-D gel electrophoresis and mass spectrometry. Results Three case groups (A, C, and D) showed 18 differentially expressed proteins. Nearly 60% of proteins (11/18) were commonly dysregulated in Group C (only with MeS) and Group D (only with miscarriage history). Nearly 40% of proteins (7/18) were commonly dysregulated in the three case groups (Groups A, C, and D), indicating a shared pathophysiology. Four proteins were exclusive but shared by case groups C and D indicating the independent routes for CVDs through MeS or miscarriages. In absolute cases, transthyretin (TTR) showed exclusive upregulation, which was further validated by Western blotting and ELISA. Networking analyses showed the strong association of TTR with haptoglobin, transferrin and ApoA1 hinting toward a cross-talk among these proteins which could be a cause or an effect of TTR upregulation. Conclusion The study pro…
format: application/pdf
format: text/html
creator: Saurabh Sharma
creator: Suniti Yadav
creator: Ketaki Chandiok
creator: Radhey Shyam Sharma
creator: Vandana Mishra
creator: Kallur Nava Saraswathy
subject: Anthropology
subject: Gynecology and Obstetrics
subject: Public Health
subject: Women’s Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.6321
publisher: PeerJ Inc.
rights: © 2019 Sharma et al.
abstract: Background Metabolic syndrome (MeS), a constellation of metabolic adversities, and history of miscarriage make women at a higher risk for cardiovascular diseases (CVDs). However, molecular evidence indicating a link between the two phenotypes (history of miscarriage and MeS) among women would offer an opportunity to predict the risk factor for CVDs at an early stage. Thus, the present retrospective study attempts to identify the proteins signatures (if any) to understand the connection between the history of miscarriage and MeS. Methods Age-matched 80 pre-menopausal women who were not on any medical intervention or drugs were recruited from a Mendelian population of the same gene pool. Recruited women were classified into four groups—(a) Group A—absolute cases with history of miscarriage and MeS, (b) Group B—absolute controls without any history of miscarriage and MeS, (c) Group C—cases with MeS but lack any history of miscarriage, (d) Group D—cases with history of miscarriage but lack MeS. Differentially expressed proteins in plasma samples of women from four groups were identified using 2-D gel electrophoresis and mass spectrometry. Results Three case groups (A, C, and D) showed 18 differentially expressed proteins. Nearly 60% of proteins (11/18) were commonly dysregulated in Group C (only with MeS) and Group D (only with miscarriage history). Nearly 40% of proteins (7/18) were commonly dysregulated in the three case groups (Groups A, C, and D), indicating a shared pathophysiology. Four proteins were exclusive but shared by case groups C and D indicating the independent routes for CVDs through MeS or miscarriages. In absolute cases, transthyretin (TTR) showed exclusive upregulation, which was further validated by Western blotting and ELISA. Networking analyses showed the strong association of TTR with haptoglobin, transferrin and ApoA1 hinting toward a cross-talk among these proteins which could be a cause or an effect of TTR upregulation. Conclusion The study pro…
bibliographic citation: Sharma et al. (2019) Protein signatures linking history of miscarriages and metabolic syndrome: a proteomic study among North Indian women. PeerJ 7:e6321 https://doi.org/10.7717/peerj.6321
date submitted: 2018-06-06
date accepted: 2018-12-20
issued: 2019-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sharma
  given name: Saurabh
author list: Agent
  family name: Yadav
  given name: Suniti
author list: Agent
  family name: Chandiok
  given name: Ketaki
author list: Agent
  family name: Sharma
  given name: Radhey Shyam
author list: Agent
  family name: Mishra
  given name: Vandana
author list: Agent
  family name: Saraswathy
  given name: Kallur Nava
doi: 10.7717/peerj.6321
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-14
copyright: © 2019 Sharma et al.
attribution name: Sharma et al.

Geometric morphometric analysis in female freshwater crabs of Sarawak (Borneo) permits addressing taxonomy-related problems
type: item
type: AcademicArticle
description: The taxonomy of freshwater crabs requires a paradigm change in methodological approaches, particularly in investigations that use morphological techniques. The traditional morphometric approach (two-dimensional measurements) tends to be inappropriate for the identification of freshwater crabs due to their variable external morphology and lack of gonopods (conventionally used for the identification of male crabs) in females. In this study, we explore the potential use of the geometric morphometric technique for identification of female freshwater crabs, and identify taxonomic key characteristics of species. The shape of the carapace could be a good characteristic for the identification of female crabs, especially when the geometric morphometric technique is used. It was observed that the shape of the carapace has an advantage over the shape of the pleon and chela because its relatively flat orientation allows more consistent and easier data preparation for geometric morphometric analysis. The geometric morphometric technique is inexpensive, relatively less time consuming to employ, and accurate. This technique is convenient when dissection to examine the gonopods is not possible, which can damage the specimen in the case of endangered or rare species. Since the technique was used herein for only two species, more compelling and extensive evidence is needed before the reliability of the method can be proven.
format: application/pdf
format: text/html
creator: Jongkar Grinang
creator: Indraneil Das
creator: Peter K.L. Ng
subject: Mathematical Biology
subject: Taxonomy
description: doi:10.7717/peerj.6205
publisher: PeerJ Inc.
rights: © 2019 Grinang et al.
abstract: The taxonomy of freshwater crabs requires a paradigm change in methodological approaches, particularly in investigations that use morphological techniques. The traditional morphometric approach (two-dimensional measurements) tends to be inappropriate for the identification of freshwater crabs due to their variable external morphology and lack of gonopods (conventionally used for the identification of male crabs) in females. In this study, we explore the potential use of the geometric morphometric technique for identification of female freshwater crabs, and identify taxonomic key characteristics of species. The shape of the carapace could be a good characteristic for the identification of female crabs, especially when the geometric morphometric technique is used. It was observed that the shape of the carapace has an advantage over the shape of the pleon and chela because its relatively flat orientation allows more consistent and easier data preparation for geometric morphometric analysis. The geometric morphometric technique is inexpensive, relatively less time consuming to employ, and accurate. This technique is convenient when dissection to examine the gonopods is not possible, which can damage the specimen in the case of endangered or rare species. Since the technique was used herein for only two species, more compelling and extensive evidence is needed before the reliability of the method can be proven.
bibliographic citation: Grinang et al. (2019) Geometric morphometric analysis in female freshwater crabs of Sarawak (Borneo) permits addressing taxonomy-related problems. PeerJ 7:e6205 https://doi.org/10.7717/peerj.6205
date submitted: 2018-06-08
date accepted: 2018-12-03
issued: 2019-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grinang
  given name: Jongkar
author list: Agent
  family name: Das
  given name: Indraneil
author list: Agent
  family name: Ng
  given name: Peter K.L.
doi: 10.7717/peerj.6205
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-14
copyright: © 2019 Grinang et al.
attribution name: Grinang et al.

Physicochemical investigation of shrimp fossils from the Romualdo and Ipubi formations (Araripe Basin)
type: item
type: AcademicArticle
description: The Ipubi and Romualdo Formations are Cretaceous units of the Araripe Basin (Santana Group). The first and most ancient was deposited in a lake environment, and some fossils were preserved in shales deposited under blackish conditions. The second was deposited in a marine environment, preserving a rich paleontological content in calcareous concretions. Considering that these two environments preserved their fossils under different processes, in this work we investigated the chemical composition of two fossilized specimens, one from each of the studied stratigraphic units, and compared them using vibrational spectroscopy techniques (Raman and IR), X-ray diffraction and large-field energy-dispersive X-ray spectroscopy (EDS) mappings. Calcite was observed as the dominant phase and carbon was observed in the fossils as a byproduct of the decomposition. The preservation of hydroxide calcium phosphate (Ca10(PO4)6(OH)2, hydroxyapatite) was observed in both fossils. In addition, it was observed that there was a smaller amount of pyrite (pyritization) in the Romualdo Formation sample than in the Ipubi one. Large-field EDS measurements showed the major presence of the chemical elements calcium, oxygen, iron, aluminum and fluoride in the Ipubi fossil, indicating a greater influence of inorganic processes in its fossilization. Our results also suggest that the Romualdo Formation fossilization process involved the substitution of the hydroxyl group by fluorine, providing durability to the fossils.
format: application/pdf
format: text/html
creator: Olga Alcântara Barros
creator: João Hermínio Silva
creator: Gilberto Dantas Saraiva
creator: Bartolomeu Cruz Viana
creator: Alexandre Rocha Paschoal
creator: Paulo Tarso Cavalcante Freire
creator: Naiara Cipriano Oliveira
creator: Amauri Jardim Paula
creator: Maria Somália Viana
subject: Paleontology
subject: Soil Science
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.6323
publisher: PeerJ Inc.
rights: © 2019 Barros et al.
abstract: The Ipubi and Romualdo Formations are Cretaceous units of the Araripe Basin (Santana Group). The first and most ancient was deposited in a lake environment, and some fossils were preserved in shales deposited under blackish conditions. The second was deposited in a marine environment, preserving a rich paleontological content in calcareous concretions. Considering that these two environments preserved their fossils under different processes, in this work we investigated the chemical composition of two fossilized specimens, one from each of the studied stratigraphic units, and compared them using vibrational spectroscopy techniques (Raman and IR), X-ray diffraction and large-field energy-dispersive X-ray spectroscopy (EDS) mappings. Calcite was observed as the dominant phase and carbon was observed in the fossils as a byproduct of the decomposition. The preservation of hydroxide calcium phosphate (Ca10(PO4)6(OH)2, hydroxyapatite) was observed in both fossils. In addition, it was observed that there was a smaller amount of pyrite (pyritization) in the Romualdo Formation sample than in the Ipubi one. Large-field EDS measurements showed the major presence of the chemical elements calcium, oxygen, iron, aluminum and fluoride in the Ipubi fossil, indicating a greater influence of inorganic processes in its fossilization. Our results also suggest that the Romualdo Formation fossilization process involved the substitution of the hydroxyl group by fluorine, providing durability to the fossils.
bibliographic citation: Barros et al. (2019) Physicochemical investigation of shrimp fossils from the Romualdo and Ipubi formations (Araripe Basin). PeerJ 7:e6323 https://doi.org/10.7717/peerj.6323
date submitted: 2018-01-29
date accepted: 2018-12-20
issued: 2019-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Barros
  given name: Olga Alcântara
author list: Agent
  family name: Silva
  given name: João Hermínio
author list: Agent
  family name: Saraiva
  given name: Gilberto Dantas
author list: Agent
  family name: Viana
  given name: Bartolomeu Cruz
author list: Agent
  family name: Paschoal
  given name: Alexandre Rocha
author list: Agent
  family name: Freire
  given name: Paulo Tarso Cavalcante
author list: Agent
  family name: Oliveira
  given name: Naiara Cipriano
author list: Agent
  family name: Paula
  given name: Amauri Jardim
author list: Agent
  family name: Viana
  given name: Maria Somália
doi: 10.7717/peerj.6323
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-14
copyright: ©2019 Barros et al.
attribution name: Barros et al.

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
type: item
type: AcademicArticle
description: Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
format: application/pdf
format: text/html
creator: Gustavo A. Bravo
creator: Alexandre Antonelli
creator: Christine D. Bacon
creator: Krzysztof Bartoszek
creator: Mozes P. K. Blom
creator: Stella Huynh
creator: Graham Jones
creator: L. Lacey Knowles
creator: Sangeet Lamichhaney
creator: Thomas Marcussen
creator: Hélène Morlon
creator: Luay K. Nakhleh
creator: Bengt Oxelman
creator: Bernard Pfeil
creator: Alexander Schliep
creator: Niklas Wahlberg
creator: Fernanda P. Werneck
creator: John Wiedenhoeft
creator: Sandi Willows-Munro
creator: Scott V. Edwards
subject: Biodiversity
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.6399
publisher: PeerJ Inc.
rights: © 2019 Bravo et al.
abstract: Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
bibliographic citation: Bravo et al. (2019) Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 7:e6399 https://doi.org/10.7717/peerj.6399
date submitted: 2018-02-05
date accepted: 2019-01-07
issued: 2019-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bravo
  given name: Gustavo A.
author list: Agent
  family name: Antonelli
  given name: Alexandre
author list: Agent
  family name: Bacon
  given name: Christine D.
author list: Agent
  family name: Bartoszek
  given name: Krzysztof
author list: Agent
  family name: Blom
  given name: Mozes P. K.
author list: Agent
  family name: Huynh
  given name: Stella
author list: Agent
  family name: Jones
  given name: Graham
author list: Agent
  family name: Knowles
  given name: L. Lacey
author list: Agent
  family name: Lamichhaney
  given name: Sangeet
author list: Agent
  family name: Marcussen
  given name: Thomas
author list: Agent
  family name: Morlon
  given name: Hélène
author list: Agent
  family name: Nakhleh
  given name: Luay K.
author list: Agent
  family name: Oxelman
  given name: Bengt
author list: Agent
  family name: Pfeil
  given name: Bernard
author list: Agent
  family name: Schliep
  given name: Alexander
author list: Agent
  family name: Wahlberg
  given name: Niklas
author list: Agent
  family name: Werneck
  given name: Fernanda P.
author list: Agent
  family name: Wiedenhoeft
  given name: John
author list: Agent
  family name: Willows-Munro
  given name: Sandi
author list: Agent
  family name: Edwards
  given name: Scott V.
doi: 10.7717/peerj.6399
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-14
copyright: © 2019 Bravo et al.
attribution name: Bravo et al.

Additional sauropod dinosaur material from the Callovian Oxford Clay Formation, Peterborough, UK: evidence for higher sauropod diversity
type: item
type: AcademicArticle
description: Four isolated sauropod axial elements from the Oxford Clay Formation (Callovian, Middle Jurassic) of Peterborough, UK, are described. Two associated posterior dorsal vertebrae show a dorsoventrally elongated centrum and short neural arch, and nutrient or pneumatic foramina, most likely belonging to a non-neosauropod eusauropod, but showing ambiguous non-neosauropod eusauropod and neosauropod affinities. An isolated anterior caudal vertebra displays a ventral keel, a ‘shoulder’ indicating a wing-like transverse process, along with a possible prespinal lamina. This, together with an overall high complexity of the anterior caudal transverse process (ACTP) complex, indicates that this caudal could have belonged to a neosauropod. A second isolated middle-posterior caudal vertebra also shows some diagnostic features, despite the neural spine and neural arch not being preserved and the neurocentral sutures being unfused. The positioning of the neurocentral sutures on the anterior one third of the centrum indicates a middle caudal position, and the presence of faint ventrolateral crests, as well as a rhomboid anterior articulation surface, suggest neosauropod affinities. The presence of possible nutrient foramina are only tentative evidence of a neosauropod origin, as they are also found in Late Jurassic non-neosauropod eusauropods. As the caudals from the two other known sauropods from the Peterborough Oxford Clay, Cetiosauriscus stewarti and an indeterminate non-neosauropod eusauropod, do not show the features seen on either of the new elements described, both isolated caudals indicate a higher sauropod species diversity in the faunal assemblage than previously recognised. An exploratory phylogenetic analysis using characters from all four isolated elements supports a basal neosauropod placement for the anterior caudal, and a diplodocid origin for the middle caudal. The dorsal vertebrae are an unstable OTU, and therefore remain part of an indeterminate eusauropod of uncer…
format: application/pdf
format: text/html
creator: Femke M. Holwerda
creator: Mark Evans
creator: Jeff J. Liston
subject: Biodiversity
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6404
publisher: PeerJ Inc.
rights: © 2019 Holwerda et al.
abstract: Four isolated sauropod axial elements from the Oxford Clay Formation (Callovian, Middle Jurassic) of Peterborough, UK, are described. Two associated posterior dorsal vertebrae show a dorsoventrally elongated centrum and short neural arch, and nutrient or pneumatic foramina, most likely belonging to a non-neosauropod eusauropod, but showing ambiguous non-neosauropod eusauropod and neosauropod affinities. An isolated anterior caudal vertebra displays a ventral keel, a ‘shoulder’ indicating a wing-like transverse process, along with a possible prespinal lamina. This, together with an overall high complexity of the anterior caudal transverse process (ACTP) complex, indicates that this caudal could have belonged to a neosauropod. A second isolated middle-posterior caudal vertebra also shows some diagnostic features, despite the neural spine and neural arch not being preserved and the neurocentral sutures being unfused. The positioning of the neurocentral sutures on the anterior one third of the centrum indicates a middle caudal position, and the presence of faint ventrolateral crests, as well as a rhomboid anterior articulation surface, suggest neosauropod affinities. The presence of possible nutrient foramina are only tentative evidence of a neosauropod origin, as they are also found in Late Jurassic non-neosauropod eusauropods. As the caudals from the two other known sauropods from the Peterborough Oxford Clay, Cetiosauriscus stewarti and an indeterminate non-neosauropod eusauropod, do not show the features seen on either of the new elements described, both isolated caudals indicate a higher sauropod species diversity in the faunal assemblage than previously recognised. An exploratory phylogenetic analysis using characters from all four isolated elements supports a basal neosauropod placement for the anterior caudal, and a diplodocid origin for the middle caudal. The dorsal vertebrae are an unstable OTU, and therefore remain part of an indeterminate eusauropod of uncer…
bibliographic citation: Holwerda et al. (2019) Additional sauropod dinosaur material from the Callovian Oxford Clay Formation, Peterborough, UK: evidence for higher sauropod diversity. PeerJ 7:e6404 https://doi.org/10.7717/peerj.6404
date submitted: 2018-03-17
date accepted: 2019-01-07
issued: 2019-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holwerda
  given name: Femke M.
author list: Agent
  family name: Evans
  given name: Mark
author list: Agent
  family name: Liston
  given name: Jeff J.
doi: 10.7717/peerj.6404
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-14
copyright: ©2019 Holwerda et al.
attribution name: Holwerda et al.

Age differences in the effect of animacy on Mandarin sentence processing
type: item
type: AcademicArticle
description: Animate nouns are preferred for grammatical subjects, whereas inanimate nouns are preferred for grammatical objects. Animacy provides important semantic cues for sentence comprehension. However, how individuals’ ability to use this animacy cue changes with advancing age is still not clear. The current study investigated whether older adults and younger adults were differentially sensitive to this semantic constraint in processing Mandarin relative clauses, using a self-paced reading paradigm. The sentences used in the study contained subject relative clauses or object relative clauses and had animate or inanimate subjects. The results indicate that the animacy manipulation affected the younger adults more than the older adults in online processing. Younger adults had longer reading times for all segments in subject relative clauses than in object relative clauses when the subjects were inanimate, whereas there was no significant difference in reading times between subject and object relative clauses when the subjects were animate. In the older group, animacy was not found to influence the processing difficulty of subject relative clauses and object relative clauses. Compared with younger adults, older adults were less sensitive to animacy constraints in relative clause processing. The findings indicate that the use of animacy cues became less efficient in the ageing population. The results can be explained by the capacity constrained comprehension theory, according to which older adults have greater difficulty in integrating semantic information with syntactic processing due to the lack of sufficient cognitive resources.
format: application/pdf
format: text/html
creator: Xinmiao Liu
creator: Wenbin Wang
creator: Haiyan Wang
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6437
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: Animate nouns are preferred for grammatical subjects, whereas inanimate nouns are preferred for grammatical objects. Animacy provides important semantic cues for sentence comprehension. However, how individuals’ ability to use this animacy cue changes with advancing age is still not clear. The current study investigated whether older adults and younger adults were differentially sensitive to this semantic constraint in processing Mandarin relative clauses, using a self-paced reading paradigm. The sentences used in the study contained subject relative clauses or object relative clauses and had animate or inanimate subjects. The results indicate that the animacy manipulation affected the younger adults more than the older adults in online processing. Younger adults had longer reading times for all segments in subject relative clauses than in object relative clauses when the subjects were inanimate, whereas there was no significant difference in reading times between subject and object relative clauses when the subjects were animate. In the older group, animacy was not found to influence the processing difficulty of subject relative clauses and object relative clauses. Compared with younger adults, older adults were less sensitive to animacy constraints in relative clause processing. The findings indicate that the use of animacy cues became less efficient in the ageing population. The results can be explained by the capacity constrained comprehension theory, according to which older adults have greater difficulty in integrating semantic information with syntactic processing due to the lack of sufficient cognitive resources.
bibliographic citation: Liu et al. (2019) Age differences in the effect of animacy on Mandarin sentence processing. PeerJ 7:e6437 https://doi.org/10.7717/peerj.6437
date submitted: 2018-09-06
date accepted: 2019-01-11
issued: 2019-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xinmiao
author list: Agent
  family name: Wang
  given name: Wenbin
author list: Agent
  family name: Wang
  given name: Haiyan
doi: 10.7717/peerj.6437
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-14
copyright: ©2019 Liu et al.
attribution name: Liu et al.

Factors that affect the growth and photosynthesis of the filamentous green algae, Chaetomorpha valida, in static sea cucumber aquaculture ponds with high salinity and high pH
type: item
type: AcademicArticle
description: Chaetomorpha valida, dominant filamentous green algae, can be harmful to sea cucumber growth in aquaculture ponds of China. In order to understand the environmental factors affecting the growth of C. valida in sea cucumber aquaculture ecosystems, a combination of field investigations and laboratory experiments were conducted. Field surveys over one year revealed that C. valida survived in sea cucumber aquaculture ponds in salinities ranging from 24.3 ± 0.01‰ to 32.0 ± 0.02‰ and a pH range of 7.5 ± 0.02–8.6 ± 0.04. The high salinity and pH during the period of low C. valida biomass from January to May lay the foundation for its rapid growth in the following months of June to October. Many factors interact in the field environment, thus, laboratory experiments were conducted to determine the isolated effects of pH and salinity on C. valida growth. In laboratory experiments, samples were incubated under different salinity and pH conditions at 25 °C, with a light intensity of 108 μmol photon·m−2·s−1, and a photoperiod of 12 L:12 D. Results showed that salinity and pH significantly affect the growth and Fv/Fm (quantum yield of photosynthesis) of C. valida (p < 0.01). C. valida grew the longest at a salinity of 34‰ and a pH of 8.0. At 34‰ salinity, C. valida grew to 26.44 ± 5.89 cm in 16 days. At a pH of 8.0, C. valida grew to 67.96 ± 4.45 cm in 32 days. Fv/Fm was 0.635 ± 0.002 at a salinity of 32‰, and 0.550 ± 0.006 to 0.660± 0.001 at pH 7.0 to 8.5. Based on these results, we conclude that C. valida can bloom in sea cucumber ponds due to the high salinity and pH of coastal sea waters, which promote growth and maintain the photosynthetic activity of C. valida.
format: application/pdf
format: text/html
creator: Ronglian Xing
creator: Weiwei Ma
creator: Yiwen Shao
creator: Xuebin Cao
creator: Lihong Chen
creator: Aili Jiang
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6468
publisher: PeerJ Inc.
rights: © 2019 Xing et al.
abstract: Chaetomorpha valida, dominant filamentous green algae, can be harmful to sea cucumber growth in aquaculture ponds of China. In order to understand the environmental factors affecting the growth of C. valida in sea cucumber aquaculture ecosystems, a combination of field investigations and laboratory experiments were conducted. Field surveys over one year revealed that C. valida survived in sea cucumber aquaculture ponds in salinities ranging from 24.3 ± 0.01‰ to 32.0 ± 0.02‰ and a pH range of 7.5 ± 0.02–8.6 ± 0.04. The high salinity and pH during the period of low C. valida biomass from January to May lay the foundation for its rapid growth in the following months of June to October. Many factors interact in the field environment, thus, laboratory experiments were conducted to determine the isolated effects of pH and salinity on C. valida growth. In laboratory experiments, samples were incubated under different salinity and pH conditions at 25 °C, with a light intensity of 108 μmol photon·m−2·s−1, and a photoperiod of 12 L:12 D. Results showed that salinity and pH significantly affect the growth and Fv/Fm (quantum yield of photosynthesis) of C. valida (p < 0.01). C. valida grew the longest at a salinity of 34‰ and a pH of 8.0. At 34‰ salinity, C. valida grew to 26.44 ± 5.89 cm in 16 days. At a pH of 8.0, C. valida grew to 67.96 ± 4.45 cm in 32 days. Fv/Fm was 0.635 ± 0.002 at a salinity of 32‰, and 0.550 ± 0.006 to 0.660± 0.001 at pH 7.0 to 8.5. Based on these results, we conclude that C. valida can bloom in sea cucumber ponds due to the high salinity and pH of coastal sea waters, which promote growth and maintain the photosynthetic activity of C. valida.
bibliographic citation: Xing et al. (2019) Factors that affect the growth and photosynthesis of the filamentous green algae, Chaetomorpha valida, in static sea cucumber aquaculture ponds with high salinity and high pH. PeerJ 7:e6468 https://doi.org/10.7717/peerj.6468
date submitted: 2018-10-02
date accepted: 2019-01-13
issued: 2019-02-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xing
  given name: Ronglian
author list: Agent
  family name: Ma
  given name: Weiwei
author list: Agent
  family name: Shao
  given name: Yiwen
author list: Agent
  family name: Cao
  given name: Xuebin
author list: Agent
  family name: Chen
  given name: Lihong
author list: Agent
  family name: Jiang
  given name: Aili
doi: 10.7717/peerj.6468
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-14
copyright: © 2019 Xing et al.
attribution name: Xing et al.

The Early Pliocene extinction of the mega-toothed shark Otodus megalodon: a view from the eastern North Pacific
type: item
type: AcademicArticle
description: The extinct giant shark Otodus megalodon is the last member of the predatory megatoothed lineage and is reported from Neogene sediments from nearly all continents. The timing of the extinction of Otodus megalodon is thought to be Pliocene, although reports of Pleistocene teeth fuel speculation that Otodus megalodon may still be extant. The longevity of the Otodus lineage (Paleocene to Pliocene) and its conspicuous absence in the modern fauna begs the question: when and why did this giant shark become extinct? Addressing this question requires a densely sampled marine vertebrate fossil record in concert with a robust geochronologic framework. Many historically important basins with stacked Otodus-bearing Neogene marine vertebrate fossil assemblages lack well-sampled and well-dated lower and upper Pliocene strata (e.g., Atlantic Coastal Plain). The fossil record of California, USA, and Baja California, Mexico, provides such an ideal sequence of assemblages preserved within well-dated lithostratigraphic sequences. This study reviews all records of Otodus megalodon from post-Messinian marine strata from western North America and evaluates their reliability. All post-Zanclean Otodus megalodon occurrences from the eastern North Pacific exhibit clear evidence of reworking or lack reliable provenance; the youngest reliable records of Otodus megalodon are early Pliocene, suggesting an extinction at the early-late Pliocene boundary (∼3.6 Ma), corresponding with youngest occurrences of Otodus megalodon in Japan, the North Atlantic, and Mediterranean. This study also reevaluates a published dataset, thoroughly vetting each occurrence and justifying the geochronologic age of each, as well as excluding several dubious records. Reanalysis of the dataset using optimal linear estimation resulted in a median extinction date of 3.51 Ma, somewhat older than a previously proposed Pliocene-Pleistocene extinction date (2.6 Ma). Post-middle Miocene oceanographic changes and cooling sea sur…
format: application/pdf
format: text/html
creator: Robert W. Boessenecker
creator: Dana J. Ehret
creator: Douglas J. Long
creator: Morgan Churchill
creator: Evan Martin
creator: Sarah J. Boessenecker
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.6088
publisher: PeerJ Inc.
rights: © 2019 Boessenecker et al.
abstract: The extinct giant shark Otodus megalodon is the last member of the predatory megatoothed lineage and is reported from Neogene sediments from nearly all continents. The timing of the extinction of Otodus megalodon is thought to be Pliocene, although reports of Pleistocene teeth fuel speculation that Otodus megalodon may still be extant. The longevity of the Otodus lineage (Paleocene to Pliocene) and its conspicuous absence in the modern fauna begs the question: when and why did this giant shark become extinct? Addressing this question requires a densely sampled marine vertebrate fossil record in concert with a robust geochronologic framework. Many historically important basins with stacked Otodus-bearing Neogene marine vertebrate fossil assemblages lack well-sampled and well-dated lower and upper Pliocene strata (e.g., Atlantic Coastal Plain). The fossil record of California, USA, and Baja California, Mexico, provides such an ideal sequence of assemblages preserved within well-dated lithostratigraphic sequences. This study reviews all records of Otodus megalodon from post-Messinian marine strata from western North America and evaluates their reliability. All post-Zanclean Otodus megalodon occurrences from the eastern North Pacific exhibit clear evidence of reworking or lack reliable provenance; the youngest reliable records of Otodus megalodon are early Pliocene, suggesting an extinction at the early-late Pliocene boundary (∼3.6 Ma), corresponding with youngest occurrences of Otodus megalodon in Japan, the North Atlantic, and Mediterranean. This study also reevaluates a published dataset, thoroughly vetting each occurrence and justifying the geochronologic age of each, as well as excluding several dubious records. Reanalysis of the dataset using optimal linear estimation resulted in a median extinction date of 3.51 Ma, somewhat older than a previously proposed Pliocene-Pleistocene extinction date (2.6 Ma). Post-middle Miocene oceanographic changes and cooling sea sur…
bibliographic citation: Boessenecker et al. (2019) The Early Pliocene extinction of the mega-toothed shark Otodus megalodon: a view from the eastern North Pacific. PeerJ 7:e6088 https://doi.org/10.7717/peerj.6088
date submitted: 2018-03-02
date accepted: 2018-11-08
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boessenecker
  given name: Robert W.
author list: Agent
  family name: Ehret
  given name: Dana J.
author list: Agent
  family name: Long
  given name: Douglas J.
author list: Agent
  family name: Churchill
  given name: Morgan
author list: Agent
  family name: Martin
  given name: Evan
author list: Agent
  family name: Boessenecker
  given name: Sarah J.
doi: 10.7717/peerj.6088
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: © 2019 Boessenecker et al.
attribution name: Boessenecker et al.

Balancing plant conservation and agricultural production in the Ecuadorian Dry Inter-Andean Valleys
type: item
type: AcademicArticle
description: Background Conserving both biodiversity and ecosystem services is a major goal of the Convention on Biological Diversity. Hotspots for biodiversity in the Andes significantly overlap with areas with dense human populations that sustain their economy through agricultural production. Therefore, developing management forms that reconcile food provisioning services—such as agriculture—with biodiversity conservation must be addressed to avoid social conflicts and to improve conservation in areas where biodiversity co-occurs with other ecosystem services. Here, we present a high-resolution conservation plan for vascular plants and agriculture in the Ecuadorian Dry Inter-Andean Valleys (DIAV) hotspot. Trade-offs in conserving important areas for both biodiversity and agriculture were explored. Methods We used a dataset containing 5,685 presence records for 95 plant species occurring in DIAVs, of which 14 species were endemic. We developed habitat suitability maps for the 95 species using Maxent. Prioritization analyses were carried out using a conservation planning framework. We developed three conservation scenarios that selected important areas for: biodiversity only, agriculture only, and for both biodiversity and agriculture combined. Results Our conservation planning analyses, capture 33.5% of biodiversity and 11% of agriculture under a scenario solely focused on the conservation of biodiversity. On the other hand, the top 17% fraction of the agriculture only scenario captures 10% of biodiversity and 28% of agriculture. When biodiversity and agriculture were considered in combination, their representation varied according to the importance given to agriculture. The most balanced solution that gives a nearly equal representation of both biodiversity and agriculture, was obtained when agriculture was given a slightly higher importance over biodiversity during the selection process. Discussion This is the first evaluation of trade-offs between important areas for biodive…
format: application/pdf
format: text/html
creator: Catalina Quintana
creator: Marco Girardello
creator: Henrik Balslev
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.6207
publisher: PeerJ Inc.
rights: © 2019 Quintana et al.
abstract: Background Conserving both biodiversity and ecosystem services is a major goal of the Convention on Biological Diversity. Hotspots for biodiversity in the Andes significantly overlap with areas with dense human populations that sustain their economy through agricultural production. Therefore, developing management forms that reconcile food provisioning services—such as agriculture—with biodiversity conservation must be addressed to avoid social conflicts and to improve conservation in areas where biodiversity co-occurs with other ecosystem services. Here, we present a high-resolution conservation plan for vascular plants and agriculture in the Ecuadorian Dry Inter-Andean Valleys (DIAV) hotspot. Trade-offs in conserving important areas for both biodiversity and agriculture were explored. Methods We used a dataset containing 5,685 presence records for 95 plant species occurring in DIAVs, of which 14 species were endemic. We developed habitat suitability maps for the 95 species using Maxent. Prioritization analyses were carried out using a conservation planning framework. We developed three conservation scenarios that selected important areas for: biodiversity only, agriculture only, and for both biodiversity and agriculture combined. Results Our conservation planning analyses, capture 33.5% of biodiversity and 11% of agriculture under a scenario solely focused on the conservation of biodiversity. On the other hand, the top 17% fraction of the agriculture only scenario captures 10% of biodiversity and 28% of agriculture. When biodiversity and agriculture were considered in combination, their representation varied according to the importance given to agriculture. The most balanced solution that gives a nearly equal representation of both biodiversity and agriculture, was obtained when agriculture was given a slightly higher importance over biodiversity during the selection process. Discussion This is the first evaluation of trade-offs between important areas for biodive…
bibliographic citation: Quintana et al. (2019) Balancing plant conservation and agricultural production in the Ecuadorian Dry Inter-Andean Valleys. PeerJ 7:e6207 https://doi.org/10.7717/peerj.6207
date submitted: 2018-07-13
date accepted: 2018-12-04
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Quintana
  given name: Catalina
author list: Agent
  family name: Girardello
  given name: Marco
author list: Agent
  family name: Balslev
  given name: Henrik
doi: 10.7717/peerj.6207
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: © 2019 Quintana et al.
attribution name: Quintana et al.

A modification of the leaf-bags method to assess spring ecosystem functioning: benthic invertebrates and leaf-litter breakdown in Vera Spring (Central Italy)
type: item
type: AcademicArticle
description: The evaluation of leaf detritus processing (decomposition and breakdown) is one of the most simple and cost-effective method to assess the functional characteristics of freshwater ecosystems. However, in comparison with other freshwater habitats, information on leaf litter breakdown in spring ecosystems is still scarce and fragmentary. In this paper, we present results of the first application of a variant of the leaf-bags method to assess structure of macroinvertebrate assemblages and leaf-litter breakdown in a Central Apennines (Italy) cold spring which was investigated from July 2016 to October 2016. Notwithstanding the stable conditions of almost all hydrological and physico-chemical parameters, we found significant temporal differences in (i) % of mass loss of poplar leaves (ii) number of Ephemeroptera, Plecoptera and Trichoptera taxa, (iii) shredder and predator densities. We demonstrate that detritus processing in cold springs may be faster than or as fast as in warmer streams/rivers. Shredders activity and biocoenotic interactions, rather than temperature and nutrients load, were the main drivers of the process. A routine application of the modified leaf-bags may contribute to expand our knowledge on detritus processing in cold springs and may help to predict impacts of climate warming on freshwater ecosystem functioning.
format: application/pdf
format: text/html
creator: Giovanni Cristiano
creator: Bruno Cicolani
creator: Francesco Paolo Miccoli
creator: Antonio Di Sabatino
subject: Ecology
subject: Ecosystem Science
subject: Climate Change Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.6250
publisher: PeerJ Inc.
rights: © 2019 Cristiano et al.
abstract: The evaluation of leaf detritus processing (decomposition and breakdown) is one of the most simple and cost-effective method to assess the functional characteristics of freshwater ecosystems. However, in comparison with other freshwater habitats, information on leaf litter breakdown in spring ecosystems is still scarce and fragmentary. In this paper, we present results of the first application of a variant of the leaf-bags method to assess structure of macroinvertebrate assemblages and leaf-litter breakdown in a Central Apennines (Italy) cold spring which was investigated from July 2016 to October 2016. Notwithstanding the stable conditions of almost all hydrological and physico-chemical parameters, we found significant temporal differences in (i) % of mass loss of poplar leaves (ii) number of Ephemeroptera, Plecoptera and Trichoptera taxa, (iii) shredder and predator densities. We demonstrate that detritus processing in cold springs may be faster than or as fast as in warmer streams/rivers. Shredders activity and biocoenotic interactions, rather than temperature and nutrients load, were the main drivers of the process. A routine application of the modified leaf-bags may contribute to expand our knowledge on detritus processing in cold springs and may help to predict impacts of climate warming on freshwater ecosystem functioning.
bibliographic citation: Cristiano et al. (2019) A modification of the leaf-bags method to assess spring ecosystem functioning: benthic invertebrates and leaf-litter breakdown in Vera Spring (Central Italy). PeerJ 7:e6250 https://doi.org/10.7717/peerj.6250
date submitted: 2018-09-18
date accepted: 2018-12-10
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cristiano
  given name: Giovanni
author list: Agent
  family name: Cicolani
  given name: Bruno
author list: Agent
  family name: Miccoli
  given name: Francesco Paolo
author list: Agent
  family name: Di Sabatino
  given name: Antonio
doi: 10.7717/peerj.6250
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: © 2019 Cristiano et al.
attribution name: Cristiano et al.

Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus
type: item
type: AcademicArticle
description: Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well–supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.
format: application/pdf
format: text/html
creator: James M. Wainaina
creator: Laura Kubatko
creator: Jagger Harvey
creator: Elijah Ateka
creator: Timothy Makori
creator: David Karanja
creator: Laura M. Boykin
creator: Monica A. Kehoe
subject: Agricultural Science
subject: Evolutionary Studies
description: doi:10.7717/peerj.6297
publisher: PeerJ Inc.
rights: © 2019 Wainaina et al.
abstract: Plant viral diseases are one of the major limitations in legume production within sub-Saharan Africa (SSA), as they account for up to 100% in production losses within smallholder farms. In this study, field surveys were conducted in the western highlands of Kenya with viral symptomatic leaf samples collected. Subsequently, next-generation sequencing was carried out to gain insights into the molecular evolution and evolutionary relationships of Bean common mosaic necrosis virus (BCMNV) and Cowpea aphid-borne mosaic virus (CABMV) present within symptomatic common bean and cowpea. Eleven near-complete genomes of BCMNV and two for CABMV were obtained from western Kenya. Bayesian phylogenomic analysis and tests for differential selection pressure within sites and across tree branches of the viral genomes were carried out. Three well–supported clades in BCMNV and one supported clade for CABMNV were resolved and in agreement with individual gene trees. Selection pressure analysis within sites and across phylogenetic branches suggested both viruses were evolving independently, but under strong purifying selection, with a slow evolutionary rate. These findings provide valuable insights on the evolution of BCMNV and CABMV genomes and their relationship to other viral genomes globally. The results will contribute greatly to the knowledge gap involving the phylogenomic relationship of these viruses, particularly for CABMV, for which there are few genome sequences available, and inform the current breeding efforts towards resistance for BCMNV and CABMV.
bibliographic citation: Wainaina et al. (2019) Evolutionary insights of Bean common mosaic necrosis virus and Cowpea aphid-borne mosaic virus. PeerJ 7:e6297 https://doi.org/10.7717/peerj.6297
date submitted: 2018-07-04
date accepted: 2018-12-18
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wainaina
  given name: James M.
author list: Agent
  family name: Kubatko
  given name: Laura
author list: Agent
  family name: Harvey
  given name: Jagger
author list: Agent
  family name: Ateka
  given name: Elijah
author list: Agent
  family name: Makori
  given name: Timothy
author list: Agent
  family name: Karanja
  given name: David
author list: Agent
  family name: Boykin
  given name: Laura M.
author list: Agent
  family name: Kehoe
  given name: Monica A.
doi: 10.7717/peerj.6297
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: ©2019 Wainaina et al.
attribution name: Wainaina et al.

X-ray vision: the accuracy and repeatability of a technology that allows clinicians to see spinal X-rays superimposed on a person's back
type: item
type: AcademicArticle
description: Objective Since the discovery of ionizing radiation, clinicians have evaluated X-ray images separately from the patient. The objective of this study was to investigate the accuracy and repeatability of a new technology which seeks to resolve this historic limitation by projecting anatomically correct X-ray images on to a person’s skin. Methods A total of 13 participants enrolled in the study, each having a pre-existing anteroposterior lumbar X-ray. Each participant’s image was uploaded into the Hololens Mixed reality system which when worn, allowed a single examiner to view a participant’s own X-ray superimposed on the participant’s back. The projected image was topographically corrected using depth information obtained by the Hololens system then aligned via existing anatomic landmarks. Using this superimposed image, vertebral levels were identified and validated against spinous process locations obtained by ultrasound. This process was repeated 1–5 days later. The projection of each vertebra was deemed to be “on-target” if it fell within the known morphological dimensions of the spinous process for that specific vertebral level. Results The projection system created on-target projections with respect to individual vertebral levels 73% of the time with no significant difference seen between testing sessions. The average repeatability for all vertebral levels between testing sessions was 77%. Conclusion These accuracy and repeatability data suggest that the accuracy and repeatability of projecting X-rays directly on to the skin is feasible for identifying underlying anatomy and as such, has potential to place radiological evaluation within the patient context. Future opportunities to improve this procedure will focus on mitigating potential sources of error.
format: application/pdf
format: text/html
creator: Jacob Aaskov
creator: Gregory N. Kawchuk
creator: Kenton D. Hamaluik
creator: Pierre Boulanger
creator: Jan Hartvigsen
subject: Kinesiology
subject: Orthopedics
subject: Radiology and Medical Imaging
subject: Science and Medical Education
subject: Human-Computer Interaction
description: doi:10.7717/peerj.6333
publisher: PeerJ Inc.
rights: © 2019 Aaskov et al.
abstract: Objective Since the discovery of ionizing radiation, clinicians have evaluated X-ray images separately from the patient. The objective of this study was to investigate the accuracy and repeatability of a new technology which seeks to resolve this historic limitation by projecting anatomically correct X-ray images on to a person’s skin. Methods A total of 13 participants enrolled in the study, each having a pre-existing anteroposterior lumbar X-ray. Each participant’s image was uploaded into the Hololens Mixed reality system which when worn, allowed a single examiner to view a participant’s own X-ray superimposed on the participant’s back. The projected image was topographically corrected using depth information obtained by the Hololens system then aligned via existing anatomic landmarks. Using this superimposed image, vertebral levels were identified and validated against spinous process locations obtained by ultrasound. This process was repeated 1–5 days later. The projection of each vertebra was deemed to be “on-target” if it fell within the known morphological dimensions of the spinous process for that specific vertebral level. Results The projection system created on-target projections with respect to individual vertebral levels 73% of the time with no significant difference seen between testing sessions. The average repeatability for all vertebral levels between testing sessions was 77%. Conclusion These accuracy and repeatability data suggest that the accuracy and repeatability of projecting X-rays directly on to the skin is feasible for identifying underlying anatomy and as such, has potential to place radiological evaluation within the patient context. Future opportunities to improve this procedure will focus on mitigating potential sources of error.
bibliographic citation: Aaskov et al. (2019) X-ray vision: the accuracy and repeatability of a technology that allows clinicians to see spinal X-rays superimposed on a person's back. PeerJ 7:e6333 https://doi.org/10.7717/peerj.6333
date submitted: 2018-09-24
date accepted: 2018-12-21
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aaskov
  given name: Jacob
author list: Agent
  family name: Kawchuk
  given name: Gregory N.
author list: Agent
  family name: Hamaluik
  given name: Kenton D.
author list: Agent
  family name: Boulanger
  given name: Pierre
author list: Agent
  family name: Hartvigsen
  given name: Jan
doi: 10.7717/peerj.6333
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: © 2019 Aaskov et al.
attribution name: Aaskov et al.

Application of relay puncture technique in treating patients with complicated lower extremity arterial diseases
type: item
type: AcademicArticle
description: Objective This study aimed to introduce and evaluate the safety and efficacy of the relay puncture technique in patients with complicated lower extremity arterial diseases. Methods A total of 21 patients (16 male and five female patients; median age: 68.5 years old), who had suffered from lower extremity arterial diseases between December 2014 and July 2017, were retrospectively collected. For all patients, the contralateral femoral artery was not available for puncture access, and the length of the devices was too short for the brachial artery approach. Therefore, the relay puncture technique, in which the first puncture was performed on the brachial artery, followed by an antegrade puncture on the femoral artery, was used to accomplish the endovascular therapy. Percutaneous transluminal angioplasty and/or percutaneous transluminal stenting were/was used to assess the efficacy of the relay puncture technique. The ankle–brachial index (ABI) and Rutherford clinical classification were used to evaluate the improvement of symptoms after treatment. Patients were followed up for 1, 3, 6, and 12 months, and annually (mean: 16.6 months) after discharge. Results The relay puncture treatment had a 100% technical success rate, and immediately decreased the ischemic symptoms of patients after the procedure. The ABI significantly increased from 0.33 ± 0.18 to 0.75 ± 0.21 at the 1-year follow-up time point (P < 0.05). No serious complications occurred during the follow-up period. The 1-year primary patency rate was 71.43%. Conclusion The relay puncture technique is a feasible technique in the hands of experienced and skilled equipment operators for the treatment of lower extremity arterial diseases, when the contralateral femoral artery is not available for puncture, and the length of the device is too short to treat the distal lesion of the femoral artery and popliteal artery through the brachial artery approach.
format: application/pdf
format: text/html
creator: Chengzhi Li
creator: Huimin You
creator: Hong Zhang
creator: Yulong Liu
creator: Wanghai Li
creator: Xiaobai Wang
creator: Yan Zhang
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.6345
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Objective This study aimed to introduce and evaluate the safety and efficacy of the relay puncture technique in patients with complicated lower extremity arterial diseases. Methods A total of 21 patients (16 male and five female patients; median age: 68.5 years old), who had suffered from lower extremity arterial diseases between December 2014 and July 2017, were retrospectively collected. For all patients, the contralateral femoral artery was not available for puncture access, and the length of the devices was too short for the brachial artery approach. Therefore, the relay puncture technique, in which the first puncture was performed on the brachial artery, followed by an antegrade puncture on the femoral artery, was used to accomplish the endovascular therapy. Percutaneous transluminal angioplasty and/or percutaneous transluminal stenting were/was used to assess the efficacy of the relay puncture technique. The ankle–brachial index (ABI) and Rutherford clinical classification were used to evaluate the improvement of symptoms after treatment. Patients were followed up for 1, 3, 6, and 12 months, and annually (mean: 16.6 months) after discharge. Results The relay puncture treatment had a 100% technical success rate, and immediately decreased the ischemic symptoms of patients after the procedure. The ABI significantly increased from 0.33 ± 0.18 to 0.75 ± 0.21 at the 1-year follow-up time point (P < 0.05). No serious complications occurred during the follow-up period. The 1-year primary patency rate was 71.43%. Conclusion The relay puncture technique is a feasible technique in the hands of experienced and skilled equipment operators for the treatment of lower extremity arterial diseases, when the contralateral femoral artery is not available for puncture, and the length of the device is too short to treat the distal lesion of the femoral artery and popliteal artery through the brachial artery approach.
bibliographic citation: Li et al. (2019) Application of relay puncture technique in treating patients with complicated lower extremity arterial diseases. PeerJ 7:e6345 https://doi.org/10.7717/peerj.6345
date submitted: 2018-06-25
date accepted: 2018-12-24
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Chengzhi
author list: Agent
  family name: You
  given name: Huimin
author list: Agent
  family name: Zhang
  given name: Hong
author list: Agent
  family name: Liu
  given name: Yulong
author list: Agent
  family name: Li
  given name: Wanghai
author list: Agent
  family name: Wang
  given name: Xiaobai
author list: Agent
  family name: Zhang
  given name: Yan
doi: 10.7717/peerj.6345
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: © 2019 Li et al.
attribution name: Li et al.

The origin of Oxalis corniculata L.
type: item
type: AcademicArticle
description: Background Oxalis corniculata L. is a weed with a world-wide distribution and unknown origin. Though it belongs to a section of the genus from South America, the evidence that this species came from there is weak. Methods We reviewed the evidence for the origin of O. corniculata using herbarium specimens, historic literature and archaeobotanical research. We also summarized ethnobotanical literature to understand where this species is most used by humans as a medicine. Results Despite numerous claims that it is native to Europe there is no strong evidence that O. corniculata occurred in Europe before the 15th century. Nor is there reliable evidence that it occurred in North or South America before the 19th century. However, there is direct archaeobotanical evidence of it occurring in south–east Asia at least 5,000 years ago. There is also evidence from historic literature and archaeobotany that it reached Polynesia before European expeditions explored these islands. Examination of the traditional use of O. corniculata demonstrates that is most widely used as a medicine in south–east Asia, which, while circumstantial, also points to a long association with human culture in this area. Discussion The most likely origin for O. corniculata is south–east Asia. This is consistent with a largely circum-Pacific distribution of section Corniculatae of Oxalis. Nevertheless, it is likely that O. corniculata spread to Europe and perhaps Polynesia before the advent of the modern era through trade routes at that time.
format: application/pdf
format: text/html
creator: Quentin J. Groom
creator: Jan Van der Straeten
creator: Ivan Hoste
subject: Biodiversity
subject: Biogeography
subject: Plant Science
description: doi:10.7717/peerj.6384
publisher: PeerJ Inc.
rights: © 2019 Groom et al.
abstract: Background Oxalis corniculata L. is a weed with a world-wide distribution and unknown origin. Though it belongs to a section of the genus from South America, the evidence that this species came from there is weak. Methods We reviewed the evidence for the origin of O. corniculata using herbarium specimens, historic literature and archaeobotanical research. We also summarized ethnobotanical literature to understand where this species is most used by humans as a medicine. Results Despite numerous claims that it is native to Europe there is no strong evidence that O. corniculata occurred in Europe before the 15th century. Nor is there reliable evidence that it occurred in North or South America before the 19th century. However, there is direct archaeobotanical evidence of it occurring in south–east Asia at least 5,000 years ago. There is also evidence from historic literature and archaeobotany that it reached Polynesia before European expeditions explored these islands. Examination of the traditional use of O. corniculata demonstrates that is most widely used as a medicine in south–east Asia, which, while circumstantial, also points to a long association with human culture in this area. Discussion The most likely origin for O. corniculata is south–east Asia. This is consistent with a largely circum-Pacific distribution of section Corniculatae of Oxalis. Nevertheless, it is likely that O. corniculata spread to Europe and perhaps Polynesia before the advent of the modern era through trade routes at that time.
bibliographic citation: Groom et al. (2019) The origin of Oxalis corniculata L.. PeerJ 7:e6384 https://doi.org/10.7717/peerj.6384
date submitted: 2018-10-30
date accepted: 2019-01-03
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Groom
  given name: Quentin J.
author list: Agent
  family name: Van der Straeten
  given name: Jan
author list: Agent
  family name: Hoste
  given name: Ivan
doi: 10.7717/peerj.6384
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: © 2019 Groom et al.
attribution name: Groom et al.

A large Late Miocene cetotheriid (Cetacea, Mysticeti) from the Netherlands clarifies the status of Tranatocetidae
type: item
type: AcademicArticle
description: Cetotheriidae are a group of small baleen whales (Mysticeti) that evolved alongside modern rorquals. They once enjoyed a nearly global distribution, but then largely went extinct during the Plio-Pleistocene. After languishing as a wastebasket taxon for more than a century, the concept of Cetotheriidae is now well established. Nevertheless, the clade remains notable for its variability, and its scope remains in flux. In particular, the recent referral of several traditional cetotheriids to a new and seemingly unrelated family, Tranatocetidae, has created major phylogenetic uncertainty. Here, we describe a new species of Tranatocetus, the type of Tranatocetidae, from the Late Miocene of the Netherlands. Tranatocetus maregermanicum sp. nov. clarifies several of the traits previously ascribed to this genus, and reveals distinctive auditory and mandibular morphologies suggesting cetotheriid affinities. This interpretation is supported by a large phylogenetic analysis, which mingles cetotheriids and tranatocetids within a unified clade. As a result, we suggest that both groups should be reintegrated into the single family Cetotheriidae.
format: application/pdf
format: text/html
creator: Felix G. Marx
creator: Klaas Post
creator: Mark Bosselaers
creator: Dirk K. Munsterman
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.6426
publisher: PeerJ Inc.
rights: © 2019 Marx et al.
abstract: Cetotheriidae are a group of small baleen whales (Mysticeti) that evolved alongside modern rorquals. They once enjoyed a nearly global distribution, but then largely went extinct during the Plio-Pleistocene. After languishing as a wastebasket taxon for more than a century, the concept of Cetotheriidae is now well established. Nevertheless, the clade remains notable for its variability, and its scope remains in flux. In particular, the recent referral of several traditional cetotheriids to a new and seemingly unrelated family, Tranatocetidae, has created major phylogenetic uncertainty. Here, we describe a new species of Tranatocetus, the type of Tranatocetidae, from the Late Miocene of the Netherlands. Tranatocetus maregermanicum sp. nov. clarifies several of the traits previously ascribed to this genus, and reveals distinctive auditory and mandibular morphologies suggesting cetotheriid affinities. This interpretation is supported by a large phylogenetic analysis, which mingles cetotheriids and tranatocetids within a unified clade. As a result, we suggest that both groups should be reintegrated into the single family Cetotheriidae.
bibliographic citation: Marx et al. (2019) A large Late Miocene cetotheriid (Cetacea, Mysticeti) from the Netherlands clarifies the status of Tranatocetidae. PeerJ 7:e6426 https://doi.org/10.7717/peerj.6426
date submitted: 2018-11-26
date accepted: 2019-01-09
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Marx
  given name: Felix G.
author list: Agent
  family name: Post
  given name: Klaas
author list: Agent
  family name: Bosselaers
  given name: Mark
author list: Agent
  family name: Munsterman
  given name: Dirk K.
doi: 10.7717/peerj.6426
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: ©2019 Marx et al.
attribution name: Marx et al.

Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask)
type: item
type: AcademicArticle
description: The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.
format: application/pdf
format: text/html
creator: Waléria Pereira Monteiro
creator: Jamille Costa Veiga
creator: Amanda Reis Silva
creator: Carolina da Silva Carvalho
creator: Éder Cristian Malta Lanes
creator: Yessica Rico
creator: Rodolfo Jaffé
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6446
publisher: PeerJ Inc.
rights: © 2019 Monteiro et al.
abstract: The bulk of the world’s biodiversity is found in tropical regions, which are increasingly threatened by the human-led degradation of natural habitats. Yet, little is known about tropical biodiversity responses to habitat loss and fragmentation. Here we review all available literature assessing landscape effects on gene flow in tropical species, aiming to help unravel the factors underpinning functional connectivity in the tropics. We map and classify studies by focus species, the molecular markers employed, statistical approaches to assess landscape effects on gene flow, and the evaluated landscape and environmental variables. We then compare qualitatively and quantitatively landscape effects on gene flow across species and units of analysis. We found 69 articles assessing landscape effects on gene flow in tropical organisms, most of which were published in the last five years, were concentrated in the Americas, and focused on amphibians or mammals. Most studies employed population-level approaches, microsatellites were the preferred type of markers, and Mantel and partial Mantel tests the most common statistical approaches used. While elevation, land cover and forest cover were the most common gene flow predictors assessed, habitat suitability was found to be a common predictor of gene flow. A third of all surveyed studies explicitly assessed the effect of habitat degradation, but only 14 of these detected a reduced gene flow with increasing habitat loss. Elevation was responsible for most significant microsatellite-based isolation by resistance effects and a single study reported significant isolation by non-forested areas in an ant. Our study reveals important knowledge gaps on the study of landscape effects on gene flow in tropical organisms, and provides useful guidelines on how to fill them.
bibliographic citation: Monteiro et al. (2019) Everything you always wanted to know about gene flow in tropical landscapes (but were afraid to ask). PeerJ 7:e6446 https://doi.org/10.7717/peerj.6446
date submitted: 2018-08-28
date accepted: 2019-01-15
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Monteiro
  given name: Waléria Pereira
author list: Agent
  family name: Veiga
  given name: Jamille Costa
author list: Agent
  family name: Silva
  given name: Amanda Reis
author list: Agent
  family name: Carvalho
  given name: Carolina da Silva
author list: Agent
  family name: Lanes
  given name: Éder Cristian Malta
author list: Agent
  family name: Rico
  given name: Yessica
author list: Agent
  family name: Jaffé
  given name: Rodolfo
doi: 10.7717/peerj.6446
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: ©2019 Monteiro et al.
attribution name: Monteiro et al.

The value of diffusion tensor tractography delineating corticospinal tract in glioma in rat: validation via correlation histology
type: item
type: AcademicArticle
description: Background An assessment of the degree of white matter tract injury is important in neurosurgical planning for patients with gliomas. The main objective of this study was to assess the injury grade of the corticospinal tract (CST) in rats with glioma using diffusion tensor imaging (DTI). Methods A total 17 rats underwent 7.0T MRI on day 10 after tumor implantation. The apparent diffusion coefficient (ADC) and fractional anisotropy (FA) were acquired in the tumor, peritumoral and contralateral areas, and the ADC ratio (ipsilateral ADC/contralateral ADC) and rFA (relative FA = ipsilateral FA/contralateral FA) in the peritumoral areas were measured. The CST injury was divided into three grades and delineated by diffusion tensor tractography reconstruction imaging. The fiber density index (FDi) of the ipsilateral and contralateral CST and rFDi (relative FDi = ipsilateral FDi/contralateral FDi) in the peritumoral areas were measured. After the mice were sacrificed, the invasion of glioma cells and fraction of proliferating cells were observed by hematoxylin-eosin and Ki67 staining in the tumor and peritumoral areas. The correlations among the pathology results, CST injury grade and DTI parameter values were calculated using a Spearman correlation analysis. One-way analysis of variance was performed to compare the different CST injury grade by the rFA, rFDi and ADC ratio values. Results The tumor cells and proliferation index were positively correlated with the CST injury grade (r = 0.8857, 0.9233, P < 0.001). A negative correlation was demonstrated between the tumor cells and the rFA and rFDi values in the peritumoral areas (r = −0.8571, −0.5588), and the proliferation index was negatively correlated with the rFA and rFDi values (r = −0.8571, −0.5588), while the ADC ratio was not correlated with the tumor cells or proliferation index. The rFA values between the CST injury grades (1 and 3, 2 and 3) and the rFDi values in grades 1 and 3 significantly differed (P < 0.05). C…
format: application/pdf
format: text/html
creator: Xiaoxiong Jia
creator: Zhiyong Su
creator: Junlin Hu
creator: Hechun Xia
creator: Hui Ma
creator: Xiaodong Wang
creator: Jiangshu Yan
creator: Dede Ma
subject: Neurology
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.6453
publisher: PeerJ Inc.
rights: © 2019 Jia et al.
abstract: Background An assessment of the degree of white matter tract injury is important in neurosurgical planning for patients with gliomas. The main objective of this study was to assess the injury grade of the corticospinal tract (CST) in rats with glioma using diffusion tensor imaging (DTI). Methods A total 17 rats underwent 7.0T MRI on day 10 after tumor implantation. The apparent diffusion coefficient (ADC) and fractional anisotropy (FA) were acquired in the tumor, peritumoral and contralateral areas, and the ADC ratio (ipsilateral ADC/contralateral ADC) and rFA (relative FA = ipsilateral FA/contralateral FA) in the peritumoral areas were measured. The CST injury was divided into three grades and delineated by diffusion tensor tractography reconstruction imaging. The fiber density index (FDi) of the ipsilateral and contralateral CST and rFDi (relative FDi = ipsilateral FDi/contralateral FDi) in the peritumoral areas were measured. After the mice were sacrificed, the invasion of glioma cells and fraction of proliferating cells were observed by hematoxylin-eosin and Ki67 staining in the tumor and peritumoral areas. The correlations among the pathology results, CST injury grade and DTI parameter values were calculated using a Spearman correlation analysis. One-way analysis of variance was performed to compare the different CST injury grade by the rFA, rFDi and ADC ratio values. Results The tumor cells and proliferation index were positively correlated with the CST injury grade (r = 0.8857, 0.9233, P < 0.001). A negative correlation was demonstrated between the tumor cells and the rFA and rFDi values in the peritumoral areas (r = −0.8571, −0.5588), and the proliferation index was negatively correlated with the rFA and rFDi values (r = −0.8571, −0.5588), while the ADC ratio was not correlated with the tumor cells or proliferation index. The rFA values between the CST injury grades (1 and 3, 2 and 3) and the rFDi values in grades 1 and 3 significantly differed (P < 0.05). C…
bibliographic citation: Jia et al. (2019) The value of diffusion tensor tractography delineating corticospinal tract in glioma in rat: validation via correlation histology. PeerJ 7:e6453 https://doi.org/10.7717/peerj.6453
date submitted: 2018-10-02
date accepted: 2019-01-15
issued: 2019-02-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jia
  given name: Xiaoxiong
author list: Agent
  family name: Su
  given name: Zhiyong
author list: Agent
  family name: Hu
  given name: Junlin
author list: Agent
  family name: Xia
  given name: Hechun
author list: Agent
  family name: Ma
  given name: Hui
author list: Agent
  family name: Wang
  given name: Xiaodong
author list: Agent
  family name: Yan
  given name: Jiangshu
author list: Agent
  family name: Ma
  given name: Dede
doi: 10.7717/peerj.6453
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-13
copyright: © 2019 Jia et al.
attribution name: Jia et al.

Morphological identification and molecular confirmation of the deep-sea blue and red shrimp Aristeus antennatus larvae
type: item
type: AcademicArticle
description: The early life stages of the blue and red shrimp Aristeus antennatus (Decapoda: Dendrobranchiata: Penaeoidea: Aristeidae) were described by Heldt in 1955 based on plankton samples, larval rearing and assumptions of species habitat. Even with adequate keys, identification of its first larval stages remained a difficult task due to the lack of specific morphological characters which would differentiate them from other Penaeoidea species. Larvae of Aristeus antennatus were collected in the continental slope off the Spanish Mediterranean coast in August 2016 with a neuston net and preserved in ethanol 96%. DNA from the larvae was extracted and the molecular markers Cytochrome Oxidase I and 16S rDNA were sequenced and compared to that of adults with the objective of confirming the previous morphological description. Then, we present additional information to the morphological description of Aristeus antennatus larval stages through scanning electron microscopy and molecular analysis. This represents the first documented occurrence of Aristeus antennatus larvae off the Catalan coast and sets the grounds for further work on larval ecology and population connectivity of the species, which is an important contribution to a more sustainable fishery.
format: application/pdf
format: text/html
creator: Marta Carreton
creator: Joan B. Company
creator: Laia Planella
creator: Sandra Heras
creator: José-Luis García-Marín
creator: Melania Agulló
creator: Morane Clavel-Henry
creator: Guiomar Rotllant
creator: Antonina dos Santos
creator: María Inés Roldán
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6063
publisher: PeerJ Inc.
rights: © 2019 Carreton et al.
abstract: The early life stages of the blue and red shrimp Aristeus antennatus (Decapoda: Dendrobranchiata: Penaeoidea: Aristeidae) were described by Heldt in 1955 based on plankton samples, larval rearing and assumptions of species habitat. Even with adequate keys, identification of its first larval stages remained a difficult task due to the lack of specific morphological characters which would differentiate them from other Penaeoidea species. Larvae of Aristeus antennatus were collected in the continental slope off the Spanish Mediterranean coast in August 2016 with a neuston net and preserved in ethanol 96%. DNA from the larvae was extracted and the molecular markers Cytochrome Oxidase I and 16S rDNA were sequenced and compared to that of adults with the objective of confirming the previous morphological description. Then, we present additional information to the morphological description of Aristeus antennatus larval stages through scanning electron microscopy and molecular analysis. This represents the first documented occurrence of Aristeus antennatus larvae off the Catalan coast and sets the grounds for further work on larval ecology and population connectivity of the species, which is an important contribution to a more sustainable fishery.
bibliographic citation: Carreton et al. (2019) Morphological identification and molecular confirmation of the deep-sea blue and red shrimp Aristeus antennatus larvae. PeerJ 7:e6063 https://doi.org/10.7717/peerj.6063
date submitted: 2018-08-07
date accepted: 2018-11-03
issued: 2019-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carreton
  given name: Marta
author list: Agent
  family name: Company
  given name: Joan B.
author list: Agent
  family name: Planella
  given name: Laia
author list: Agent
  family name: Heras
  given name: Sandra
author list: Agent
  family name: García-Marín
  given name: José-Luis
author list: Agent
  family name: Agulló
  given name: Melania
author list: Agent
  family name: Clavel-Henry
  given name: Morane
author list: Agent
  family name: Rotllant
  given name: Guiomar
author list: Agent
  family name: dos Santos
  given name: Antonina
author list: Agent
  family name: Roldán
  given name: María Inés
doi: 10.7717/peerj.6063
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-12
copyright: © 2019 Carreton et al.
attribution name: Carreton et al.

The running kinematics of free-roaming giraffes, measured using a low cost unmanned aerial vehicle (UAV)
type: item
type: AcademicArticle
description: The study of animal locomotion can be logistically challenging, especially in the case of large or unhandleable animals in uncontrolled environments. Here we demonstrate the utility of a low cost unmanned aerial vehicle (UAV) in measuring two-dimensional running kinematics from free-roaming giraffes (Giraffa camelopardalis giraffa) in the Free State Province, South Africa. We collected 120 Hz video of running giraffes, and calibrated each video frame using metatarsal length as a constant object of scale. We tested a number of methods to measure metatarsal length. The method with the least variation used close range photography and a trigonometric equation to spatially calibrate the still image, and derive metatarsal length. In the absence of this option, a spatially calibrated surface model of the study terrain was used to estimate topographical dimensions in video footage of interest. Data for the terrain models were collected using the same equipment, during the same study period. We subsequently validated the accuracy of the UAV method by comparing similar speed measurements of a human subject running on a treadmill, with treadmill speed. At 8 m focal distance we observed an error of 8% between the two measures of speed. This error was greater at a shorter focal distance, and when the subject was not in the central field of view. We recommend that future users maximise the camera focal distance, and keep the subject in the central field of view. The studied giraffes used a grounded rotary gallop with a speed range of 3.4–6.9 ms−1 (never cantering, trotting or pacing), and lower duty factors when compared with other cursorial quadrupeds. As this pattern might result in adverse increases in peak vertical limb forces with speed, it was notable to find that contralateral limbs became more in-phase with speed. Considering the latter pattern and the modest maximal speed of giraffes, we speculate that tissue safety factors are maintained within tolerable bounds this way…
format: application/pdf
format: text/html
creator: Christopher K. Basu
creator: Francois Deacon
creator: John R. Hutchinson
creator: Alan M. Wilson
subject: Biophysics
subject: Zoology
subject: Kinesiology
description: doi:10.7717/peerj.6312
publisher: PeerJ Inc.
rights: © 2019 Basu et al.
abstract: The study of animal locomotion can be logistically challenging, especially in the case of large or unhandleable animals in uncontrolled environments. Here we demonstrate the utility of a low cost unmanned aerial vehicle (UAV) in measuring two-dimensional running kinematics from free-roaming giraffes (Giraffa camelopardalis giraffa) in the Free State Province, South Africa. We collected 120 Hz video of running giraffes, and calibrated each video frame using metatarsal length as a constant object of scale. We tested a number of methods to measure metatarsal length. The method with the least variation used close range photography and a trigonometric equation to spatially calibrate the still image, and derive metatarsal length. In the absence of this option, a spatially calibrated surface model of the study terrain was used to estimate topographical dimensions in video footage of interest. Data for the terrain models were collected using the same equipment, during the same study period. We subsequently validated the accuracy of the UAV method by comparing similar speed measurements of a human subject running on a treadmill, with treadmill speed. At 8 m focal distance we observed an error of 8% between the two measures of speed. This error was greater at a shorter focal distance, and when the subject was not in the central field of view. We recommend that future users maximise the camera focal distance, and keep the subject in the central field of view. The studied giraffes used a grounded rotary gallop with a speed range of 3.4–6.9 ms−1 (never cantering, trotting or pacing), and lower duty factors when compared with other cursorial quadrupeds. As this pattern might result in adverse increases in peak vertical limb forces with speed, it was notable to find that contralateral limbs became more in-phase with speed. Considering the latter pattern and the modest maximal speed of giraffes, we speculate that tissue safety factors are maintained within tolerable bounds this way…
bibliographic citation: Basu et al. (2019) The running kinematics of free-roaming giraffes, measured using a low cost unmanned aerial vehicle (UAV). PeerJ 7:e6312 https://doi.org/10.7717/peerj.6312
date submitted: 2018-10-30
date accepted: 2018-12-19
issued: 2019-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Basu
  given name: Christopher K.
author list: Agent
  family name: Deacon
  given name: Francois
author list: Agent
  family name: Hutchinson
  given name: John R.
author list: Agent
  family name: Wilson
  given name: Alan M.
doi: 10.7717/peerj.6312
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-12
copyright: ©2019 Basu et al.
attribution name: Basu et al.

Responses of Phaseolus calcaltus to lime and biochar application in an acid soil
type: item
type: AcademicArticle
description: Introduction Rice bean (Phaseolus calcaltus), as an annual summer legume, is always subjected to acid soils in tropical to subtropical regions, limiting its growth and nodulation. However, little is known about its responses to lime and biochar addition, the two in improving soil fertility in acid soils. Materials and Methods In the current study, a pot experiment was conducted using rice bean on a sandy yellow soil (Orthic Acrisol) with a pH of 5.5. The experiment included three lime rates (0, 0.75 and 1.5 g kg−1) and three biochar rates (0, 5 and 10 g kg−1). The biochar was produced from aboveground parts of Solanum tuberosum using a home-made device with temperature of pyrolysis about 500 °C. Results and Discussion The results indicated that both lime and biochar could reduce soil exchange Al concentration, increase soil pH and the contents of soil microbial biomass carbon and microbial biomass nitrogen, and enhance urease and dehydrogenase activities, benefiting P. calcaltus growth and nodulation in acid soils. Lime application did decrease the concentrations of soil available phosphorus (AP) and alkali dispelled nitrogen (AN), whereas biochar application increased the concentrations of soil AP, AN and available potassium (AK). However, sole biochar application could not achieve as much yield increase as lime application did. High lime rate (1.5 g lime kg−1) incorporated with low biochar rate (5 g biochar kg−1) could obtain higher shoot biomass, nutrient uptake, and nodule number when compared with high lime rate and high biochar rate. Conclusion Lime incorporated with biochar application could achieve optimum improvement for P. calcaltus growing in acid soils when compared with sole lime or biochar addition.
format: application/pdf
format: text/html
creator: Luhua Yao
creator: Xiangyu Yu
creator: Lei Huang
creator: Xuefeng Zhang
creator: Dengke Wang
creator: Xiao Zhao
creator: Yang Li
creator: Zhibin He
creator: Lin Kang
creator: Xiaoting Li
creator: Dan Liu
creator: Qianlin Xiao
creator: Yanjun Guo
subject: Agricultural Science
subject: Soil Science
description: doi:10.7717/peerj.6346
publisher: PeerJ Inc.
rights: © 2019 Yao et al.
abstract: Introduction Rice bean (Phaseolus calcaltus), as an annual summer legume, is always subjected to acid soils in tropical to subtropical regions, limiting its growth and nodulation. However, little is known about its responses to lime and biochar addition, the two in improving soil fertility in acid soils. Materials and Methods In the current study, a pot experiment was conducted using rice bean on a sandy yellow soil (Orthic Acrisol) with a pH of 5.5. The experiment included three lime rates (0, 0.75 and 1.5 g kg−1) and three biochar rates (0, 5 and 10 g kg−1). The biochar was produced from aboveground parts of Solanum tuberosum using a home-made device with temperature of pyrolysis about 500 °C. Results and Discussion The results indicated that both lime and biochar could reduce soil exchange Al concentration, increase soil pH and the contents of soil microbial biomass carbon and microbial biomass nitrogen, and enhance urease and dehydrogenase activities, benefiting P. calcaltus growth and nodulation in acid soils. Lime application did decrease the concentrations of soil available phosphorus (AP) and alkali dispelled nitrogen (AN), whereas biochar application increased the concentrations of soil AP, AN and available potassium (AK). However, sole biochar application could not achieve as much yield increase as lime application did. High lime rate (1.5 g lime kg−1) incorporated with low biochar rate (5 g biochar kg−1) could obtain higher shoot biomass, nutrient uptake, and nodule number when compared with high lime rate and high biochar rate. Conclusion Lime incorporated with biochar application could achieve optimum improvement for P. calcaltus growing in acid soils when compared with sole lime or biochar addition.
bibliographic citation: Yao et al. (2019) Responses of Phaseolus calcaltus to lime and biochar application in an acid soil. PeerJ 7:e6346 https://doi.org/10.7717/peerj.6346
date submitted: 2018-09-18
date accepted: 2018-12-24
issued: 2019-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Luhua
author list: Agent
  family name: Yu
  given name: Xiangyu
author list: Agent
  family name: Huang
  given name: Lei
author list: Agent
  family name: Zhang
  given name: Xuefeng
author list: Agent
  family name: Wang
  given name: Dengke
author list: Agent
  family name: Zhao
  given name: Xiao
author list: Agent
  family name: Li
  given name: Yang
author list: Agent
  family name: He
  given name: Zhibin
author list: Agent
  family name: Kang
  given name: Lin
author list: Agent
  family name: Li
  given name: Xiaoting
author list: Agent
  family name: Liu
  given name: Dan
author list: Agent
  family name: Xiao
  given name: Qianlin
author list: Agent
  family name: Guo
  given name: Yanjun
doi: 10.7717/peerj.6346
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-12
copyright: ©2019 Yao et al.
attribution name: Yao et al.

Nation-scale primary prevention to reduce newly incident adolescent drug use: the issue of lag time
type: item
type: AcademicArticle
description: Background There is limited evidence about the effects of United States (US) nation-level policy changes on the incidence of alcohol drinking and tobacco smoking. To investigate the potential primary prevention effects on precocious drug use and to clarify lag-time issues, we estimated incidence rates for specified intervals anticipating and lagging after drug policy enactment. Our hypotheses are (a) reductions in underage drinking or smoking onset and (b) increases of incidence at the legal age (i.e., 21 for drinking and 18 for smoking). Methods The study population is 12–23-year-old non-institutionalized US civilian residents. Estimates are from 30 community samples drawn to be nationally representative for the US National Surveys on Drug Use and Health 1979–2015. Estimates were year-by-year annual incidence rates for alcohol drinking and tobacco smoking by 12–23-year-olds, age by age. Meta-regressions estimate age-specific incidence over time. Results Incidence of underage alcohol drinking declined and followed a trend line that started before 1984 enactment of the National Minimum Drinking Age Act, but increased drinking incidence for 21 year olds was observed approximately 10 years after policy enactment. Eight years after the Synar amendment enactment, evidence of reduced smoking incidence started to emerge. Among 18 year olds, a slight increase in tobacco smoking incidence occurred about 10 years after the Synar amendment. Conclusion Once nation-level policies affecting drug sales to minors are enacted, one might have to wait almost a decade before seeing tangible policy effects on drug use incidence rates.
format: application/pdf
format: text/html
creator: Hui G. Cheng
creator: Dukernse Augustin
creator: Eric H. Glass
creator: James C. Anthony
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.6356
publisher: PeerJ Inc.
rights: © 2019 Cheng et al.
abstract: Background There is limited evidence about the effects of United States (US) nation-level policy changes on the incidence of alcohol drinking and tobacco smoking. To investigate the potential primary prevention effects on precocious drug use and to clarify lag-time issues, we estimated incidence rates for specified intervals anticipating and lagging after drug policy enactment. Our hypotheses are (a) reductions in underage drinking or smoking onset and (b) increases of incidence at the legal age (i.e., 21 for drinking and 18 for smoking). Methods The study population is 12–23-year-old non-institutionalized US civilian residents. Estimates are from 30 community samples drawn to be nationally representative for the US National Surveys on Drug Use and Health 1979–2015. Estimates were year-by-year annual incidence rates for alcohol drinking and tobacco smoking by 12–23-year-olds, age by age. Meta-regressions estimate age-specific incidence over time. Results Incidence of underage alcohol drinking declined and followed a trend line that started before 1984 enactment of the National Minimum Drinking Age Act, but increased drinking incidence for 21 year olds was observed approximately 10 years after policy enactment. Eight years after the Synar amendment enactment, evidence of reduced smoking incidence started to emerge. Among 18 year olds, a slight increase in tobacco smoking incidence occurred about 10 years after the Synar amendment. Conclusion Once nation-level policies affecting drug sales to minors are enacted, one might have to wait almost a decade before seeing tangible policy effects on drug use incidence rates.
bibliographic citation: Cheng et al. (2019) Nation-scale primary prevention to reduce newly incident adolescent drug use: the issue of lag time. PeerJ 7:e6356 https://doi.org/10.7717/peerj.6356
date submitted: 2018-08-20
date accepted: 2018-12-28
issued: 2019-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Hui G.
author list: Agent
  family name: Augustin
  given name: Dukernse
author list: Agent
  family name: Glass
  given name: Eric H.
author list: Agent
  family name: Anthony
  given name: James C.
doi: 10.7717/peerj.6356
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-12
copyright: © 2019 Cheng et al.
attribution name: Cheng et al.

Modeling the spatial structure of the endemic mara (Dolichotis patagonum) across modified landscapes
type: item
type: AcademicArticle
description: Across modified landscapes, anthropic factors can affect habitat selection by animals and consequently their abundance and distribution patterns. The study of the spatial structure of wild populations is crucial to gain knowledge on species’ response to habitat quality, and a key for the design and implementation of conservation actions. This is particularly important for a low-density and widely distributed species such as the mara (Dolichotis patagonum), a large rodent endemic to Argentina across the Monte and Patagonian drylands where extensive sheep ranching predominates. We aimed to assess the spatial variation in the abundance of maras and to identify the natural and anthropic factors influencing the observed patterns in Península Valdés, a representative landscape of Patagonia. We conducted ground surveys during the austral autumn from 2015 to 2017. We built density surface models to account for the variation in mara abundance, and obtained a map of mara density at a resolution of four km2. We estimated an overall density of 0.93 maras.km−2 for the prediction area of 3,476 km2. The location of ranch buildings, indicators of human presence, had a strong positive effect on the abundance of maras, while the significant contribution of the geographic longitude suggested that mara density increases with higher rainfall. Although human presence favored mara abundance, presumably by providing protection against predators, it is likely that the association could bring negative consequences for maras and other species. The use of spatial models allowed us to provide the first estimate of mara abundance at a landscape scale and its spatial variation at a high resolution. Our approach can contribute to the assessment of mara population abundance and the factors shaping its spatial structure elsewhere across the species range, all crucial attributes to identify and prioritize conservation actions.
format: application/pdf
format: text/html
creator: Milagros Antún
creator: Ricardo Baldi
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Population Biology
description: doi:10.7717/peerj.6367
publisher: PeerJ Inc.
rights: © 2019 Antún and Baldi
abstract: Across modified landscapes, anthropic factors can affect habitat selection by animals and consequently their abundance and distribution patterns. The study of the spatial structure of wild populations is crucial to gain knowledge on species’ response to habitat quality, and a key for the design and implementation of conservation actions. This is particularly important for a low-density and widely distributed species such as the mara (Dolichotis patagonum), a large rodent endemic to Argentina across the Monte and Patagonian drylands where extensive sheep ranching predominates. We aimed to assess the spatial variation in the abundance of maras and to identify the natural and anthropic factors influencing the observed patterns in Península Valdés, a representative landscape of Patagonia. We conducted ground surveys during the austral autumn from 2015 to 2017. We built density surface models to account for the variation in mara abundance, and obtained a map of mara density at a resolution of four km2. We estimated an overall density of 0.93 maras.km−2 for the prediction area of 3,476 km2. The location of ranch buildings, indicators of human presence, had a strong positive effect on the abundance of maras, while the significant contribution of the geographic longitude suggested that mara density increases with higher rainfall. Although human presence favored mara abundance, presumably by providing protection against predators, it is likely that the association could bring negative consequences for maras and other species. The use of spatial models allowed us to provide the first estimate of mara abundance at a landscape scale and its spatial variation at a high resolution. Our approach can contribute to the assessment of mara population abundance and the factors shaping its spatial structure elsewhere across the species range, all crucial attributes to identify and prioritize conservation actions.
bibliographic citation: Antún et al. (2019) Modeling the spatial structure of the endemic mara (Dolichotis patagonum) across modified landscapes. PeerJ 7:e6367 https://doi.org/10.7717/peerj.6367
date submitted: 2018-11-08
date accepted: 2018-12-28
issued: 2019-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Antún
  given name: Milagros
author list: Agent
  family name: Baldi
  given name: Ricardo
doi: 10.7717/peerj.6367
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-12
copyright: © 2019 Antún and Baldi
attribution name: Antún and Baldi

Overexpression of OsFTL10 induces early flowering and improves drought tolerance in Oryza sativa L.
type: item
type: AcademicArticle
description: Flowering time control is critically important for the reproductive accomplishment of higher plants as floral transition can be affected by both environmental and endogenous signals. Flowering Locus T-like (FTL) genes are major genetic determinants of flowering in plants. In rice, 13 OsFTL genes have been annotated in the genome and amongst them, Hd3a (OsFTL2) and RFT1 (OsFTL3) have been studied extensively and their functions are confirmed as central florigens that control rice flowering under short day and long day environment, respectively. In this report, a rice OsFTL gene, OsFTL10, was characterized, and its function on flowering and abiotic stress was investigated. The expression level of OsFTL10 was high in young seedlings and shown to be induced by GA3 and drought stress. Overexpression of OsFTL10 resulted in earlier flowering in rice plants by up to 2 weeks, through up-regulation of the downstream gene OsMADS15. OsFTL10 also regulated Ehd1 and OsMADS51 through a feedback mechanism. The OsFTL10 protein was also detected in both nucleus and cytoplasm. Furthermore, yeast two hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) results show that OsFTL10 could interact with multiple 14-3-3s, suggesting that OsFTL10 might function in a similar way to Hd3a in promoting rice flowering by forming a FAC complex with 14-3-3, and OsFD1. Further experiments revealed that constitutive expression of OsFTL10 improved the drought tolerance of transgenic plants by stimulating the expression of drought responsive genes. These results suggest that rice FTL genes might function in flowering promotion and responses to environmental signals.
format: application/pdf
format: text/html
creator: Maichun Fang
creator: Zejiao Zhou
creator: Xusheng Zhou
creator: Huiyong Yang
creator: Meiru Li
creator: Hongqing Li
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6422
publisher: PeerJ Inc.
rights: © 2019 Fang et al.
abstract: Flowering time control is critically important for the reproductive accomplishment of higher plants as floral transition can be affected by both environmental and endogenous signals. Flowering Locus T-like (FTL) genes are major genetic determinants of flowering in plants. In rice, 13 OsFTL genes have been annotated in the genome and amongst them, Hd3a (OsFTL2) and RFT1 (OsFTL3) have been studied extensively and their functions are confirmed as central florigens that control rice flowering under short day and long day environment, respectively. In this report, a rice OsFTL gene, OsFTL10, was characterized, and its function on flowering and abiotic stress was investigated. The expression level of OsFTL10 was high in young seedlings and shown to be induced by GA3 and drought stress. Overexpression of OsFTL10 resulted in earlier flowering in rice plants by up to 2 weeks, through up-regulation of the downstream gene OsMADS15. OsFTL10 also regulated Ehd1 and OsMADS51 through a feedback mechanism. The OsFTL10 protein was also detected in both nucleus and cytoplasm. Furthermore, yeast two hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) results show that OsFTL10 could interact with multiple 14-3-3s, suggesting that OsFTL10 might function in a similar way to Hd3a in promoting rice flowering by forming a FAC complex with 14-3-3, and OsFD1. Further experiments revealed that constitutive expression of OsFTL10 improved the drought tolerance of transgenic plants by stimulating the expression of drought responsive genes. These results suggest that rice FTL genes might function in flowering promotion and responses to environmental signals.
bibliographic citation: Fang et al. (2019) Overexpression of OsFTL10 induces early flowering and improves drought tolerance in Oryza sativa L.. PeerJ 7:e6422 https://doi.org/10.7717/peerj.6422
date submitted: 2018-10-16
date accepted: 2019-01-08
issued: 2019-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fang
  given name: Maichun
author list: Agent
  family name: Zhou
  given name: Zejiao
author list: Agent
  family name: Zhou
  given name: Xusheng
author list: Agent
  family name: Yang
  given name: Huiyong
author list: Agent
  family name: Li
  given name: Meiru
author list: Agent
  family name: Li
  given name: Hongqing
doi: 10.7717/peerj.6422
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-12
copyright: ©2019 Fang et al.
attribution name: Fang et al.

Production of eugenol from fungal endophytes Neopestalotiopsis sp. and Diaporthe sp. isolated from Cinnamomum loureiroi leaves
type: item
type: AcademicArticle
description: Endophytic fungi, which colonize within a host plant without causing any apparent diseases, have been considered as an important source of bioactive secondary metabolites containing antimicrobial and antioxidant activities. The aim of this research was to isolate the endophytic fungi of Cinnamomum loureiroi and then to screen their antimicrobial and antioxidant activities. A total of 11 fungal endophytes were isolated from healthy leaves of Cinnamomum loureiroi belonging to six genera: Botryosphaeria, Colletotrichum, Diaporthe, Fusarium, Neopestalotiopsis, and Pestalotiopsis. All isolated strains were cultured and further extracted with ethyl acetate solvent. Antimicrobial activity of all crude endophytic fungal extracts was analyzed using disc diffusion assay against six bacterial and two fungal pathogens. Crude extracts of strains MFLUCC15-1130 and MFLUCC15-1131 showed broad-spectrum antimicrobial activity against all tested pathogens. Activity against Bacillus cereus and Staphylococcus epidermidis was notable, showing the lowest minimum inhibitory concentration at 3.91 μg/mL. Antioxidant activity of all crude endophytic fungal extracts was also evaluated based on 2,2-diphenyl-1-picrylhydrazyl assay. Significant antioxidant activity was detected in the crude extracts of fungus MFLUCC15-1130 and MFLUCC15-1131 with IC50 of 22.92 ± 0.67 and 37.61 ± 0.49 μg/mL, respectively. Using molecular identification, MFLUCC15-1130 and MFLUCC15-1131 were identified as Neopestalotiopsis sp. and Diaporthe sp., respectively. The major chemical constituents produced by both crude extracts were identified by gas chromatography-mass spectrometry. Eugenol, myristaldehyde, lauric acid, and caprylic acid were the primary antimicrobial and antioxidant compounds in both crude extracts. This is the first report of eugenol being a biologically active compound of Neopestalotiopsis sp. and Diaporthe sp. fungal endophytes. Eugenol has been reported as antimicrobial and antioxidant agents with ag…
format: application/pdf
format: text/html
creator: Chutima Tanapichatsakul
creator: Sarunpron Khruengsai
creator: Sakon Monggoot
creator: Patcharee Pripdeevech
subject: Biotechnology
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.6427
publisher: PeerJ Inc.
rights: © 2019 Tanapichatsakul et al.
abstract: Endophytic fungi, which colonize within a host plant without causing any apparent diseases, have been considered as an important source of bioactive secondary metabolites containing antimicrobial and antioxidant activities. The aim of this research was to isolate the endophytic fungi of Cinnamomum loureiroi and then to screen their antimicrobial and antioxidant activities. A total of 11 fungal endophytes were isolated from healthy leaves of Cinnamomum loureiroi belonging to six genera: Botryosphaeria, Colletotrichum, Diaporthe, Fusarium, Neopestalotiopsis, and Pestalotiopsis. All isolated strains were cultured and further extracted with ethyl acetate solvent. Antimicrobial activity of all crude endophytic fungal extracts was analyzed using disc diffusion assay against six bacterial and two fungal pathogens. Crude extracts of strains MFLUCC15-1130 and MFLUCC15-1131 showed broad-spectrum antimicrobial activity against all tested pathogens. Activity against Bacillus cereus and Staphylococcus epidermidis was notable, showing the lowest minimum inhibitory concentration at 3.91 μg/mL. Antioxidant activity of all crude endophytic fungal extracts was also evaluated based on 2,2-diphenyl-1-picrylhydrazyl assay. Significant antioxidant activity was detected in the crude extracts of fungus MFLUCC15-1130 and MFLUCC15-1131 with IC50 of 22.92 ± 0.67 and 37.61 ± 0.49 μg/mL, respectively. Using molecular identification, MFLUCC15-1130 and MFLUCC15-1131 were identified as Neopestalotiopsis sp. and Diaporthe sp., respectively. The major chemical constituents produced by both crude extracts were identified by gas chromatography-mass spectrometry. Eugenol, myristaldehyde, lauric acid, and caprylic acid were the primary antimicrobial and antioxidant compounds in both crude extracts. This is the first report of eugenol being a biologically active compound of Neopestalotiopsis sp. and Diaporthe sp. fungal endophytes. Eugenol has been reported as antimicrobial and antioxidant agents with ag…
bibliographic citation: Tanapichatsakul et al. (2019) Production of eugenol from fungal endophytes Neopestalotiopsis sp. and Diaporthe sp. isolated from Cinnamomum loureiroi leaves. PeerJ 7:e6427 https://doi.org/10.7717/peerj.6427
date submitted: 2018-11-21
date accepted: 2019-01-03
issued: 2019-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanapichatsakul
  given name: Chutima
author list: Agent
  family name: Khruengsai
  given name: Sarunpron
author list: Agent
  family name: Monggoot
  given name: Sakon
author list: Agent
  family name: Pripdeevech
  given name: Patcharee
doi: 10.7717/peerj.6427
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-12
copyright: © 2019 Tanapichatsakul et al.
attribution name: Tanapichatsakul et al.

The association between meteorological variables and road traffic injuries: a study from Macao
type: item
type: AcademicArticle
description: Objective Correlation analysis and multiple linear regression analysis were conducted to estimate the influence of meteorological factors on road traffic injuries stratified by severity. Crash rate was defined as mean monthly road traffic accidents per 1,000 vectors. Design Ecological time-series study. Setting Macao traffic accident registry database between January 1st, 2001 and November 31st, 2016. Participants In total, 393,176 traffic accidents and 72,501 cases of road traffic injuries (RTIs) were enrolled; patients’ severity was divided into mild injury, required hospitalisation, and death. Exposure Variation of monthly meteorological factors. Main outcome measure Weather-condition-related road traffic accidents, injuries, and deaths. Results Windy weather significantly correlated with increased number of traffic accidents among all transport vectors (r = .375 to .637; p < 0.001). Multiple linear regression showed temperature (B = 0.704; p < 0.05) and humidity (B = − 0.537; p < 0.001) were independent factors for mild injury. The role of windy weather was relatively more obvious among patients with severe injuries (B = 0.304; p < 0.001) or those who died (B = 0.015; p < 0.001). A longer duration of sunshine was also associated to RTI-related deaths (B = 0.015; p < 0.001). In total, 13.4% of RTIs were attributable to meteorological factors and may be preventable. Conclusion The World Health Organization stated that RTIs are a major but neglected public health challenge. This study demonstrates meteorological factors have significant effects on any degree of RTIs. The results may not be generalized to other climates or populations while the findings may have implications in both preventing injuries and to announce safety precautions regarding trauma and motor vehicle collisions to the general public by public agencies.
format: application/pdf
format: text/html
creator: Chon-Fu Lio
creator: Hou-Hon Cheong
creator: Chon-Hou Un
creator: Iek-Long Lo
creator: Shin-Yi Tsai
subject: Epidemiology
subject: Global Health
subject: Public Health
subject: Environmental Impacts
description: doi:10.7717/peerj.6438
publisher: PeerJ Inc.
rights: © 2019 Lio et al.
abstract: Objective Correlation analysis and multiple linear regression analysis were conducted to estimate the influence of meteorological factors on road traffic injuries stratified by severity. Crash rate was defined as mean monthly road traffic accidents per 1,000 vectors. Design Ecological time-series study. Setting Macao traffic accident registry database between January 1st, 2001 and November 31st, 2016. Participants In total, 393,176 traffic accidents and 72,501 cases of road traffic injuries (RTIs) were enrolled; patients’ severity was divided into mild injury, required hospitalisation, and death. Exposure Variation of monthly meteorological factors. Main outcome measure Weather-condition-related road traffic accidents, injuries, and deaths. Results Windy weather significantly correlated with increased number of traffic accidents among all transport vectors (r = .375 to .637; p < 0.001). Multiple linear regression showed temperature (B = 0.704; p < 0.05) and humidity (B = − 0.537; p < 0.001) were independent factors for mild injury. The role of windy weather was relatively more obvious among patients with severe injuries (B = 0.304; p < 0.001) or those who died (B = 0.015; p < 0.001). A longer duration of sunshine was also associated to RTI-related deaths (B = 0.015; p < 0.001). In total, 13.4% of RTIs were attributable to meteorological factors and may be preventable. Conclusion The World Health Organization stated that RTIs are a major but neglected public health challenge. This study demonstrates meteorological factors have significant effects on any degree of RTIs. The results may not be generalized to other climates or populations while the findings may have implications in both preventing injuries and to announce safety precautions regarding trauma and motor vehicle collisions to the general public by public agencies.
bibliographic citation: Lio et al. (2019) The association between meteorological variables and road traffic injuries: a study from Macao. PeerJ 7:e6438 https://doi.org/10.7717/peerj.6438
date submitted: 2018-04-11
date accepted: 2019-01-11
issued: 2019-02-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lio
  given name: Chon-Fu
author list: Agent
  family name: Cheong
  given name: Hou-Hon
author list: Agent
  family name: Un
  given name: Chon-Hou
author list: Agent
  family name: Lo
  given name: Iek-Long
author list: Agent
  family name: Tsai
  given name: Shin-Yi
doi: 10.7717/peerj.6438
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-12
copyright: ©2019 Lio et al.
attribution name: Lio et al.

Engineering of CHO cells for the production of vertebrate recombinant sialyltransferases
type: item
type: AcademicArticle
description: Background Sialyltransferases (SIATs) are a family of enzymes that transfer sialic acid (Sia) to glycan chains on glycoproteins, glycolipids, and oligosaccharides. They play key roles in determining cell–cell and cell-matrix interactions and are important in neuronal development, immune regulation, protein stability and clearance. Most fully characterized SIATs are of mammalian origin and these have been used for in vitro and in vivo modification of glycans. Additional versatility could be achieved by the use of animal SIATs from other species that live in much more variable environments. Our aim was to generate a panel of stable CHO cell lines expressing a range of vertebrate SIATs with different physicochemical and functional properties. Methods The soluble forms of various animal ST6Gal and ST3Gal enzymes were stably expressed from a Gateway-modified secretion vector in CHO cells. The secreted proteins were IMAC-purified from serum-free media. Functionality of the protein was initially assessed by lectin binding to the host CHO cells. Activity of purified proteins was determined by a number of approaches that included a phosphate-linked sialyltransferase assay, HILIC-HPLC identification of sialyllactose products and enzyme-linked lectin assay (ELLA). Results A range of sialyltransferase from mammals, birds and fish were stably expressed in CHO Flp-In cells. The stable cell lines expressing ST6Gal1 modify the glycans on the surface of the CHO cells as detected by fluorescently labelled lectin microscopy. The catalytic domains, as isolated by Ni Sepharose from culture media, have enzymatic activities comparable to commercial enzymes. Sialyllactoses were identified by HILIC-HPLC on incubation of the enzymes from lactose or whey permeate. The enzymes also increased SNA-I labelling of asialofetuin when incubated in a plate format. Conclusion Stable cell lines are available that may provide options for the in vivo sialylation of glycoproteins. Proteins are active and s…
format: application/pdf
format: text/html
creator: Benoit Houeix
creator: Michael T. Cairns
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.5788
publisher: PeerJ Inc.
rights: © 2019 Houeix and Cairns
abstract: Background Sialyltransferases (SIATs) are a family of enzymes that transfer sialic acid (Sia) to glycan chains on glycoproteins, glycolipids, and oligosaccharides. They play key roles in determining cell–cell and cell-matrix interactions and are important in neuronal development, immune regulation, protein stability and clearance. Most fully characterized SIATs are of mammalian origin and these have been used for in vitro and in vivo modification of glycans. Additional versatility could be achieved by the use of animal SIATs from other species that live in much more variable environments. Our aim was to generate a panel of stable CHO cell lines expressing a range of vertebrate SIATs with different physicochemical and functional properties. Methods The soluble forms of various animal ST6Gal and ST3Gal enzymes were stably expressed from a Gateway-modified secretion vector in CHO cells. The secreted proteins were IMAC-purified from serum-free media. Functionality of the protein was initially assessed by lectin binding to the host CHO cells. Activity of purified proteins was determined by a number of approaches that included a phosphate-linked sialyltransferase assay, HILIC-HPLC identification of sialyllactose products and enzyme-linked lectin assay (ELLA). Results A range of sialyltransferase from mammals, birds and fish were stably expressed in CHO Flp-In cells. The stable cell lines expressing ST6Gal1 modify the glycans on the surface of the CHO cells as detected by fluorescently labelled lectin microscopy. The catalytic domains, as isolated by Ni Sepharose from culture media, have enzymatic activities comparable to commercial enzymes. Sialyllactoses were identified by HILIC-HPLC on incubation of the enzymes from lactose or whey permeate. The enzymes also increased SNA-I labelling of asialofetuin when incubated in a plate format. Conclusion Stable cell lines are available that may provide options for the in vivo sialylation of glycoproteins. Proteins are active and s…
bibliographic citation: Houeix et al. (2019) Engineering of CHO cells for the production of vertebrate recombinant sialyltransferases. PeerJ 7:e5788 https://doi.org/10.7717/peerj.5788
date submitted: 2018-06-01
date accepted: 2018-09-19
issued: 2019-02-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Houeix
  given name: Benoit
author list: Agent
  family name: Cairns
  given name: Michael T.
doi: 10.7717/peerj.5788
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-11
copyright: © 2019 Houeix and Cairns
attribution name: Houeix and Cairns

Potential ecotoxicological effects of antimicrobial surface coatings: a literature survey backed up by analysis of market reports
type: item
type: AcademicArticle
description: This review was initiated by the COST action CA15114 AMICI “Anti-Microbial Coating Innovations to prevent infectious diseases,” where one important aspect is to analyze ecotoxicological impacts of antimicrobial coatings (AMCs) to ensure their sustainable use. Scopus database was used to collect scientific literature on the types and uses of AMCs, while market reports were used to collect data on production volumes. Special attention was paid on data obtained for the release of the most prevalent ingredients of AMCs into the aqueous phase that was used as the proxy for their possible ecotoxicological effects. Based on the critical analysis of 2,720 papers, it can be concluded that silver-based AMCs are by far the most studied and used coatings followed by those based on titanium, copper, zinc, chitosan and quaternary ammonium compounds. The literature analysis pointed to biomedicine, followed by marine industry, construction industry (paints), food industry and textiles as the main fields of application of AMCs. The published data on ecotoxicological effects of AMCs was scarce, and also only a small number of the papers provided information on release of antimicrobial ingredients from AMCs. The available release data allowed to conclude that silver, copper and zinc are often released in substantial amounts (up to 100%) from the coatings to the aqueous environment. Chitosan and titanium were mostly not used as active released ingredients in AMCs, but rather as carriers for other release-based antimicrobial ingredients (e.g., conventional antibiotics). While minimizing the prevalence of healthcare-associated infections appeared to be the most prosperous field of AMCs application, the release of environmentally hazardous ingredients of AMCs into hospital wastewaters and thus, also the environmental risks associated with AMCs, comprise currently only a fraction of the release and risks of traditional disinfectants. However, being proactive, while the use of antimicrobial…
format: application/pdf
format: text/html
creator: Merilin Rosenberg
creator: Krunoslav Ilić
creator: Katre Juganson
creator: Angela Ivask
creator: Merja Ahonen
creator: Ivana Vinković Vrček
creator: Anne Kahru
subject: Microbiology
subject: Toxicology
subject: Public Health
subject: Ecotoxicology
subject: Environmental Impacts
description: doi:10.7717/peerj.6315
publisher: PeerJ Inc.
rights: © 2019 Rosenberg et al.
abstract: This review was initiated by the COST action CA15114 AMICI “Anti-Microbial Coating Innovations to prevent infectious diseases,” where one important aspect is to analyze ecotoxicological impacts of antimicrobial coatings (AMCs) to ensure their sustainable use. Scopus database was used to collect scientific literature on the types and uses of AMCs, while market reports were used to collect data on production volumes. Special attention was paid on data obtained for the release of the most prevalent ingredients of AMCs into the aqueous phase that was used as the proxy for their possible ecotoxicological effects. Based on the critical analysis of 2,720 papers, it can be concluded that silver-based AMCs are by far the most studied and used coatings followed by those based on titanium, copper, zinc, chitosan and quaternary ammonium compounds. The literature analysis pointed to biomedicine, followed by marine industry, construction industry (paints), food industry and textiles as the main fields of application of AMCs. The published data on ecotoxicological effects of AMCs was scarce, and also only a small number of the papers provided information on release of antimicrobial ingredients from AMCs. The available release data allowed to conclude that silver, copper and zinc are often released in substantial amounts (up to 100%) from the coatings to the aqueous environment. Chitosan and titanium were mostly not used as active released ingredients in AMCs, but rather as carriers for other release-based antimicrobial ingredients (e.g., conventional antibiotics). While minimizing the prevalence of healthcare-associated infections appeared to be the most prosperous field of AMCs application, the release of environmentally hazardous ingredients of AMCs into hospital wastewaters and thus, also the environmental risks associated with AMCs, comprise currently only a fraction of the release and risks of traditional disinfectants. However, being proactive, while the use of antimicrobial…
bibliographic citation: Rosenberg et al. (2019) Potential ecotoxicological effects of antimicrobial surface coatings: a literature survey backed up by analysis of market reports. PeerJ 7:e6315 https://doi.org/10.7717/peerj.6315
date submitted: 2018-08-28
date accepted: 2018-12-19
issued: 2019-02-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rosenberg
  given name: Merilin
author list: Agent
  family name: Ilić
  given name: Krunoslav
author list: Agent
  family name: Juganson
  given name: Katre
author list: Agent
  family name: Ivask
  given name: Angela
author list: Agent
  family name: Ahonen
  given name: Merja
author list: Agent
  family name: Vinković Vrček
  given name: Ivana
author list: Agent
  family name: Kahru
  given name: Anne
doi: 10.7717/peerj.6315
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-11
copyright: © 2019 Rosenberg et al.
attribution name: Rosenberg et al.

Integrating gross morphology and bone histology to assess skeletal maturity in early dinosauromorphs: new insights from Dromomeron (Archosauria: Dinosauromorpha)
type: item
type: AcademicArticle
description: Understanding growth patterns is central to properly interpreting paleobiological signals in tetrapods, but assessing skeletal maturity in some extinct clades may be difficult when growth patterns are poorly constrained by a lack of ontogenetic series. To overcome this difficulty in assessing the maturity of extinct archosaurian reptiles—crocodylians, birds and their extinct relatives—many studies employ bone histology to observe indicators of the developmental stage reached by a given individual. However, the relationship between gross morphological and histological indicators of maturity has not been examined in most archosaurian groups. In this study, we examined the gross morphology of a hypothesized growth series of Dromomeron romeri femora (96.6–144.4 mm long), the first series of a non-dinosauriform dinosauromorph available for such a study. We also histologically sampled several individuals in this growth series. Previous studies reported that D. romeri lacks well-developed rugose muscle scars that appear during ontogeny in closely related dinosauromorph taxa, so integrating gross morphology and histological signal is needed to determine reliable maturity indicators for early bird-line archosaurs. We found that, although there are small, linear scars indicating muscle attachment sites across the femur, the only rugose muscle scar that appears during ontogeny is the attachment of the M. caudofemoralis longus, and only in the largest-sampled individual. This individual is also the only femur with histological indicators that asymptotic size had been reached, although smaller individuals possess some signal of decreasing growth rates (e.g., decreasing vascular density). The overall femoral bone histology of D. romeri is similar to that of other early bird-line archosaurs (e.g., woven-bone tissue, moderately to well-vascularized, longitudinal vascular canals). All these data indicate that the lack of well-developed femoral scars is autapomorphic for this species…
format: application/pdf
format: text/html
creator: Christopher T. Griffin
creator: Lauren S. Bano
creator: Alan H. Turner
creator: Nathan D. Smith
creator: Randall B. Irmis
creator: Sterling J. Nesbitt
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.6331
publisher: PeerJ Inc.
rights: © 2019 Griffin et al.
abstract: Understanding growth patterns is central to properly interpreting paleobiological signals in tetrapods, but assessing skeletal maturity in some extinct clades may be difficult when growth patterns are poorly constrained by a lack of ontogenetic series. To overcome this difficulty in assessing the maturity of extinct archosaurian reptiles—crocodylians, birds and their extinct relatives—many studies employ bone histology to observe indicators of the developmental stage reached by a given individual. However, the relationship between gross morphological and histological indicators of maturity has not been examined in most archosaurian groups. In this study, we examined the gross morphology of a hypothesized growth series of Dromomeron romeri femora (96.6–144.4 mm long), the first series of a non-dinosauriform dinosauromorph available for such a study. We also histologically sampled several individuals in this growth series. Previous studies reported that D. romeri lacks well-developed rugose muscle scars that appear during ontogeny in closely related dinosauromorph taxa, so integrating gross morphology and histological signal is needed to determine reliable maturity indicators for early bird-line archosaurs. We found that, although there are small, linear scars indicating muscle attachment sites across the femur, the only rugose muscle scar that appears during ontogeny is the attachment of the M. caudofemoralis longus, and only in the largest-sampled individual. This individual is also the only femur with histological indicators that asymptotic size had been reached, although smaller individuals possess some signal of decreasing growth rates (e.g., decreasing vascular density). The overall femoral bone histology of D. romeri is similar to that of other early bird-line archosaurs (e.g., woven-bone tissue, moderately to well-vascularized, longitudinal vascular canals). All these data indicate that the lack of well-developed femoral scars is autapomorphic for this species…
bibliographic citation: Griffin et al. (2019) Integrating gross morphology and bone histology to assess skeletal maturity in early dinosauromorphs: new insights from Dromomeron (Archosauria: Dinosauromorpha). PeerJ 7:e6331 https://doi.org/10.7717/peerj.6331
date submitted: 2018-08-07
date accepted: 2018-12-20
issued: 2019-02-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Griffin
  given name: Christopher T.
author list: Agent
  family name: Bano
  given name: Lauren S.
author list: Agent
  family name: Turner
  given name: Alan H.
author list: Agent
  family name: Smith
  given name: Nathan D.
author list: Agent
  family name: Irmis
  given name: Randall B.
author list: Agent
  family name: Nesbitt
  given name: Sterling J.
doi: 10.7717/peerj.6331
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-11
copyright: © 2019 Griffin et al.
attribution name: Griffin et al.

In silico analysis reveals a shared immune signature in CASP8-mutated carcinomas with varying correlations to prognosis
type: item
type: AcademicArticle
description: Background Sequencing studies across multiple cancers continue to reveal mutations and genes involved in the pathobiology of these cancers. Exome sequencing of oral cancers, a subset of Head and Neck Squamous cell Carcinomas (HNSCs) common among tobacco-chewing populations, revealed that ∼34% of the affected patients harbor mutations in the CASP8 gene. Uterine Corpus Endometrial Carcinoma (UCEC) is another cancer where ∼10% cases harbor CASP8 mutations. Caspase-8, the protease encoded by CASP8 gene, plays a dual role in programmed cell death, which in turn has an important role in tumor cell death and drug resistance. CASP8 is a protease required for the extrinsic pathway of apoptosis and is also a negative regulator of necroptosis. Using multiple tools such as differential gene expression, gene set enrichment, gene ontology, in silico immune cell estimates, and survival analyses to mine data in The Cancer Genome Atlas, we compared the molecular features and survival of these carcinomas with and without CASP8 mutations. Results Differential gene expression followed by gene set enrichment analysis showed that HNSCs with CASP8 mutations displayed a prominent signature of genes involved in immune response and inflammation. Analysis of abundance estimates of immune cells in these tumors further revealed that mutant-CASP8 HNSCs were rich in immune cell infiltrates. However, in contrast to Human Papilloma Virus-positive HNSCs that also exhibit high immune cell infiltration, which in turn is correlated with better overall survival, HNSC patients with mutant-CASP8 tumors did not display any survival advantage. Similar analyses of UCECs revealed that while UCECs with CASP8 mutations also displayed an immune signature, they had better overall survival, in contrast to the HNSC scenario. There was also a significant up-regulation of neutrophils (p-value = 0.0001638) as well as high levels of IL33 mRNA (p-value = 7.63747E−08) in mutant-CASP8 HNSCs, which were not observed in mut…
format: application/pdf
format: text/html
creator: Yashoda Ghanekar
creator: Subhashini Sadasivam
subject: Bioinformatics
subject: Genomics
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.6402
publisher: PeerJ Inc.
rights: © 2019 Ghanekar and Sadasivam
abstract: Background Sequencing studies across multiple cancers continue to reveal mutations and genes involved in the pathobiology of these cancers. Exome sequencing of oral cancers, a subset of Head and Neck Squamous cell Carcinomas (HNSCs) common among tobacco-chewing populations, revealed that ∼34% of the affected patients harbor mutations in the CASP8 gene. Uterine Corpus Endometrial Carcinoma (UCEC) is another cancer where ∼10% cases harbor CASP8 mutations. Caspase-8, the protease encoded by CASP8 gene, plays a dual role in programmed cell death, which in turn has an important role in tumor cell death and drug resistance. CASP8 is a protease required for the extrinsic pathway of apoptosis and is also a negative regulator of necroptosis. Using multiple tools such as differential gene expression, gene set enrichment, gene ontology, in silico immune cell estimates, and survival analyses to mine data in The Cancer Genome Atlas, we compared the molecular features and survival of these carcinomas with and without CASP8 mutations. Results Differential gene expression followed by gene set enrichment analysis showed that HNSCs with CASP8 mutations displayed a prominent signature of genes involved in immune response and inflammation. Analysis of abundance estimates of immune cells in these tumors further revealed that mutant-CASP8 HNSCs were rich in immune cell infiltrates. However, in contrast to Human Papilloma Virus-positive HNSCs that also exhibit high immune cell infiltration, which in turn is correlated with better overall survival, HNSC patients with mutant-CASP8 tumors did not display any survival advantage. Similar analyses of UCECs revealed that while UCECs with CASP8 mutations also displayed an immune signature, they had better overall survival, in contrast to the HNSC scenario. There was also a significant up-regulation of neutrophils (p-value = 0.0001638) as well as high levels of IL33 mRNA (p-value = 7.63747E−08) in mutant-CASP8 HNSCs, which were not observed in mut…
bibliographic citation: Ghanekar et al. (2019) In silico analysis reveals a shared immune signature in CASP8-mutated carcinomas with varying correlations to prognosis. PeerJ 7:e6402 https://doi.org/10.7717/peerj.6402
date submitted: 2018-11-06
date accepted: 2019-01-07
issued: 2019-02-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghanekar
  given name: Yashoda
author list: Agent
  family name: Sadasivam
  given name: Subhashini
doi: 10.7717/peerj.6402
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-11
copyright: ©2019 Ghanekar and Sadasivam
attribution name: Ghanekar and Sadasivam

The blood parameters and liver function changed inconsistently among children between burns and traumatic injuries
type: item
type: AcademicArticle
description: Objective Burn and traumatic injury are two kinds of injury by modality. They cause acute phase response and lead to a series of pathological and physiological changes. In this study, we explored whether there are differences in routine blood parameters and liver enzyme levels between burned and traumatically injured children. Methods Patients under 18 years old with injuries were recruited. Their demographic and clinical data were recorded. Collected clinical data included routine blood parameters (white blood cell count (WBC), red blood cell count (RBC), platelets (PLT), hemoglobin (HB)), serological enzyme levels (alanine aminotransferase (ALT), aspartate transaminase (AST), glutamyltransferase (GGT), alkaline phosphatase (ALP), cholinesterase (CHE)), and total protein (TP) levels (albumin (ALB), globulin (GLB)). A generalized linear model and multivariate analysis of variance were used to conduct comparisons. Results A total of 162 children (109 with burns and 53 with traumatic injuries) with a mean age of 4.36 ± 4.29 years were enrolled in the study. Burned children had higher levels of RBC, HB, WBC, AST and lower levels of TP, CHE, ALB than traumatically injured children (P < 0.05). Moreover, the concentration of WBC and HB was higher in males compared to females (P < 0.001). Conversely, the level of AST and TP in males was lower, AST levels were significantly lower in males (P = 0.005). Age positively correlated with the levels of HB, AST and TP (P < 0.001), and negatively correlated with WBC (P < 0.001). With decreasing body mass index (BMI), the levels of WBC, HB, AST and TP significantly increased in both groups of injured children (P < 0.001). In addition, ISS was positively correlated with WBC and HB levels (P < 0.001), but negatively correlated with AST and TP levels (P < 0.001). Conclusions Children with burn injuries suffered a greater acute response and liver damage than traumatically injured children. This may in part underlie clinical observations …
format: application/pdf
format: text/html
creator: Chan Nie
creator: Tao Wang
creator: Huiting Yu
creator: Xue Wang
creator: Xueqin Zeng
creator: Zairong Wei
creator: Xiuquan Shi
subject: Dermatology
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.6415
publisher: PeerJ Inc.
rights: © 2019 Nie et al.
abstract: Objective Burn and traumatic injury are two kinds of injury by modality. They cause acute phase response and lead to a series of pathological and physiological changes. In this study, we explored whether there are differences in routine blood parameters and liver enzyme levels between burned and traumatically injured children. Methods Patients under 18 years old with injuries were recruited. Their demographic and clinical data were recorded. Collected clinical data included routine blood parameters (white blood cell count (WBC), red blood cell count (RBC), platelets (PLT), hemoglobin (HB)), serological enzyme levels (alanine aminotransferase (ALT), aspartate transaminase (AST), glutamyltransferase (GGT), alkaline phosphatase (ALP), cholinesterase (CHE)), and total protein (TP) levels (albumin (ALB), globulin (GLB)). A generalized linear model and multivariate analysis of variance were used to conduct comparisons. Results A total of 162 children (109 with burns and 53 with traumatic injuries) with a mean age of 4.36 ± 4.29 years were enrolled in the study. Burned children had higher levels of RBC, HB, WBC, AST and lower levels of TP, CHE, ALB than traumatically injured children (P < 0.05). Moreover, the concentration of WBC and HB was higher in males compared to females (P < 0.001). Conversely, the level of AST and TP in males was lower, AST levels were significantly lower in males (P = 0.005). Age positively correlated with the levels of HB, AST and TP (P < 0.001), and negatively correlated with WBC (P < 0.001). With decreasing body mass index (BMI), the levels of WBC, HB, AST and TP significantly increased in both groups of injured children (P < 0.001). In addition, ISS was positively correlated with WBC and HB levels (P < 0.001), but negatively correlated with AST and TP levels (P < 0.001). Conclusions Children with burn injuries suffered a greater acute response and liver damage than traumatically injured children. This may in part underlie clinical observations …
bibliographic citation: Nie et al. (2019) The blood parameters and liver function changed inconsistently among children between burns and traumatic injuries. PeerJ 7:e6415 https://doi.org/10.7717/peerj.6415
date submitted: 2018-10-24
date accepted: 2019-01-08
issued: 2019-02-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nie
  given name: Chan
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Yu
  given name: Huiting
author list: Agent
  family name: Wang
  given name: Xue
author list: Agent
  family name: Zeng
  given name: Xueqin
author list: Agent
  family name: Wei
  given name: Zairong
author list: Agent
  family name: Shi
  given name: Xiuquan
doi: 10.7717/peerj.6415
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-11
copyright: ©2019 Nie et al.
attribution name: Nie et al.

Discordant financial conflicts of interest disclosures between clinical trial conference abstract and subsequent publication
type: item
type: AcademicArticle
description: Background Financial conflicts of interest (FCOI) are known to be prevalent in medicine. Authorship of pivotal trials reap non-financial benefits including publication productivity that can be used for assessment of tenure positions and promotion. The purpose of this investigation was to quantify the prevalence and discordance of academic trial author (authors) FCOI in industry-sponsored drug trials that were initially presented as oral abstracts and subsequently resulted in a peer-reviewed publication. Methods Oral abstracts from the American Society of Clinical Oncology (ASCO) 2017 Annual Meeting that were subsequently published were identified. Studies that were non-industry sponsored, non-adult, or non-therapeutic trials were excluded. Studies that did not have a subsequent peer-reviewed publication or had a publication preceding the ASCO 2017 Annual Meeting were also excluded. FCOI was categorized and impact factor (IF) for the journal at the time of publication was retrieved. FCOI discordance between the oral abstract and publication was calculated based on geographic location and IF. Results A total of 22 paired abstract and publications met inclusion criteria for further analysis. A total of 384 authors were identified, of these 280 authors (74.1%) were included in both the oral abstract and subsequent publication. A total of 76% of these 280 authors had FCOI and 66.4% had FCOI discordance. There were statistically significant differences for the sum of FCOI discordance for U.S.-based authors (p = 0.0004) but not for journal IF. When analyzing the sum of absolute differences of FCOI discordance, statistical significance was reached for authors from any of the three geographic regions, as well as, low and high IF journals (all p-values < 0.0001). Conclusions This study draws attention to the lack of uniformity and vetting of FCOI reporting in abstracts and journals publishing solid tumor oncology trial results. This is particularly concerning, since FCOI is p…
format: application/pdf
format: text/html
creator: Glen J. Weiss
creator: Roger B. Davis
subject: Clinical Trials
subject: Oncology
subject: Ethical Issues
description: doi:10.7717/peerj.6423
publisher: PeerJ Inc.
rights: © 2019 Weiss and Davis
abstract: Background Financial conflicts of interest (FCOI) are known to be prevalent in medicine. Authorship of pivotal trials reap non-financial benefits including publication productivity that can be used for assessment of tenure positions and promotion. The purpose of this investigation was to quantify the prevalence and discordance of academic trial author (authors) FCOI in industry-sponsored drug trials that were initially presented as oral abstracts and subsequently resulted in a peer-reviewed publication. Methods Oral abstracts from the American Society of Clinical Oncology (ASCO) 2017 Annual Meeting that were subsequently published were identified. Studies that were non-industry sponsored, non-adult, or non-therapeutic trials were excluded. Studies that did not have a subsequent peer-reviewed publication or had a publication preceding the ASCO 2017 Annual Meeting were also excluded. FCOI was categorized and impact factor (IF) for the journal at the time of publication was retrieved. FCOI discordance between the oral abstract and publication was calculated based on geographic location and IF. Results A total of 22 paired abstract and publications met inclusion criteria for further analysis. A total of 384 authors were identified, of these 280 authors (74.1%) were included in both the oral abstract and subsequent publication. A total of 76% of these 280 authors had FCOI and 66.4% had FCOI discordance. There were statistically significant differences for the sum of FCOI discordance for U.S.-based authors (p = 0.0004) but not for journal IF. When analyzing the sum of absolute differences of FCOI discordance, statistical significance was reached for authors from any of the three geographic regions, as well as, low and high IF journals (all p-values < 0.0001). Conclusions This study draws attention to the lack of uniformity and vetting of FCOI reporting in abstracts and journals publishing solid tumor oncology trial results. This is particularly concerning, since FCOI is p…
bibliographic citation: Weiss et al. (2019) Discordant financial conflicts of interest disclosures between clinical trial conference abstract and subsequent publication. PeerJ 7:e6423 https://doi.org/10.7717/peerj.6423
date submitted: 2018-09-27
date accepted: 2019-01-09
issued: 2019-02-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weiss
  given name: Glen J.
author list: Agent
  family name: Davis
  given name: Roger B.
doi: 10.7717/peerj.6423
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-11
copyright: © 2019 Weiss and Davis
attribution name: Weiss and Davis

Elevational patterns of the percentages of plant genera with tropical and temperate affinities in Nepal
type: item
type: AcademicArticle
description: Background Geographical patterns of species diversity are one of the key topics in biogeography and ecology. The effects of biogeographical affinities on the elevational patterns of species diversity have attracted much attention recently, but the factors driving elevational patterns of the percentages of plants with tropical and temperate biogeographical affinities have not been adequately explored. Methods We first used univariate least squares regressions to evaluate the effects of each predictor on the elevational patterns of the percentages of plant genera with tropical and temperate affinities in Nepal. Then, the lowest corrected Akaike information criterion value was used to find the best-fit models for all possible combinations of the aforementioned predictors. We also conducted partial regression analysis to investigate the relative influences of each predictor in the best-fit model of the percentages of plant genera with tropical and temperate affinities. Results With the increase of elevation, the percentage of plant genera with tropical affinity significantly decreased, while that of plant genera with temperate affinity increased. The strongest predictor of the percentages of plant genera with tropical affinity in the examined area was the minimum temperature of the coldest month. For the elevational patterns of the percentages of plant genera with temperate affinity, the strongest predictor was the maximum temperature of the warmest month. Compared with mid-domain effects (MDE), climatic factors explained much more of the elevational variation of the percentages of plant genera with tropical and temperate affinities. Discussion The elevational patterns of the percentages of plant genera with tropical affinities and the factors driving them supported the revision of the freezing-tolerance hypothesis. That is, freezing may filter out plant genera with tropical affinity, resulting in the decrease of their percentages, with winter coldness playing a predomi…
format: application/pdf
format: text/html
creator: Yunyun Lai
creator: Jianmeng Feng
subject: Biogeography
subject: Ecology
description: doi:10.7717/peerj.6116
publisher: PeerJ Inc.
rights: © 2019 Lai and Feng
abstract: Background Geographical patterns of species diversity are one of the key topics in biogeography and ecology. The effects of biogeographical affinities on the elevational patterns of species diversity have attracted much attention recently, but the factors driving elevational patterns of the percentages of plants with tropical and temperate biogeographical affinities have not been adequately explored. Methods We first used univariate least squares regressions to evaluate the effects of each predictor on the elevational patterns of the percentages of plant genera with tropical and temperate affinities in Nepal. Then, the lowest corrected Akaike information criterion value was used to find the best-fit models for all possible combinations of the aforementioned predictors. We also conducted partial regression analysis to investigate the relative influences of each predictor in the best-fit model of the percentages of plant genera with tropical and temperate affinities. Results With the increase of elevation, the percentage of plant genera with tropical affinity significantly decreased, while that of plant genera with temperate affinity increased. The strongest predictor of the percentages of plant genera with tropical affinity in the examined area was the minimum temperature of the coldest month. For the elevational patterns of the percentages of plant genera with temperate affinity, the strongest predictor was the maximum temperature of the warmest month. Compared with mid-domain effects (MDE), climatic factors explained much more of the elevational variation of the percentages of plant genera with tropical and temperate affinities. Discussion The elevational patterns of the percentages of plant genera with tropical affinities and the factors driving them supported the revision of the freezing-tolerance hypothesis. That is, freezing may filter out plant genera with tropical affinity, resulting in the decrease of their percentages, with winter coldness playing a predomi…
bibliographic citation: Lai et al. (2019) Elevational patterns of the percentages of plant genera with tropical and temperate affinities in Nepal. PeerJ 7:e6116 https://doi.org/10.7717/peerj.6116
date submitted: 2018-05-15
date accepted: 2018-11-14
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lai
  given name: Yunyun
author list: Agent
  family name: Feng
  given name: Jianmeng
doi: 10.7717/peerj.6116
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Lai and Feng
attribution name: Lai and Feng

Invasion genetics of the mummichog (Fundulus heteroclitus): recent anthropogenic introduction in Iberia
type: item
type: AcademicArticle
description: Human activities such as trade and transport have increased considerably in the last decades, greatly facilitating the introduction and spread of non-native species at a global level. In the Iberian Peninsula, Fundulus heteroclitus, a small euryhaline coastal fish with short dispersal, was found for the first time in the mid-1970s. Since then, F. heteroclitus has undergone range expansions, colonizing the southern region of Portugal, southwestern coast of Spain and the Ebro Delta in the Mediterranean Sea. Cytochrome b sequences were used to elucidate the species invasion pathway in Iberia. Three Iberian locations (Faro, Cádiz and Ebro Delta) and 13 other locations along the native range of F. heteroclitus in North America were sampled. Results revealed a single haplotype, common to all invasive populations, which can be traced to the northern region of the species’ native range. We posit that the origin of the founder individuals is between New York and Nova Scotia. Additionally, the lack of genetic structure within Iberia is consistent with a recent invasion scenario and a strong founder effect. We suggest the most probable introduction vector is associated with the aquarium trade. We further discuss the hypothesis of a second human-mediated introduction responsible for the establishment of individuals in the Ebro Delta supported by the absence of adequate muddy habitats linking Cádiz and the Ebro Delta. Although the species has a high tolerance to salinity and temperature, ecological niche modelling indicates that benthic habitat constraints prevent along-shore colonisation suggesting that such expansions would need to be aided by human release.
format: application/pdf
format: text/html
creator: Teófilo Morim
creator: Grant R. Bigg
creator: Pedro M. Madeira
creator: Jorge Palma
creator: David D. Duvernell
creator: Enric Gisbert
creator: Regina L. Cunha
creator: Rita Castilho
subject: Biogeography
subject: Genetics
description: doi:10.7717/peerj.6155
publisher: PeerJ Inc.
rights: © 2019 Morim et al.
abstract: Human activities such as trade and transport have increased considerably in the last decades, greatly facilitating the introduction and spread of non-native species at a global level. In the Iberian Peninsula, Fundulus heteroclitus, a small euryhaline coastal fish with short dispersal, was found for the first time in the mid-1970s. Since then, F. heteroclitus has undergone range expansions, colonizing the southern region of Portugal, southwestern coast of Spain and the Ebro Delta in the Mediterranean Sea. Cytochrome b sequences were used to elucidate the species invasion pathway in Iberia. Three Iberian locations (Faro, Cádiz and Ebro Delta) and 13 other locations along the native range of F. heteroclitus in North America were sampled. Results revealed a single haplotype, common to all invasive populations, which can be traced to the northern region of the species’ native range. We posit that the origin of the founder individuals is between New York and Nova Scotia. Additionally, the lack of genetic structure within Iberia is consistent with a recent invasion scenario and a strong founder effect. We suggest the most probable introduction vector is associated with the aquarium trade. We further discuss the hypothesis of a second human-mediated introduction responsible for the establishment of individuals in the Ebro Delta supported by the absence of adequate muddy habitats linking Cádiz and the Ebro Delta. Although the species has a high tolerance to salinity and temperature, ecological niche modelling indicates that benthic habitat constraints prevent along-shore colonisation suggesting that such expansions would need to be aided by human release.
bibliographic citation: Morim et al. (2019) Invasion genetics of the mummichog (Fundulus heteroclitus): recent anthropogenic introduction in Iberia. PeerJ 7:e6155 https://doi.org/10.7717/peerj.6155
date submitted: 2018-08-31
date accepted: 2018-11-25
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morim
  given name: Teófilo
author list: Agent
  family name: Bigg
  given name: Grant R.
author list: Agent
  family name: Madeira
  given name: Pedro M.
author list: Agent
  family name: Palma
  given name: Jorge
author list: Agent
  family name: Duvernell
  given name: David D.
author list: Agent
  family name: Gisbert
  given name: Enric
author list: Agent
  family name: Cunha
  given name: Regina L.
author list: Agent
  family name: Castilho
  given name: Rita
doi: 10.7717/peerj.6155
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: ©2019 Morim et al.
attribution name: Morim et al.

Response of adult honey bees treated in larval stage with prochloraz to infection with Nosema ceranae
type: item
type: AcademicArticle
description: Among numerous factors that contribute to honey bee colony losses and problems in beekeeping, pesticides and Nosema ceranae have been often reported. In contrast to insecticides, whose effects on bees have been widely studied, fungicides did not attract considerable attention. Prochloraz, an imidazole fungicide widely used in agriculture, was detected in honey and pollen stored inside hives and has been already proven to alter immune gene expression of honey bees at different developmental stages. The aim of this study was to simulate the realistic conditions of migratory beekeeping, where colonies, both uninfected and infected with N. ceranae, are frequently transported to the vicinity of crop fields treated with prochloraz. We investigated the combined effect of prochloraz and N. ceranae on honey bees that faced fungicide during the larval stage through food consumption and microsporidium infection afterwards. The most pronounced changes in gene expression were observed in newly emerged Nosema-free bees originating from colonies previously contaminated with prochloraz. As exclusively upregulation was registered, prochloraz alone most likely acts as a challenge that induces activation of immune pathways in newly emerged bees. The combination of both stressors (prochloraz and Nosema infection) exerted the greatest effect on six-day-old honey bees. Among ten genes with significantly altered expression, half were upregulated and half downregulated. N. ceranae as a sole stressor had the weakest effects on immune gene expression modulation with only three genes significantly dysregulated. In conclusion, food contaminated with prochloraz consumed in larval stage could present a threat to the development of immunity and detoxification mechanisms in honey bees.
format: application/pdf
format: text/html
creator: Uros Glavinic
creator: Tanja Tesovnik
creator: Jevrosima Stevanovic
creator: Minja Zorc
creator: Ivanka Cizelj
creator: Zoran Stanimirovic
creator: Mojca Narat
subject: Agricultural Science
subject: Biotechnology
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.6325
publisher: PeerJ Inc.
rights: © 2019 Glavinic et al.
abstract: Among numerous factors that contribute to honey bee colony losses and problems in beekeeping, pesticides and Nosema ceranae have been often reported. In contrast to insecticides, whose effects on bees have been widely studied, fungicides did not attract considerable attention. Prochloraz, an imidazole fungicide widely used in agriculture, was detected in honey and pollen stored inside hives and has been already proven to alter immune gene expression of honey bees at different developmental stages. The aim of this study was to simulate the realistic conditions of migratory beekeeping, where colonies, both uninfected and infected with N. ceranae, are frequently transported to the vicinity of crop fields treated with prochloraz. We investigated the combined effect of prochloraz and N. ceranae on honey bees that faced fungicide during the larval stage through food consumption and microsporidium infection afterwards. The most pronounced changes in gene expression were observed in newly emerged Nosema-free bees originating from colonies previously contaminated with prochloraz. As exclusively upregulation was registered, prochloraz alone most likely acts as a challenge that induces activation of immune pathways in newly emerged bees. The combination of both stressors (prochloraz and Nosema infection) exerted the greatest effect on six-day-old honey bees. Among ten genes with significantly altered expression, half were upregulated and half downregulated. N. ceranae as a sole stressor had the weakest effects on immune gene expression modulation with only three genes significantly dysregulated. In conclusion, food contaminated with prochloraz consumed in larval stage could present a threat to the development of immunity and detoxification mechanisms in honey bees.
bibliographic citation: Glavinic et al. (2019) Response of adult honey bees treated in larval stage with prochloraz to infection with Nosema ceranae. PeerJ 7:e6325 https://doi.org/10.7717/peerj.6325
date submitted: 2018-11-30
date accepted: 2018-12-20
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Glavinic
  given name: Uros
author list: Agent
  family name: Tesovnik
  given name: Tanja
author list: Agent
  family name: Stevanovic
  given name: Jevrosima
author list: Agent
  family name: Zorc
  given name: Minja
author list: Agent
  family name: Cizelj
  given name: Ivanka
author list: Agent
  family name: Stanimirovic
  given name: Zoran
author list: Agent
  family name: Narat
  given name: Mojca
doi: 10.7717/peerj.6325
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: ©2019 Glavinic et al.
attribution name: Glavinic et al.

Membrane potential (Vmem) measurements during mesenchymal stem cell (MSC) proliferation and osteogenic differentiation
type: item
type: AcademicArticle
description: Background Electrochemical signals play an important role in cell communication and behavior. Electrically charged ions transported across cell membranes maintain an electrochemical imbalance that gives rise to bioelectric signaling, called membrane potential or Vmem. Vmem plays a key role in numerous inter- and intracellular functions that regulate cell behaviors like proliferation, differentiation and migration, all playing a critical role in embryonic development, healing, and regeneration. Methods With the goal of analyzing the changes in Vmem during cell proliferation and differentiation, here we used direct current electrical stimulation (EStim) to promote cell proliferation and differentiation and simultaneously tracked the corresponding changes in Vmem in adipose derived mesenchymal stem cells (AT-MSC). Results We found that EStim caused increased AT-MSC proliferation that corresponded to Vmem depolarization and increased osteogenic differentiation that corresponded to Vmem hyperpolarization. Taken together, this shows that Vmem changes associated with EStim induced cell proliferation and differentiation can be accurately tracked during these important cell functions. Using this tool to monitor Vmem changes associated with these important cell behaviors we hope to learn more about how these electrochemical cues regulate cell function with the ultimate goal of developing new EStim based treatments capable of controlling healing and regeneration.
format: application/pdf
format: text/html
creator: Mit Balvantray Bhavsar
creator: Gloria Cato
creator: Alexander Hauschild
creator: Liudmila Leppik
creator: Karla Mychellyne Costa Oliveira
creator: Maria José Eischen-Loges
creator: John Howard Barker
subject: Bioengineering
subject: Cell Biology
subject: Statistics
description: doi:10.7717/peerj.6341
publisher: PeerJ Inc.
rights: © 2019 Bhavsar et al.
abstract: Background Electrochemical signals play an important role in cell communication and behavior. Electrically charged ions transported across cell membranes maintain an electrochemical imbalance that gives rise to bioelectric signaling, called membrane potential or Vmem. Vmem plays a key role in numerous inter- and intracellular functions that regulate cell behaviors like proliferation, differentiation and migration, all playing a critical role in embryonic development, healing, and regeneration. Methods With the goal of analyzing the changes in Vmem during cell proliferation and differentiation, here we used direct current electrical stimulation (EStim) to promote cell proliferation and differentiation and simultaneously tracked the corresponding changes in Vmem in adipose derived mesenchymal stem cells (AT-MSC). Results We found that EStim caused increased AT-MSC proliferation that corresponded to Vmem depolarization and increased osteogenic differentiation that corresponded to Vmem hyperpolarization. Taken together, this shows that Vmem changes associated with EStim induced cell proliferation and differentiation can be accurately tracked during these important cell functions. Using this tool to monitor Vmem changes associated with these important cell behaviors we hope to learn more about how these electrochemical cues regulate cell function with the ultimate goal of developing new EStim based treatments capable of controlling healing and regeneration.
bibliographic citation: Bhavsar et al. (2019) Membrane potential (Vmem) measurements during mesenchymal stem cell (MSC) proliferation and osteogenic differentiation. PeerJ 7:e6341 https://doi.org/10.7717/peerj.6341
date submitted: 2018-10-24
date accepted: 2018-12-22
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bhavsar
  given name: Mit Balvantray
author list: Agent
  family name: Cato
  given name: Gloria
author list: Agent
  family name: Hauschild
  given name: Alexander
author list: Agent
  family name: Leppik
  given name: Liudmila
author list: Agent
  family name: Costa Oliveira
  given name: Karla Mychellyne
author list: Agent
  family name: Eischen-Loges
  given name: Maria José
author list: Agent
  family name: Barker
  given name: John Howard
doi: 10.7717/peerj.6341
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Bhavsar et al.
attribution name: Bhavsar et al.

Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4
type: item
type: AcademicArticle
description: The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
format: application/pdf
format: text/html
creator: Han Ming Gan
creator: Melvin V.L. Lee
creator: Michael A. Savka
subject: Agricultural Science
subject: Genomics
subject: Microbiology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6366
publisher: PeerJ Inc.
rights: © 2019 Gan et al.
abstract: The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
bibliographic citation: Gan et al. (2019) Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4. PeerJ 7:e6366 https://doi.org/10.7717/peerj.6366
date submitted: 2018-10-23
date accepted: 2018-12-20
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gan
  given name: Han Ming
author list: Agent
  family name: Lee
  given name: Melvin V.L.
author list: Agent
  family name: Savka
  given name: Michael A.
doi: 10.7717/peerj.6366
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Gan et al.
attribution name: Gan et al.

Positive association between epiphytes and competitiveness of the brown algal genus Lobophora against corals
type: item
type: AcademicArticle
description: Observations of coral–algal competition can provide valuable information about the state of coral reef ecosystems. Here, we report contact rates and apparent competition states for six shallow lagoonal reefs in Fiji. A total of 81.4% of examined coral perimeters were found to be in contact with algae, with turf algae (54.7%) and macroalgae of the genus Lobophora (16.8%) representing the most frequently observed contacts. Turf algae competitiveness was low, with 21.8% of coral–turf contacts being won by the algae (i.e. overgrowth or bleaching of coral tissue). In contrast, Lobophora competitiveness against corals was high, with 62.5% of contacts being won by the alga. The presence of epiphytic algae on Lobophora was associated with significantly greater algal competitiveness against corals, with 75.8% and 21.1% of interactions recorded as algal wins in the presence and absence of epiphytes, respectively. Sedimentation rate, herbivorous fish biomass, and coral colony size did not have a significant effect on Lobophora–coral interactions. This research indicates a novel and important role of epiphytes in driving the outcome of coral–algal contacts.
format: application/pdf
format: text/html
creator: Andreas Eich
creator: Amanda K. Ford
creator: Maggy M. Nugues
creator: Ryan S. McAndrews
creator: Christian Wild
creator: Sebastian C.A. Ferse
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6380
publisher: PeerJ Inc.
rights: © 2019 Eich et al.
abstract: Observations of coral–algal competition can provide valuable information about the state of coral reef ecosystems. Here, we report contact rates and apparent competition states for six shallow lagoonal reefs in Fiji. A total of 81.4% of examined coral perimeters were found to be in contact with algae, with turf algae (54.7%) and macroalgae of the genus Lobophora (16.8%) representing the most frequently observed contacts. Turf algae competitiveness was low, with 21.8% of coral–turf contacts being won by the algae (i.e. overgrowth or bleaching of coral tissue). In contrast, Lobophora competitiveness against corals was high, with 62.5% of contacts being won by the alga. The presence of epiphytic algae on Lobophora was associated with significantly greater algal competitiveness against corals, with 75.8% and 21.1% of interactions recorded as algal wins in the presence and absence of epiphytes, respectively. Sedimentation rate, herbivorous fish biomass, and coral colony size did not have a significant effect on Lobophora–coral interactions. This research indicates a novel and important role of epiphytes in driving the outcome of coral–algal contacts.
bibliographic citation: Eich et al. (2019) Positive association between epiphytes and competitiveness of the brown algal genus Lobophora against corals. PeerJ 7:e6380 https://doi.org/10.7717/peerj.6380
date submitted: 2018-06-15
date accepted: 2018-12-28
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eich
  given name: Andreas
author list: Agent
  family name: Ford
  given name: Amanda K.
author list: Agent
  family name: Nugues
  given name: Maggy M.
author list: Agent
  family name: McAndrews
  given name: Ryan S.
author list: Agent
  family name: Wild
  given name: Christian
author list: Agent
  family name: Ferse
  given name: Sebastian C.A.
doi: 10.7717/peerj.6380
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Eich et al.
attribution name: Eich et al.

Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean
type: item
type: AcademicArticle
description: Background Understanding the role of communities of arbuscular mycorrhizal fungi (AMF) in agricultural systems is imperative for enhancing crop production. The key variables influencing change in AMF communities are the type of cover crop species or the type of subsequent host crop species. However, how maize and soybean performance is related to the diversity of AMF communities in cover cropping systems remains unclear. We therefore investigated which cover cropping or host identity is the most important factor in shaping AMF community structure in subsequent crop roots using an Illumina Miseq platform amplicon sequencing. Methods In this study, we established three cover crop systems (Italian ryegrass, hairy vetch, and brown mustard) or bare fallow prior to planting maize and soybean as cash crops. After cover cropping, we divided the cover crop experimental plots into two subsequent crop plots (maize and soybean) to understand which cover cropping or host crop identity is an important factor for determining the AMF communities and diversity both in maize and soybeans. Results We found that most of the operational taxonomic units (OTUs) in root samples were common in both maize and soybean, and the proportion of common generalists in this experiment for maize and soybean roots was 79.5% according to the multinomial species classification method (CLAM test). The proportion of OTUs specifically detected in only maize and soybean was 9.6% and 10.8%, respectively. Additionally, the cover cropping noticeably altered the AMF community structure in the maize and soybean roots. However, the differentiation of AMF communities between maize and soybean was not significantly different. Discussion Our results suggest cover cropping prior to planting maize and soybean may be a strong factor for shaping AMF community structure in subsequent maize and soybean roots rather than two host crop identities. Additionally, we could not determine the suitable rotational combination for …
format: application/pdf
format: text/html
creator: Masao Higo
creator: Yuya Tatewaki
creator: Kento Gunji
creator: Akari Kaseda
creator: Katsunori Isobe
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.6403
publisher: PeerJ Inc.
rights: © 2019 Higo et al.
abstract: Background Understanding the role of communities of arbuscular mycorrhizal fungi (AMF) in agricultural systems is imperative for enhancing crop production. The key variables influencing change in AMF communities are the type of cover crop species or the type of subsequent host crop species. However, how maize and soybean performance is related to the diversity of AMF communities in cover cropping systems remains unclear. We therefore investigated which cover cropping or host identity is the most important factor in shaping AMF community structure in subsequent crop roots using an Illumina Miseq platform amplicon sequencing. Methods In this study, we established three cover crop systems (Italian ryegrass, hairy vetch, and brown mustard) or bare fallow prior to planting maize and soybean as cash crops. After cover cropping, we divided the cover crop experimental plots into two subsequent crop plots (maize and soybean) to understand which cover cropping or host crop identity is an important factor for determining the AMF communities and diversity both in maize and soybeans. Results We found that most of the operational taxonomic units (OTUs) in root samples were common in both maize and soybean, and the proportion of common generalists in this experiment for maize and soybean roots was 79.5% according to the multinomial species classification method (CLAM test). The proportion of OTUs specifically detected in only maize and soybean was 9.6% and 10.8%, respectively. Additionally, the cover cropping noticeably altered the AMF community structure in the maize and soybean roots. However, the differentiation of AMF communities between maize and soybean was not significantly different. Discussion Our results suggest cover cropping prior to planting maize and soybean may be a strong factor for shaping AMF community structure in subsequent maize and soybean roots rather than two host crop identities. Additionally, we could not determine the suitable rotational combination for …
bibliographic citation: Higo et al. (2019) Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean. PeerJ 7:e6403 https://doi.org/10.7717/peerj.6403
date submitted: 2018-08-24
date accepted: 2019-01-07
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Higo
  given name: Masao
author list: Agent
  family name: Tatewaki
  given name: Yuya
author list: Agent
  family name: Gunji
  given name: Kento
author list: Agent
  family name: Kaseda
  given name: Akari
author list: Agent
  family name: Isobe
  given name: Katsunori
doi: 10.7717/peerj.6403
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Higo et al.
attribution name: Higo et al.

Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies
type: item
type: AcademicArticle
description: Sugarcane-soybean intercropping has been widely used to control disease and improve nutrition in the field. However, the response of the soil microbial community diversity and structure to intercropping is not well understood. Since microbial diversity corresponds to soil quality and plant health, a pot experiment was conducted with sugarcane intercropped with soybean. Rhizosphere soil was collected 40 days after sowing, and MiSeq sequencing was utilized to analyze the soil microbial community diversity and composition. Soil columns were used to assess the influence of intercropping on soil microbial activity (soil respiration and carbon-use efficiency: nitrogen-use efficiency ratio). PICRUSt and FUNGuild analysis were conducted to predict microbial functional profiling. Our results showed that intercropping decreased pH by approximately 8.9% and enhanced the soil organic carbon, dissolved organic carbon, and available nitrogen (N) by 5.5%, 13.4%, and 10.0%, respectively. These changes in physicochemical properties corresponded to increased microbial diversity and shifts in soil microbial communities. Microbial community correlated significantly (p < 0.05) with soil respiration rates and nutrient use efficiency. Furthermore, intercropping influenced microbial functions, such as carbon fixation pathways in prokaryotes, citrate cycle (TCA cycle) of bacteria and wood saprotrophs of fungi. These overrepresented functions might accelerate nutrient conversion and control phytopathogens in soil.
format: application/pdf
format: text/html
creator: Tengxiang Lian
creator: Yinghui Mu
creator: Jian Jin
creator: Qibin Ma
creator: Yanbo Cheng
creator: Zhandong Cai
creator: Hai Nian
subject: Agricultural Science
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.6412
publisher: PeerJ Inc.
rights: © 2019 Lian et al.
abstract: Sugarcane-soybean intercropping has been widely used to control disease and improve nutrition in the field. However, the response of the soil microbial community diversity and structure to intercropping is not well understood. Since microbial diversity corresponds to soil quality and plant health, a pot experiment was conducted with sugarcane intercropped with soybean. Rhizosphere soil was collected 40 days after sowing, and MiSeq sequencing was utilized to analyze the soil microbial community diversity and composition. Soil columns were used to assess the influence of intercropping on soil microbial activity (soil respiration and carbon-use efficiency: nitrogen-use efficiency ratio). PICRUSt and FUNGuild analysis were conducted to predict microbial functional profiling. Our results showed that intercropping decreased pH by approximately 8.9% and enhanced the soil organic carbon, dissolved organic carbon, and available nitrogen (N) by 5.5%, 13.4%, and 10.0%, respectively. These changes in physicochemical properties corresponded to increased microbial diversity and shifts in soil microbial communities. Microbial community correlated significantly (p < 0.05) with soil respiration rates and nutrient use efficiency. Furthermore, intercropping influenced microbial functions, such as carbon fixation pathways in prokaryotes, citrate cycle (TCA cycle) of bacteria and wood saprotrophs of fungi. These overrepresented functions might accelerate nutrient conversion and control phytopathogens in soil.
bibliographic citation: Lian et al. (2019) Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies. PeerJ 7:e6412 https://doi.org/10.7717/peerj.6412
date submitted: 2018-08-02
date accepted: 2018-12-31
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lian
  given name: Tengxiang
author list: Agent
  family name: Mu
  given name: Yinghui
author list: Agent
  family name: Jin
  given name: Jian
author list: Agent
  family name: Ma
  given name: Qibin
author list: Agent
  family name: Cheng
  given name: Yanbo
author list: Agent
  family name: Cai
  given name: Zhandong
author list: Agent
  family name: Nian
  given name: Hai
doi: 10.7717/peerj.6412
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Lian et al.
attribution name: Lian et al.

Synthesis of silver nanoparticles using a modified Tollens’ method in conjunction with phytochemicals and assessment of their antimicrobial activity
type: item
type: AcademicArticle
description: Background Silver nanoparticles (AgNPs) have attracted great attention due to their outstanding electrical, optical, magnetic, catalytic, and antimicrobial properties. However, there is a need for alternative production methods that use less toxic precursors and reduce their undesirable by-products. Phyto-extracts from the leaves of olive and rosemary plants can be used as reducing agents and (in conjunction with Tollens’ reagent) can even enhance AgNP antimicrobial activity. Methods Conditions for the proposed hybrid synthesis method were optimized for olive leaf extracts (OLEs) and rosemary leaf extracts (RLEs). The resultant AgNPs were characterized using UV–visible spectroscopy, an environmental scanning electron microscope, and Dynamic Light Scattering analysis. An atomic absorption spectrophotometer was used to measure AgNP concentration. Fourier transform infrared spectroscopy (FTIR) was used to determine the specific functional groups responsible for the reduction of both silver nitrate and capping agents in the leaf extract. Additionally, the antimicrobial properties of the synthesized AgNPs were assessed against Gram-negative bacteria (Escherichia coli and Salmonella enterica) and Gram-positive bacteria (Staphylococcus aureus), by using both the Kirby–Bauer and broth microdilution methods on Mueller–Hinton (MH) agar plates. Results and Discussion A simple, feasible, and rapid method has been successfully developed for silver nanoparticle synthesis by reducing Tollens’ reagent using leaf extracts from olive and rosemary plants (widely available in Jordan). Scanning electron microscopy images showed that the method produces AgNPs with a spherical shape and average core sizes of 45 ± 2 and 38 ± 3 nm for OLE and RLE, respectively. A negative zeta potential (ζ) of −43.15 ± 3.65 mV for OLE-AgNPs and −33.65 ± 2.88mV for RLE-AgNPs proved the stability of silver nanoparticles. FTIR spectra for AgNPs and leaf extracts indicated that the compounds present in the leaf…
format: application/pdf
format: text/html
creator: Muna A. AbuDalo
creator: Ismaeel R. Al-Mheidat
creator: Alham W. Al-Shurafat
creator: Colleen Grinham
creator: Vinka Oyanedel-Craver
subject: Microbiology
subject: Green Chemistry
description: doi:10.7717/peerj.6413
publisher: PeerJ Inc.
rights: © 2019 AbuDalo et al.
abstract: Background Silver nanoparticles (AgNPs) have attracted great attention due to their outstanding electrical, optical, magnetic, catalytic, and antimicrobial properties. However, there is a need for alternative production methods that use less toxic precursors and reduce their undesirable by-products. Phyto-extracts from the leaves of olive and rosemary plants can be used as reducing agents and (in conjunction with Tollens’ reagent) can even enhance AgNP antimicrobial activity. Methods Conditions for the proposed hybrid synthesis method were optimized for olive leaf extracts (OLEs) and rosemary leaf extracts (RLEs). The resultant AgNPs were characterized using UV–visible spectroscopy, an environmental scanning electron microscope, and Dynamic Light Scattering analysis. An atomic absorption spectrophotometer was used to measure AgNP concentration. Fourier transform infrared spectroscopy (FTIR) was used to determine the specific functional groups responsible for the reduction of both silver nitrate and capping agents in the leaf extract. Additionally, the antimicrobial properties of the synthesized AgNPs were assessed against Gram-negative bacteria (Escherichia coli and Salmonella enterica) and Gram-positive bacteria (Staphylococcus aureus), by using both the Kirby–Bauer and broth microdilution methods on Mueller–Hinton (MH) agar plates. Results and Discussion A simple, feasible, and rapid method has been successfully developed for silver nanoparticle synthesis by reducing Tollens’ reagent using leaf extracts from olive and rosemary plants (widely available in Jordan). Scanning electron microscopy images showed that the method produces AgNPs with a spherical shape and average core sizes of 45 ± 2 and 38 ± 3 nm for OLE and RLE, respectively. A negative zeta potential (ζ) of −43.15 ± 3.65 mV for OLE-AgNPs and −33.65 ± 2.88mV for RLE-AgNPs proved the stability of silver nanoparticles. FTIR spectra for AgNPs and leaf extracts indicated that the compounds present in the leaf…
bibliographic citation: AbuDalo et al. (2019) Synthesis of silver nanoparticles using a modified Tollens’ method in conjunction with phytochemicals and assessment of their antimicrobial activity. PeerJ 7:e6413 https://doi.org/10.7717/peerj.6413
date submitted: 2017-12-24
date accepted: 2018-12-30
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: AbuDalo
  given name: Muna A.
author list: Agent
  family name: Al-Mheidat
  given name: Ismaeel R.
author list: Agent
  family name: Al-Shurafat
  given name: Alham W.
author list: Agent
  family name: Grinham
  given name: Colleen
author list: Agent
  family name: Oyanedel-Craver
  given name: Vinka
doi: 10.7717/peerj.6413
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 AbuDalo et al.
attribution name: AbuDalo et al.

Predictors of foot care behaviours in patients with diabetes in Turkey
type: item
type: AcademicArticle
description: Background The management of diabetic foot complications is challenging, time-consuming and costly. Such complications frequently recur, and the feet of individuals with diabetes can be easily infected. The variables that predict foot care behaviours must be identified to improve foot care attitudes and behaviours. Thus, this study aimed to evaluate the predictors of foot care behaviours in individuals with diabetes and the role of these variables. Methods This descriptive and analytic study was carried out between July 2015 and July 2016, and 368 outpatients with diabetes from a public hospital in Turkey were included. The participants had no communication, psychiatric or neurological problems and had been diagnosed with diabetes for at least 1 year. Foot care behaviour was the dependent variable and was evaluated with the foot care behaviour questionnaire. The relationship among foot care behaviours and sociodemographic characteristics, diabetes-related attitudes, disease perception, health beliefs and perceived social support was evaluated. Factors that independently predicted effective foot care behaviours were estimated via a linear regression analysis. Results The foot care behaviour score of the participants was above average (54.8 ± 5.0). Gender (t = −2.38, p = 0.018), history of a foot wound (t = −2.74, p = 0.006), nephropathy (t = 3.13, p = 0.002), duration subscale of the illness perception scores (t = 2.26, p = 0.024) and personal control subscale of the health belief scores (t = −2.07, p = 0.038) were significant predictors of foot care behaviours. These variables, which provided model compatibility, accounted for approximately 22.0% of the total variance of the foot care behaviour score (R = 0.47, R2 = 0.22, F = 5.48, p ≤ 0.001). Discussion Our results show factors that may affect diabetic foot care behaviours. Several of these factors prevent individuals from practising these behaviours. Further studies on the roles of barriers as predictors of foot c…
format: application/pdf
format: text/html
creator: Yasemin Yıldırım Usta
creator: Yurdanur Dikmen
creator: Songül Yorgun
creator: İkbal Berdo
subject: Diabetes and Endocrinology
subject: Nursing
description: doi:10.7717/peerj.6416
publisher: PeerJ Inc.
rights: © 2019 Yıldırım Usta et al.
abstract: Background The management of diabetic foot complications is challenging, time-consuming and costly. Such complications frequently recur, and the feet of individuals with diabetes can be easily infected. The variables that predict foot care behaviours must be identified to improve foot care attitudes and behaviours. Thus, this study aimed to evaluate the predictors of foot care behaviours in individuals with diabetes and the role of these variables. Methods This descriptive and analytic study was carried out between July 2015 and July 2016, and 368 outpatients with diabetes from a public hospital in Turkey were included. The participants had no communication, psychiatric or neurological problems and had been diagnosed with diabetes for at least 1 year. Foot care behaviour was the dependent variable and was evaluated with the foot care behaviour questionnaire. The relationship among foot care behaviours and sociodemographic characteristics, diabetes-related attitudes, disease perception, health beliefs and perceived social support was evaluated. Factors that independently predicted effective foot care behaviours were estimated via a linear regression analysis. Results The foot care behaviour score of the participants was above average (54.8 ± 5.0). Gender (t = −2.38, p = 0.018), history of a foot wound (t = −2.74, p = 0.006), nephropathy (t = 3.13, p = 0.002), duration subscale of the illness perception scores (t = 2.26, p = 0.024) and personal control subscale of the health belief scores (t = −2.07, p = 0.038) were significant predictors of foot care behaviours. These variables, which provided model compatibility, accounted for approximately 22.0% of the total variance of the foot care behaviour score (R = 0.47, R2 = 0.22, F = 5.48, p ≤ 0.001). Discussion Our results show factors that may affect diabetic foot care behaviours. Several of these factors prevent individuals from practising these behaviours. Further studies on the roles of barriers as predictors of foot c…
bibliographic citation: Yıldırım Usta et al. (2019) Predictors of foot care behaviours in patients with diabetes in Turkey. PeerJ 7:e6416 https://doi.org/10.7717/peerj.6416
date submitted: 2018-09-10
date accepted: 2019-01-09
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yıldırım Usta
  given name: Yasemin
author list: Agent
  family name: Dikmen
  given name: Yurdanur
author list: Agent
  family name: Yorgun
  given name: Songül
author list: Agent
  family name: Berdo
  given name: İkbal
doi: 10.7717/peerj.6416
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Yıldırım Usta et al.
attribution name: Yıldırım Usta et al.

The detailed distribution of T cell subpopulations in immune-stable renal allograft recipients: a single center study
type: item
type: AcademicArticle
description: Background Most renal allograft recipients reach a stable immune state (neither rejection nor infection) after transplantation. However, the detailed distribution of overall T lymphocyte subsets in the peripheral blood of these immune-stable renal transplant recipients remains unclear. We aim to identify differences between this stable immune state and a healthy immune state. Methods In total, 103 recipients underwent renal transplantation from 2012 to 2016 and received regular follow-up in our clinic. A total of 88 of these 103 recipients were enrolled in our study according to the inclusion and exclusion criteria. A total of 47 patients were 1 year post-transplantation, and 41 were 5 years post-transplantation. In addition, 41 healthy volunteers were recruited from our physical examination clinic. Detailed T cell subpopulations from the peripheral blood were assessed via flow cytometry. The parental frequency of each subset was calculated and compared among the diverse groups. Results The demographics and baseline characteristics of every group were analyzed. The frequency of total T cells (CD3+) was decreased in the renal allograft recipients. No difference in the variation of the CD4+, CD8+, and activated (HLA-DR+) T cell subsets was noted among the diverse groups. Regarding T cell receptor (TCR) markers, significant reductions were found in the proportion of γδ T cells and their Vδ2 subset in the renal allograft recipients. The proportions of both CD4+ and CD8+ programmed cell death protein (PD) 1+ T cell subsets were increased in the renal allograft recipients. The CD27+CD28+ T cell proportions in both the CD4+ and CD8+ populations were significantly decreased in the allograft recipients, but the opposite results were found for both CD4+ and CD8+ CD27-CD28- T cells. An increased percentage of CD4+ effector memory T cells and a declined fraction of CD8+ central memory T cells were found in the renal allograft recipients. Conclusion Limited differences in genera…
format: application/pdf
format: text/html
creator: Quan Zhuang
creator: Bo Peng
creator: Wei Wei
creator: Hang Gong
creator: Meng Yu
creator: Min Yang
creator: Lian Liu
creator: Yingzi Ming
subject: Immunology
subject: Urology
description: doi:10.7717/peerj.6417
publisher: PeerJ Inc.
rights: © 2019 Zhuang et al.
abstract: Background Most renal allograft recipients reach a stable immune state (neither rejection nor infection) after transplantation. However, the detailed distribution of overall T lymphocyte subsets in the peripheral blood of these immune-stable renal transplant recipients remains unclear. We aim to identify differences between this stable immune state and a healthy immune state. Methods In total, 103 recipients underwent renal transplantation from 2012 to 2016 and received regular follow-up in our clinic. A total of 88 of these 103 recipients were enrolled in our study according to the inclusion and exclusion criteria. A total of 47 patients were 1 year post-transplantation, and 41 were 5 years post-transplantation. In addition, 41 healthy volunteers were recruited from our physical examination clinic. Detailed T cell subpopulations from the peripheral blood were assessed via flow cytometry. The parental frequency of each subset was calculated and compared among the diverse groups. Results The demographics and baseline characteristics of every group were analyzed. The frequency of total T cells (CD3+) was decreased in the renal allograft recipients. No difference in the variation of the CD4+, CD8+, and activated (HLA-DR+) T cell subsets was noted among the diverse groups. Regarding T cell receptor (TCR) markers, significant reductions were found in the proportion of γδ T cells and their Vδ2 subset in the renal allograft recipients. The proportions of both CD4+ and CD8+ programmed cell death protein (PD) 1+ T cell subsets were increased in the renal allograft recipients. The CD27+CD28+ T cell proportions in both the CD4+ and CD8+ populations were significantly decreased in the allograft recipients, but the opposite results were found for both CD4+ and CD8+ CD27-CD28- T cells. An increased percentage of CD4+ effector memory T cells and a declined fraction of CD8+ central memory T cells were found in the renal allograft recipients. Conclusion Limited differences in genera…
bibliographic citation: Zhuang et al. (2019) The detailed distribution of T cell subpopulations in immune-stable renal allograft recipients: a single center study. PeerJ 7:e6417 https://doi.org/10.7717/peerj.6417
date submitted: 2018-08-22
date accepted: 2019-01-09
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhuang
  given name: Quan
author list: Agent
  family name: Peng
  given name: Bo
author list: Agent
  family name: Wei
  given name: Wei
author list: Agent
  family name: Gong
  given name: Hang
author list: Agent
  family name: Yu
  given name: Meng
author list: Agent
  family name: Yang
  given name: Min
author list: Agent
  family name: Liu
  given name: Lian
author list: Agent
  family name: Ming
  given name: Yingzi
doi: 10.7717/peerj.6417
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Zhuang et al.
attribution name: Zhuang et al.

Molecular evidence for sex reversal in wild populations of green frogs (Rana clamitans)
type: item
type: AcademicArticle
description: In vertebrates, sex determination occurs along a continuum from strictly genotypic (GSD), where sex is entirely guided by genes, to strictly environmental (ESD), where rearing conditions, like temperature, determine phenotypic sex. Along this continuum are taxa which have combined genetic and environmental contributions to sex determination (GSD + EE), where some individuals experience environmental effects which cause them to sex reverse and develop their phenotypic sex opposite their genotypic sex. Amphibians are often assumed to be strictly GSD with sex reversal typically considered abnormal. Despite calls to understand the relative natural and anthropogenic causes of amphibian sex reversal, sex reversal has not been closely studied across populations of any wild amphibian, particularly in contrasting environmental conditions. Here, we use sex-linked molecular markers to discover sex reversal in wild populations of green frogs (Rana clamitans) inhabiting ponds in either undeveloped, forested landscapes or in suburban neighborhoods. Our work here begins to suggest that sex reversal may be common within and across green frog populations, occurring in 12 of 16 populations and with frequencies of 2–16% of individuals sampled within populations. Additionally, our results also suggest that intersex phenotypic males and sex reversal are not correlated with each other and are also not correlated with suburban land use. While sex reversal and intersex are often considered aberrant responses to human activities and associated pollution, we found no such associations here. Our data perhaps begin to suggest that, relative to what is often suggested, sex reversal may be a relatively natural process in amphibians. Future research should focus on assessing interactions between genes and the environment to understand the molecular and exogenous basis of sex determination in green frogs and in other amphibians.
format: application/pdf
format: text/html
creator: Max R. Lambert
creator: Tien Tran
creator: Andrzej Kilian
creator: Tariq Ezaz
creator: David K. Skelly
subject: Conservation Biology
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
subject: Ecotoxicology
description: doi:10.7717/peerj.6449
publisher: PeerJ Inc.
rights: © 2019 Lambert et al.
abstract: In vertebrates, sex determination occurs along a continuum from strictly genotypic (GSD), where sex is entirely guided by genes, to strictly environmental (ESD), where rearing conditions, like temperature, determine phenotypic sex. Along this continuum are taxa which have combined genetic and environmental contributions to sex determination (GSD + EE), where some individuals experience environmental effects which cause them to sex reverse and develop their phenotypic sex opposite their genotypic sex. Amphibians are often assumed to be strictly GSD with sex reversal typically considered abnormal. Despite calls to understand the relative natural and anthropogenic causes of amphibian sex reversal, sex reversal has not been closely studied across populations of any wild amphibian, particularly in contrasting environmental conditions. Here, we use sex-linked molecular markers to discover sex reversal in wild populations of green frogs (Rana clamitans) inhabiting ponds in either undeveloped, forested landscapes or in suburban neighborhoods. Our work here begins to suggest that sex reversal may be common within and across green frog populations, occurring in 12 of 16 populations and with frequencies of 2–16% of individuals sampled within populations. Additionally, our results also suggest that intersex phenotypic males and sex reversal are not correlated with each other and are also not correlated with suburban land use. While sex reversal and intersex are often considered aberrant responses to human activities and associated pollution, we found no such associations here. Our data perhaps begin to suggest that, relative to what is often suggested, sex reversal may be a relatively natural process in amphibians. Future research should focus on assessing interactions between genes and the environment to understand the molecular and exogenous basis of sex determination in green frogs and in other amphibians.
bibliographic citation: Lambert et al. (2019) Molecular evidence for sex reversal in wild populations of green frogs (Rana clamitans). PeerJ 7:e6449 https://doi.org/10.7717/peerj.6449
date submitted: 2018-08-28
date accepted: 2019-01-15
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lambert
  given name: Max R.
author list: Agent
  family name: Tran
  given name: Tien
author list: Agent
  family name: Kilian
  given name: Andrzej
author list: Agent
  family name: Ezaz
  given name: Tariq
author list: Agent
  family name: Skelly
  given name: David K.
doi: 10.7717/peerj.6449
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Lambert et al.
attribution name: Lambert et al.

Tamilokus mabinia, a new, anatomically divergent genus and species of wood-boring bivalve from the Philippines
type: item
type: AcademicArticle
description: Here we describe an anatomically divergent wood-boring bivalve belonging to the family Teredinidae. Specimens were collected off the coast of Mabini, Batangas, Philippines, in February 2018, from sunken driftwood at a depth of less than 2 m. A combination of characteristics differentiates these specimens from members of previously named teredinid genera and species. Most notable among these include: an enlarged cephalic hood which extends across the posterior slope of the shell valves and integrates into the posterior adductor muscle; a unique structure, which we term the ‘cephalic collar’, formed by protruding folds of the mantle immediately ventral to the foot and extending past the posterior margin of the valves; a large globular stomach located entirely posterior to the posterior adductor muscle and extending substantially beyond the posterior gape of the valves; an elongate crystalline style and style sac extending from the base of the foot, past the posterior adductor muscle, to the posteriorly located stomach; calcareous pallets distinct from those of described genera; a prominently flared mantle collar which extends midway along the stalk of the pallets; and, separated siphons that bear a pigmented pinstripe pattern with highly elaborate compound papillae on the incurrent siphon aperture. We used Micro-Computed Tomography (Micro-CT) to build a virtual 3D anatomical model of this organism, confirming the spatial arrangement of the structures described above. Phylogenetic analysis of the small (18S) and large (28S) nuclear rRNA gene sequences, place this bivalve within the Teredindae on a branch well differentiated from previously named genera and species. We propose the new genus and species Tamilokus mabinia to accommodate these organisms, raising the total number of genera in this economically and environmentally important family to 17. This study demonstrates the efficacy of Micro-CT for anatomical description of a systematically challenging group of bival…
format: application/pdf
format: text/html
creator: J. Reuben Shipway
creator: Marvin A. Altamia
creator: Gary Rosenberg
creator: Gisela P. Concepcion
creator: Margo G. Haygood
creator: Daniel L. Distel
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6256
publisher: PeerJ Inc.
rights: © 2019 Shipway et al.
abstract: Here we describe an anatomically divergent wood-boring bivalve belonging to the family Teredinidae. Specimens were collected off the coast of Mabini, Batangas, Philippines, in February 2018, from sunken driftwood at a depth of less than 2 m. A combination of characteristics differentiates these specimens from members of previously named teredinid genera and species. Most notable among these include: an enlarged cephalic hood which extends across the posterior slope of the shell valves and integrates into the posterior adductor muscle; a unique structure, which we term the ‘cephalic collar’, formed by protruding folds of the mantle immediately ventral to the foot and extending past the posterior margin of the valves; a large globular stomach located entirely posterior to the posterior adductor muscle and extending substantially beyond the posterior gape of the valves; an elongate crystalline style and style sac extending from the base of the foot, past the posterior adductor muscle, to the posteriorly located stomach; calcareous pallets distinct from those of described genera; a prominently flared mantle collar which extends midway along the stalk of the pallets; and, separated siphons that bear a pigmented pinstripe pattern with highly elaborate compound papillae on the incurrent siphon aperture. We used Micro-Computed Tomography (Micro-CT) to build a virtual 3D anatomical model of this organism, confirming the spatial arrangement of the structures described above. Phylogenetic analysis of the small (18S) and large (28S) nuclear rRNA gene sequences, place this bivalve within the Teredindae on a branch well differentiated from previously named genera and species. We propose the new genus and species Tamilokus mabinia to accommodate these organisms, raising the total number of genera in this economically and environmentally important family to 17. This study demonstrates the efficacy of Micro-CT for anatomical description of a systematically challenging group of bival…
bibliographic citation: Shipway et al. (2019) Tamilokus mabinia, a new, anatomically divergent genus and species of wood-boring bivalve from the Philippines. PeerJ 7:e6256 https://doi.org/10.7717/peerj.6256
date submitted: 2018-08-15
date accepted: 2018-12-10
issued: 2019-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shipway
  given name: J. Reuben
author list: Agent
  family name: Altamia
  given name: Marvin A.
author list: Agent
  family name: Rosenberg
  given name: Gary
author list: Agent
  family name: Concepcion
  given name: Gisela P.
author list: Agent
  family name: Haygood
  given name: Margo G.
author list: Agent
  family name: Distel
  given name: Daniel L.
doi: 10.7717/peerj.6256
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-07
copyright: ©2019 Shipway et al.
attribution name: Shipway et al.

Co-expression of HIF-1α, MDR1 and LAPTM4B in peripheral blood of solid tumors
type: item
type: AcademicArticle
description: The hypoxic tumor microenvironment is the major contributor of chemotherapy resistance in solid tumors. One of the key regulators of hypoxic responses within the cell is the hypoxia inducible factor-1α (HIF-1α) that is involved in transcription of genes promoting cell survival and chemotherapy resistance. Multidrug resistance gene-1 (MDR1) and Lysosome-associated protein transmembrane 4B-35 (LAPTM4B-35) are among those notable players which augment their responses to cellular hypoxia. MDR1 is the hypoxia responsive gene involved in multidrug resistance phenotype while LAPTM4B-35 is involved in chemotherapy resistance by stabilizing HIF-1α and overexpressing MDR1. Overexpression of HIF-1α, MDR1 and LAPTM4B has been associated with poor disease outcome in many cancers when studied individually at tissue level. However, accessibility of the tissues following the course of chemotherapy for ascertaining chemotherapy resistance is difficult and sometimes not clinically feasible. Therefore, indication of hypoxic biomarkers in patient’s blood can significantly alter the clinical outcome. Hence there is a need to identify a blood based marker to understand the disease progression. In the current study the expression of hypoxia associated chemotherapy resistance genes were studied in the peripheral blood lymphocytes of solid tumor patients and any potential correlation with disease progression were explored. The expression of HIF-1α, MDR1 and LAPTM4B was studied in blood of 72 breast, 42 ovarian, 32 colon and 21 prostate cancer patients through real time PCR analysis using delta cycle threshold method. The statistical scrutiny was executed through Fisher’s Exact test and the Spearman correlation method. There was 12–13 fold increased in expression of HIF-1α, two fold increased in MDR1 and 13–14 fold increased in LAPTM4B mRNA level in peripheral blood of breast, ovarian, prostate and colon cancer patients. In the current study there was an association of HIF-1α, MDR1 and LAPTM…
format: application/pdf
format: text/html
creator: Zaira Rehman
creator: Ammad Fahim
creator: Attya Bhatti
creator: Hajra Sadia
creator: Peter John
subject: Biotechnology
subject: Oncology
description: doi:10.7717/peerj.6309
publisher: PeerJ Inc.
rights: © 2019 Rehman et al.
abstract: The hypoxic tumor microenvironment is the major contributor of chemotherapy resistance in solid tumors. One of the key regulators of hypoxic responses within the cell is the hypoxia inducible factor-1α (HIF-1α) that is involved in transcription of genes promoting cell survival and chemotherapy resistance. Multidrug resistance gene-1 (MDR1) and Lysosome-associated protein transmembrane 4B-35 (LAPTM4B-35) are among those notable players which augment their responses to cellular hypoxia. MDR1 is the hypoxia responsive gene involved in multidrug resistance phenotype while LAPTM4B-35 is involved in chemotherapy resistance by stabilizing HIF-1α and overexpressing MDR1. Overexpression of HIF-1α, MDR1 and LAPTM4B has been associated with poor disease outcome in many cancers when studied individually at tissue level. However, accessibility of the tissues following the course of chemotherapy for ascertaining chemotherapy resistance is difficult and sometimes not clinically feasible. Therefore, indication of hypoxic biomarkers in patient’s blood can significantly alter the clinical outcome. Hence there is a need to identify a blood based marker to understand the disease progression. In the current study the expression of hypoxia associated chemotherapy resistance genes were studied in the peripheral blood lymphocytes of solid tumor patients and any potential correlation with disease progression were explored. The expression of HIF-1α, MDR1 and LAPTM4B was studied in blood of 72 breast, 42 ovarian, 32 colon and 21 prostate cancer patients through real time PCR analysis using delta cycle threshold method. The statistical scrutiny was executed through Fisher’s Exact test and the Spearman correlation method. There was 12–13 fold increased in expression of HIF-1α, two fold increased in MDR1 and 13–14 fold increased in LAPTM4B mRNA level in peripheral blood of breast, ovarian, prostate and colon cancer patients. In the current study there was an association of HIF-1α, MDR1 and LAPTM…
bibliographic citation: Rehman et al. (2019) Co-expression of HIF-1α, MDR1 and LAPTM4B in peripheral blood of solid tumors. PeerJ 7:e6309 https://doi.org/10.7717/peerj.6309
date submitted: 2018-09-27
date accepted: 2018-12-19
issued: 2019-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rehman
  given name: Zaira
author list: Agent
  family name: Fahim
  given name: Ammad
author list: Agent
  family name: Bhatti
  given name: Attya
author list: Agent
  family name: Sadia
  given name: Hajra
author list: Agent
  family name: John
  given name: Peter
doi: 10.7717/peerj.6309
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-07
copyright: © 2019 Rehman et al.
attribution name: Rehman et al.

Splitting on categorical predictors in random forests
type: item
type: AcademicArticle
description: One reason for the widespread success of random forests (RFs) is their ability to analyze most datasets without preprocessing. For example, in contrast to many other statistical methods and machine learning approaches, no recoding such as dummy coding is required to handle ordinal and nominal predictors. The standard approach for nominal predictors is to consider all 2k − 1 − 1 2-partitions of the k predictor categories. However, this exponential relationship produces a large number of potential splits to be evaluated, increasing computational complexity and restricting the possible number of categories in most implementations. For binary classification and regression, it was shown that ordering the predictor categories in each split leads to exactly the same splits as the standard approach. This reduces computational complexity because only k − 1 splits have to be considered for a nominal predictor with k categories. For multiclass classification and survival prediction no ordering method producing equivalent splits exists. We therefore propose to use a heuristic which orders the categories according to the first principal component of the weighted covariance matrix in multiclass classification and by log-rank scores in survival prediction. This ordering of categories can be done either in every split or a priori, that is, just once before growing the forest. With this approach, the nominal predictor can be treated as ordinal in the entire RF procedure, speeding up the computation and avoiding category limits. We compare the proposed methods with the standard approach, dummy coding and simply ignoring the nominal nature of the predictors in several simulation settings and on real data in terms of prediction performance and computational efficiency. We show that ordering the categories a priori is at least as good as the standard approach of considering all 2-partitions in all datasets considered, while being computationally faster. We recommend to use this approach…
format: application/pdf
format: text/html
creator: Marvin N. Wright
creator: Inke R. König
subject: Statistics
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.6339
publisher: PeerJ Inc.
rights: © 2019 Wright et al.
abstract: One reason for the widespread success of random forests (RFs) is their ability to analyze most datasets without preprocessing. For example, in contrast to many other statistical methods and machine learning approaches, no recoding such as dummy coding is required to handle ordinal and nominal predictors. The standard approach for nominal predictors is to consider all 2k − 1 − 1 2-partitions of the k predictor categories. However, this exponential relationship produces a large number of potential splits to be evaluated, increasing computational complexity and restricting the possible number of categories in most implementations. For binary classification and regression, it was shown that ordering the predictor categories in each split leads to exactly the same splits as the standard approach. This reduces computational complexity because only k − 1 splits have to be considered for a nominal predictor with k categories. For multiclass classification and survival prediction no ordering method producing equivalent splits exists. We therefore propose to use a heuristic which orders the categories according to the first principal component of the weighted covariance matrix in multiclass classification and by log-rank scores in survival prediction. This ordering of categories can be done either in every split or a priori, that is, just once before growing the forest. With this approach, the nominal predictor can be treated as ordinal in the entire RF procedure, speeding up the computation and avoiding category limits. We compare the proposed methods with the standard approach, dummy coding and simply ignoring the nominal nature of the predictors in several simulation settings and on real data in terms of prediction performance and computational efficiency. We show that ordering the categories a priori is at least as good as the standard approach of considering all 2-partitions in all datasets considered, while being computationally faster. We recommend to use this approach…
bibliographic citation: Wright et al. (2019) Splitting on categorical predictors in random forests. PeerJ 7:e6339 https://doi.org/10.7717/peerj.6339
date submitted: 2018-06-26
date accepted: 2018-12-22
issued: 2019-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wright
  given name: Marvin N.
author list: Agent
  family name: König
  given name: Inke R.
doi: 10.7717/peerj.6339
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-07
copyright: © 2019 Wright et al.
attribution name: Wright et al.

Intrauterine growth and the maturation process of adrenal function
type: item
type: AcademicArticle
description: Backgrounds Environmental factors during early life alter the hypothalamus-pituitary-adrenal (HPA) axis regulation and increase the risk of diseases in later life. However, adrenal function at each developmental stage has not fully been investigated in relation to pathological antenatal conditions. Cortisol levels of newborns with intrauterine growth restriction (IUGR) are elevated during the neonatal period; however, when studied during early childhood, cortisol levels are reduced compared with their peers, suggesting that the HPA axis regulation might be altered from activation to suppression, the timing of which remains uncertain. Aim The aim of this study was to assess the presence of an interaction between intrauterine growth and postnatal age on cortisol levels in newborns hospitalised at a neonatal intensive care unit. Methods We performed a secondary analysis using a dataset from saliva samples of 62 newborns collected between 30 and 40 weeks corrected age. Interactions between postnatal age and clinical variables with regard to cortisol levels were assessed. Results The z-score of the birth weight and IUGR showed significant interactions with postnatal age on cortisol levels; cortisol levels were higher ≤5 days of birth and lower >14 days of birth than those in their peers without IUGR. Conclusion The adrenal function of newborns with IUGR might be altered from activation to suppression within the first several weeks of life. Longitudinal studies need to address when/how IUGR alters adrenal functions, and how these responses are associated with diseases during adulthood.
format: application/pdf
format: text/html
creator: Sachiko Iwata
creator: Masahiro Kinoshita
creator: Hisayoshi Okamura
creator: Kennosuke Tsuda
creator: Mamoru Saikusa
creator: Eimei Harada
creator: Shinji Saitoh
creator: Osuke Iwata
subject: Diabetes and Endocrinology
subject: Pediatrics
description: doi:10.7717/peerj.6368
publisher: PeerJ Inc.
rights: © 2019 Iwata et al.
abstract: Backgrounds Environmental factors during early life alter the hypothalamus-pituitary-adrenal (HPA) axis regulation and increase the risk of diseases in later life. However, adrenal function at each developmental stage has not fully been investigated in relation to pathological antenatal conditions. Cortisol levels of newborns with intrauterine growth restriction (IUGR) are elevated during the neonatal period; however, when studied during early childhood, cortisol levels are reduced compared with their peers, suggesting that the HPA axis regulation might be altered from activation to suppression, the timing of which remains uncertain. Aim The aim of this study was to assess the presence of an interaction between intrauterine growth and postnatal age on cortisol levels in newborns hospitalised at a neonatal intensive care unit. Methods We performed a secondary analysis using a dataset from saliva samples of 62 newborns collected between 30 and 40 weeks corrected age. Interactions between postnatal age and clinical variables with regard to cortisol levels were assessed. Results The z-score of the birth weight and IUGR showed significant interactions with postnatal age on cortisol levels; cortisol levels were higher ≤5 days of birth and lower >14 days of birth than those in their peers without IUGR. Conclusion The adrenal function of newborns with IUGR might be altered from activation to suppression within the first several weeks of life. Longitudinal studies need to address when/how IUGR alters adrenal functions, and how these responses are associated with diseases during adulthood.
bibliographic citation: Iwata et al. (2019) Intrauterine growth and the maturation process of adrenal function. PeerJ 7:e6368 https://doi.org/10.7717/peerj.6368
date submitted: 2018-08-27
date accepted: 2018-12-28
issued: 2019-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Iwata
  given name: Sachiko
author list: Agent
  family name: Kinoshita
  given name: Masahiro
author list: Agent
  family name: Okamura
  given name: Hisayoshi
author list: Agent
  family name: Tsuda
  given name: Kennosuke
author list: Agent
  family name: Saikusa
  given name: Mamoru
author list: Agent
  family name: Harada
  given name: Eimei
author list: Agent
  family name: Saitoh
  given name: Shinji
author list: Agent
  family name: Iwata
  given name: Osuke
doi: 10.7717/peerj.6368
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-07
copyright: © 2019 Iwata et al.
attribution name: Iwata et al.

Physical activity during pregnancy and its influence on delivery time: a randomized clinical trial
type: item
type: AcademicArticle
description: Introduction During pregnancy, women often change their lifestyle for fear of harmful effects on the child or themselves. In this respect, many women reduce the amount of physical exercise they take, despite its beneficial effects. Objective To determine the duration of labor in pregnant women who completed a program of moderate physical exercise in water and subsequently presented eutocic birth. Methods A randomized trial was performed with 140 healthy pregnant women, divided into an exercise group (EG) (n = 70) and a control group (CG) (n = 70). The women who composed the study population were recruited at 12 weeks of gestation. The intervention program, termed SWEP (Study of Water Exercise during Pregnancy) began in week 20 of gestation and ended in week 37. Perinatal outcomes were determined by examining the corresponding partographs, recorded by the Maternity Service at the Granada University Hospital Complex. Results The intervention phase of the study took place from June through October 2016, with the 120 women finally included in EG and CG (60 in each group). At term, 63% of the women in EG and 56% of those in CG had a eutocic birth. The average total duration of labor was 389.33 ± 216.18 min for the women in EG and 561.30 ± 199.94 min for those in CG, a difference of approximately three hours (p < 0.001). Conclusions The women who exercised in water during their pregnancy presented a shorter duration of labor than those who did not. The difference was especially marked with respect to the duration of the first and second stages of labor.
format: application/pdf
format: text/html
creator: Raquel Rodríguez-Blanque
creator: Juan Carlos Sánchez-García
creator: Antonio Manuel Sánchez-López
creator: María José Aguilar-Cordero
subject: Clinical Trials
subject: Gynecology and Obstetrics
subject: Kinesiology
subject: Nursing
subject: Women’s Health
description: doi:10.7717/peerj.6370
publisher: PeerJ Inc.
rights: © 2019 Rodríguez-Blanque et al.
abstract: Introduction During pregnancy, women often change their lifestyle for fear of harmful effects on the child or themselves. In this respect, many women reduce the amount of physical exercise they take, despite its beneficial effects. Objective To determine the duration of labor in pregnant women who completed a program of moderate physical exercise in water and subsequently presented eutocic birth. Methods A randomized trial was performed with 140 healthy pregnant women, divided into an exercise group (EG) (n = 70) and a control group (CG) (n = 70). The women who composed the study population were recruited at 12 weeks of gestation. The intervention program, termed SWEP (Study of Water Exercise during Pregnancy) began in week 20 of gestation and ended in week 37. Perinatal outcomes were determined by examining the corresponding partographs, recorded by the Maternity Service at the Granada University Hospital Complex. Results The intervention phase of the study took place from June through October 2016, with the 120 women finally included in EG and CG (60 in each group). At term, 63% of the women in EG and 56% of those in CG had a eutocic birth. The average total duration of labor was 389.33 ± 216.18 min for the women in EG and 561.30 ± 199.94 min for those in CG, a difference of approximately three hours (p < 0.001). Conclusions The women who exercised in water during their pregnancy presented a shorter duration of labor than those who did not. The difference was especially marked with respect to the duration of the first and second stages of labor.
bibliographic citation: Rodríguez-Blanque et al. (2019) Physical activity during pregnancy and its influence on delivery time: a randomized clinical trial. PeerJ 7:e6370 https://doi.org/10.7717/peerj.6370
date submitted: 2018-09-21
date accepted: 2018-12-31
issued: 2019-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rodríguez-Blanque
  given name: Raquel
author list: Agent
  family name: Sánchez-García
  given name: Juan Carlos
author list: Agent
  family name: Sánchez-López
  given name: Antonio Manuel
author list: Agent
  family name: Aguilar-Cordero
  given name: María José
doi: 10.7717/peerj.6370
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-07
copyright: ©2019 Rodríguez-Blanque et al.
attribution name: Rodríguez-Blanque et al.

Nursing knowledge of and attitude in cardiopulmonary arrest: cross-sectional survey analysis
type: item
type: AcademicArticle
description: Background Nurses are often the first to activate the chain of survival when a cardiorespiratory arrest happens. That is why it is crucial that they keep their knowledge and skills up-to-date and their attitudes to resuscitation are very important. The main aim of this study was to analyse whether the level of theoretical and practical understanding affected the attitudes of nursing staff. Methods A questionnaire was designed using the Delphi technique (three rounds). The questionnaire was adjusted and it was piloted on a test-retest basis with a convenience sample of 30 registered nurses. The psychometric characteristics were evaluated using a sample of 347 nurses using Cronbach’s alpha. Descriptive analysis was performed to describe the sociodemographic variables and Spearman’s correlation coefficient to assess the relationship between two scale variables. Pearson’s chi-squared test has been used to study the relationship between two categorical variables. Wilcoxon Mann Whitney test and the Kruskal–Wallis test were performed to establish relationships between the demographic/work related characteristics and the level of understanding. Results The Knowledge and Attitude of Nurses in the Event of a Cardiorespiratory Arrest (CAEPCR) questionnaire comprised three sections: sociodemographic information, theoretical and practical understanding, and attitudes of ethical issues. Cronbach’s alpha for the internal consistency of the attitudes questionnaire was 0.621. The knowledge that nurses self-reported with regard to cardiopulmonary arrest directly affected their attitudes. Their responses raised a number of bioethical issues. Conclusions CAEPCR questionnaire is the first one which successfully linked knowledge of cardiopulmonary resuscitation to the attitudes towards ethical issues Health policies should ensure that CPR training is mandatory for nurses and all healthcare workers, and this training should include the ethical aspects.
format: application/pdf
format: text/html
creator: Verónica Tíscar-González
creator: Joan Blanco-Blanco
creator: Montserrat Gea-Sánchez
creator: Ascensión Rodriguez Molinuevo
creator: Teresa Moreno-Casbas
subject: Cardiology
subject: Emergency and Critical Care
subject: Nursing
subject: Ethical Issues
description: doi:10.7717/peerj.6410
publisher: PeerJ Inc.
rights: © 2019 Tíscar-González et al.
abstract: Background Nurses are often the first to activate the chain of survival when a cardiorespiratory arrest happens. That is why it is crucial that they keep their knowledge and skills up-to-date and their attitudes to resuscitation are very important. The main aim of this study was to analyse whether the level of theoretical and practical understanding affected the attitudes of nursing staff. Methods A questionnaire was designed using the Delphi technique (three rounds). The questionnaire was adjusted and it was piloted on a test-retest basis with a convenience sample of 30 registered nurses. The psychometric characteristics were evaluated using a sample of 347 nurses using Cronbach’s alpha. Descriptive analysis was performed to describe the sociodemographic variables and Spearman’s correlation coefficient to assess the relationship between two scale variables. Pearson’s chi-squared test has been used to study the relationship between two categorical variables. Wilcoxon Mann Whitney test and the Kruskal–Wallis test were performed to establish relationships between the demographic/work related characteristics and the level of understanding. Results The Knowledge and Attitude of Nurses in the Event of a Cardiorespiratory Arrest (CAEPCR) questionnaire comprised three sections: sociodemographic information, theoretical and practical understanding, and attitudes of ethical issues. Cronbach’s alpha for the internal consistency of the attitudes questionnaire was 0.621. The knowledge that nurses self-reported with regard to cardiopulmonary arrest directly affected their attitudes. Their responses raised a number of bioethical issues. Conclusions CAEPCR questionnaire is the first one which successfully linked knowledge of cardiopulmonary resuscitation to the attitudes towards ethical issues Health policies should ensure that CPR training is mandatory for nurses and all healthcare workers, and this training should include the ethical aspects.
bibliographic citation: Tíscar-González et al. (2019) Nursing knowledge of and attitude in cardiopulmonary arrest: cross-sectional survey analysis. PeerJ 7:e6410 https://doi.org/10.7717/peerj.6410
date submitted: 2018-08-22
date accepted: 2019-01-07
issued: 2019-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tíscar-González
  given name: Verónica
author list: Agent
  family name: Blanco-Blanco
  given name: Joan
author list: Agent
  family name: Gea-Sánchez
  given name: Montserrat
author list: Agent
  family name: Rodriguez Molinuevo
  given name: Ascensión
author list: Agent
  family name: Moreno-Casbas
  given name: Teresa
doi: 10.7717/peerj.6410
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-07
copyright: ©2019 Tíscar-González et al.
attribution name: Tíscar-González et al.

Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure
type: item
type: AcademicArticle
description: NAD glycohydrolase (EC 3.2.2.5) (NADase) sequences have been identified in 10 elapid and crotalid venom gland transcriptomes, eight of which are complete. These sequences show very high homology, but elapid and crotalid sequences also display consistent differences. As in Aplysia kurodai ADP-ribosyl cyclase and vertebrate CD38 genes, snake venom NADase genes comprise eight exons; however, in the Protobothrops mucrosquamatus genome, the sixth exon is sometimes not transcribed, yielding a shortened NADase mRNA that encodes all six disulfide bonds, but an active site that lacks the catalytic glutamate residue. The function of this shortened protein, if expressed, is unknown. While many vertebrate CD38s are multifunctional, liberating both ADP-ribose and small quantities of cyclic ADP-ribose (cADPR), snake venom CD38 homologs are dedicated NADases. They possess the invariant TLEDTL sequence (residues 144–149) that bounds the active site and the catalytic residue, Glu228. In addition, they possess a disulfide bond (Cys121–Cys202) that specifically prevents ADP-ribosyl cyclase activity in combination with Ile224, in lieu of phenylalanine, which is requisite for ADPR cyclases. In concert with venom phosphodiesterase and 5′-nucleotidase and their ecto-enzyme homologs in prey tissues, snake venom NADases comprise part of an envenomation strategy to liberate purine nucleosides, and particularly adenosine, in the prey, promoting prey immobilization via hypotension and paralysis.
format: application/pdf
format: text/html
creator: Ivan Koludarov
creator: Steven D. Aird
subject: Biochemistry
subject: Genomics
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.6154
publisher: PeerJ Inc.
rights: © 2019 Koludarov and Aird
abstract: NAD glycohydrolase (EC 3.2.2.5) (NADase) sequences have been identified in 10 elapid and crotalid venom gland transcriptomes, eight of which are complete. These sequences show very high homology, but elapid and crotalid sequences also display consistent differences. As in Aplysia kurodai ADP-ribosyl cyclase and vertebrate CD38 genes, snake venom NADase genes comprise eight exons; however, in the Protobothrops mucrosquamatus genome, the sixth exon is sometimes not transcribed, yielding a shortened NADase mRNA that encodes all six disulfide bonds, but an active site that lacks the catalytic glutamate residue. The function of this shortened protein, if expressed, is unknown. While many vertebrate CD38s are multifunctional, liberating both ADP-ribose and small quantities of cyclic ADP-ribose (cADPR), snake venom CD38 homologs are dedicated NADases. They possess the invariant TLEDTL sequence (residues 144–149) that bounds the active site and the catalytic residue, Glu228. In addition, they possess a disulfide bond (Cys121–Cys202) that specifically prevents ADP-ribosyl cyclase activity in combination with Ile224, in lieu of phenylalanine, which is requisite for ADPR cyclases. In concert with venom phosphodiesterase and 5′-nucleotidase and their ecto-enzyme homologs in prey tissues, snake venom NADases comprise part of an envenomation strategy to liberate purine nucleosides, and particularly adenosine, in the prey, promoting prey immobilization via hypotension and paralysis.
bibliographic citation: Koludarov et al. (2019) Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure. PeerJ 7:e6154 https://doi.org/10.7717/peerj.6154
date submitted: 2018-09-26
date accepted: 2018-11-25
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koludarov
  given name: Ivan
author list: Agent
  family name: Aird
  given name: Steven D.
doi: 10.7717/peerj.6154
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Koludarov and Aird
attribution name: Koludarov and Aird

A survey on zoo mortality over a 12-year period in Italy
type: item
type: AcademicArticle
description: Background The zoo is a unique environment in which to study animals. Zoos have a long history of research into aspects of animal biology, even if this was not the primary purpose for which they were established. The data collected from zoo animals can have a great biological relevance and it can tell us more about what these animals are like outside the captive environment. In order to ensure the health of all captive animals, it is important to perform a post-mortem examination on all the animals that die in captivity. Methods The causes of mortality of two hundred and eighty two mammals which died between 2004 and 2015 in three different Italian zoos (a Biopark, a Safari Park and a private conservation center) have been investigated. Results Post mortem findings have been evaluated reporting the cause of death, zoo type, year and animal category. The animals frequently died from infectious diseases, in particular the causes of death in ruminants were mostly related to gastro-intestinal pathologies. pulmonary diseases were also very common in each of the zoos in the study. Moreover, death was sometimes attributable to traumas, as a result of fighting between conspecifics or during mating. Cases of genetic diseases and malformations have also been registered. Discussion This research was a confirmation of how conservation, histology and pathology are all connected through individual animals. These areas of expertise are extremely important to ensure the survival of rare and endangered species and to learn more about their morphological and physiological conditions. They are also useful to control pathologies, parasites and illnesses that can have a great impact on the species in captivity. Finally, this study underlines the importance of a close collaboration between veterinarians, zoo biologists and pathologists. Necropsy findings can help conservationists to determine how to support wild animal populations.
format: application/pdf
format: text/html
creator: Frine Eleonora Scaglione
creator: Cristina Biolatti
creator: Paola Pregel
creator: Enrica Berio
creator: Francesca Tiziana Cannizzo
creator: Bartolomeo Biolatti
creator: Enrico Bollo
subject: Conservation Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6198
publisher: PeerJ Inc.
rights: © 2019 Scaglione et al.
abstract: Background The zoo is a unique environment in which to study animals. Zoos have a long history of research into aspects of animal biology, even if this was not the primary purpose for which they were established. The data collected from zoo animals can have a great biological relevance and it can tell us more about what these animals are like outside the captive environment. In order to ensure the health of all captive animals, it is important to perform a post-mortem examination on all the animals that die in captivity. Methods The causes of mortality of two hundred and eighty two mammals which died between 2004 and 2015 in three different Italian zoos (a Biopark, a Safari Park and a private conservation center) have been investigated. Results Post mortem findings have been evaluated reporting the cause of death, zoo type, year and animal category. The animals frequently died from infectious diseases, in particular the causes of death in ruminants were mostly related to gastro-intestinal pathologies. pulmonary diseases were also very common in each of the zoos in the study. Moreover, death was sometimes attributable to traumas, as a result of fighting between conspecifics or during mating. Cases of genetic diseases and malformations have also been registered. Discussion This research was a confirmation of how conservation, histology and pathology are all connected through individual animals. These areas of expertise are extremely important to ensure the survival of rare and endangered species and to learn more about their morphological and physiological conditions. They are also useful to control pathologies, parasites and illnesses that can have a great impact on the species in captivity. Finally, this study underlines the importance of a close collaboration between veterinarians, zoo biologists and pathologists. Necropsy findings can help conservationists to determine how to support wild animal populations.
bibliographic citation: Scaglione et al. (2019) A survey on zoo mortality over a 12-year period in Italy. PeerJ 7:e6198 https://doi.org/10.7717/peerj.6198
date submitted: 2017-04-07
date accepted: 2018-12-02
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scaglione
  given name: Frine Eleonora
author list: Agent
  family name: Biolatti
  given name: Cristina
author list: Agent
  family name: Pregel
  given name: Paola
author list: Agent
  family name: Berio
  given name: Enrica
author list: Agent
  family name: Cannizzo
  given name: Francesca Tiziana
author list: Agent
  family name: Biolatti
  given name: Bartolomeo
author list: Agent
  family name: Bollo
  given name: Enrico
doi: 10.7717/peerj.6198
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Scaglione et al.
attribution name: Scaglione et al.

Turtles of the genera Geoemyda and Pangshura (Testudines: Geoemydidae) lack differentiated sex chromosomes: the end of a 40-year error cascade for Pangshura
type: item
type: AcademicArticle
description: For a long time, turtles of the family Geoemydidae have been considered exceptional because representatives of this family were thought to possess a wide variety of sex determination systems. In the present study, we cytogenetically studied Geoemyda spengleri and G. japonica and re-examined the putative presence of sex chromosomes in Pangshura smithii. Karyotypes were examined by assessing the occurrence of constitutive heterochromatin, by comparative genome hybridization and in situ hybridization with repetitive motifs, which are often accumulated on differentiated sex chromosomes in reptiles. We found similar karyotypes, similar distributions of constitutive heterochromatin and a similar topology of tested repetitive motifs for all three species. We did not detect differentiated sex chromosomes in any of the species. For P. smithii, a ZZ/ZW sex determination system, with differentiated sex chromosomes, was described more than 40 years ago, but this finding has never been re-examined and was cited in all reviews of sex determination in reptiles. Here, we show that the identification of sex chromosomes in the original report was based on the erroneous pairing of chromosomes in the karyogram, causing over decades an error cascade regarding the inferences derived from the putative existence of female heterogamety in geoemydid turtles.
format: application/pdf
format: text/html
creator: Sofia Mazzoleni
creator: Barbora Augstenová
creator: Lorenzo Clemente
creator: Markus Auer
creator: Uwe Fritz
creator: Peter Praschag
creator: Tomáš Protiva
creator: Petr Velenský
creator: Lukáš Kratochvíl
creator: Michail Rovatsos
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6241
publisher: PeerJ Inc.
rights: © 2019 Mazzoleni et al.
abstract: For a long time, turtles of the family Geoemydidae have been considered exceptional because representatives of this family were thought to possess a wide variety of sex determination systems. In the present study, we cytogenetically studied Geoemyda spengleri and G. japonica and re-examined the putative presence of sex chromosomes in Pangshura smithii. Karyotypes were examined by assessing the occurrence of constitutive heterochromatin, by comparative genome hybridization and in situ hybridization with repetitive motifs, which are often accumulated on differentiated sex chromosomes in reptiles. We found similar karyotypes, similar distributions of constitutive heterochromatin and a similar topology of tested repetitive motifs for all three species. We did not detect differentiated sex chromosomes in any of the species. For P. smithii, a ZZ/ZW sex determination system, with differentiated sex chromosomes, was described more than 40 years ago, but this finding has never been re-examined and was cited in all reviews of sex determination in reptiles. Here, we show that the identification of sex chromosomes in the original report was based on the erroneous pairing of chromosomes in the karyogram, causing over decades an error cascade regarding the inferences derived from the putative existence of female heterogamety in geoemydid turtles.
bibliographic citation: Mazzoleni et al. (2019) Turtles of the genera Geoemyda and Pangshura (Testudines: Geoemydidae) lack differentiated sex chromosomes: the end of a 40-year error cascade for Pangshura. PeerJ 7:e6241 https://doi.org/10.7717/peerj.6241
date submitted: 2018-10-29
date accepted: 2018-12-08
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mazzoleni
  given name: Sofia
author list: Agent
  family name: Augstenová
  given name: Barbora
author list: Agent
  family name: Clemente
  given name: Lorenzo
author list: Agent
  family name: Auer
  given name: Markus
author list: Agent
  family name: Fritz
  given name: Uwe
author list: Agent
  family name: Praschag
  given name: Peter
author list: Agent
  family name: Protiva
  given name: Tomáš
author list: Agent
  family name: Velenský
  given name: Petr
author list: Agent
  family name: Kratochvíl
  given name: Lukáš
author list: Agent
  family name: Rovatsos
  given name: Michail
doi: 10.7717/peerj.6241
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Mazzoleni et al.
attribution name: Mazzoleni et al.

kuenm: an R package for detailed development of ecological niche models using Maxent
type: item
type: AcademicArticle
description: Background Ecological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way. Results This package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric. Discussion Use of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes.
format: application/pdf
format: text/html
creator: Marlon E. Cobos
creator: A. Townsend Peterson
creator: Narayani Barve
creator: Luis Osorio-Olvera
subject: Biogeography
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.6281
publisher: PeerJ Inc.
rights: © 2019 Cobos et al.
abstract: Background Ecological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way. Results This package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric. Discussion Use of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes.
bibliographic citation: Cobos et al. (2019) kuenm: an R package for detailed development of ecological niche models using Maxent. PeerJ 7:e6281 https://doi.org/10.7717/peerj.6281
date submitted: 2018-10-05
date accepted: 2018-12-13
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cobos
  given name: Marlon E.
author list: Agent
  family name: Peterson
  given name: A. Townsend
author list: Agent
  family name: Barve
  given name: Narayani
author list: Agent
  family name: Osorio-Olvera
  given name: Luis
doi: 10.7717/peerj.6281
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Cobos et al.
attribution name: Cobos et al.

The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
type: item
type: AcademicArticle
description: In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes (T1D), and 12 children with newly diagnosed T2D. These data were used for differentially expressed genes (DGEs) analysis and weighted co-expression network analysis (WGCNA). We identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to figure out the functions and related pathways of genes, which were identified in the results of DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the protein-protein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the transcription factors and references related to genes with conspicuous logFC or high-degree genes, which were present in both the modules of WGCNA and PPI network. Current research shows that EGR1 and NAMPT can be used as marker genes for childhood-onset T2D. Gestational diabetes and chronic inflammation are risk factors that lead to the development of childhood-onset T2D.
format: application/pdf
format: text/html
creator: Keren Jia
creator: Yingcheng Wu
creator: Jingyi Ju
creator: Liyang Wang
creator: Lili Shi
creator: Huiqun Wu
creator: Kui Jiang
creator: Jiancheng Dong
subject: Bioinformatics
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6343
publisher: PeerJ Inc.
rights: © 2019 Jia et al.
abstract: In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes (T1D), and 12 children with newly diagnosed T2D. These data were used for differentially expressed genes (DGEs) analysis and weighted co-expression network analysis (WGCNA). We identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to figure out the functions and related pathways of genes, which were identified in the results of DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the protein-protein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the transcription factors and references related to genes with conspicuous logFC or high-degree genes, which were present in both the modules of WGCNA and PPI network. Current research shows that EGR1 and NAMPT can be used as marker genes for childhood-onset T2D. Gestational diabetes and chronic inflammation are risk factors that lead to the development of childhood-onset T2D.
bibliographic citation: Jia et al. (2019) The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes. PeerJ 7:e6343 https://doi.org/10.7717/peerj.6343
date submitted: 2018-10-03
date accepted: 2018-12-24
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jia
  given name: Keren
author list: Agent
  family name: Wu
  given name: Yingcheng
author list: Agent
  family name: Ju
  given name: Jingyi
author list: Agent
  family name: Wang
  given name: Liyang
author list: Agent
  family name: Shi
  given name: Lili
author list: Agent
  family name: Wu
  given name: Huiqun
author list: Agent
  family name: Jiang
  given name: Kui
author list: Agent
  family name: Dong
  given name: Jiancheng
doi: 10.7717/peerj.6343
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Jia et al.
attribution name: Jia et al.

Species turnover reveals hidden effects of decreasing nitrogen deposition in mountain hay meadows
type: item
type: AcademicArticle
description: Nitrogen (N) deposition is a major threat to biodiversity in many habitats. The recent introduction of cleaner technologies in Switzerland has led to a reduction in the emissions of nitrogen oxides, with a consequent decrease in N deposition. We examined different drivers of plant community change, that is, N deposition, climate warming, and land-use change, in Swiss mountain hay meadows, using data from the Swiss biodiversity monitoring program. We compared indicator values of species that disappeared from or colonized a site (species turnover) with the indicator values of randomly chosen species from the same site. While oligotrophic plant species were more likely to colonize, compared to random expectation, we found only weak shifts in plant community composition. In particular, the average nutrient value of plant communities remained stable over time (2003–2017). We found the largest deviations from random expectation in the nutrient values of colonizing species, suggesting that N deposition or other factors that change the nutrient content of soils were important drivers of the species composition change over the last 15 years in Swiss mountain hay meadows. In addition, we observed an overall replacement of species with lower indicator values for temperature with species with higher values. Apparently, the community effects of the replacement of eutrophic species with oligotrophic species was outweighed by climate warming. Our results add to the increasing evidence that plant communities in changing environments may be relatively stable regarding average species richness or average indicator values, but that this apparent stability is often accompanied by a marked turnover of species.
format: application/pdf
format: text/html
creator: Tobias Roth
creator: Lukas Kohli
creator: Christoph Bühler
creator: Beat Rihm
creator: Reto Giulio Meuli
creator: Reto Meier
creator: Valentin Amrhein
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.6347
publisher: PeerJ Inc.
rights: © 2019 Roth et al.
abstract: Nitrogen (N) deposition is a major threat to biodiversity in many habitats. The recent introduction of cleaner technologies in Switzerland has led to a reduction in the emissions of nitrogen oxides, with a consequent decrease in N deposition. We examined different drivers of plant community change, that is, N deposition, climate warming, and land-use change, in Swiss mountain hay meadows, using data from the Swiss biodiversity monitoring program. We compared indicator values of species that disappeared from or colonized a site (species turnover) with the indicator values of randomly chosen species from the same site. While oligotrophic plant species were more likely to colonize, compared to random expectation, we found only weak shifts in plant community composition. In particular, the average nutrient value of plant communities remained stable over time (2003–2017). We found the largest deviations from random expectation in the nutrient values of colonizing species, suggesting that N deposition or other factors that change the nutrient content of soils were important drivers of the species composition change over the last 15 years in Swiss mountain hay meadows. In addition, we observed an overall replacement of species with lower indicator values for temperature with species with higher values. Apparently, the community effects of the replacement of eutrophic species with oligotrophic species was outweighed by climate warming. Our results add to the increasing evidence that plant communities in changing environments may be relatively stable regarding average species richness or average indicator values, but that this apparent stability is often accompanied by a marked turnover of species.
bibliographic citation: Roth et al. (2019) Species turnover reveals hidden effects of decreasing nitrogen deposition in mountain hay meadows. PeerJ 7:e6347 https://doi.org/10.7717/peerj.6347
date submitted: 2018-09-14
date accepted: 2018-12-24
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roth
  given name: Tobias
author list: Agent
  family name: Kohli
  given name: Lukas
author list: Agent
  family name: Bühler
  given name: Christoph
author list: Agent
  family name: Rihm
  given name: Beat
author list: Agent
  family name: Meuli
  given name: Reto Giulio
author list: Agent
  family name: Meier
  given name: Reto
author list: Agent
  family name: Amrhein
  given name: Valentin
doi: 10.7717/peerj.6347
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Roth et al.
attribution name: Roth et al.

Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis
type: item
type: AcademicArticle
description: Background Alcohol-related hepatocellular carcinoma (HCC) was reported to be diagnosed at a later stage, but the mechanism was unknown. This study aimed to identify special key genes (SKGs) during alcohol-related HCC development and progression. Methods The mRNA data of 369 HCC patients and the clinical information were downloaded from the Cancer Genome Atlas project (TCGA). The 310 patients with certain HCC-related risk factors were included for analysis and divided into seven groups according to the risk factors. Survival analyses were applied for the HCC patients of different groups. The patients with hepatitis B virus or hepatitis C virus infection only were combined into the HCC-V group for further analysis. The differentially expressed genes (DEGs) between the HCCs with alcohol consumption only (HCC-A) and HCC-V tumors were identified through limma package in R with cutoff criteria│log2 fold change (logFC)|>1.0 and p < 0.05. The DEGs between eight alcohol-related HCCs and their paired normal livers of GSE59259 from the Gene Expression Omnibus (GEO) were identified through GEO2R (a built-in tool in GEO database) with cutoff criteria |logFC|> 2.0 and adj.p < 0.05. The intersection of the two sets of DEGs was considered SKGs which were then investigated for their specificity through comparisons between HCC-A and other four HCC groups. The SKGs were analyzed for their correlations with HCC-A stage and grade and their prognostic power for HCC-A patients. The expressional differences of the SKGs in the HCCs in whole were also investigated through Gene Expression Profiling Interactive Analysis (GEPIA). The SKGs in HCC were validated through Oncomine database analysis. Results Pathological stage is an independent prognostic factor for HCC patients. HCC-A patients were diagnosed later than HCC patients with other risk factors. Ten SKGs were identified and nine of them were confirmed for their differences in paired samples of HCC-A patients. Three (SLC22A10, CD5L, and U…
format: application/pdf
format: text/html
creator: Xiuzhi Zhang
creator: Chunyan Kang
creator: Ningning Li
creator: Xiaoli Liu
creator: Jinzhong Zhang
creator: Fenglan Gao
creator: Liping Dai
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Global Health
subject: Oncology
description: doi:10.7717/peerj.6375
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Alcohol-related hepatocellular carcinoma (HCC) was reported to be diagnosed at a later stage, but the mechanism was unknown. This study aimed to identify special key genes (SKGs) during alcohol-related HCC development and progression. Methods The mRNA data of 369 HCC patients and the clinical information were downloaded from the Cancer Genome Atlas project (TCGA). The 310 patients with certain HCC-related risk factors were included for analysis and divided into seven groups according to the risk factors. Survival analyses were applied for the HCC patients of different groups. The patients with hepatitis B virus or hepatitis C virus infection only were combined into the HCC-V group for further analysis. The differentially expressed genes (DEGs) between the HCCs with alcohol consumption only (HCC-A) and HCC-V tumors were identified through limma package in R with cutoff criteria│log2 fold change (logFC)|>1.0 and p < 0.05. The DEGs between eight alcohol-related HCCs and their paired normal livers of GSE59259 from the Gene Expression Omnibus (GEO) were identified through GEO2R (a built-in tool in GEO database) with cutoff criteria |logFC|> 2.0 and adj.p < 0.05. The intersection of the two sets of DEGs was considered SKGs which were then investigated for their specificity through comparisons between HCC-A and other four HCC groups. The SKGs were analyzed for their correlations with HCC-A stage and grade and their prognostic power for HCC-A patients. The expressional differences of the SKGs in the HCCs in whole were also investigated through Gene Expression Profiling Interactive Analysis (GEPIA). The SKGs in HCC were validated through Oncomine database analysis. Results Pathological stage is an independent prognostic factor for HCC patients. HCC-A patients were diagnosed later than HCC patients with other risk factors. Ten SKGs were identified and nine of them were confirmed for their differences in paired samples of HCC-A patients. Three (SLC22A10, CD5L, and U…
bibliographic citation: Zhang et al. (2019) Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis. PeerJ 7:e6375 https://doi.org/10.7717/peerj.6375
date submitted: 2018-09-18
date accepted: 2018-12-31
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiuzhi
author list: Agent
  family name: Kang
  given name: Chunyan
author list: Agent
  family name: Li
  given name: Ningning
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Zhang
  given name: Jinzhong
author list: Agent
  family name: Gao
  given name: Fenglan
author list: Agent
  family name: Dai
  given name: Liping
doi: 10.7717/peerj.6375
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient
type: item
type: AcademicArticle
description: Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonst…
format: application/pdf
format: text/html
creator: Joseph D. DiBattista
creator: James D. Reimer
creator: Michael Stat
creator: Giovanni D. Masucci
creator: Piera Biondi
creator: Maarten De Brauwer
creator: Michael Bunce
subject: Biodiversity
subject: Marine Biology
description: doi:10.7717/peerj.6379
publisher: PeerJ Inc.
rights: © 2019 DiBattista et al.
abstract: Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonst…
bibliographic citation: DiBattista et al. (2019) Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ 7:e6379 https://doi.org/10.7717/peerj.6379
date submitted: 2018-10-15
date accepted: 2018-12-24
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DiBattista
  given name: Joseph D.
author list: Agent
  family name: Reimer
  given name: James D.
author list: Agent
  family name: Stat
  given name: Michael
author list: Agent
  family name: Masucci
  given name: Giovanni D.
author list: Agent
  family name: Biondi
  given name: Piera
author list: Agent
  family name: De Brauwer
  given name: Maarten
author list: Agent
  family name: Bunce
  given name: Michael
doi: 10.7717/peerj.6379
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 DiBattista et al.
attribution name: DiBattista et al.

Genetic alteration of histone lysine methyltransferases and their significance in renal cell carcinoma
type: item
type: AcademicArticle
description: Background Histone lysine methyltransferases (HMTs), a category of enzymes, play essential roles in regulating transcription, cellular differentiation, and chromatin construction. The genomic landscape and clinical significance of HMTs in renal cell carcinoma (RCC) remain uncovered. Methods We conducted an integrative analysis of 50 HMTs in RCC and discovered the internal relations among copy number alterations (CNAs), expressive abundance, mutations, and clinical outcome. Results We confirmed 12 HMTs with the highest frequency of genetic alterations, including seven HMTs with high-level amplification, two HMTs with somatic mutation, and three HMTs with putative homozygous deletion. Patterns of copy number and expression varied among different subtypes of RCC, including clear cell renal cell carcinoma, papillary cell carcinoma, and chromophobe renal carcinoma. Kaplan–Meier survival analysis and multivariate analysis identified that CNA or mRNA expression in some HMTs were significantly associated with shorter overall patient survival. Systematic analysis identified six HMTs (ASH1L, PRDM6, NSD1, EZH2, WHSC1L1, SETD2) which were dysregulated by genetic alterations as candidate therapeutic targets. Discussion In summary, our findings strongly evidenced that genetic alteration of HMTs may play an important role in generation and development of RCC, which lays a solid foundation for the mechanism for further research in the future.
format: application/pdf
format: text/html
creator: Libin Yan
creator: Yangjun Zhang
creator: Beichen Ding
creator: Hui Zhou
creator: Weimin Yao
creator: Hua Xu
subject: Genetics
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.6396
publisher: PeerJ Inc.
rights: © 2019 Yan et al.
abstract: Background Histone lysine methyltransferases (HMTs), a category of enzymes, play essential roles in regulating transcription, cellular differentiation, and chromatin construction. The genomic landscape and clinical significance of HMTs in renal cell carcinoma (RCC) remain uncovered. Methods We conducted an integrative analysis of 50 HMTs in RCC and discovered the internal relations among copy number alterations (CNAs), expressive abundance, mutations, and clinical outcome. Results We confirmed 12 HMTs with the highest frequency of genetic alterations, including seven HMTs with high-level amplification, two HMTs with somatic mutation, and three HMTs with putative homozygous deletion. Patterns of copy number and expression varied among different subtypes of RCC, including clear cell renal cell carcinoma, papillary cell carcinoma, and chromophobe renal carcinoma. Kaplan–Meier survival analysis and multivariate analysis identified that CNA or mRNA expression in some HMTs were significantly associated with shorter overall patient survival. Systematic analysis identified six HMTs (ASH1L, PRDM6, NSD1, EZH2, WHSC1L1, SETD2) which were dysregulated by genetic alterations as candidate therapeutic targets. Discussion In summary, our findings strongly evidenced that genetic alteration of HMTs may play an important role in generation and development of RCC, which lays a solid foundation for the mechanism for further research in the future.
bibliographic citation: Yan et al. (2019) Genetic alteration of histone lysine methyltransferases and their significance in renal cell carcinoma. PeerJ 7:e6396 https://doi.org/10.7717/peerj.6396
date submitted: 2018-08-01
date accepted: 2019-01-05
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Libin
author list: Agent
  family name: Zhang
  given name: Yangjun
author list: Agent
  family name: Ding
  given name: Beichen
author list: Agent
  family name: Zhou
  given name: Hui
author list: Agent
  family name: Yao
  given name: Weimin
author list: Agent
  family name: Xu
  given name: Hua
doi: 10.7717/peerj.6396
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Yan et al.
attribution name: Yan et al.

Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) play an important role in the competitive endogenous RNA (ceRNA) networks in that they regulate protein-coding gene expression by sponging microRNAs (miRNAs). However, the understanding of the ceRNA network in tongue squamous cell carcinoma (TSCC) remains limited. Methods Expression profile data regarding mRNAs, miRNAs and lncRNAs as well as clinical information on 122 TSCC tissues and 15 normal controls from The Cancer Genome Atlas (TCGA) database were collected. We used the edgR package to identify differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs) and miRNAs (DEmiRNAs) between TSCC samples and normal samples. In order to explore the functions of DEmRNAs, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed. Subsequently, a ceRNA network was established based on the identified DElncRNAs–DEmiRNAs and DEmiRNAs–DEmRNAs interactions. The RNAs within the ceRNA network were analyzed for their correlation with overall disease survival. Finally, lncRNAs were specifically analyzed for their correlation with clinical features in the included TSCC patient samples. Results A total of 1867 mRNAs, 828 lncRNAs and 81 miRNAs were identified as differentially expressed in TSCC tissues (—log 2fold change— ≥ 2; adjusted P value <0.01). The resulting ceRNA network included 16 mRNAs, 56 lncRNAs and 6 miRNAs. Ten out of the 56 lncRNAs were found to be associated with the overall survival in TSCC patients (P < 0.05); 10 lncRNAs were correlated with TSCC progression (P < 0.05). Conclusion Our study deepens the understanding of ceRNA network regulatory mechanisms in TSCC. Furthermore, we identified ten lncRNAs (PART1, LINC00261, AL163952.1, C2orf48, FAM87A, LINC00052, LINC00472, STEAP3-AS1, TSPEAR-AS1 and ERVH48-1) as novel, potential prognostic biomarkers and therapeutic targets for TSCC.
format: application/pdf
format: text/html
creator: Shusen Zhang
creator: Ruoyan Cao
creator: Qiulan Li
creator: Mianfeng Yao
creator: Yu Chen
creator: Hongbo Zhou
subject: Bioinformatics
subject: Dentistry
subject: Oncology
description: doi:10.7717/peerj.6397
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) play an important role in the competitive endogenous RNA (ceRNA) networks in that they regulate protein-coding gene expression by sponging microRNAs (miRNAs). However, the understanding of the ceRNA network in tongue squamous cell carcinoma (TSCC) remains limited. Methods Expression profile data regarding mRNAs, miRNAs and lncRNAs as well as clinical information on 122 TSCC tissues and 15 normal controls from The Cancer Genome Atlas (TCGA) database were collected. We used the edgR package to identify differentially expressed mRNAs (DEmRNAs), lncRNAs (DElncRNAs) and miRNAs (DEmiRNAs) between TSCC samples and normal samples. In order to explore the functions of DEmRNAs, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was performed. Subsequently, a ceRNA network was established based on the identified DElncRNAs–DEmiRNAs and DEmiRNAs–DEmRNAs interactions. The RNAs within the ceRNA network were analyzed for their correlation with overall disease survival. Finally, lncRNAs were specifically analyzed for their correlation with clinical features in the included TSCC patient samples. Results A total of 1867 mRNAs, 828 lncRNAs and 81 miRNAs were identified as differentially expressed in TSCC tissues (—log 2fold change— ≥ 2; adjusted P value <0.01). The resulting ceRNA network included 16 mRNAs, 56 lncRNAs and 6 miRNAs. Ten out of the 56 lncRNAs were found to be associated with the overall survival in TSCC patients (P < 0.05); 10 lncRNAs were correlated with TSCC progression (P < 0.05). Conclusion Our study deepens the understanding of ceRNA network regulatory mechanisms in TSCC. Furthermore, we identified ten lncRNAs (PART1, LINC00261, AL163952.1, C2orf48, FAM87A, LINC00052, LINC00472, STEAP3-AS1, TSPEAR-AS1 and ERVH48-1) as novel, potential prognostic biomarkers and therapeutic targets for TSCC.
bibliographic citation: Zhang et al. (2019) Comprehensive analysis of lncRNA-associated competing endogenous RNA network in tongue squamous cell carcinoma. PeerJ 7:e6397 https://doi.org/10.7717/peerj.6397
date submitted: 2018-10-03
date accepted: 2019-01-07
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shusen
author list: Agent
  family name: Cao
  given name: Ruoyan
author list: Agent
  family name: Li
  given name: Qiulan
author list: Agent
  family name: Yao
  given name: Mianfeng
author list: Agent
  family name: Chen
  given name: Yu
author list: Agent
  family name: Zhou
  given name: Hongbo
doi: 10.7717/peerj.6397
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Zhang et al.
attribution name: Zhang et al.

Quantitative color profiling of digital images with earth mover’s distance using the R package colordistance
type: item
type: AcademicArticle
description: Biological color may be adaptive or incidental, seasonal or permanent, species- or population-specific, or modified for breeding, defense or camouflage. Although color is a hugely informative aspect of biology, quantitative color comparisons are notoriously difficult. Color comparison is limited by categorization methods, with available tools requiring either subjective classifications, or expensive equipment, software, and expertise. We present an R package for processing images of organisms (or other objects) in order to quantify color profiles, gather color trait data, and compare color palettes on the basis of color similarity and amount. The package treats image pixels as 3D coordinates in a “color space,” producing a multidimensional color histogram for each image. Pairwise distances between histograms are computed using earth mover’s distance, a technique borrowed from computer vision, that compares histograms using transportation costs. Users choose a color space, parameters for generating color histograms, and a pairwise comparison method to produce a color distance matrix for a set of images. The package is intended as a more rigorous alternative to subjective, manual digital image analyses, not as a replacement for more advanced techniques that rely on detailed spectrophotometry methods unavailable to many users. Here, we outline the basic functions of colordistance, provide guidelines for the available color spaces and quantification methods, and compare this toolkit with other available methods. The tools presented for quantitative color analysis may be applied to a broad range of questions in biology and other disciplines.
format: application/pdf
format: text/html
creator: Hannah I. Weller
creator: Mark W. Westneat
subject: Biodiversity
subject: Evolutionary Studies
subject: Statistics
description: doi:10.7717/peerj.6398
publisher: PeerJ Inc.
rights: © 2019 Weller and Westneat
abstract: Biological color may be adaptive or incidental, seasonal or permanent, species- or population-specific, or modified for breeding, defense or camouflage. Although color is a hugely informative aspect of biology, quantitative color comparisons are notoriously difficult. Color comparison is limited by categorization methods, with available tools requiring either subjective classifications, or expensive equipment, software, and expertise. We present an R package for processing images of organisms (or other objects) in order to quantify color profiles, gather color trait data, and compare color palettes on the basis of color similarity and amount. The package treats image pixels as 3D coordinates in a “color space,” producing a multidimensional color histogram for each image. Pairwise distances between histograms are computed using earth mover’s distance, a technique borrowed from computer vision, that compares histograms using transportation costs. Users choose a color space, parameters for generating color histograms, and a pairwise comparison method to produce a color distance matrix for a set of images. The package is intended as a more rigorous alternative to subjective, manual digital image analyses, not as a replacement for more advanced techniques that rely on detailed spectrophotometry methods unavailable to many users. Here, we outline the basic functions of colordistance, provide guidelines for the available color spaces and quantification methods, and compare this toolkit with other available methods. The tools presented for quantitative color analysis may be applied to a broad range of questions in biology and other disciplines.
bibliographic citation: Weller et al. (2019) Quantitative color profiling of digital images with earth mover’s distance using the R package colordistance. PeerJ 7:e6398 https://doi.org/10.7717/peerj.6398
date submitted: 2018-02-05
date accepted: 2019-01-03
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Weller
  given name: Hannah I.
author list: Agent
  family name: Westneat
  given name: Mark W.
doi: 10.7717/peerj.6398
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Weller and Westneat
attribution name: Weller and Westneat

Behavioral correlates of semi-zygodactyly in Ospreys (Pandion haliaetus) based on analysis of internet images
type: item
type: AcademicArticle
description: Ospreys are renowned for their fishing abilities, which have largely been attributed to their specialized talon morphology and semi-zygodactyly−the ability to rotate the fourth toe to accompany the first toe in opposition of toes II and III. Anecdotal observations indicate that zygodactyly in Ospreys is associated with prey capture, although to our knowledge this has not been rigorously tested. As a first pass toward understanding the functional significance of semi-zygodactyly in Ospreys, we scoured the internet for images of Osprey feet in a variety of circumstances. From these we cross-tabulated the number of times each of three toe configurations (anisodactylous, zygodactylous, and an intermediate condition between these) was associated with different grasping scenarios (e.g., grasping prey or perched), contact conditions (e.g., fish, other objects, or substrate), object sizes (relative to foot size), and grasping behaviors (e.g., using one or both feet). Our analysis confirms an association between zygodactyly and grasping behavior; the odds that an osprey exhibited zygodactyly while grasping objects in flight were 5.7 times greater than whilst perched. Furthermore, the odds of zygodactyly during single-foot grasps were 4.1 times greater when pictured grasping fish compared to other objects. These results suggest a functional association between predatory behavior and zygodactyly and has implications for the selective role of predatory performance in the evolution of zygodactyly more generally.
format: application/pdf
format: text/html
creator: Diego Sustaita
creator: Yuri Gloumakov
creator: Leah R. Tsang
creator: Aaron M. Dollar
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.6243
publisher: PeerJ Inc.
rights: © 2019 Sustaita et al.
abstract: Ospreys are renowned for their fishing abilities, which have largely been attributed to their specialized talon morphology and semi-zygodactyly−the ability to rotate the fourth toe to accompany the first toe in opposition of toes II and III. Anecdotal observations indicate that zygodactyly in Ospreys is associated with prey capture, although to our knowledge this has not been rigorously tested. As a first pass toward understanding the functional significance of semi-zygodactyly in Ospreys, we scoured the internet for images of Osprey feet in a variety of circumstances. From these we cross-tabulated the number of times each of three toe configurations (anisodactylous, zygodactylous, and an intermediate condition between these) was associated with different grasping scenarios (e.g., grasping prey or perched), contact conditions (e.g., fish, other objects, or substrate), object sizes (relative to foot size), and grasping behaviors (e.g., using one or both feet). Our analysis confirms an association between zygodactyly and grasping behavior; the odds that an osprey exhibited zygodactyly while grasping objects in flight were 5.7 times greater than whilst perched. Furthermore, the odds of zygodactyly during single-foot grasps were 4.1 times greater when pictured grasping fish compared to other objects. These results suggest a functional association between predatory behavior and zygodactyly and has implications for the selective role of predatory performance in the evolution of zygodactyly more generally.
bibliographic citation: Sustaita et al. (2019) Behavioral correlates of semi-zygodactyly in Ospreys (Pandion haliaetus) based on analysis of internet images. PeerJ 7:e6243 https://doi.org/10.7717/peerj.6243
date submitted: 2018-07-15
date accepted: 2018-12-09
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sustaita
  given name: Diego
author list: Agent
  family name: Gloumakov
  given name: Yuri
author list: Agent
  family name: Tsang
  given name: Leah R.
author list: Agent
  family name: Dollar
  given name: Aaron M.
doi: 10.7717/peerj.6243
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Sustaita et al.
attribution name: Sustaita et al.

Low-carbohydrate diets differing in carbohydrate restriction improve cardiometabolic and anthropometric markers in healthy adults: A randomised clinical trial
type: item
type: AcademicArticle
description: Background Low-carbohydrate, high-fat (LCHF) diets are useful for treating a range of health conditions, but there is little research evaluating the degree of carbohydrate restriction on outcome measures. This study compares anthropometric and cardiometabolic outcomes between differing carbohydrate-restricted diets. Objective Our hypothesis was that moderate carbohydrate restriction is easier to maintain and more effective for improving cardiometabolic health markers than greater restriction. Design A total of 77 healthy participants were randomised to a very low-carbohydrate ketogenic diet (VLCKD), low-carbohydrate diet (LCD), or moderate-low carbohydrate diet (MCD), containing 5%, 15% and 25% total energy from carbohydrate, respectively, for 12-weeks. Anthropometric and metabolic health measures were taken at baseline and at 12 weeks. Using ANOVA, both within and between-group outcomes were analysed. Results Of 77 participants, 39 (51%) completed the study. In these completers overall, significant reductions in weight and body mass index occurred ((mean change) 3.7 kg/m2; 95% confidence limits (CL): 3.8, 1.8), along with increases in high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, (0.49 mmol/L; 95% CL; 0.06, 0.92; p = 0.03), and total cholesterol concentrations (0.11 mmol/L; 95% CL; 0.00, 0.23; p = 0.05). Triglyceride (TG) levels were reduced by 0.12 mmol/L (95% CL; −0.20, 0.02; p = 0.02). No significant changes occurred between groups. The largest improvements in high density lipoprotein cholesterol (HDL-c) and TG and anthropometric changes occurred for the VLCKD group. Conclusions Low-carbohydrate, high-fat diets have a positive effect on markers of health. Adherence to the allocation of carbohydrate was more easily achieved in MCD, and LCD groups compared to VLCKD and there were comparable improvements in weight loss and waist circumference and greater improvements in HDL-c and TG with greater carbohydrate restriction.
format: application/pdf
format: text/html
creator: Cliff J. d. C. Harvey
creator: Grant M. Schofield
creator: Caryn Zinn
creator: Simon J. Thornley
creator: Catherine Crofts
creator: Fabrice L. R. Merien
subject: Nutrition
subject: Public Health
subject: Metabolic Sciences
description: doi:10.7717/peerj.6273
publisher: PeerJ Inc.
rights: © 2019 Harvey et al.
abstract: Background Low-carbohydrate, high-fat (LCHF) diets are useful for treating a range of health conditions, but there is little research evaluating the degree of carbohydrate restriction on outcome measures. This study compares anthropometric and cardiometabolic outcomes between differing carbohydrate-restricted diets. Objective Our hypothesis was that moderate carbohydrate restriction is easier to maintain and more effective for improving cardiometabolic health markers than greater restriction. Design A total of 77 healthy participants were randomised to a very low-carbohydrate ketogenic diet (VLCKD), low-carbohydrate diet (LCD), or moderate-low carbohydrate diet (MCD), containing 5%, 15% and 25% total energy from carbohydrate, respectively, for 12-weeks. Anthropometric and metabolic health measures were taken at baseline and at 12 weeks. Using ANOVA, both within and between-group outcomes were analysed. Results Of 77 participants, 39 (51%) completed the study. In these completers overall, significant reductions in weight and body mass index occurred ((mean change) 3.7 kg/m2; 95% confidence limits (CL): 3.8, 1.8), along with increases in high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, (0.49 mmol/L; 95% CL; 0.06, 0.92; p = 0.03), and total cholesterol concentrations (0.11 mmol/L; 95% CL; 0.00, 0.23; p = 0.05). Triglyceride (TG) levels were reduced by 0.12 mmol/L (95% CL; −0.20, 0.02; p = 0.02). No significant changes occurred between groups. The largest improvements in high density lipoprotein cholesterol (HDL-c) and TG and anthropometric changes occurred for the VLCKD group. Conclusions Low-carbohydrate, high-fat diets have a positive effect on markers of health. Adherence to the allocation of carbohydrate was more easily achieved in MCD, and LCD groups compared to VLCKD and there were comparable improvements in weight loss and waist circumference and greater improvements in HDL-c and TG with greater carbohydrate restriction.
bibliographic citation: Harvey et al. (2019) Low-carbohydrate diets differing in carbohydrate restriction improve cardiometabolic and anthropometric markers in healthy adults: A randomised clinical trial. PeerJ 7:e6273 https://doi.org/10.7717/peerj.6273
date submitted: 2018-10-02
date accepted: 2018-12-11
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harvey
  given name: Cliff J. d. C.
author list: Agent
  family name: Schofield
  given name: Grant M.
author list: Agent
  family name: Zinn
  given name: Caryn
author list: Agent
  family name: Thornley
  given name: Simon J.
author list: Agent
  family name: Crofts
  given name: Catherine
author list: Agent
  family name: Merien
  given name: Fabrice L. R.
doi: 10.7717/peerj.6273
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Harvey et al.
attribution name: Harvey et al.

Genome-wide identification and comparative evolutionary analysis of the Dof transcription factor family in physic nut and castor bean
type: item
type: AcademicArticle
description: DNA-binding with one finger (Dof) proteins comprise a plant-specific transcription factor family involved in plant growth, development and stress responses. This study presents a genome-wide comparison of Dof family genes in physic nut (Jatropha curcas) and castor bean (Ricinus communis), two Euphorbiaceae plants that have not experienced any recent whole-genome duplication. A total of 25 or 24 Dof genes were identified from physic nut and castor genomes, respectively, where JcDof genes are distributed across nine out of 11 chromosomes. Phylogenetic analysis assigned these genes into nine groups representing four subfamilies, and 24 orthologous groups were also proposed based on comparison of physic nut, castor, Arabidopsis and rice Dofs. Conserved microsynteny was observed between physic nut and castor Dof-coding scaffolds, which allowed anchoring of 23 RcDof genes to nine physic nut chromosomes. In contrast to how no recent duplicate was present in castor, two tandem duplications and one gene loss were found in the Dof gene family of physic nut. Global transcriptome profiling revealed diverse patterns of Jc/RcDof genes over various tissues, and key Dof genes involved in flower development and stress response were also identified in physic nut. These findings provide valuable information for further studies of Dof genes in physic nut and castor.
format: application/pdf
format: text/html
creator: Zhi Zou
creator: Xicai Zhang
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6354
publisher: PeerJ Inc.
rights: © 2019 Zou and Zhang
abstract: DNA-binding with one finger (Dof) proteins comprise a plant-specific transcription factor family involved in plant growth, development and stress responses. This study presents a genome-wide comparison of Dof family genes in physic nut (Jatropha curcas) and castor bean (Ricinus communis), two Euphorbiaceae plants that have not experienced any recent whole-genome duplication. A total of 25 or 24 Dof genes were identified from physic nut and castor genomes, respectively, where JcDof genes are distributed across nine out of 11 chromosomes. Phylogenetic analysis assigned these genes into nine groups representing four subfamilies, and 24 orthologous groups were also proposed based on comparison of physic nut, castor, Arabidopsis and rice Dofs. Conserved microsynteny was observed between physic nut and castor Dof-coding scaffolds, which allowed anchoring of 23 RcDof genes to nine physic nut chromosomes. In contrast to how no recent duplicate was present in castor, two tandem duplications and one gene loss were found in the Dof gene family of physic nut. Global transcriptome profiling revealed diverse patterns of Jc/RcDof genes over various tissues, and key Dof genes involved in flower development and stress response were also identified in physic nut. These findings provide valuable information for further studies of Dof genes in physic nut and castor.
bibliographic citation: Zou et al. (2019) Genome-wide identification and comparative evolutionary analysis of the Dof transcription factor family in physic nut and castor bean. PeerJ 7:e6354 https://doi.org/10.7717/peerj.6354
date submitted: 2018-10-15
date accepted: 2018-12-27
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zou
  given name: Zhi
author list: Agent
  family name: Zhang
  given name: Xicai
doi: 10.7717/peerj.6354
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Zou and Zhang
attribution name: Zou and Zhang

Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird
type: item
type: AcademicArticle
description: The Hoatzin (Opisthocomus hoazin) is the only extant member of the order Opisthocomiformes. This unique South American bird lives in the riparian lowland vegetation characteristic of the Amazon and Orinoco basins. Hoatzins nest in communal social units close to water bodies; they are strictly folivores being the only bird with pregastric fermentation in the crop. Because of the complex logistics involved in capturing this bird, there is a knowledge gap on its parasites. This study documents two distant lineages of haemosporidian parasites (Plasmodium spp.) in a juvenile and two adults sampled in the Cojedes state, Venezuela. Although negative by microscopy, the parasite identification was possible by using molecular methods. We estimated the phylogenetic relationships on the parasite cytochrome b (cytb, 480 bp) gene and the mitochondrial DNA. We found one of the parasites lineages in two individuals (nestling and adult), and the corresponding fragment of cytb was identical to a one found in Wood Stork (Mycteria americana) from Brazil. The other lineage, found in an adult, has an identity of 469 out of 478 bp (98%) with Plasmodium sp. GAL-2012 (isolate THAMB08) from Brazil. Although a morphological description of these parasites was not possible, this is the first molecular study focusing on Hoatzin haemosporidian parasites and the first documentation of Plasmodium infections in the Hoatzin from Venezuela. Furthermore, we reported microfilaria in two adults as well as hematological parameters for six individuals. Information on hematological parameters could contribute to establishing the necessary baseline to detect underlying conditions, such as infections, in this bird species.
format: application/pdf
format: text/html
creator: M. Andreína Pacheco
creator: M. Alexandra García-Amado
creator: Jaime Manzano
creator: Nubia E. Matta
creator: Ananias A. Escalante
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.6361
publisher: PeerJ Inc.
rights: © 2019 Pacheco et al.
abstract: The Hoatzin (Opisthocomus hoazin) is the only extant member of the order Opisthocomiformes. This unique South American bird lives in the riparian lowland vegetation characteristic of the Amazon and Orinoco basins. Hoatzins nest in communal social units close to water bodies; they are strictly folivores being the only bird with pregastric fermentation in the crop. Because of the complex logistics involved in capturing this bird, there is a knowledge gap on its parasites. This study documents two distant lineages of haemosporidian parasites (Plasmodium spp.) in a juvenile and two adults sampled in the Cojedes state, Venezuela. Although negative by microscopy, the parasite identification was possible by using molecular methods. We estimated the phylogenetic relationships on the parasite cytochrome b (cytb, 480 bp) gene and the mitochondrial DNA. We found one of the parasites lineages in two individuals (nestling and adult), and the corresponding fragment of cytb was identical to a one found in Wood Stork (Mycteria americana) from Brazil. The other lineage, found in an adult, has an identity of 469 out of 478 bp (98%) with Plasmodium sp. GAL-2012 (isolate THAMB08) from Brazil. Although a morphological description of these parasites was not possible, this is the first molecular study focusing on Hoatzin haemosporidian parasites and the first documentation of Plasmodium infections in the Hoatzin from Venezuela. Furthermore, we reported microfilaria in two adults as well as hematological parameters for six individuals. Information on hematological parameters could contribute to establishing the necessary baseline to detect underlying conditions, such as infections, in this bird species.
bibliographic citation: Pacheco et al. (2019) Blood parasites infecting the Hoatzin (Opisthocomus hoazin), a unique neotropical folivorous bird. PeerJ 7:e6361 https://doi.org/10.7717/peerj.6361
date submitted: 2018-09-07
date accepted: 2018-12-30
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pacheco
  given name: M. Andreína
author list: Agent
  family name: García-Amado
  given name: M. Alexandra
author list: Agent
  family name: Manzano
  given name: Jaime
author list: Agent
  family name: Matta
  given name: Nubia E.
author list: Agent
  family name: Escalante
  given name: Ananias A.
doi: 10.7717/peerj.6361
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: ©2019 Pacheco et al.
attribution name: Pacheco et al.

Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean
type: item
type: AcademicArticle
description: Neopetrosia proxima (Porifera: Demospongiae: Haplosclerida) is described as a morphologically variable sponge common on shallow reefs of the Caribbean. However, the range of morphological and reproductive variation within putative N. proxima led us to hypothesize that such variability may be indicative of cryptic species rather than plasticity. Using DNA sequences and morphological characters we confirmed the presence of three previously undescribed species of Neopetrosia. Morphological differences of each new congener were best resolved by partial gene sequences of the mitochondrial cytochrome oxidase subunit 1 over nuclear ones (18S rRNA and 28S rRNA). Several new characters for Neopetrosia were revealed by each new species. For example, N. dendrocrevacea sp. nov. and N. cristata sp. nov. showed the presence of grooves on the surface of the sponge body that converge at the oscula, and a more disorganized skeleton than previously defined for the genus. N. sigmafera sp. nov. adds the (1) presence of sigma microscleres, (2) significantly wider/longer oxeas (>200 μm), and (3) the presence of parenchymella larvae. Sampling of conspecifics throughout several locations in the Caribbean revealed larger spicules in habitats closer to the continental shelf than those in remote island locations. Our study highlights the importance of integrating molecular and morphological systematics for the discrimination of new Neopetrosia spp. despite belonging to one of several polyphyletic groups (families, genera) within the current definition of the order Haplosclerida.
format: application/pdf
format: text/html
creator: Jan Vicente
creator: Jaime Andrés Ríos
creator: Sven Zea
creator: Robert J. Toonen
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6371
publisher: PeerJ Inc.
rights: © 2019 Vicente et al.
abstract: Neopetrosia proxima (Porifera: Demospongiae: Haplosclerida) is described as a morphologically variable sponge common on shallow reefs of the Caribbean. However, the range of morphological and reproductive variation within putative N. proxima led us to hypothesize that such variability may be indicative of cryptic species rather than plasticity. Using DNA sequences and morphological characters we confirmed the presence of three previously undescribed species of Neopetrosia. Morphological differences of each new congener were best resolved by partial gene sequences of the mitochondrial cytochrome oxidase subunit 1 over nuclear ones (18S rRNA and 28S rRNA). Several new characters for Neopetrosia were revealed by each new species. For example, N. dendrocrevacea sp. nov. and N. cristata sp. nov. showed the presence of grooves on the surface of the sponge body that converge at the oscula, and a more disorganized skeleton than previously defined for the genus. N. sigmafera sp. nov. adds the (1) presence of sigma microscleres, (2) significantly wider/longer oxeas (>200 μm), and (3) the presence of parenchymella larvae. Sampling of conspecifics throughout several locations in the Caribbean revealed larger spicules in habitats closer to the continental shelf than those in remote island locations. Our study highlights the importance of integrating molecular and morphological systematics for the discrimination of new Neopetrosia spp. despite belonging to one of several polyphyletic groups (families, genera) within the current definition of the order Haplosclerida.
bibliographic citation: Vicente et al. (2019) Molecular and morphological congruence of three new cryptic Neopetrosia spp. in the Caribbean. PeerJ 7:e6371 https://doi.org/10.7717/peerj.6371
date submitted: 2018-10-25
date accepted: 2018-12-28
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vicente
  given name: Jan
author list: Agent
  family name: Ríos
  given name: Jaime Andrés
author list: Agent
  family name: Zea
  given name: Sven
author list: Agent
  family name: Toonen
  given name: Robert J.
doi: 10.7717/peerj.6371
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Vicente et al.
attribution name: Vicente et al.

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis
type: item
type: AcademicArticle
description: Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO2 (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.
format: application/pdf
format: text/html
creator: Bettina Glasl
creator: Caitlin E. Smith
creator: David G. Bourne
creator: Nicole S. Webster
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.6377
publisher: PeerJ Inc.
rights: © 2019 Glasl et al.
abstract: Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO2 (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.
bibliographic citation: Glasl et al. (2019) Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis. PeerJ 7:e6377 https://doi.org/10.7717/peerj.6377
date submitted: 2018-11-05
date accepted: 2018-12-30
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Glasl
  given name: Bettina
author list: Agent
  family name: Smith
  given name: Caitlin E.
author list: Agent
  family name: Bourne
  given name: David G.
author list: Agent
  family name: Webster
  given name: Nicole S.
doi: 10.7717/peerj.6377
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Glasl et al.
attribution name: Glasl et al.

Motor expertise modulates unconscious rather than conscious executive control
type: item
type: AcademicArticle
description: Background Executive control, the ability to regulate the execution of a goal-directed task, is an important element in an athlete’s skill set. Although previous studies have shown that executive control in athletes is better than that in non-athletes, those studies were mainly confined to conscious executive control. Many recent studies have suggested that executive control can be triggered by the presentation of visual stimuli without participant’s conscious awareness. However, few studies have examined unconscious executive control in sports. Thus, the present study investigated whether, similar to conscious executive control, unconscious executive control in table tennis athletes is superior to that in non-athletes. Methods In total, 42 age-matched undergraduate students were recruited for this study; 22 nonathletic students lacking practical athletic experience comprised one group, and 20 table tennis athletes with many years of training in this sport comprised a second group. Each participant first completed an unconscious response priming task, the unconscious processing of visual-spatial information, and then completed a conscious version of this same response priming task. Results Table tennis athletes showed a significant response priming effect, whereas non-athletes did not, when participants were unable to consciously perceive the visual-spatial priming stimuli. In addition, the number of years the table tennis athletes had trained in this sport (a measure of their motor expertise) was positively correlated with the strength of the unconscious response priming effect. However, both table tennis athletes and non-athletes showed a response priming effect when the primes were unmasked and the participants were able to consciously perceive the visual-spatial priming stimuli. Conclusion Our results suggest that motor expertise modulates unconscious, rather than conscious, executive control and that motor expertise is positively correlated with unconscious exe…
format: application/pdf
format: text/html
creator: Fanying Meng
creator: Anmin Li
creator: Yihong You
creator: Chun Xie
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6387
publisher: PeerJ Inc.
rights: © 2019 Meng et al.
abstract: Background Executive control, the ability to regulate the execution of a goal-directed task, is an important element in an athlete’s skill set. Although previous studies have shown that executive control in athletes is better than that in non-athletes, those studies were mainly confined to conscious executive control. Many recent studies have suggested that executive control can be triggered by the presentation of visual stimuli without participant’s conscious awareness. However, few studies have examined unconscious executive control in sports. Thus, the present study investigated whether, similar to conscious executive control, unconscious executive control in table tennis athletes is superior to that in non-athletes. Methods In total, 42 age-matched undergraduate students were recruited for this study; 22 nonathletic students lacking practical athletic experience comprised one group, and 20 table tennis athletes with many years of training in this sport comprised a second group. Each participant first completed an unconscious response priming task, the unconscious processing of visual-spatial information, and then completed a conscious version of this same response priming task. Results Table tennis athletes showed a significant response priming effect, whereas non-athletes did not, when participants were unable to consciously perceive the visual-spatial priming stimuli. In addition, the number of years the table tennis athletes had trained in this sport (a measure of their motor expertise) was positively correlated with the strength of the unconscious response priming effect. However, both table tennis athletes and non-athletes showed a response priming effect when the primes were unmasked and the participants were able to consciously perceive the visual-spatial priming stimuli. Conclusion Our results suggest that motor expertise modulates unconscious, rather than conscious, executive control and that motor expertise is positively correlated with unconscious exe…
bibliographic citation: Meng et al. (2019) Motor expertise modulates unconscious rather than conscious executive control. PeerJ 7:e6387 https://doi.org/10.7717/peerj.6387
date submitted: 2018-08-20
date accepted: 2019-01-03
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Fanying
author list: Agent
  family name: Li
  given name: Anmin
author list: Agent
  family name: You
  given name: Yihong
author list: Agent
  family name: Xie
  given name: Chun
doi: 10.7717/peerj.6387
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: ©2019 Meng et al.
attribution name: Meng et al.

Fruit availability for migratory birds: a GIS approach
type: item
type: AcademicArticle
description: Bird migration is a widely studied phenomenon, however many factors that influence migratory flows remain unknown or poorly understood. Food availability en route is particularly important for many species and can affect their migration success, pattern and timing but this relationship has not been addressed at a wide scale due to the lack of spatial models of food availability on the terrain. This work presents a GIS-database approach that combines spatial and non-spatial ecological information in order to map fruit availability from vegetation over time in the SE Alps, an important node of European migratory routes. We created a unique database that contains information on the presence and periods of fructification of 52 wild plants carrying berries and a series of original cartographic themes. The presence and coverage of the plant species was modelled with the geo-statistical method of the Gaussian Kernel, which was validated against the ground truth of field sampling data with a correct classification power above 80% in most cases. The highest fruit availability in the study area during September and October co-occurs with the peak of captures of berry eating birds. The maps created and distributed along this work can be useful to address more detailed studies about stopover sites as well as the spatial ecology of other fruit eating animals.
format: application/pdf
format: text/html
creator: Clara Tattoni
creator: Erica Soardi
creator: Filippo Prosser
creator: Maurizio Odasso
creator: Paolo Zatelli
creator: Marco Ciolli
subject: Biodiversity
subject: Ecology
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6394
publisher: PeerJ Inc.
rights: © 2019 Tattoni et al.
abstract: Bird migration is a widely studied phenomenon, however many factors that influence migratory flows remain unknown or poorly understood. Food availability en route is particularly important for many species and can affect their migration success, pattern and timing but this relationship has not been addressed at a wide scale due to the lack of spatial models of food availability on the terrain. This work presents a GIS-database approach that combines spatial and non-spatial ecological information in order to map fruit availability from vegetation over time in the SE Alps, an important node of European migratory routes. We created a unique database that contains information on the presence and periods of fructification of 52 wild plants carrying berries and a series of original cartographic themes. The presence and coverage of the plant species was modelled with the geo-statistical method of the Gaussian Kernel, which was validated against the ground truth of field sampling data with a correct classification power above 80% in most cases. The highest fruit availability in the study area during September and October co-occurs with the peak of captures of berry eating birds. The maps created and distributed along this work can be useful to address more detailed studies about stopover sites as well as the spatial ecology of other fruit eating animals.
bibliographic citation: Tattoni et al. (2019) Fruit availability for migratory birds: a GIS approach. PeerJ 7:e6394 https://doi.org/10.7717/peerj.6394
date submitted: 2018-02-24
date accepted: 2019-01-04
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tattoni
  given name: Clara
author list: Agent
  family name: Soardi
  given name: Erica
author list: Agent
  family name: Prosser
  given name: Filippo
author list: Agent
  family name: Odasso
  given name: Maurizio
author list: Agent
  family name: Zatelli
  given name: Paolo
author list: Agent
  family name: Ciolli
  given name: Marco
doi: 10.7717/peerj.6394
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: ©2019 Tattoni et al.
attribution name: Tattoni et al.

Evaluation of DESS as a storage medium for microbial community analysis
type: item
type: AcademicArticle
description: Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.
format: application/pdf
format: text/html
creator: Kevin M. Lee
creator: Madison Adams
creator: Jonathan L. Klassen
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.6414
publisher: PeerJ Inc.
rights: © 2019 Lee et al.
abstract: Microbial ecology research requires sampling strategies that accurately represent the microbial community under study. These communities must typically be transported from the collection location to the laboratory and then stored until they can be processed. However, there is a lack of consensus on how best to preserve microbial communities during transport and storage. Here, we evaluated dimethyl sulfoxide, ethylenediamine tetraacetic acid, saturated salt (DESS) solution as a broadly applicable preservative for microbial ecology experiments. We stored fungus gardens grown by the ant Trachymyrmex septentrionalis in DESS, 15% glycerol, and phosphate buffered saline (PBS) to test their impact on the fungus garden microbial community. Variation in microbial community structure due to differences in preservative type was minimal when compared to variation between ant colonies. Additionally, DESS preserved the structure of a defined mock community more faithfully than either 15% glycerol or PBS. DESS is inexpensive, easy to transport, and effective in preserving microbial community structure. We therefore conclude that DESS is a valuable preservative for use in microbial ecology research.
bibliographic citation: Lee et al. (2019) Evaluation of DESS as a storage medium for microbial community analysis. PeerJ 7:e6414 https://doi.org/10.7717/peerj.6414
date submitted: 2018-07-12
date accepted: 2018-12-24
issued: 2019-02-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lee
  given name: Kevin M.
author list: Agent
  family name: Adams
  given name: Madison
author list: Agent
  family name: Klassen
  given name: Jonathan L.
doi: 10.7717/peerj.6414
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-05
copyright: © 2019 Lee et al.
attribution name: Lee et al.

LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics
type: item
type: AcademicArticle
description: Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to drastic over- or under-representation of RNA in non-linear length-dependent fashion due to enzymatic reactions during cDNA production. It is currently not corrected by any RNA-seq software, which mostly focus on local bias in coverage along RNAs. This paper describes LiBiNorm, a simple command line program that mimics the popular htseq-count software and allows diagnostics, quantification, and global bias removal. LiBiNorm outputs gene expression data that has been normalized to correct for global bias introduced by the Smart-seq2 protocol. In addition, it produces data and several plots that allow insights into the experimental history underlying library preparation. The LiBiNorm package includes an R script that allows visualization of the main results. LiBiNorm is the first software application to correct for the global bias that is introduced by the Smart-seq2 protocol. It is freely downloadable at http://www2.warwick.ac.uk/fac/sci/lifesci/research/libinorm.
format: application/pdf
format: text/html
creator: Nigel P. Dyer
creator: Vahid Shahrezaei
creator: Daniel Hebenstreit
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.6222
publisher: PeerJ Inc.
rights: © 2019 Dyer et al.
abstract: Protocols for preparing RNA sequencing (RNA-seq) libraries, most prominently “Smart-seq” variations, introduce global biases that can have a significant impact on the quantification of gene expression levels. This global bias can lead to drastic over- or under-representation of RNA in non-linear length-dependent fashion due to enzymatic reactions during cDNA production. It is currently not corrected by any RNA-seq software, which mostly focus on local bias in coverage along RNAs. This paper describes LiBiNorm, a simple command line program that mimics the popular htseq-count software and allows diagnostics, quantification, and global bias removal. LiBiNorm outputs gene expression data that has been normalized to correct for global bias introduced by the Smart-seq2 protocol. In addition, it produces data and several plots that allow insights into the experimental history underlying library preparation. The LiBiNorm package includes an R script that allows visualization of the main results. LiBiNorm is the first software application to correct for the global bias that is introduced by the Smart-seq2 protocol. It is freely downloadable at http://www2.warwick.ac.uk/fac/sci/lifesci/research/libinorm.
bibliographic citation: Dyer et al. (2019) LiBiNorm: an htseq-count analogue with improved normalisation of Smart-seq2 data and library preparation diagnostics. PeerJ 7:e6222 https://doi.org/10.7717/peerj.6222
date submitted: 2018-09-11
date accepted: 2018-12-05
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dyer
  given name: Nigel P.
author list: Agent
  family name: Shahrezaei
  given name: Vahid
author list: Agent
  family name: Hebenstreit
  given name: Daniel
doi: 10.7717/peerj.6222
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Dyer et al.
attribution name: Dyer et al.

Methods of body temperature assessment in Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid
type: item
type: AcademicArticle
description: Since cardiovascular, respiratory, and metabolic systems of reptiles are affected by temperature, accurate measurements are of great importance in both captive husbandry and research. Ectothermic animals generally have core body temperatures close to ambient temperature but can differ from the immediate environment if they are using sunlight to thermoregulate. Many zoological facilities and exotic pet caregivers have begun using infrared temperature guns to assess ambient temperatures of reptile enclosures but there are currently few studies assessing the efficacy of these devices for measuring the body temperatures of reptiles. Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid are robust land iguanas endemic to the Galápagos archipelago. By comparing the infrared body temperature measurements of land iguanas against virtual simultaneous collection of cloacal temperatures obtained using a thermocouple thermometer, we sought to assess the efficacy of this non-invasive method. We found that internal body temperature can be predicted with a high level of accuracy from three external body temperature sites, providing a good non-invasive method that avoids the capture of animals.
format: application/pdf
format: text/html
creator: Carlos A. Valle
creator: Colon J. Grijalva
creator: Paul P. Calle
creator: Juan Pablo Muñoz-Pérez
creator: Galo Quezada
creator: Carlos A. Vera
creator: Gregory A. Lewbart
subject: Ecology
subject: Ecosystem Science
subject: Veterinary Medicine
subject: Zoology
subject: Anatomy and Physiology
description: doi:10.7717/peerj.6291
publisher: PeerJ Inc.
rights: © 2019 Valle et al.
abstract: Since cardiovascular, respiratory, and metabolic systems of reptiles are affected by temperature, accurate measurements are of great importance in both captive husbandry and research. Ectothermic animals generally have core body temperatures close to ambient temperature but can differ from the immediate environment if they are using sunlight to thermoregulate. Many zoological facilities and exotic pet caregivers have begun using infrared temperature guns to assess ambient temperatures of reptile enclosures but there are currently few studies assessing the efficacy of these devices for measuring the body temperatures of reptiles. Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid are robust land iguanas endemic to the Galápagos archipelago. By comparing the infrared body temperature measurements of land iguanas against virtual simultaneous collection of cloacal temperatures obtained using a thermocouple thermometer, we sought to assess the efficacy of this non-invasive method. We found that internal body temperature can be predicted with a high level of accuracy from three external body temperature sites, providing a good non-invasive method that avoids the capture of animals.
bibliographic citation: Valle et al. (2019) Methods of body temperature assessment in Conolophus subcristatus, Conolophus pallidus (Galápagos land iguanas), and Amblyrhynchus cristatus X C. subcristatus hybrid. PeerJ 7:e6291 https://doi.org/10.7717/peerj.6291
date submitted: 2018-10-02
date accepted: 2018-12-11
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valle
  given name: Carlos A.
author list: Agent
  family name: Grijalva
  given name: Colon J.
author list: Agent
  family name: Calle
  given name: Paul P.
author list: Agent
  family name: Muñoz-Pérez
  given name: Juan Pablo
author list: Agent
  family name: Quezada
  given name: Galo
author list: Agent
  family name: Vera
  given name: Carlos A.
author list: Agent
  family name: Lewbart
  given name: Gregory A.
doi: 10.7717/peerj.6291
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Valle et al.
attribution name: Valle et al.

Effects of particle size on physicochemical and functional properties of superfine black kidney bean (Phaseolus vulgaris L.) powder
type: item
type: AcademicArticle
description: Black kidney bean (Phaseolus vulgaris L.) powder (BKBP) with particle sizes of 250–180, 180–125, 125–75, 75–38, and <38 μm was prepared by using coarse and eccentric vibratory milling, respectively. Physicochemical properties, cholesterol adsorption, and antioxidant activities of powders were investigated. Size and scanning electron microscopy analyses showed that particle size of BKBP could be effectively decreased after the superfine grinding treatment, and the specific surface area was increased. Flow properties, hydration properties, thermal stability, and cholesterol adsorption efficiency significantly improved with the reducing of particle size. The superfine powder with sizes of 75–38 or <38 μm exhibited higher antioxidant activity via 2,2-diphenyl-1-picryhydrazyl, hydroxyl radical-scavenging, and ferrous ion-chelating assays. The results indicated that the BKBP with a size of <38 μm could serve as a better potential biological resource for food additives, and could be applied for the development of low-cholesterol products.
format: application/pdf
format: text/html
creator: Xianbao Sun
creator: Yuwei Zhang
creator: Jing Li
creator: Nayab Aslam
creator: Hanju Sun
creator: Jinlong Zhao
creator: Zeyu Wu
creator: Shudong He
subject: Bioengineering
subject: Food Science and Technology
description: doi:10.7717/peerj.6369
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Black kidney bean (Phaseolus vulgaris L.) powder (BKBP) with particle sizes of 250–180, 180–125, 125–75, 75–38, and <38 μm was prepared by using coarse and eccentric vibratory milling, respectively. Physicochemical properties, cholesterol adsorption, and antioxidant activities of powders were investigated. Size and scanning electron microscopy analyses showed that particle size of BKBP could be effectively decreased after the superfine grinding treatment, and the specific surface area was increased. Flow properties, hydration properties, thermal stability, and cholesterol adsorption efficiency significantly improved with the reducing of particle size. The superfine powder with sizes of 75–38 or <38 μm exhibited higher antioxidant activity via 2,2-diphenyl-1-picryhydrazyl, hydroxyl radical-scavenging, and ferrous ion-chelating assays. The results indicated that the BKBP with a size of <38 μm could serve as a better potential biological resource for food additives, and could be applied for the development of low-cholesterol products.
bibliographic citation: Sun et al. (2019) Effects of particle size on physicochemical and functional properties of superfine black kidney bean (Phaseolus vulgaris L.) powder. PeerJ 7:e6369 https://doi.org/10.7717/peerj.6369
date submitted: 2018-07-05
date accepted: 2018-12-29
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xianbao
author list: Agent
  family name: Zhang
  given name: Yuwei
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Aslam
  given name: Nayab
author list: Agent
  family name: Sun
  given name: Hanju
author list: Agent
  family name: Zhao
  given name: Jinlong
author list: Agent
  family name: Wu
  given name: Zeyu
author list: Agent
  family name: He
  given name: Shudong
doi: 10.7717/peerj.6369
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Sun et al.
attribution name: Sun et al.

Density dependent attributes of fish aggregative behaviour
type: item
type: AcademicArticle
description: Grouping behaviour, as fascinating as it is unclear, has lately drawn the attention of numerous researchers. While most of the authors focused their work on a mechanistic approach to the matter of schooling, this study explores the issue from a population point of view. Present camera observation study on the fish community carried out in the epipelagic habitat of a European temperate reservoir in the Czech Republic explored the relationship between density and aggregative features of predominantly cyprinid fish stock. Results demonstrated that schooling behaviour is triggered by the ‘critical density’ of fish in the habitat. School size as well as counts of schools and proportion of schooling individuals increased with the density of fish. Counts of clusters (observed units in time, including singletons, pairs and schools) and cluster size, on the other hand, showed a slowing tendency to increase. The slower increase implies the tendency of fish for not being frequent but rather to create larger groups. Altogether, our findings suggest that fish density is a triggering factor in the formation of large fish schools. As the tendency of cyprinid species for school formation could be an evolutional advantage responsible for dominance in later succession phases of water bodies, we suggest that more in situ studies should be encouraged for the proper understanding of the ecological interactions that drive the structure of aquatic ecosystems and for ensuring unbiased assessment.
format: application/pdf
format: text/html
creator: Michaela Holubová
creator: Martin Čech
creator: Mojmír Vašek
creator: Jiří Peterka
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.6378
publisher: PeerJ Inc.
rights: © 2019 Holubová et al.
abstract: Grouping behaviour, as fascinating as it is unclear, has lately drawn the attention of numerous researchers. While most of the authors focused their work on a mechanistic approach to the matter of schooling, this study explores the issue from a population point of view. Present camera observation study on the fish community carried out in the epipelagic habitat of a European temperate reservoir in the Czech Republic explored the relationship between density and aggregative features of predominantly cyprinid fish stock. Results demonstrated that schooling behaviour is triggered by the ‘critical density’ of fish in the habitat. School size as well as counts of schools and proportion of schooling individuals increased with the density of fish. Counts of clusters (observed units in time, including singletons, pairs and schools) and cluster size, on the other hand, showed a slowing tendency to increase. The slower increase implies the tendency of fish for not being frequent but rather to create larger groups. Altogether, our findings suggest that fish density is a triggering factor in the formation of large fish schools. As the tendency of cyprinid species for school formation could be an evolutional advantage responsible for dominance in later succession phases of water bodies, we suggest that more in situ studies should be encouraged for the proper understanding of the ecological interactions that drive the structure of aquatic ecosystems and for ensuring unbiased assessment.
bibliographic citation: Holubová et al. (2019) Density dependent attributes of fish aggregative behaviour. PeerJ 7:e6378 https://doi.org/10.7717/peerj.6378
date submitted: 2018-08-30
date accepted: 2018-12-28
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holubová
  given name: Michaela
author list: Agent
  family name: Čech
  given name: Martin
author list: Agent
  family name: Vašek
  given name: Mojmír
author list: Agent
  family name: Peterka
  given name: Jiří
doi: 10.7717/peerj.6378
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Holubová et al.
attribution name: Holubová et al.

Recent dating of extinct Atlantic gray whale fossils, (Eschrichtius robustus), Georgia Bight and Florida, western Atlantic Ocean
type: item
type: AcademicArticle
description: The Atlantic gray whale (Eschrichtius robustus) presents an interesting case study of climate related dispersal and extinction. While (limited) fossil records confirm its presence in the Atlantic up until the 18th Century, its abundance and distribution within the Eastern and Western basins are still not well understood. The discovery of presumed gray whale fossil remains from the Georgia Bight and the Atlantic coast of Florida, from the mid-1980s to late-2000s, provides a new opportunity to recover additional data regarding their chronology within the Western basin. Here, we apply accelerator mass spectrometry radiocarbon techniques to six fossil whale finds, identifying dates within marine isotope stage 3 (59–24 ka) and the late Holocene, ∼2,000 yr BP. We additionally confirm the taxonomic identification of two fossil bone samples as E. robustus using collagen peptide mass fingerprinting (ZooMS). The obtained dates, when combined with a larger corpus of previously published Atlantic gray whale fossil dates, support the hypothesis for the decline of the Atlantic gray whale in the late Pleistocene and the late Holocene. These new data augment the findings of the Eastern Atlantic Basin and better incorporate the Western Atlantic Basin into a pan-ocean understanding for the species.
format: application/pdf
format: text/html
creator: Ervan G. Garrison
creator: Gary S. Morgan
creator: Krista McGrath
creator: Camilla Speller
creator: Alexander Cherkinsky
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Paleontology
description: doi:10.7717/peerj.6381
publisher: PeerJ Inc.
rights: © 2019 Garrison et al.
abstract: The Atlantic gray whale (Eschrichtius robustus) presents an interesting case study of climate related dispersal and extinction. While (limited) fossil records confirm its presence in the Atlantic up until the 18th Century, its abundance and distribution within the Eastern and Western basins are still not well understood. The discovery of presumed gray whale fossil remains from the Georgia Bight and the Atlantic coast of Florida, from the mid-1980s to late-2000s, provides a new opportunity to recover additional data regarding their chronology within the Western basin. Here, we apply accelerator mass spectrometry radiocarbon techniques to six fossil whale finds, identifying dates within marine isotope stage 3 (59–24 ka) and the late Holocene, ∼2,000 yr BP. We additionally confirm the taxonomic identification of two fossil bone samples as E. robustus using collagen peptide mass fingerprinting (ZooMS). The obtained dates, when combined with a larger corpus of previously published Atlantic gray whale fossil dates, support the hypothesis for the decline of the Atlantic gray whale in the late Pleistocene and the late Holocene. These new data augment the findings of the Eastern Atlantic Basin and better incorporate the Western Atlantic Basin into a pan-ocean understanding for the species.
bibliographic citation: Garrison et al. (2019) Recent dating of extinct Atlantic gray whale fossils, (Eschrichtius robustus), Georgia Bight and Florida, western Atlantic Ocean. PeerJ 7:e6381 https://doi.org/10.7717/peerj.6381
date submitted: 2018-07-03
date accepted: 2018-12-28
issued: 2019-02-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garrison
  given name: Ervan G.
author list: Agent
  family name: Morgan
  given name: Gary S.
author list: Agent
  family name: McGrath
  given name: Krista
author list: Agent
  family name: Speller
  given name: Camilla
author list: Agent
  family name: Cherkinsky
  given name: Alexander
doi: 10.7717/peerj.6381
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-04
copyright: © 2019 Garrison et al.
attribution name: Garrison et al.

The rise of feathered dinosaurs: Kulindadromeus zabaikalicus, the oldest dinosaur with ‘feather-like’ structures
type: item
type: AcademicArticle
description: Diverse epidermal appendages including grouped filaments closely resembling primitive feathers in non-avian theropods, are associated with skeletal elements in the primitive ornithischian dinosaur Kulindadromeus zabaikalicus from the Kulinda locality in south-eastern Siberia. This discovery suggests that “feather-like” structures did not evolve exclusively in theropod dinosaurs, but were instead potentially widespread in the whole dinosaur clade. The dating of the Kulinda locality is therefore particularly important for reconstructing the evolution of “feather-like” structures in dinosaurs within a chronostratigraphic framework. Here we present the first dating of the Kulinda locality, combining U-Pb analyses (LA-ICP-MS) on detrital zircons and monazites from sedimentary rocks of volcaniclastic origin and palynological observations. Concordia ages constrain the maximum age of the volcaniclastic deposits at 172.8 ± 1.6 Ma, corresponding to the Aalenian (Middle Jurassic). The palynological assemblage includes taxa that are correlated to Bathonian palynozones from western Siberia, and therefore constrains the minimum age of the deposits. The new U-Pb ages, together with the palynological data, provide evidence of a Bathonian age—between 168.3 ± 1.3 Ma and 166.1 ± 1.2 Ma—for Kulindadromeus. This is older than the previous Late Jurassic to Early Cretaceous ages tentatively based on local stratigraphic correlations. A Bathonian age is highly consistent with the phylogenetic position of Kulindadromeus at the base of the neornithischian clade and suggests that cerapodan dinosaurs originated in Asia during the Middle Jurassic, from a common ancestor that closely looked like Kulindadromeus. Our results consequently show that Kulindadromeus is the oldest known dinosaur with “feather-like” structures discovered so far.
format: application/pdf
format: text/html
creator: Aude Cincotta
creator: Ekaterina B. Pestchevitskaya
creator: Sofia M. Sinitsa
creator: Valentina S. Markevich
creator: Vinciane Debaille
creator: Svetlana A. Reshetova
creator: Irina M. Mashchuk
creator: Andrei O. Frolov
creator: Axel Gerdes
creator: Johan Yans
creator: Pascal Godefroit
subject: Paleontology
description: doi:10.7717/peerj.6239
publisher: PeerJ Inc.
rights: © 2019 Cincotta et al.
abstract: Diverse epidermal appendages including grouped filaments closely resembling primitive feathers in non-avian theropods, are associated with skeletal elements in the primitive ornithischian dinosaur Kulindadromeus zabaikalicus from the Kulinda locality in south-eastern Siberia. This discovery suggests that “feather-like” structures did not evolve exclusively in theropod dinosaurs, but were instead potentially widespread in the whole dinosaur clade. The dating of the Kulinda locality is therefore particularly important for reconstructing the evolution of “feather-like” structures in dinosaurs within a chronostratigraphic framework. Here we present the first dating of the Kulinda locality, combining U-Pb analyses (LA-ICP-MS) on detrital zircons and monazites from sedimentary rocks of volcaniclastic origin and palynological observations. Concordia ages constrain the maximum age of the volcaniclastic deposits at 172.8 ± 1.6 Ma, corresponding to the Aalenian (Middle Jurassic). The palynological assemblage includes taxa that are correlated to Bathonian palynozones from western Siberia, and therefore constrains the minimum age of the deposits. The new U-Pb ages, together with the palynological data, provide evidence of a Bathonian age—between 168.3 ± 1.3 Ma and 166.1 ± 1.2 Ma—for Kulindadromeus. This is older than the previous Late Jurassic to Early Cretaceous ages tentatively based on local stratigraphic correlations. A Bathonian age is highly consistent with the phylogenetic position of Kulindadromeus at the base of the neornithischian clade and suggests that cerapodan dinosaurs originated in Asia during the Middle Jurassic, from a common ancestor that closely looked like Kulindadromeus. Our results consequently show that Kulindadromeus is the oldest known dinosaur with “feather-like” structures discovered so far.
bibliographic citation: Cincotta et al. (2019) The rise of feathered dinosaurs: Kulindadromeus zabaikalicus, the oldest dinosaur with ‘feather-like’ structures. PeerJ 7:e6239 https://doi.org/10.7717/peerj.6239
date submitted: 2018-10-12
date accepted: 2018-12-08
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cincotta
  given name: Aude
author list: Agent
  family name: Pestchevitskaya
  given name: Ekaterina B.
author list: Agent
  family name: Sinitsa
  given name: Sofia M.
author list: Agent
  family name: Markevich
  given name: Valentina S.
author list: Agent
  family name: Debaille
  given name: Vinciane
author list: Agent
  family name: Reshetova
  given name: Svetlana A.
author list: Agent
  family name: Mashchuk
  given name: Irina M.
author list: Agent
  family name: Frolov
  given name: Andrei O.
author list: Agent
  family name: Gerdes
  given name: Axel
author list: Agent
  family name: Yans
  given name: Johan
author list: Agent
  family name: Godefroit
  given name: Pascal
doi: 10.7717/peerj.6239
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: ©2019 Cincotta et al.
attribution name: Cincotta et al.

African savanna elephants (Loxodonta africana) as an example of a herbivore making movement choices based on nutritional needs
type: item
type: AcademicArticle
description: Background The increasing human population and global intensification of agriculture have had a major impact on the world’s natural ecosystems and caused devastating effects on populations of mega-herbivores such as the African savanna elephants, through habitat reduction and fragmentation and increased human–animal conflict. Animals with vast home ranges are forced into increasingly smaller geographical areas, often restricted by fencing or encroaching anthropogenic activities, resulting in huge pressures on these areas to meet the animals’ resource needs. This can present a nutritional challenge and cause animals to adapt their movement patterns to meet their dietary needs for specific minerals, potentially causing human–animal conflict. The aim of this review is to consolidate understanding of nutritional drivers for animal movement, especially that of African savanna elephants and focus the direction of future research. Peer reviewed literature available was generally geographically specific and studies conducted on isolated populations of individual species. African savanna elephants have the capacity to extensively alter the landscape and have been more greatly studied than other herbivores, making them a good example species to use for this review. Alongside this, their movement choices, potentially linked with nutritional drivers could be applicable to a range of other species. Relevant case study examples of other herbivores moving based on nutritional needs are discussed. Methods Three databases were searched in this review: Scopus, Web of Science and Google Scholar, using identified search terms. Inclusion and exclusion criteria were determined and applied as required. Additional grey literature was reviewed as appropriate. Results Initial searches yielded 1,870 records prior to application of inclusion and exclusion criteria. A less detailed review of grey literature, and additional peer-reviewed literature which did not meet the inclusion criteria but w…
format: application/pdf
format: text/html
creator: Fiona Sach
creator: Ellen S. Dierenfeld
creator: Simon C. Langley-Evans
creator: Michael J. Watts
creator: Lisa Yon
subject: Animal Behavior
subject: Biogeography
subject: Zoology
subject: Nutrition
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.6260
publisher: PeerJ Inc.
rights: © 2019 Sach et al.
abstract: Background The increasing human population and global intensification of agriculture have had a major impact on the world’s natural ecosystems and caused devastating effects on populations of mega-herbivores such as the African savanna elephants, through habitat reduction and fragmentation and increased human–animal conflict. Animals with vast home ranges are forced into increasingly smaller geographical areas, often restricted by fencing or encroaching anthropogenic activities, resulting in huge pressures on these areas to meet the animals’ resource needs. This can present a nutritional challenge and cause animals to adapt their movement patterns to meet their dietary needs for specific minerals, potentially causing human–animal conflict. The aim of this review is to consolidate understanding of nutritional drivers for animal movement, especially that of African savanna elephants and focus the direction of future research. Peer reviewed literature available was generally geographically specific and studies conducted on isolated populations of individual species. African savanna elephants have the capacity to extensively alter the landscape and have been more greatly studied than other herbivores, making them a good example species to use for this review. Alongside this, their movement choices, potentially linked with nutritional drivers could be applicable to a range of other species. Relevant case study examples of other herbivores moving based on nutritional needs are discussed. Methods Three databases were searched in this review: Scopus, Web of Science and Google Scholar, using identified search terms. Inclusion and exclusion criteria were determined and applied as required. Additional grey literature was reviewed as appropriate. Results Initial searches yielded 1,870 records prior to application of inclusion and exclusion criteria. A less detailed review of grey literature, and additional peer-reviewed literature which did not meet the inclusion criteria but w…
bibliographic citation: Sach et al. (2019) African savanna elephants (Loxodonta africana) as an example of a herbivore making movement choices based on nutritional needs. PeerJ 7:e6260 https://doi.org/10.7717/peerj.6260
date submitted: 2018-07-03
date accepted: 2018-12-07
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sach
  given name: Fiona
author list: Agent
  family name: Dierenfeld
  given name: Ellen S.
author list: Agent
  family name: Langley-Evans
  given name: Simon C.
author list: Agent
  family name: Watts
  given name: Michael J.
author list: Agent
  family name: Yon
  given name: Lisa
doi: 10.7717/peerj.6260
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: © 2019 Sach et al.
attribution name: Sach et al.

Suppression of hesA mutation on nitrogenase activity in Paenibacillus polymyxa WLY78 with the addition of high levels of molybdate or cystine
type: item
type: AcademicArticle
description: The diazotrophic Paenibacillus polymyxa WLY78 possesses a minimal nitrogen fixation gene cluster consisting of nine genes (nifB nifH nifD nifK nifE nifN nifX hesA and nifV). Notably, the hesA gene contained within the nif gene cluster is also found within nif gene clusters among diazotrophic cyanobacteria and Frankia. The predicted product HesA is a member of the ThiF-MoeB-HesA family containing an N-terminal nucleotide binding domain and a C-terminal MoeZ/MoeB-like domain. However, the function of hesA gene in nitrogen fixation is unknown. In this study, we demonstrate that the hesA mutation of P. polymyxa WLY78 leads to nearly complete loss of nitrogenase activity. The effect of the mutation can be partially suppressed by the addition of high levels of molybdate or cystine. However, the nitrogenase activity of the hesA mutant could not be restored by Klebsiella oxytoca nifQ or Escherichia coli moeB completely. In addition, the hesA mutation does not affect nitrate reductase activity of P. polymyxa WLY78. Our results demonstrate hesA is a novel gene specially required for nitrogen fixation and its role is related to introduction of S and Mo into the FeMo-co of nitrogenase.
format: application/pdf
format: text/html
creator: Xiaomeng Liu
creator: Xiyun Zhao
creator: Xiaohan Li
creator: Sanfeng Chen
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6294
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: The diazotrophic Paenibacillus polymyxa WLY78 possesses a minimal nitrogen fixation gene cluster consisting of nine genes (nifB nifH nifD nifK nifE nifN nifX hesA and nifV). Notably, the hesA gene contained within the nif gene cluster is also found within nif gene clusters among diazotrophic cyanobacteria and Frankia. The predicted product HesA is a member of the ThiF-MoeB-HesA family containing an N-terminal nucleotide binding domain and a C-terminal MoeZ/MoeB-like domain. However, the function of hesA gene in nitrogen fixation is unknown. In this study, we demonstrate that the hesA mutation of P. polymyxa WLY78 leads to nearly complete loss of nitrogenase activity. The effect of the mutation can be partially suppressed by the addition of high levels of molybdate or cystine. However, the nitrogenase activity of the hesA mutant could not be restored by Klebsiella oxytoca nifQ or Escherichia coli moeB completely. In addition, the hesA mutation does not affect nitrate reductase activity of P. polymyxa WLY78. Our results demonstrate hesA is a novel gene specially required for nitrogen fixation and its role is related to introduction of S and Mo into the FeMo-co of nitrogenase.
bibliographic citation: Liu et al. (2019) Suppression of hesA mutation on nitrogenase activity in Paenibacillus polymyxa WLY78 with the addition of high levels of molybdate or cystine. PeerJ 7:e6294 https://doi.org/10.7717/peerj.6294
date submitted: 2018-10-30
date accepted: 2018-12-17
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiaomeng
author list: Agent
  family name: Zhao
  given name: Xiyun
author list: Agent
  family name: Li
  given name: Xiaohan
author list: Agent
  family name: Chen
  given name: Sanfeng
doi: 10.7717/peerj.6294
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: © 2019 Liu et al.
attribution name: Liu et al.

Wild edible fool’s watercress, a potential crop with high nutraceutical properties
type: item
type: AcademicArticle
description: Background Fool’s watercress (Apium nodiflorum) is an edible vegetable with potential as a new crop. However, little information is available regarding the antioxidant properties of the plant and the individual phenolics accounting for this capacity are unknown. Methods The antioxidant properties of twenty-five wild populations were analysed and individual phenolics present in the species reported and compared with celery and parsley. The antioxidant activity was measured as the 2,2-diphenyl-1-picrylhydrazyl hydrate (DPPH) free radical scavenging capacity, and the total phenolics content (TPC) via the Folin-Ciocalteu procedure. The individual phenolics constituents were determined via high performance liquid chromatography (HPLC) as aglycones. Results The average DPPH and TPC of fool’s watercress were 28.1 mg Trolox g−1 DW and 22.3 mg of chlorogenic acid equivalents g−1 DW, respectively, much higher than those of celery and parsley. Significant differences for both DPPH and TPC, which may be explained by either genotype or environmental factors, were detected among groups established according to geographical origin. Quercetin was identified as the major phenolic present in the leaves of the species, unlike parsley and celery, in which high amounts of apigenin and luteolin were determined. Quercetin represented 61.6% of the phenolics targeted in fool’s watercress, followed by caffeic acid derivatives as main hydroxycinnamic acids. Discussion The study reports the high antioxidant properties of fool’s watercress based on a large number of populations. Results suggest that quercetin accounts for an important share of the antioxidant capacity of this potential new crop. The study also provides a basis for future breeding programs, suggesting that selection by geographical locations may result in differences in the antioxidant properties.
format: application/pdf
format: text/html
creator: Carla Guijarro-Real
creator: Jaime Prohens
creator: Adrian Rodriguez-Burruezo
creator: Ana María Adalid-Martínez
creator: M Pilar López-Gresa
creator: Ana Fita
subject: Biochemistry
subject: Food Science and Technology
description: doi:10.7717/peerj.6296
publisher: PeerJ Inc.
rights: © 2019 Guijarro-Real et al.
abstract: Background Fool’s watercress (Apium nodiflorum) is an edible vegetable with potential as a new crop. However, little information is available regarding the antioxidant properties of the plant and the individual phenolics accounting for this capacity are unknown. Methods The antioxidant properties of twenty-five wild populations were analysed and individual phenolics present in the species reported and compared with celery and parsley. The antioxidant activity was measured as the 2,2-diphenyl-1-picrylhydrazyl hydrate (DPPH) free radical scavenging capacity, and the total phenolics content (TPC) via the Folin-Ciocalteu procedure. The individual phenolics constituents were determined via high performance liquid chromatography (HPLC) as aglycones. Results The average DPPH and TPC of fool’s watercress were 28.1 mg Trolox g−1 DW and 22.3 mg of chlorogenic acid equivalents g−1 DW, respectively, much higher than those of celery and parsley. Significant differences for both DPPH and TPC, which may be explained by either genotype or environmental factors, were detected among groups established according to geographical origin. Quercetin was identified as the major phenolic present in the leaves of the species, unlike parsley and celery, in which high amounts of apigenin and luteolin were determined. Quercetin represented 61.6% of the phenolics targeted in fool’s watercress, followed by caffeic acid derivatives as main hydroxycinnamic acids. Discussion The study reports the high antioxidant properties of fool’s watercress based on a large number of populations. Results suggest that quercetin accounts for an important share of the antioxidant capacity of this potential new crop. The study also provides a basis for future breeding programs, suggesting that selection by geographical locations may result in differences in the antioxidant properties.
bibliographic citation: Guijarro-Real et al. (2019) Wild edible fool’s watercress, a potential crop with high nutraceutical properties. PeerJ 7:e6296 https://doi.org/10.7717/peerj.6296
date submitted: 2018-09-24
date accepted: 2018-12-18
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guijarro-Real
  given name: Carla
author list: Agent
  family name: Prohens
  given name: Jaime
author list: Agent
  family name: Rodriguez-Burruezo
  given name: Adrian
author list: Agent
  family name: Adalid-Martínez
  given name: Ana María
author list: Agent
  family name: López-Gresa
  given name: M Pilar
author list: Agent
  family name: Fita
  given name: Ana
doi: 10.7717/peerj.6296
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: ©2019 Guijarro-Real et al.
attribution name: Guijarro-Real et al.

Total incombustible (mineral) content of Cherax quadricarinatus differs between feral populations in Central-Eastern Australia
type: item
type: AcademicArticle
description: Cherax quadricarinatus has been widely translocated within Australia, and a number of self-sustaining feral populations have established, and persisted, in central-eastern Australia for over 20 years: however, the biology and ecology of feral populations remain poorly understood. Using the loss-by-ignition method, this study investigated differences in the total content of incombustible material (as a proxy for total mineral content), between feral C. quadricarinatus populations in southeast Queensland and northeastern New South Wales. A total of 102 C. quadricarinatus were ignited, and percent total incombustible material was not proportional to the body size, or gender of the crayfish. Incombustible content was however, significantly different between some locations of capture (i.e., waterbodies). The site where incombustible content in crayfish was atypical, Lake Ainsworth, is a naturally acidic coastal lake, and we suggest that acidity and low concentration of calcium in that waterbody are likely responsible for the difference in mineral content detected in that population. Mechanism(s) driving the difference detected in the Lake Ainsworth population are unknown, but we suggest the acidic environment could directly impact maintenance of internal calcium reserves in the crayfish (intermoult), during recalcification of the cuticle (postmoult), or both. Limited calcium availability in the lake may also be a direct, or indirect, contributing factor. The ability of C. quadricarinatus to occupy acidic habitats while managing biomineralization challenges possibly could enable additional range-expansion of the species, and potential impacts on both endangered ecological communities and other biota occupying the acidic coastal habitats of Eastern Australia.
format: application/pdf
format: text/html
creator: Leyton J. Tierney
creator: Clyde H. Wild
creator: James M. Furse
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Biosphere Interactions
subject: Freshwater Biology
description: doi:10.7717/peerj.6351
publisher: PeerJ Inc.
rights: © 2019 Tierney et al.
abstract: Cherax quadricarinatus has been widely translocated within Australia, and a number of self-sustaining feral populations have established, and persisted, in central-eastern Australia for over 20 years: however, the biology and ecology of feral populations remain poorly understood. Using the loss-by-ignition method, this study investigated differences in the total content of incombustible material (as a proxy for total mineral content), between feral C. quadricarinatus populations in southeast Queensland and northeastern New South Wales. A total of 102 C. quadricarinatus were ignited, and percent total incombustible material was not proportional to the body size, or gender of the crayfish. Incombustible content was however, significantly different between some locations of capture (i.e., waterbodies). The site where incombustible content in crayfish was atypical, Lake Ainsworth, is a naturally acidic coastal lake, and we suggest that acidity and low concentration of calcium in that waterbody are likely responsible for the difference in mineral content detected in that population. Mechanism(s) driving the difference detected in the Lake Ainsworth population are unknown, but we suggest the acidic environment could directly impact maintenance of internal calcium reserves in the crayfish (intermoult), during recalcification of the cuticle (postmoult), or both. Limited calcium availability in the lake may also be a direct, or indirect, contributing factor. The ability of C. quadricarinatus to occupy acidic habitats while managing biomineralization challenges possibly could enable additional range-expansion of the species, and potential impacts on both endangered ecological communities and other biota occupying the acidic coastal habitats of Eastern Australia.
bibliographic citation: Tierney et al. (2019) Total incombustible (mineral) content of Cherax quadricarinatus differs between feral populations in Central-Eastern Australia. PeerJ 7:e6351 https://doi.org/10.7717/peerj.6351
date submitted: 2018-01-29
date accepted: 2018-12-26
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tierney
  given name: Leyton J.
author list: Agent
  family name: Wild
  given name: Clyde H.
author list: Agent
  family name: Furse
  given name: James M.
doi: 10.7717/peerj.6351
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: © 2019 Tierney et al.
attribution name: Tierney et al.

New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east–west lineage split and genetic mixture within western subtropical China
type: item
type: AcademicArticle
description: Background Subtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species. Liriodendron chinense is a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern of L. chinense and to explore the role of mountains in the conservation of L. chinense genetic resources. Methods Three chloroplast regions (psbJ-petA, rpl32-ndhF, and trnK5’-matK) were sequenced in 40 populations of L. chinense for phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods. Results Obvious phylogeographic structure was found in L. chinense. SAMOVA revealed seven groups matching the major landscape features of the L. chinense distribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin of L. chinense in the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage. Discussion The clear geographical distributions of haplotypes suggested multiple mountainous refugia of L. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots…
format: application/pdf
format: text/html
creator: Aihong Yang
creator: Yongda Zhong
creator: Shujuan Liu
creator: Lipan Liu
creator: Tengyun Liu
creator: Yanqiang Li
creator: Faxin Yu
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Plant Science
description: doi:10.7717/peerj.6355
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Background Subtropical China is a global center of biodiversity and one of the most important refugia worldwide. Mountains play an important role in conserving the genetic resources of species. Liriodendron chinense is a Tertiary relict tree largely endemic to subtropical China. In this study, we aimed to achieve a better understanding of the phylogeographical pattern of L. chinense and to explore the role of mountains in the conservation of L. chinense genetic resources. Methods Three chloroplast regions (psbJ-petA, rpl32-ndhF, and trnK5’-matK) were sequenced in 40 populations of L. chinense for phylogeographical analyses. Relationships among chloroplast DNA (cpDNA) haplotypes were determined using median-joining networks, and genetic structure was examined by spatial analysis of molecular variance (SAMOVA). The ancestral area of the species was reconstructed using the Bayesian binary Markov Chain Monte Carlo (BBM) method according to its geographic distribution and a maximum parsimony (MP) tree based on Bayesian methods. Results Obvious phylogeographic structure was found in L. chinense. SAMOVA revealed seven groups matching the major landscape features of the L. chinense distribution area. The haplotype network showed three clades distributed in the eastern, southwestern, and northwestern regions. Separate northern and southern refugia were found in the Wu Mountains and Yungui Plateau, with genetic admixture in the Dalou Mountains and Wuling Mountains. BBM revealed a more ancient origin of L. chinense in the eastern region, with a west–east split most likely having occurred during the Mindel glacial stage. Discussion The clear geographical distributions of haplotypes suggested multiple mountainous refugia of L. chinense. The east–west lineage split was most likely a process of gradual genetic isolation and allopatric lineage divergence when the Nanling corridor was frequently occupied by evergreen or coniferous forest during Late Quaternary oscillations. Hotspots…
bibliographic citation: Yang et al. (2019) New insight into the phylogeographic pattern of Liriodendron chinense (Magnoliaceae) revealed by chloroplast DNA: east–west lineage split and genetic mixture within western subtropical China. PeerJ 7:e6355 https://doi.org/10.7717/peerj.6355
date submitted: 2018-09-13
date accepted: 2018-12-26
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Aihong
author list: Agent
  family name: Zhong
  given name: Yongda
author list: Agent
  family name: Liu
  given name: Shujuan
author list: Agent
  family name: Liu
  given name: Lipan
author list: Agent
  family name: Liu
  given name: Tengyun
author list: Agent
  family name: Li
  given name: Yanqiang
author list: Agent
  family name: Yu
  given name: Faxin
doi: 10.7717/peerj.6355
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: © 2019 Yang et al.
attribution name: Yang et al.

Identification of species and materia medica within Saussurea subg. Amphilaena based on DNA barcodes
type: item
type: AcademicArticle
description: Saussurea is one of the most species-rich genera in the family Asteraceae, where some have a complex evolutionary history, including radiation and convergent evolution, and the identification of these species is notoriously difficult. This genus contains many plants with medical uses, and thus an objective identification method is urgently needed. Saussurea subg. Amphilaena is one of the four subgenera of Saussurea and it is particularly rich in medical resources, where 15/39 species are used in medicine. To test the application of DNA barcodes in this subgenus, five candidates were sequenced and analyzed using 131 individuals representing 15 medical plants and four additional species from this subgenus. Our results suggested that internal transcribed spacer (ITS) + rbcL or ITS + rbcL + psbA-trnH could distinguish all of the species, while the ITS alone could identify all of the 15 medical plants. However, the species identification rates based on plastid barcodes were low, i.e., 0% to 36% when analyzed individually, and 63% when all four loci were combined. Thus, we recommend using ITS + rbcL as the DNA barcode for S. subg. Amphilaena or the ITS alone for medical plants. Possible taxonomic problems and substitutes for medicinal plant materials are also discussed.
format: application/pdf
format: text/html
creator: Jie Chen
creator: Yong-Bao Zhao
creator: Yu-Jin Wang
creator: Xiao-Gang Li
subject: Biochemistry
subject: Molecular Biology
subject: Plant Science
subject: Taxonomy
subject: Pharmacology
description: doi:10.7717/peerj.6357
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Saussurea is one of the most species-rich genera in the family Asteraceae, where some have a complex evolutionary history, including radiation and convergent evolution, and the identification of these species is notoriously difficult. This genus contains many plants with medical uses, and thus an objective identification method is urgently needed. Saussurea subg. Amphilaena is one of the four subgenera of Saussurea and it is particularly rich in medical resources, where 15/39 species are used in medicine. To test the application of DNA barcodes in this subgenus, five candidates were sequenced and analyzed using 131 individuals representing 15 medical plants and four additional species from this subgenus. Our results suggested that internal transcribed spacer (ITS) + rbcL or ITS + rbcL + psbA-trnH could distinguish all of the species, while the ITS alone could identify all of the 15 medical plants. However, the species identification rates based on plastid barcodes were low, i.e., 0% to 36% when analyzed individually, and 63% when all four loci were combined. Thus, we recommend using ITS + rbcL as the DNA barcode for S. subg. Amphilaena or the ITS alone for medical plants. Possible taxonomic problems and substitutes for medicinal plant materials are also discussed.
bibliographic citation: Chen et al. (2019) Identification of species and materia medica within Saussurea subg. Amphilaena based on DNA barcodes. PeerJ 7:e6357 https://doi.org/10.7717/peerj.6357
date submitted: 2018-09-11
date accepted: 2018-12-28
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Zhao
  given name: Yong-Bao
author list: Agent
  family name: Wang
  given name: Yu-Jin
author list: Agent
  family name: Li
  given name: Xiao-Gang
doi: 10.7717/peerj.6357
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: ©2019 Chen et al.
attribution name: Chen et al.

A gelatin/collagen/polycaprolactone scaffold for skin regeneration
type: item
type: AcademicArticle
description: Background A tissue-engineered skin substitute, based on gelatin (“G”), collagen (“C”), and poly(ε-caprolactone) (PCL; “P”), was developed. Method G/C/P biocomposites were fabricated by impregnation of lyophilized gelatin/collagen (GC) mats with PCL solutions, followed by solvent evaporation. Two different GC:PCL ratios (1:8 and 1:20) were used. Results Differential scanning calorimetry revealed that all G/C/P biocomposites had characteristic melting point of PCL at around 60 °C. Scanning electron microscopy showed that all biocomposites had similar fibrous structures. Good cytocompatibility was present in all G/C/P biocomposites when incubated with primary human epidermal keratinocytes (PHEK), human dermal fibroblasts (PHDF) and human adipose-derived stem cells (ASCs) in vitro. All G/C/P biocomposites exhibited similar cell growth and mechanical characteristics in comparison with C/P biocomposites. G/C/P biocomposites with a lower collagen content showed better cell proliferation than those with a higher collagen content in vitro. Due to reasonable mechanical strength and biocompatibility in vitro, G/C/P with a lower content of collagen and a higher content of PCL (GCLPH) was selected for animal wound healing studies. According to our data, a significant promotion in wound healing and skin regeneration could be observed in GCLPH seeded with adipose-derived stem cells by Gomori’s trichrome staining. Conclusion This study may provide an effective and low-cost wound dressings to assist skin regeneration for clinical use.
format: application/pdf
format: text/html
creator: Lin-Gwei Wei
creator: Hsin-I Chang
creator: Yiwei Wang
creator: Shan-hui Hsu
creator: Lien-Guo Dai
creator: Keng-Yen Fu
creator: Niann-Tzyy Dai
subject: Bioengineering
subject: Biotechnology
subject: Cell Biology
subject: Dermatology
description: doi:10.7717/peerj.6358
publisher: PeerJ Inc.
rights: © 2019 Wei et al.
abstract: Background A tissue-engineered skin substitute, based on gelatin (“G”), collagen (“C”), and poly(ε-caprolactone) (PCL; “P”), was developed. Method G/C/P biocomposites were fabricated by impregnation of lyophilized gelatin/collagen (GC) mats with PCL solutions, followed by solvent evaporation. Two different GC:PCL ratios (1:8 and 1:20) were used. Results Differential scanning calorimetry revealed that all G/C/P biocomposites had characteristic melting point of PCL at around 60 °C. Scanning electron microscopy showed that all biocomposites had similar fibrous structures. Good cytocompatibility was present in all G/C/P biocomposites when incubated with primary human epidermal keratinocytes (PHEK), human dermal fibroblasts (PHDF) and human adipose-derived stem cells (ASCs) in vitro. All G/C/P biocomposites exhibited similar cell growth and mechanical characteristics in comparison with C/P biocomposites. G/C/P biocomposites with a lower collagen content showed better cell proliferation than those with a higher collagen content in vitro. Due to reasonable mechanical strength and biocompatibility in vitro, G/C/P with a lower content of collagen and a higher content of PCL (GCLPH) was selected for animal wound healing studies. According to our data, a significant promotion in wound healing and skin regeneration could be observed in GCLPH seeded with adipose-derived stem cells by Gomori’s trichrome staining. Conclusion This study may provide an effective and low-cost wound dressings to assist skin regeneration for clinical use.
bibliographic citation: Wei et al. (2019) A gelatin/collagen/polycaprolactone scaffold for skin regeneration. PeerJ 7:e6358 https://doi.org/10.7717/peerj.6358
date submitted: 2018-03-11
date accepted: 2018-12-28
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Lin-Gwei
author list: Agent
  family name: Chang
  given name: Hsin-I
author list: Agent
  family name: Wang
  given name: Yiwei
author list: Agent
  family name: Hsu
  given name: Shan-hui
author list: Agent
  family name: Dai
  given name: Lien-Guo
author list: Agent
  family name: Fu
  given name: Keng-Yen
author list: Agent
  family name: Dai
  given name: Niann-Tzyy
doi: 10.7717/peerj.6358
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: ©2019 Wei et al.
attribution name: Wei et al.

Time arrow in published clinical studies/trials indexed in MEDLINE: a systematic analysis of retrospective vs. prospective study design, from 1960 to 2017
type: item
type: AcademicArticle
description: Clinical studies/trials are experiments or observations on human subjects considered by the scientific community the most appropriate instrument to answer specific research questions on interventions on health outcomes. The time-line of the observations might be focused on a single time point or to follow time, backward or forward, in the so called, respectively, retrospective and prospective study design. Since the retrospective approach has been criticized for the possible sources of errors due to bias and confounding, we aimed this study to assess if there is a prevalence of retrospective vs. prospective design in the clinical studies/trials by querying MEDLINE. Our results on a sample of 1,438,872 studies/trials, (yrs 1960–2017), support a prevalence of retrospective, respectively 55% vs. 45%. To explain this result, a random sub-sample of studies where the country of origin was reported (n = 1,576) was categorized in high and low-income based onthe nominal Gross Domestic Product (GDP) and matched with the topic of the research. As expected, the absolute majority of studies/trials are carried on by high-income countries, respectively 86% vs. 14%; even if a slight prevalence of retrospective was recorded in both income groups, for the most part prospective studies are carried out by high-GDP countries, 85% vs. 15%. Finally, the differences in the design of the study are understandable when considering the topic of the research.
format: application/pdf
format: text/html
creator: Michele M. Ciulla
creator: Patrizia Vivona
subject: Bioinformatics
subject: Clinical Trials
subject: Epidemiology
subject: Statistics
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6363
publisher: PeerJ Inc.
rights: © 2019 Ciulla and Vivona
abstract: Clinical studies/trials are experiments or observations on human subjects considered by the scientific community the most appropriate instrument to answer specific research questions on interventions on health outcomes. The time-line of the observations might be focused on a single time point or to follow time, backward or forward, in the so called, respectively, retrospective and prospective study design. Since the retrospective approach has been criticized for the possible sources of errors due to bias and confounding, we aimed this study to assess if there is a prevalence of retrospective vs. prospective design in the clinical studies/trials by querying MEDLINE. Our results on a sample of 1,438,872 studies/trials, (yrs 1960–2017), support a prevalence of retrospective, respectively 55% vs. 45%. To explain this result, a random sub-sample of studies where the country of origin was reported (n = 1,576) was categorized in high and low-income based onthe nominal Gross Domestic Product (GDP) and matched with the topic of the research. As expected, the absolute majority of studies/trials are carried on by high-income countries, respectively 86% vs. 14%; even if a slight prevalence of retrospective was recorded in both income groups, for the most part prospective studies are carried out by high-GDP countries, 85% vs. 15%. Finally, the differences in the design of the study are understandable when considering the topic of the research.
bibliographic citation: Ciulla et al. (2019) Time arrow in published clinical studies/trials indexed in MEDLINE: a systematic analysis of retrospective vs. prospective study design, from 1960 to 2017. PeerJ 7:e6363 https://doi.org/10.7717/peerj.6363
date submitted: 2018-03-13
date accepted: 2018-12-30
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ciulla
  given name: Michele M.
author list: Agent
  family name: Vivona
  given name: Patrizia
doi: 10.7717/peerj.6363
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: ©2019 Ciulla and Vivona
attribution name: Ciulla and Vivona

Genes of the pig, Sus scrofa, reconstructed with EvidentialGene
type: item
type: AcademicArticle
description: The pig is a well-studied model animal of biomedical and agricultural importance. Genes of this species, Sus scrofa, are known from experiments and predictions, and collected at the NCBI reference sequence database section. Gene reconstruction from transcribed gene evidence of RNA-seq now can accurately and completely reproduce the biological gene sets of animals and plants. Such a gene set for the pig is reported here, including human orthologs missing from current NCBI and Ensembl reference pig gene sets, additional alternate transcripts, and other improvements. Methodology for accurate and complete gene set reconstruction from RNA is used: the automated SRA2Genes pipeline of EvidentialGene project.
format: application/pdf
format: text/html
creator: Donald G. Gilbert
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Data Science
description: doi:10.7717/peerj.6374
publisher: PeerJ Inc.
rights: © 2019 Gilbert
abstract: The pig is a well-studied model animal of biomedical and agricultural importance. Genes of this species, Sus scrofa, are known from experiments and predictions, and collected at the NCBI reference sequence database section. Gene reconstruction from transcribed gene evidence of RNA-seq now can accurately and completely reproduce the biological gene sets of animals and plants. Such a gene set for the pig is reported here, including human orthologs missing from current NCBI and Ensembl reference pig gene sets, additional alternate transcripts, and other improvements. Methodology for accurate and complete gene set reconstruction from RNA is used: the automated SRA2Genes pipeline of EvidentialGene project.
bibliographic citation: Gilbert (2019) Genes of the pig, Sus scrofa, reconstructed with EvidentialGene. PeerJ 7:e6374 https://doi.org/10.7717/peerj.6374
date submitted: 2018-09-10
date accepted: 2018-12-29
issued: 2019-02-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gilbert
  given name: Donald G.
doi: 10.7717/peerj.6374
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-01
copyright: © 2019 Gilbert
attribution name: Gilbert

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359