PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Ultraviolet disinfection impacts the microbial community composition and function of treated wastewater effluent and the receiving urban river
items: Ngwevu intloko: a new early sauropodomorph dinosaur from the Lower Jurassic Elliot Formation of South Africa and comments on cranial ontogeny in Massospondylus carinatus
items: Taxonomic reassessment of the genus Dichotomius (Coleoptera: Scarabaeinae) through integrative taxonomy
items: Elevated frequencies of total and MAIT cell subsets in patients with knee osteoarthritis
items: Sex differences in the response to angiotensin II receptor blockade in a rat model of eccentric cardiac hypertrophy
items: Effect of dietary concentrate to forage ratio on growth performance, rumen fermentation and bacterial diversity of Tibetan sheep under barn feeding on the Qinghai-Tibetan plateau
items: Binding interactions of epididymal protease inhibitor and semenogelin-1: a homology modeling, docking and molecular dynamics simulation study
items: Impact of digital video analytics on accuracy of chemobehavioural phenotyping in aquatic toxicology
items: The role of past experience in development of feeding behavior in common vampire bats
items: Pruning and dormancy breaking make two sustainable grape-cropping productions in a protected environment possible without overlap in a single year

Ultraviolet disinfection impacts the microbial community composition and function of treated wastewater effluent and the receiving urban river
type: item
type: AcademicArticle
description: Background In the United States, an estimated 14,748 wastewater treatment plants (WWTPs) provide wastewater collection, treatment, and disposal service to more than 230 million people. The quality of treated wastewater is often assessed by the presence or absence of fecal indicator bacteria. UV disinfection of wastewater is a common final treatment step used by many wastewater treatment plants in order to reduce fecal coliform bacteria and other pathogens; however, its potential impacts on the total effluent bacterial community are seemingly varied. This is especially important given that urban WWTPs typically return treated effluent to coastal and riverine environments and thus are a major source of microorganisms, genes, and chemical compounds to these systems. Following rainfall, stormflow conditions can result in substantial increases to effluent flow into combined systems. Methods Here, we conducted a lab-scale UV disinfection on WWTP effluent using UV dosage of 100 mJ/cm2 and monitored the active microbiome in UV-treated effluent and untreated effluent over the course of 48 h post-exposure using 16S rRNA sequencing. In addition, we simulated stormflow conditions with effluent UV-treated and untreated effluent additions to river water and compared the microbial communities to those in baseflow river water. We also tracked the functional profiles of genes involved in tetracycline resistance (tetW) and nitrification (amoA) in these microcosms using RT-qPCR. Results We showed that while some organisms, such as members of the Bacteroidetes, are inhibited by UV disinfection and overall diversity of the microbial community decreases following treatment, many organisms not only survive, but remain active. These include common WWTP-derived organisms such as Comamonadaceae and Pseudomonas. When combined with river water to mimic stormflow conditions, these organisms can persist in the environment and potentially enhance microbial functions such as nitrification and anti…
format: application/pdf
format: text/html
creator: Imrose Kauser
creator: Mark Ciesielski
creator: Rachel S. Poretsky
subject: Microbiology
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.7455
publisher: PeerJ Inc.
rights: © 2019 Kauser et al.
abstract: Background In the United States, an estimated 14,748 wastewater treatment plants (WWTPs) provide wastewater collection, treatment, and disposal service to more than 230 million people. The quality of treated wastewater is often assessed by the presence or absence of fecal indicator bacteria. UV disinfection of wastewater is a common final treatment step used by many wastewater treatment plants in order to reduce fecal coliform bacteria and other pathogens; however, its potential impacts on the total effluent bacterial community are seemingly varied. This is especially important given that urban WWTPs typically return treated effluent to coastal and riverine environments and thus are a major source of microorganisms, genes, and chemical compounds to these systems. Following rainfall, stormflow conditions can result in substantial increases to effluent flow into combined systems. Methods Here, we conducted a lab-scale UV disinfection on WWTP effluent using UV dosage of 100 mJ/cm2 and monitored the active microbiome in UV-treated effluent and untreated effluent over the course of 48 h post-exposure using 16S rRNA sequencing. In addition, we simulated stormflow conditions with effluent UV-treated and untreated effluent additions to river water and compared the microbial communities to those in baseflow river water. We also tracked the functional profiles of genes involved in tetracycline resistance (tetW) and nitrification (amoA) in these microcosms using RT-qPCR. Results We showed that while some organisms, such as members of the Bacteroidetes, are inhibited by UV disinfection and overall diversity of the microbial community decreases following treatment, many organisms not only survive, but remain active. These include common WWTP-derived organisms such as Comamonadaceae and Pseudomonas. When combined with river water to mimic stormflow conditions, these organisms can persist in the environment and potentially enhance microbial functions such as nitrification and anti…
bibliographic citation: Kauser et al. (2019) Ultraviolet disinfection impacts the microbial community composition and function of treated wastewater effluent and the receiving urban river. PeerJ 7:e7455 https://doi.org/10.7717/peerj.7455
date submitted: 2019-03-20
date accepted: 2019-07-10
issued: 2019-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kauser
  given name: Imrose
author list: Agent
  family name: Ciesielski
  given name: Mark
author list: Agent
  family name: Poretsky
  given name: Rachel S.
doi: 10.7717/peerj.7455
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-06
copyright: ©2019 Kauser et al.
attribution name: Kauser et al.

Ngwevu intloko: a new early sauropodomorph dinosaur from the Lower Jurassic Elliot Formation of South Africa and comments on cranial ontogeny in Massospondylus carinatus
type: item
type: AcademicArticle
description: Our knowledge of Early Jurassic palaeobiodiversity in the upper Elliot Formation of South Africa has increased markedly in recent years with the discovery of new fossils, re-assessments of previously collected material and a better understanding of Stormberg Group stratigraphy. Here, Ngwevu intloko, a new genus of upper Elliot basal sauropodomorph is named on the basis of a complete skull and partial skeleton (BP/1/4779) previously assigned to Massospondylus carinatus. It can be distinguished from all other basal sauropodomorphs by a combination of 16 cranial and six postcranial characters. The new species is compared to a small ontogenetic series of M. carinatus as well as to a range of closely related taxa. Taphonomic deformation, sexual dimorphism and ontogeny are rejected as possible explanations for the morphological differences present between BP/1/4779 and other taxa. Osteohistological examination reveals that BP/1/4779 had nearly reached adult size at the time of its death at a minimum age of 10 years.
format: application/pdf
format: text/html
creator: Kimberley E.J. Chapelle
creator: Paul M. Barrett
creator: Jennifer Botha
creator: Jonah N. Choiniere
subject: Developmental Biology
subject: Paleontology
subject: Taxonomy
subject: Histology
description: doi:10.7717/peerj.7240
publisher: PeerJ Inc.
rights: © 2019 Chapelle et al.
abstract: Our knowledge of Early Jurassic palaeobiodiversity in the upper Elliot Formation of South Africa has increased markedly in recent years with the discovery of new fossils, re-assessments of previously collected material and a better understanding of Stormberg Group stratigraphy. Here, Ngwevu intloko, a new genus of upper Elliot basal sauropodomorph is named on the basis of a complete skull and partial skeleton (BP/1/4779) previously assigned to Massospondylus carinatus. It can be distinguished from all other basal sauropodomorphs by a combination of 16 cranial and six postcranial characters. The new species is compared to a small ontogenetic series of M. carinatus as well as to a range of closely related taxa. Taphonomic deformation, sexual dimorphism and ontogeny are rejected as possible explanations for the morphological differences present between BP/1/4779 and other taxa. Osteohistological examination reveals that BP/1/4779 had nearly reached adult size at the time of its death at a minimum age of 10 years.
bibliographic citation: Chapelle et al. (2019) Ngwevu intloko: a new early sauropodomorph dinosaur from the Lower Jurassic Elliot Formation of South Africa and comments on cranial ontogeny in Massospondylus carinatus. PeerJ 7:e7240 https://doi.org/10.7717/peerj.7240
date submitted: 2019-03-25
date accepted: 2019-06-03
issued: 2019-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chapelle
  given name: Kimberley E.J.
author list: Agent
  family name: Barrett
  given name: Paul M.
author list: Agent
  family name: Botha
  given name: Jennifer
author list: Agent
  family name: Choiniere
  given name: Jonah N.
doi: 10.7717/peerj.7240
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-05
copyright: © 2019 Chapelle et al.
attribution name: Chapelle et al.

Taxonomic reassessment of the genus Dichotomius (Coleoptera: Scarabaeinae) through integrative taxonomy
type: item
type: AcademicArticle
description: Dung beetles of the subfamily Scarabaeinae are widely recognised as important providers of multiple ecosystem services and are currently experiencing revisions that have improved our understanding of higher-level relationships in the subfamily. However, the study of phylogenetic relationships at the level of genus or species is still lagging behind. In this study we investigated the New World beetle genus Dichotomius, one of the richest within the New World Scarabaeinae, using the most comprehensive molecular and morphological dataset for the genus to date (in terms of number of species and individuals). Besides evaluating phylogenetic relationships, we also assessed species delimitation through a novel Bayesian approach (iBPP) that enables morphological and molecular data to be combined. Our findings support the monophyly of the genus Dichotomius but not that of the subgenera Selenocopris and Dichotomius sensu stricto (s.s). Also, our results do not support the recent synonymy of Selenocopris with Luederwaldtinia. Some species-groups within the genus were recovered, and seem associated with elevational distribution. Our species delimitation analyses were largely congruent irrespective of the set of parameters applied, but the most robust results were obtained when molecular and morphological data were combined. Although our current sampling and analyses were not powerful enough to make definite interpretations on the validity of all species evaluated, we can confidently recognise D. nisus, D. belus and D. mamillatus as valid and well differentiated species. Overall, our study provides new insights into the phylogenetic relationships and classification of dung beetles and has broad implications for their systematics and evolutionary analyses.
format: application/pdf
format: text/html
creator: Carolina Pardo-Diaz
creator: Alejandro Lopera Toro
creator: Sergio Andrés Peña Tovar
creator: Rodrigo Sarmiento-Garcés
creator: Melissa Sanchez Herrera
creator: Camilo Salazar
subject: Biodiversity
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.7332
publisher: PeerJ Inc.
rights: © 2019 Pardo-Diaz et al.
abstract: Dung beetles of the subfamily Scarabaeinae are widely recognised as important providers of multiple ecosystem services and are currently experiencing revisions that have improved our understanding of higher-level relationships in the subfamily. However, the study of phylogenetic relationships at the level of genus or species is still lagging behind. In this study we investigated the New World beetle genus Dichotomius, one of the richest within the New World Scarabaeinae, using the most comprehensive molecular and morphological dataset for the genus to date (in terms of number of species and individuals). Besides evaluating phylogenetic relationships, we also assessed species delimitation through a novel Bayesian approach (iBPP) that enables morphological and molecular data to be combined. Our findings support the monophyly of the genus Dichotomius but not that of the subgenera Selenocopris and Dichotomius sensu stricto (s.s). Also, our results do not support the recent synonymy of Selenocopris with Luederwaldtinia. Some species-groups within the genus were recovered, and seem associated with elevational distribution. Our species delimitation analyses were largely congruent irrespective of the set of parameters applied, but the most robust results were obtained when molecular and morphological data were combined. Although our current sampling and analyses were not powerful enough to make definite interpretations on the validity of all species evaluated, we can confidently recognise D. nisus, D. belus and D. mamillatus as valid and well differentiated species. Overall, our study provides new insights into the phylogenetic relationships and classification of dung beetles and has broad implications for their systematics and evolutionary analyses.
bibliographic citation: Pardo-Diaz et al. (2019) Taxonomic reassessment of the genus Dichotomius (Coleoptera: Scarabaeinae) through integrative taxonomy. PeerJ 7:e7332 https://doi.org/10.7717/peerj.7332
date submitted: 2019-03-01
date accepted: 2019-06-20
issued: 2019-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pardo-Diaz
  given name: Carolina
author list: Agent
  family name: Lopera Toro
  given name: Alejandro
author list: Agent
  family name: Peña Tovar
  given name: Sergio Andrés
author list: Agent
  family name: Sarmiento-Garcés
  given name: Rodrigo
author list: Agent
  family name: Sanchez Herrera
  given name: Melissa
author list: Agent
  family name: Salazar
  given name: Camilo
doi: 10.7717/peerj.7332
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-05
copyright: ©2019 Pardo-Diaz et al.
attribution name: Pardo-Diaz et al.

Elevated frequencies of total and MAIT cell subsets in patients with knee osteoarthritis
type: item
type: AcademicArticle
description: Background Osteoarthritis (OA) is characterized by the degeneration of joint cartilage, with concomitant changes in the synovium and subchondral bone. Recently, the inflammatory response and involvement of several types of T-cells has been implicated in the development of OA. This study investigated the frequency of MR1-restricted mucosal-associated invariant T (MAIT) cells in patients with knee OA. Methods Forty-five patients recently diagnosed with knee OA and 21 age- and gender-matched healthy controls were recruited for this study. Percentages of circulating MAIT cells were assessed by flow cytometry. Plasma cytokine levels were measured using cytometric bead arrays. Associations between the percentages of MAIT cells, plasma cytokine levels, and clinical parameters of OA (erythrocyte sedimentation rate [ESR] and the Western Ontario and McMaster Universities Osteoarthritis Index [WOMAC]) were analyzed using the Spearman correlation test. Results The percentages of total, CD8αα, and CD8αβ MAIT cells were higher in patients with OA compared to healthy controls. The percentages of total and CD8αα MAIT cells were higher in patients with multi-joint OA (MOA) compared to patients with knee-only OA (KOA). Plasma IFN-γ and TNF-α levels were elevated in patients with OA compared to healthy controls, and there was a positive correlation between plasma IFN-γ levels and the percentages of total, CD8αα, and CD8αβ MAIT cells. Plasma IFN-γ and IL-17 levels were higher in patients with MOA compared to healthy controls or patients with KOA. There were positive correlations between the percentages of total and CD8αα MAIT cells and clinical parameters (ESR and WOMAC scores) in patients with OA or MOA. Binary logistic regression analysis shown the frequency of MAIT cells was associated with the risk of OA. Conclusions MAIT cells and their subpopulations were significantly increased in patients with OA and have potential as biological markers of OA disease severity, especially in pat…
format: application/pdf
format: text/html
creator: Ding Zhao
creator: Wei Zhong
creator: Dongfeng Han
creator: Yingbo Li
creator: Yanfang Jiang
creator: Guishan Gu
subject: Immunology
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.7443
publisher: PeerJ Inc.
rights: © 2019 Zhao et al.
abstract: Background Osteoarthritis (OA) is characterized by the degeneration of joint cartilage, with concomitant changes in the synovium and subchondral bone. Recently, the inflammatory response and involvement of several types of T-cells has been implicated in the development of OA. This study investigated the frequency of MR1-restricted mucosal-associated invariant T (MAIT) cells in patients with knee OA. Methods Forty-five patients recently diagnosed with knee OA and 21 age- and gender-matched healthy controls were recruited for this study. Percentages of circulating MAIT cells were assessed by flow cytometry. Plasma cytokine levels were measured using cytometric bead arrays. Associations between the percentages of MAIT cells, plasma cytokine levels, and clinical parameters of OA (erythrocyte sedimentation rate [ESR] and the Western Ontario and McMaster Universities Osteoarthritis Index [WOMAC]) were analyzed using the Spearman correlation test. Results The percentages of total, CD8αα, and CD8αβ MAIT cells were higher in patients with OA compared to healthy controls. The percentages of total and CD8αα MAIT cells were higher in patients with multi-joint OA (MOA) compared to patients with knee-only OA (KOA). Plasma IFN-γ and TNF-α levels were elevated in patients with OA compared to healthy controls, and there was a positive correlation between plasma IFN-γ levels and the percentages of total, CD8αα, and CD8αβ MAIT cells. Plasma IFN-γ and IL-17 levels were higher in patients with MOA compared to healthy controls or patients with KOA. There were positive correlations between the percentages of total and CD8αα MAIT cells and clinical parameters (ESR and WOMAC scores) in patients with OA or MOA. Binary logistic regression analysis shown the frequency of MAIT cells was associated with the risk of OA. Conclusions MAIT cells and their subpopulations were significantly increased in patients with OA and have potential as biological markers of OA disease severity, especially in pat…
bibliographic citation: Zhao et al. (2019) Elevated frequencies of total and MAIT cell subsets in patients with knee osteoarthritis. PeerJ 7:e7443 https://doi.org/10.7717/peerj.7443
date submitted: 2019-01-07
date accepted: 2019-07-09
issued: 2019-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Ding
author list: Agent
  family name: Zhong
  given name: Wei
author list: Agent
  family name: Han
  given name: Dongfeng
author list: Agent
  family name: Li
  given name: Yingbo
author list: Agent
  family name: Jiang
  given name: Yanfang
author list: Agent
  family name: Gu
  given name: Guishan
doi: 10.7717/peerj.7443
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-05
copyright: ©2019 Zhao et al.
attribution name: Zhao et al.

Sex differences in the response to angiotensin II receptor blockade in a rat model of eccentric cardiac hypertrophy
type: item
type: AcademicArticle
description: Background. Men and women differ in their susceptibility to cardiovascular disease, though the underlying mechanism has remained elusive. Heart disease symptoms, evolution and response to treatment are often sex-specific. This has been studied in animal models of hypertension or myocardial infarction in the past but has received less attention in the context of heart valve regurgitation. The aim of the study was to evaluate the development of cardiac hypertrophy (CH) in response to left ventricle (LV) volume overload (VO) caused by chronic aortic valve regurgitation (AR) in male and female rats treated or not with angiotensin II receptor blocker (ARB), valsartan. We studied eight groups of Wistar rats: male or female, AR or sham-operated (sham) and treated or not with valsartan (30 mg/kg/day) for 9 weeks starting one week before AR surgical induction. Results. As expected, VO from AR resulted for both male and female rats in significant LV dilation (39% vs. 40% end-diastolic LV diameter increase, respectively; p < 0.0001) and CH (53% vs. 64% heart weight increase, respectively; p < 0.0001) compared to sham. Sex differences were observed in LV wall thickening in response to VO. In untreated AR males, relative LV wall thickness (a ratio of wall thickness to end-diastolic diameter) was reduced compared to sham, whereas this ratio in females remained unchanged. ARB treatment did not prevent LV dilation in both male and female animals but reversed LV wall thickening in females. Systolic and diastolic functions in AR animals were altered similarly for both sexes. ARB treatment did not improve systolic function but helped normalizing diastolic parameters such as left atrial mass and E wave slope in female AR rats. Increased LV gene expression of Anp and Bnp was normalized by ARB treatment in AR females but not in males. Other hypertrophy gene markers (Fos, Trpc6, Klf15, Myh6 and Myh7) were not modulated by ARB treatment. The same was true for genes related to LV extracellu…
format: application/pdf
format: text/html
creator: Élisabeth Walsh-Wilkinson
creator: Marie-Claude Drolet
creator: Charlie Le Houillier
creator: Ève-Marie Roy
creator: Marie Arsenault
creator: Jacques Couet
subject: Anatomy and Physiology
subject: Cardiology
description: doi:10.7717/peerj.7461
publisher: PeerJ Inc.
rights: © 2019 Walsh-Wilkinson et al.
abstract: Background. Men and women differ in their susceptibility to cardiovascular disease, though the underlying mechanism has remained elusive. Heart disease symptoms, evolution and response to treatment are often sex-specific. This has been studied in animal models of hypertension or myocardial infarction in the past but has received less attention in the context of heart valve regurgitation. The aim of the study was to evaluate the development of cardiac hypertrophy (CH) in response to left ventricle (LV) volume overload (VO) caused by chronic aortic valve regurgitation (AR) in male and female rats treated or not with angiotensin II receptor blocker (ARB), valsartan. We studied eight groups of Wistar rats: male or female, AR or sham-operated (sham) and treated or not with valsartan (30 mg/kg/day) for 9 weeks starting one week before AR surgical induction. Results. As expected, VO from AR resulted for both male and female rats in significant LV dilation (39% vs. 40% end-diastolic LV diameter increase, respectively; p < 0.0001) and CH (53% vs. 64% heart weight increase, respectively; p < 0.0001) compared to sham. Sex differences were observed in LV wall thickening in response to VO. In untreated AR males, relative LV wall thickness (a ratio of wall thickness to end-diastolic diameter) was reduced compared to sham, whereas this ratio in females remained unchanged. ARB treatment did not prevent LV dilation in both male and female animals but reversed LV wall thickening in females. Systolic and diastolic functions in AR animals were altered similarly for both sexes. ARB treatment did not improve systolic function but helped normalizing diastolic parameters such as left atrial mass and E wave slope in female AR rats. Increased LV gene expression of Anp and Bnp was normalized by ARB treatment in AR females but not in males. Other hypertrophy gene markers (Fos, Trpc6, Klf15, Myh6 and Myh7) were not modulated by ARB treatment. The same was true for genes related to LV extracellu…
bibliographic citation: Walsh-Wilkinson et al. (2019) Sex differences in the response to angiotensin II receptor blockade in a rat model of eccentric cardiac hypertrophy. PeerJ 7:e7461 https://doi.org/10.7717/peerj.7461
date submitted: 2019-04-12
date accepted: 2019-07-11
issued: 2019-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Walsh-Wilkinson
  given name: Élisabeth
author list: Agent
  family name: Drolet
  given name: Marie-Claude
author list: Agent
  family name: Le Houillier
  given name: Charlie
author list: Agent
  family name: Roy
  given name: Ève-Marie
author list: Agent
  family name: Arsenault
  given name: Marie
author list: Agent
  family name: Couet
  given name: Jacques
doi: 10.7717/peerj.7461
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-05
copyright: ©2019 Walsh-Wilkinson et al.
attribution name: Walsh-Wilkinson et al.

Effect of dietary concentrate to forage ratio on growth performance, rumen fermentation and bacterial diversity of Tibetan sheep under barn feeding on the Qinghai-Tibetan plateau
type: item
type: AcademicArticle
description: This study aimed to research the effects of different dietary concentrate to forage (C:F) ratio on growth performance, rumen fermentation and bacteria diversity of barn feeding Tibetan sheep. The experiment contains fiver treatments (HS1, HS2 HS3, HS4 and HS5; n = 8, respectively) based on dietary C:F ratios 0:100, 15:85, 30:70, 45:55, and 60:40, respectively. The ruminal bacterial community structure was investigated through high-throughput sequencing of 16S rRNA genes in V4 hypervariable region. The results showed that increasing dietary concentrate feed level from 0% to 60% exerted a positive effect on DMI, BW gain, gain rate and feed conversation ratio (FCR) in Tibetan sheep. The increases dietary concentrate feed level elevatedNH3-N, propionate and valerate concentrations, whereas, reduced molar ratio of acetate to propionate (A/P ratio) (P < 0.05). For rumen bacterial diversity, increases in dietary concentrate content contributed to lower alpha diversity indexes including Shannon wiener, Chao1 and observed species, meanwhile, significantly increased the abundances of the phylum Bacteroidetes and the genus Prevotella_1 (P < 0.05). In conclusion, increases dietary concentrate content improved the growth performance and Tibetan sheep fed diets of 45% concentrate obtained a better performance; the inclusion of concentrate in feed changed rumen fermentation from acetate fermentation to propionate fermentation, and improved the energy utilization efficiency of Tibetan sheep; the increased in concentrate content significantly reduced rumen bacteria diversity and changed the abundance of some core bacteria.
format: application/pdf
format: text/html
creator: Hongjin Liu
creator: Tianwei Xu
creator: Shixiao Xu
creator: Li Ma
creator: Xueping Han
creator: Xungang Wang
creator: Xiaoling Zhang
creator: Linyong Hu
creator: Na Zhao
creator: Yongwei Chen
creator: Li Pi
creator: Xinquan Zhao
subject: Biodiversity
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
subject: Nutrition
description: doi:10.7717/peerj.7462
publisher: PeerJ Inc.
rights: © 2019 Liu et al.
abstract: This study aimed to research the effects of different dietary concentrate to forage (C:F) ratio on growth performance, rumen fermentation and bacteria diversity of barn feeding Tibetan sheep. The experiment contains fiver treatments (HS1, HS2 HS3, HS4 and HS5; n = 8, respectively) based on dietary C:F ratios 0:100, 15:85, 30:70, 45:55, and 60:40, respectively. The ruminal bacterial community structure was investigated through high-throughput sequencing of 16S rRNA genes in V4 hypervariable region. The results showed that increasing dietary concentrate feed level from 0% to 60% exerted a positive effect on DMI, BW gain, gain rate and feed conversation ratio (FCR) in Tibetan sheep. The increases dietary concentrate feed level elevatedNH3-N, propionate and valerate concentrations, whereas, reduced molar ratio of acetate to propionate (A/P ratio) (P < 0.05). For rumen bacterial diversity, increases in dietary concentrate content contributed to lower alpha diversity indexes including Shannon wiener, Chao1 and observed species, meanwhile, significantly increased the abundances of the phylum Bacteroidetes and the genus Prevotella_1 (P < 0.05). In conclusion, increases dietary concentrate content improved the growth performance and Tibetan sheep fed diets of 45% concentrate obtained a better performance; the inclusion of concentrate in feed changed rumen fermentation from acetate fermentation to propionate fermentation, and improved the energy utilization efficiency of Tibetan sheep; the increased in concentrate content significantly reduced rumen bacteria diversity and changed the abundance of some core bacteria.
bibliographic citation: Liu et al. (2019) Effect of dietary concentrate to forage ratio on growth performance, rumen fermentation and bacterial diversity of Tibetan sheep under barn feeding on the Qinghai-Tibetan plateau. PeerJ 7:e7462 https://doi.org/10.7717/peerj.7462
date submitted: 2019-02-24
date accepted: 2019-07-11
issued: 2019-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hongjin
author list: Agent
  family name: Xu
  given name: Tianwei
author list: Agent
  family name: Xu
  given name: Shixiao
author list: Agent
  family name: Ma
  given name: Li
author list: Agent
  family name: Han
  given name: Xueping
author list: Agent
  family name: Wang
  given name: Xungang
author list: Agent
  family name: Zhang
  given name: Xiaoling
author list: Agent
  family name: Hu
  given name: Linyong
author list: Agent
  family name: Zhao
  given name: Na
author list: Agent
  family name: Chen
  given name: Yongwei
author list: Agent
  family name: Pi
  given name: Li
author list: Agent
  family name: Zhao
  given name: Xinquan
doi: 10.7717/peerj.7462
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-05
copyright: ©2019 Liu et al.
attribution name: Liu et al.

Binding interactions of epididymal protease inhibitor and semenogelin-1: a homology modeling, docking and molecular dynamics simulation study
type: item
type: AcademicArticle
description: Epididymal protease inhibitor (EPPIN) that is located on the sperm surface and specific to the male reproductive system is a non-hormonal contraceptive target, since the binding of EPPIN with the seminal plasma protein semenogelin-1 (SEMG1) causes a loss of sperm function. Here, we investigated the binding interactions between EPPIN and SEMG1 by homology modeling, docking and molecular dynamics simulation. Since no crystal structure was reported for EPPIN, its 3D structure was constructed by homology modeling and refined by dynamics simulation, illustrating the C-terminus domain of EPPIN could bind with its N-terminus domain through the residues 30–32 and 113–116. The binding interaction of SEMG110-8 peptide and EPPIN was investigated by Z-DOCK and dynamics simulation. After evaluating the models according to the calculated binding free energies, we demonstrated that C-terminus domain of EPPIN was important for the binding of SEMG1 via residues Tyr107, Gly112, Asn116, Gln118 and Asn122, while residue Arg32 in N-terminus domain also had contribution for their binding interaction. Additionally, the binding pocket of EPPIN was defined according to these key residues and verified by molecular docking with reported inhibitor EP055, suggesting that the pocket formed by Arg32, Asn114, Asn116, Phe117 and Asn122 could be important for the design of new ligands. This study might be helpful for the understanding of biological function of EPPIN and would encourage the discovery of non-hormonal contraceptive leads/drugs in the future.
format: application/pdf
format: text/html
creator: Changyu Shan
creator: Hongwei Li
creator: Yuping Zhang
creator: Yuyan Li
creator: Yingchun Chen
creator: Wei He
subject: Bioinformatics
subject: Computational Biology
subject: Andrology
subject: Computational Science
description: doi:10.7717/peerj.7329
publisher: PeerJ Inc.
rights: © 2019 Shan et al.
abstract: Epididymal protease inhibitor (EPPIN) that is located on the sperm surface and specific to the male reproductive system is a non-hormonal contraceptive target, since the binding of EPPIN with the seminal plasma protein semenogelin-1 (SEMG1) causes a loss of sperm function. Here, we investigated the binding interactions between EPPIN and SEMG1 by homology modeling, docking and molecular dynamics simulation. Since no crystal structure was reported for EPPIN, its 3D structure was constructed by homology modeling and refined by dynamics simulation, illustrating the C-terminus domain of EPPIN could bind with its N-terminus domain through the residues 30–32 and 113–116. The binding interaction of SEMG110-8 peptide and EPPIN was investigated by Z-DOCK and dynamics simulation. After evaluating the models according to the calculated binding free energies, we demonstrated that C-terminus domain of EPPIN was important for the binding of SEMG1 via residues Tyr107, Gly112, Asn116, Gln118 and Asn122, while residue Arg32 in N-terminus domain also had contribution for their binding interaction. Additionally, the binding pocket of EPPIN was defined according to these key residues and verified by molecular docking with reported inhibitor EP055, suggesting that the pocket formed by Arg32, Asn114, Asn116, Phe117 and Asn122 could be important for the design of new ligands. This study might be helpful for the understanding of biological function of EPPIN and would encourage the discovery of non-hormonal contraceptive leads/drugs in the future.
bibliographic citation: Shan et al. (2019) Binding interactions of epididymal protease inhibitor and semenogelin-1: a homology modeling, docking and molecular dynamics simulation study. PeerJ 7:e7329 https://doi.org/10.7717/peerj.7329
date submitted: 2019-05-06
date accepted: 2019-06-19
issued: 2019-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shan
  given name: Changyu
author list: Agent
  family name: Li
  given name: Hongwei
author list: Agent
  family name: Zhang
  given name: Yuping
author list: Agent
  family name: Li
  given name: Yuyan
author list: Agent
  family name: Chen
  given name: Yingchun
author list: Agent
  family name: He
  given name: Wei
doi: 10.7717/peerj.7329
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-05
copyright: © 2019 Shan et al.
attribution name: Shan et al.

Impact of digital video analytics on accuracy of chemobehavioural phenotyping in aquatic toxicology
type: item
type: AcademicArticle
description: Chemobehavioural phenotypic analysis using small aquatic model organisms is becoming an important toolbox in aquatic ecotoxicology and neuroactive drug discovery. The analysis of the organisms’ behavior is usually performed by combining digital video recording with animal tracking software. This software detects the organisms in the video frames, and reconstructs their movement trajectory using image processing algorithms. In this work we investigated the impact of video file characteristics, video optimization techniques and differences in animal tracking algorithms on the accuracy of quantitative neurobehavioural endpoints. We employed larval stages of a free-swimming euryhaline crustacean Artemia franciscana,commonly used for marine ecotoxicity testing, as a proxy modelto assess the effects of video analytics on quantitative behavioural parameters. We evaluated parameters such as data processing speed, tracking precision, capability to perform high-throughput batch processing of video files. Using a model toxicant the software algorithms were also finally benchmarked against one another. Our data indicates that variability in video file parameters; such as resolution, frame rate, file containers types, codecs and compression levels, can be a source of experimental biases in behavioural analysis. Similarly, the variability in data outputs between different tracking algorithms should be taken into account when designing standardized behavioral experiments and conducting chemobehavioural phenotyping.
format: application/pdf
format: text/html
creator: Jason Henry
creator: Alvaro Rodriguez
creator: Donald Wlodkowic
subject: Animal Behavior
subject: Zoology
subject: Ecotoxicology
description: doi:10.7717/peerj.7367
publisher: PeerJ Inc.
rights: © 2019 Henry et al.
abstract: Chemobehavioural phenotypic analysis using small aquatic model organisms is becoming an important toolbox in aquatic ecotoxicology and neuroactive drug discovery. The analysis of the organisms’ behavior is usually performed by combining digital video recording with animal tracking software. This software detects the organisms in the video frames, and reconstructs their movement trajectory using image processing algorithms. In this work we investigated the impact of video file characteristics, video optimization techniques and differences in animal tracking algorithms on the accuracy of quantitative neurobehavioural endpoints. We employed larval stages of a free-swimming euryhaline crustacean Artemia franciscana,commonly used for marine ecotoxicity testing, as a proxy modelto assess the effects of video analytics on quantitative behavioural parameters. We evaluated parameters such as data processing speed, tracking precision, capability to perform high-throughput batch processing of video files. Using a model toxicant the software algorithms were also finally benchmarked against one another. Our data indicates that variability in video file parameters; such as resolution, frame rate, file containers types, codecs and compression levels, can be a source of experimental biases in behavioural analysis. Similarly, the variability in data outputs between different tracking algorithms should be taken into account when designing standardized behavioral experiments and conducting chemobehavioural phenotyping.
bibliographic citation: Henry et al. (2019) Impact of digital video analytics on accuracy of chemobehavioural phenotyping in aquatic toxicology. PeerJ 7:e7367 https://doi.org/10.7717/peerj.7367
date submitted: 2019-06-03
date accepted: 2019-06-27
issued: 2019-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Henry
  given name: Jason
author list: Agent
  family name: Rodriguez
  given name: Alvaro
author list: Agent
  family name: Wlodkowic
  given name: Donald
doi: 10.7717/peerj.7367
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-05
copyright: ©2019 Henry et al.
attribution name: Henry et al.

The role of past experience in development of feeding behavior in common vampire bats
type: item
type: AcademicArticle
description: The life history strategy of common vampire bats (Desmodus rotundus) suggests that learning might play a role in development of their foraging skills. We took advantage of 12 captive births in a study colony of vampire bats to test the role of past experience in two aspects of feeding. First, we compared preferences for blood temperature in 32 wild-born vampire bats versus 11 captive-born vampire bats that had only previously fed on blood of ambient temperature or colder. We found no evidence for a preference in either group for blood presented at 4 °C versus 37 °C. Second, we tested whether captive-born vampire bats with no previous experience of feeding on live animals could successfully feed on a live chicken. Five of 12 naïve captive-born bats were able to bite the chicken and draw blood, but only one bat gained more than 5% of body mass. We were unable to reasonably compare their feeding performance with that of wild-born bats because only two of three wild-born, short-term captive bats fed on the chicken and none of the seven wild-born, long-term captive mothers attempted to feed. This unexpected lack of feeding might be due to a previously reported age-dependent neophobia. When six of the captive-born bats were released in the wild, they appeared to feed successfully because they survived for more than three consecutive nights. We suggest further tests that would better clarify the role of learning in the development of foraging in vampire bats.
format: application/pdf
format: text/html
creator: Jineth Berrío-Martínez
creator: Samuel Kaiser
creator: Michelle Nowak
creator: Rachel A. Page
creator: Gerald G. Carter
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.7448
publisher: PeerJ Inc.
rights: © 2019 Berrío-Martínez et al.
abstract: The life history strategy of common vampire bats (Desmodus rotundus) suggests that learning might play a role in development of their foraging skills. We took advantage of 12 captive births in a study colony of vampire bats to test the role of past experience in two aspects of feeding. First, we compared preferences for blood temperature in 32 wild-born vampire bats versus 11 captive-born vampire bats that had only previously fed on blood of ambient temperature or colder. We found no evidence for a preference in either group for blood presented at 4 °C versus 37 °C. Second, we tested whether captive-born vampire bats with no previous experience of feeding on live animals could successfully feed on a live chicken. Five of 12 naïve captive-born bats were able to bite the chicken and draw blood, but only one bat gained more than 5% of body mass. We were unable to reasonably compare their feeding performance with that of wild-born bats because only two of three wild-born, short-term captive bats fed on the chicken and none of the seven wild-born, long-term captive mothers attempted to feed. This unexpected lack of feeding might be due to a previously reported age-dependent neophobia. When six of the captive-born bats were released in the wild, they appeared to feed successfully because they survived for more than three consecutive nights. We suggest further tests that would better clarify the role of learning in the development of foraging in vampire bats.
bibliographic citation: Berrío-Martínez et al. (2019) The role of past experience in development of feeding behavior in common vampire bats. PeerJ 7:e7448 https://doi.org/10.7717/peerj.7448
date submitted: 2019-03-12
date accepted: 2019-07-10
issued: 2019-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berrío-Martínez
  given name: Jineth
author list: Agent
  family name: Kaiser
  given name: Samuel
author list: Agent
  family name: Nowak
  given name: Michelle
author list: Agent
  family name: Page
  given name: Rachel A.
author list: Agent
  family name: Carter
  given name: Gerald G.
doi: 10.7717/peerj.7448
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-05
copyright: ©2019 Berrío-Martínez et al.
attribution name: Berrío-Martínez et al.

Pruning and dormancy breaking make two sustainable grape-cropping productions in a protected environment possible without overlap in a single year
type: item
type: AcademicArticle
description: In table grape production, protected cultivation in a vineyard in different regions and climates is currently a commonly used practice. The aims of this study were to provide key approaches to sustainably produce two crops of grape without overlap under protected environment in a single year. Spraying the degreening chemicals 400 mg/L ethephon +0.4% sulfur at 4 weeks of vine nutrient restoration after the harvest of the summer crop resulted in the highest percentage of sprouting inflorescence. The retention of 7–10 buds in the base shoot results in the high percentage of sprouting inflorescence. Bud breaking chemicals with 2.5% hydrogen cyanamide+2.0% Baoguoliang +0.02% Shenzhonggen significantly led to sprout inflorescence more efficiently. Cluster and fruit weights of the winter crop weighed significantly less than those of the summer crop. However, the contents of total soluble sugar and titratable acidity were higher than those of the summer crop. The anthocyanin content in the peel of the winter fruit was significantly higher than that in the summer fruit. The yield of the winter crop is controlled by the yield of the summer fruit. To maintain the stability of the two crops for one year, the ratio of yield in the winter to the summer should be controlled from 2:5 to 3:5 to ensure the sustainable production of two crops without overlap for ‘Summer Black’ grape. These results may help grape growers to overcome the impacts of rainy and hot climates with the help of protected facilities, and it could enable the use of solar radiation and heat resources in subtropical and tropical areas.
format: application/pdf
format: text/html
creator: Zhipeng Qiu
creator: Guangzheng Chen
creator: Dongliang Qiu
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.7412
publisher: PeerJ Inc.
rights: © 2019 Qiu et al.
abstract: In table grape production, protected cultivation in a vineyard in different regions and climates is currently a commonly used practice. The aims of this study were to provide key approaches to sustainably produce two crops of grape without overlap under protected environment in a single year. Spraying the degreening chemicals 400 mg/L ethephon +0.4% sulfur at 4 weeks of vine nutrient restoration after the harvest of the summer crop resulted in the highest percentage of sprouting inflorescence. The retention of 7–10 buds in the base shoot results in the high percentage of sprouting inflorescence. Bud breaking chemicals with 2.5% hydrogen cyanamide+2.0% Baoguoliang +0.02% Shenzhonggen significantly led to sprout inflorescence more efficiently. Cluster and fruit weights of the winter crop weighed significantly less than those of the summer crop. However, the contents of total soluble sugar and titratable acidity were higher than those of the summer crop. The anthocyanin content in the peel of the winter fruit was significantly higher than that in the summer fruit. The yield of the winter crop is controlled by the yield of the summer fruit. To maintain the stability of the two crops for one year, the ratio of yield in the winter to the summer should be controlled from 2:5 to 3:5 to ensure the sustainable production of two crops without overlap for ‘Summer Black’ grape. These results may help grape growers to overcome the impacts of rainy and hot climates with the help of protected facilities, and it could enable the use of solar radiation and heat resources in subtropical and tropical areas.
bibliographic citation: Qiu et al. (2019) Pruning and dormancy breaking make two sustainable grape-cropping productions in a protected environment possible without overlap in a single year. PeerJ 7:e7412 https://doi.org/10.7717/peerj.7412
date submitted: 2019-02-03
date accepted: 2019-07-04
issued: 2019-08-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qiu
  given name: Zhipeng
author list: Agent
  family name: Chen
  given name: Guangzheng
author list: Agent
  family name: Qiu
  given name: Dongliang
doi: 10.7717/peerj.7412
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-08-02
copyright: ©2019 Qiu et al.
attribution name: Qiu et al.

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