PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis
items: Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy
items: Analysis and comparison of protein secondary structures in the rachis of avian flight feathers
items: Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium)
items: Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)
items: Response of bacterial community structure to different ecological niches and their functions in Korean pine forests
items: Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China
items: Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants
items: Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.
items: Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury
items: Applications and limitations of current markerless motion capture methods for clinical gait biomechanics
items: Profiles of anemia in adolescent students with sports club membership in an outpatient clinic setting: a retrospective study
items: Effects of long-term nitrogen & phosphorus fertilization on soil microbial, bacterial and fungi respiration and their temperature sensitivity on the Qinghai-Tibet Plateau
items: Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives
items: Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes
items: AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis
items: Biomarkers of non-communicable chronic disease: an update on contemporary methods
items: Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard
items: Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy
items: Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species
items: Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits
items: Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis
items: Disentangling bias for non-destructive insect metabarcoding
items: Microbial biogeography of the wombat gastrointestinal tract
items: A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift
items: Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum
items: Estimation of Coregonus ussuriensis age, growth, and maturation in China’s Amur River
items: A retrospective study on molecular epidemiology trends of carbapenem resistant Enterobacteriaceae in a teaching hospital in Malaysia
items: Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands
items: Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia
items: Methodological approaches for estimating populations of the endangered dhole Cuon alpinus
items: SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.
items: Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study
items: Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition
items: Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish
items: Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans)
items: Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow
items: Functional network motifs defined through integration of protein-protein and genetic interactions
items: Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat
items: Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1
items: Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.)
items: Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations
items: Drivers of phenotypic divergence in a Mesoamerican highland bird
items: Climate in Africa sequentially shapes spring passage of Willow Warbler Phylloscopus trochilus across the Baltic coast
items: Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [Setaria italica (L.) P. Beauv.] varieties with different panicle types
items: A neuronal theta band signature of error monitoring during integration of facial expression cues
items: Deciphering the Heteropterys pannosa species complex (Malpighiaceae)
items: Characterizing the suckling behavior by video and 3D-accelerometry in humpback whale calves on a breeding ground
items: Sarcopenia is not associated with inspiratory muscle strength but with expiratory muscle strength among older adults requiring long-term care/support
items: Prevalence of iron deficiency anemia in Brazilian women of childbearing age: a systematic review with meta-analysis
items: PCAtest: testing the statistical significance of Principal Component Analysis in R
items: Molecular characterization and expression profiling of transformer 2 and fruitless-like homologs in the black tiger shrimp, Penaeus monodon
items: The relationships between toad behaviour, antipredator defences, and spatial and sexual variation in predation pressure
items: Measurement of dispersion of PM 2.5 in Thailand using confidence intervals for the coefficient of variation of an inverse Gaussian distribution
items: Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe
items: Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets
items: Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs
items: Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey
items: Effect of interaction between occupational stress and polymorphisms of MTHFR gene and SELE gene on hypertension
items: Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China
items: New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea)
items: The impact of COVID-19 and control measures on public health in Thailand, 2020
items: In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury
items: A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)
items: Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?
items: Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure
items: https://peerj.com/articles/12872
items: New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans
items: 7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway
items: Morphological characterization and sexual dimorphism of the antennal sensilla in Bactericera gobica Loginova (Hemiptera: Psyllidae)—a scanning and transmission electron microscopic study
items: The coalescent with replication-independent mutations
items: Wei2GO: weighted sequence similarity-based protein function prediction

Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis
type: item
type: AcademicArticle
description: Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
format: application/pdf
format: text/html
creator: John Geoffrey Gill
creator: Kristina M. Hill-Spanik
creator: Kerry A. Whittaker
creator: Martin L. Jones
creator: Craig Plante
subject: Biogeography
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Biological Oceanography
description: doi:10.7717/peerj.12835
publisher: PeerJ Inc.
rights: © 2022 Gill et al.
abstract: Marine microbes provide the backbone for pelagic ecosystems by cycling and fixing nutrients and establishing the base of food webs. Microbial communities are often assumed to be highly connected and genetically mixed, with localized environmental filters driving minor changes in structure. Our study applied high-throughput Illumina 16S ribosomal RNA gene amplicon sequencing on whole-community bacterial samples to characterize geographic, environmental, and stochastic drivers of community diversity. DNA was extracted from seawater collected from the surface (N = 18) and at depth just below the deep chlorophyll-a maximum (DCM mean depth = 115.4 m; N = 22) in the Sargasso Sea and adjacent oceanographic regions. Discrete bacterioplankton assemblages were observed at varying depths in the North Sargasso Sea, with a signal for distance-decay of bacterioplankton community similarity found only in surface waters. Bacterial communities from different oceanic regions could be distinguished statistically but exhibited a low magnitude of divergence. Redundancy analysis identified temperature as the key environmental variable correlated with community structuring. The effect of dispersal limitation was weak, while variation partitioning and neutral community modeling demonstrated stochastic processes influencing the communities. This study advances understanding of microbial biogeography in the pelagic ocean and highlights the use of high-throughput sequencing methods in studying microbial community structure.
bibliographic citation: Gill et al. (2022) Sargasso Sea bacterioplankton community structure and drivers of variance as revealed by DNA metabarcoding analysis. PeerJ 10:e12835 https://doi.org/10.7717/peerj.12835
date submitted: 2021-08-17
date accepted: 2022-01-04
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gill
  given name: John Geoffrey
author list: Agent
  family name: Hill-Spanik
  given name: Kristina M.
author list: Agent
  family name: Whittaker
  given name: Kerry A.
author list: Agent
  family name: Jones
  given name: Martin L.
author list: Agent
  family name: Plante
  given name: Craig
doi: 10.7717/peerj.12835
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: © 2022 Gill et al.
attribution name: Gill et al.

Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy
type: item
type: AcademicArticle
description: Iberian natural steppes have traditionally been used for extensive sheep grazing, which has been noted to be positively associated with steppe bird abundance and diversity. Sheep numbers in Spain, which harbors the largest European populations of many steppe bird species, decreased by 9.2 million (37.3%) between 1992 and 2020. Steppe birds in Spain have faced dramatic declines during the same period, but there is a lack of knowledge about the potential association between sheep and open-habitat bird declines. We used sheep data from the Spanish Ministry of Agriculture and bird data (1998–2018) from the Spanish Common Bird Monitoring Program to assess the association at the Spanish scale between sheep decline and the Farmland Bird Index (FBI) and the Natural Shrub-steppe Bird Index (SBI). We also used an independent dataset on population trends of the Dupont’s Lark (Chersophilus duponti) to assess the relationship between sheep numbers and the decline of this threatened steppe specialist passerine in Spain, whose European population is restricted to Iberian natural steppes. To test for a spurious relationship between temporal series, variables were tested for cointegration. After confirming cointegration, we found a strong positive relationship between sheep abundance and the trends of the FBI and SBI indices during the period 1998–2018. The association between sheep abundance and trends of the Dupont’s Lark (2004–2015) was positive although it was not statistically significant. Although the main causes of decline of farmland and steppe birds are mainly related to agricultural intensification and land use changes, the correlation found, using two independent cointegrated datasets, between the reduction in farmland and shrub-steppe birds and sheep numbers at the country scale suggests that the decline of steppe birds in Spain may be also associated with the decline in sheep numbers. This agrees with previous studies that found a positive relationship between intermedi…
format: application/pdf
format: text/html
creator: Juan Traba
creator: Cristian Pérez-Granados
subject: Agricultural Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12870
publisher: PeerJ Inc.
rights: © 2022 Traba and Pérez-Granados
abstract: Iberian natural steppes have traditionally been used for extensive sheep grazing, which has been noted to be positively associated with steppe bird abundance and diversity. Sheep numbers in Spain, which harbors the largest European populations of many steppe bird species, decreased by 9.2 million (37.3%) between 1992 and 2020. Steppe birds in Spain have faced dramatic declines during the same period, but there is a lack of knowledge about the potential association between sheep and open-habitat bird declines. We used sheep data from the Spanish Ministry of Agriculture and bird data (1998–2018) from the Spanish Common Bird Monitoring Program to assess the association at the Spanish scale between sheep decline and the Farmland Bird Index (FBI) and the Natural Shrub-steppe Bird Index (SBI). We also used an independent dataset on population trends of the Dupont’s Lark (Chersophilus duponti) to assess the relationship between sheep numbers and the decline of this threatened steppe specialist passerine in Spain, whose European population is restricted to Iberian natural steppes. To test for a spurious relationship between temporal series, variables were tested for cointegration. After confirming cointegration, we found a strong positive relationship between sheep abundance and the trends of the FBI and SBI indices during the period 1998–2018. The association between sheep abundance and trends of the Dupont’s Lark (2004–2015) was positive although it was not statistically significant. Although the main causes of decline of farmland and steppe birds are mainly related to agricultural intensification and land use changes, the correlation found, using two independent cointegrated datasets, between the reduction in farmland and shrub-steppe birds and sheep numbers at the country scale suggests that the decline of steppe birds in Spain may be also associated with the decline in sheep numbers. This agrees with previous studies that found a positive relationship between intermedi…
bibliographic citation: Traba et al. (2022) Extensive sheep grazing is associated with trends in steppe birds in Spain: recommendations for the Common Agricultural Policy. PeerJ 10:e12870 https://doi.org/10.7717/peerj.12870
date submitted: 2021-10-12
date accepted: 2022-01-11
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Traba
  given name: Juan
author list: Agent
  family name: Pérez-Granados
  given name: Cristian
doi: 10.7717/peerj.12870
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: © 2022 Traba and Pérez-Granados
attribution name: Traba and Pérez-Granados

Analysis and comparison of protein secondary structures in the rachis of avian flight feathers
type: item
type: AcademicArticle
description: Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.
format: application/pdf
format: text/html
creator: Pin-Yen Lin
creator: Pei-Yu Huang
creator: Yao-Chang Lee
creator: Chen Siang Ng
subject: Biochemistry
subject: Biophysics
subject: Zoology
description: doi:10.7717/peerj.12919
publisher: PeerJ Inc.
rights: © 2022 Lin et al.
abstract: Avians have evolved many different modes of flying as well as various types of feathers for adapting to varied environments. However, the protein content and ratio of protein secondary structures (PSSs) in mature flight feathers are less understood. Further research is needed to understand the proportions of PSSs in feather shafts adapted to various flight modes in different avian species. Flight feathers were analyzed in chicken, mallard, sacred ibis, crested goshawk, collared scops owl, budgie, and zebra finch to investigate the PSSs that have evolved in the feather cortex and medulla by using nondestructive attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). In addition, synchrotron radiation-based, Fourier transform infrared microspectroscopy (SR-FTIRM) was utilized to measure and analyze cross-sections of the feather shafts of seven bird species at a high lateral resolution to resolve the composition of proteins distributed within the sampled area of interest. In this study, significant amounts of α-keratin and collagen components were observed in flight feather shafts, suggesting that these proteins play significant roles in the mechanical strength of flight feathers. This investigation increases our understanding of adaptations to flight by elucidating the structural and mechanistic basis of the feather composition.
bibliographic citation: Lin et al. (2022) Analysis and comparison of protein secondary structures in the rachis of avian flight feathers. PeerJ 10:e12919 https://doi.org/10.7717/peerj.12919
date submitted: 2021-10-29
date accepted: 2022-01-20
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Pin-Yen
author list: Agent
  family name: Huang
  given name: Pei-Yu
author list: Agent
  family name: Lee
  given name: Yao-Chang
author list: Agent
  family name: Ng
  given name: Chen Siang
doi: 10.7717/peerj.12919
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: ©2022 Lin et al.
attribution name: Lin et al.

Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium)
type: item
type: AcademicArticle
description: Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to decipher the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found high abundance proteins related to nitrate and amino acids metabolismsin the salt-tolerant cultivars. The significant increase in abundance of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. Moreover, the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including sterol side chain reductase, gamma aminobutyrate transaminase and starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future.
format: application/pdf
format: text/html
creator: Qiang Wang
creator: Baike Wang
creator: Huifang Liu
creator: Hongwei Han
creator: Hongmei Zhuang
creator: Juan Wang
creator: Tao Yang
creator: Hao Wang
creator: Yong Qin
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12955
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Salt stress causes the quality change and significant yield loss of tomato. However, the resources of salt-resistant tomato were still deficient and the mechanisms of tomato resistance to salt stress were still unclear. In this study, the proteomic profiles of two salt-tolerant and salt-sensitive tomato cultivars were investigated to decipher the salt-resistance mechanism of tomato and provide novel resources for tomato breeding. We found high abundance proteins related to nitrate and amino acids metabolismsin the salt-tolerant cultivars. The significant increase in abundance of proteins involved in Brassinolides and GABA biosynthesis were verified in salt-tolerant cultivars, strengthening the salt resistance of tomato. Meanwhile, salt-tolerant cultivars with higher abundance and activity of antioxidant-related proteins have more advantages in dealing with reactive oxygen species caused by salt stress. Moreover, the salt-tolerant cultivars had higher photosynthetic activity based on overexpression of proteins functioned in chloroplast, guaranteeing the sufficient nutrient for plant growth under salt stress. Furthermore, three key proteins were identified as important salt-resistant resources for breeding salt-tolerant cultivars, including sterol side chain reductase, gamma aminobutyrate transaminase and starch synthase. Our results provided series valuable strategies for salt-tolerant cultivars which can be used in future.
bibliographic citation: Wang et al. (2022) Comparative proteomic analysis for revealing the advantage mechanisms of salt-tolerant tomato (Solanum lycoperscium). PeerJ 10:e12955 https://doi.org/10.7717/peerj.12955
date submitted: 2021-07-29
date accepted: 2022-01-27
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Qiang
author list: Agent
  family name: Wang
  given name: Baike
author list: Agent
  family name: Liu
  given name: Huifang
author list: Agent
  family name: Han
  given name: Hongwei
author list: Agent
  family name: Zhuang
  given name: Hongmei
author list: Agent
  family name: Wang
  given name: Juan
author list: Agent
  family name: Yang
  given name: Tao
author list: Agent
  family name: Wang
  given name: Hao
author list: Agent
  family name: Qin
  given name: Yong
doi: 10.7717/peerj.12955
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.)
type: item
type: AcademicArticle
description: Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by 60Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful i…
format: application/pdf
format: text/html
creator: Yaqi Wang
creator: Maoning Zhang
creator: Pei Du
creator: Hua Liu
creator: Zhongxin Zhang
creator: Jing Xu
creator: Li Qin
creator: Bingyan Huang
creator: Zheng Zheng
creator: Wenzhao Dong
creator: Xinyou Zhang
creator: Suoyi Han
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.12965
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Pod size is an important yield-influencing trait in peanuts. It is affected by plant hormones and identifying the genes related to these hormones may contribute to pod-related trait improvements in peanut breeding programs. However, there is limited information on the molecular mechanisms of plant hormones that regulate pod size in peanuts. We identified a mutant with an extremely small pod (spm) from Yuanza 9102 (WT) by 60Co γ-radiation mutagenesis. The length and width of the natural mature pod in spm were only 71.34% and 73.36% of those in WT, respectively. We performed comparative analyses for morphological characteristics, anatomy, physiology, and global transcriptome between spm and WT pods. Samples were collected at 10, 20, and 30 days after peg elongation into the soil, representing stages S1, S2, and S3, respectively. The differences in pod size between WT and spm were seen at stage S1 and became even more striking at stages S2 and S3. The cell sizes of the pods were significantly smaller in spm than in WT at stages S1, S2, and S3. These results suggested that reduced cell size may be one of the important contributors for the small pod in spm. The contents of indole-3-acetic acid (IAA), gibberellin (GA), and brassinosteroid (BR) were also significantly lower in spm pods than those in WT pods at all three stages. RNA-Seq analyses showed that 1,373, 8,053, and 3,358 differently expressed genes (DEGs) were identified at stages S1, S2, and S3, respectively. Functional analyses revealed that a set of DEGs was related to plant hormone biosynthesis, plant hormone signal transduction pathway, and cell wall biosynthesis and metabolism. Furthermore, several hub genes associated with plant hormone biosynthesis and signal transduction pathways were identified through weighted gene co-expression network analysis. Our results revealed that IAA, GA, and BR may be important regulators in controlling pod size by regulating cell size in peanuts. This study provides helpful i…
bibliographic citation: Wang et al. (2022) Transcriptome analysis of pod mutant reveals plant hormones are important regulators in controlling pod size in peanut (Arachis hypogaea L.). PeerJ 10:e12965 https://doi.org/10.7717/peerj.12965
date submitted: 2021-10-01
date accepted: 2022-01-28
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yaqi
author list: Agent
  family name: Zhang
  given name: Maoning
author list: Agent
  family name: Du
  given name: Pei
author list: Agent
  family name: Liu
  given name: Hua
author list: Agent
  family name: Zhang
  given name: Zhongxin
author list: Agent
  family name: Xu
  given name: Jing
author list: Agent
  family name: Qin
  given name: Li
author list: Agent
  family name: Huang
  given name: Bingyan
author list: Agent
  family name: Zheng
  given name: Zheng
author list: Agent
  family name: Dong
  given name: Wenzhao
author list: Agent
  family name: Zhang
  given name: Xinyou
author list: Agent
  family name: Han
  given name: Suoyi
doi: 10.7717/peerj.12965
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Response of bacterial community structure to different ecological niches and their functions in Korean pine forests
type: item
type: AcademicArticle
description: A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemo…
format: application/pdf
format: text/html
creator: Rui-Qing Ji
creator: Meng-Le Xie
creator: Guan-Lin Li
creator: Yang Xu
creator: Ting-Ting Gao
creator: Peng-Jie Xing
creator: Li-Peng Meng
creator: Shu-Yan Liu
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.12978
publisher: PeerJ Inc.
rights: © 2022 Ji et al.
abstract: A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemo…
bibliographic citation: Ji et al. (2022) Response of bacterial community structure to different ecological niches and their functions in Korean pine forests. PeerJ 10:e12978 https://doi.org/10.7717/peerj.12978
date submitted: 2021-07-05
date accepted: 2022-01-31
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Rui-Qing
author list: Agent
  family name: Xie
  given name: Meng-Le
author list: Agent
  family name: Li
  given name: Guan-Lin
author list: Agent
  family name: Xu
  given name: Yang
author list: Agent
  family name: Gao
  given name: Ting-Ting
author list: Agent
  family name: Xing
  given name: Peng-Jie
author list: Agent
  family name: Meng
  given name: Li-Peng
author list: Agent
  family name: Liu
  given name: Shu-Yan
doi: 10.7717/peerj.12978
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: ©2022 Ji et al.
attribution name: Ji et al.

Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China
type: item
type: AcademicArticle
description: Background With the exacerbating effects of the global climate change and the more and more attention to the study of plant carbon sink, an increasing number of researches on plant carbon sinks has grown. Although many studies exist on shrub vegetation, soil and litters, most studies focus on the community structure, biomass, surface soil of single plant and shrub layer vegetation, and lack the studies which included the potential relationships between climate change and ecological stoichiometric elements, comprehensive research on main species, even herb and litter layer. In order to provide relevant theoretical basis and data support, it is necessary to take the main terrestrial shrub ecosystem in Central Yunnan as the starting point to analyze and explore its carbon sink distribution characteristics, formation causes, the correlation between climatic factors (temperature and precipitation) and stoichiometric elements, which from community and species levels. Methods Plants which originated from 12 main shrub species, litter and soil samples which collected in 69 plots were from 23 plots (Q1–Q23) of 11 cities (countries) in the central Yunnan, China. The biomass and carbon density distribution pattern of each shrub ecosystem and the potential correlations with main climate factors was explored and identified. Some indexes were analyzed such as biomass and carbon density of each part of the shrub ecosystem distribution pattern, correlation, significant changes, formation reasons with the mean value (±standard deviation: SD). Through the redundancy analysis(RDA) of carbon (c), nitrogen (n), phosphorus (P) and main climate factors (precipitation and temperature), the distribution pattern of stoichiometric elements in shrub ecosystem can be judged. Results (1) The above-ground biomass (AGB), under-ground biomass (UGB) and root-shoot ratio (R/S) were between 1.13–2.03 t/hm2, 0.62–1.49 t/hm2, and 0.38–0.84, the carbon element was distributed in herb layer under-ground p…
format: application/pdf
format: text/html
creator: Zihao Guo
creator: Wei Chen
creator: Qianwei Chen
creator: Xingyue Liu
creator: Sisi Hong
creator: Xiuwen Zhu
creator: Hede Gong
subject: Biogeography
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.13005
publisher: PeerJ Inc.
rights: © 2022 Guo et al.
abstract: Background With the exacerbating effects of the global climate change and the more and more attention to the study of plant carbon sink, an increasing number of researches on plant carbon sinks has grown. Although many studies exist on shrub vegetation, soil and litters, most studies focus on the community structure, biomass, surface soil of single plant and shrub layer vegetation, and lack the studies which included the potential relationships between climate change and ecological stoichiometric elements, comprehensive research on main species, even herb and litter layer. In order to provide relevant theoretical basis and data support, it is necessary to take the main terrestrial shrub ecosystem in Central Yunnan as the starting point to analyze and explore its carbon sink distribution characteristics, formation causes, the correlation between climatic factors (temperature and precipitation) and stoichiometric elements, which from community and species levels. Methods Plants which originated from 12 main shrub species, litter and soil samples which collected in 69 plots were from 23 plots (Q1–Q23) of 11 cities (countries) in the central Yunnan, China. The biomass and carbon density distribution pattern of each shrub ecosystem and the potential correlations with main climate factors was explored and identified. Some indexes were analyzed such as biomass and carbon density of each part of the shrub ecosystem distribution pattern, correlation, significant changes, formation reasons with the mean value (±standard deviation: SD). Through the redundancy analysis(RDA) of carbon (c), nitrogen (n), phosphorus (P) and main climate factors (precipitation and temperature), the distribution pattern of stoichiometric elements in shrub ecosystem can be judged. Results (1) The above-ground biomass (AGB), under-ground biomass (UGB) and root-shoot ratio (R/S) were between 1.13–2.03 t/hm2, 0.62–1.49 t/hm2, and 0.38–0.84, the carbon element was distributed in herb layer under-ground p…
bibliographic citation: Guo et al. (2022) Biomass distribution pattern and stoichiometric characteristics in main shrub ecosystems in Central Yunnan, China. PeerJ 10:e13005 https://doi.org/10.7717/peerj.13005
date submitted: 2021-10-11
date accepted: 2022-02-03
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Zihao
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: Chen
  given name: Qianwei
author list: Agent
  family name: Liu
  given name: Xingyue
author list: Agent
  family name: Hong
  given name: Sisi
author list: Agent
  family name: Zhu
  given name: Xiuwen
author list: Agent
  family name: Gong
  given name: Hede
doi: 10.7717/peerj.13005
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: ©2022 Guo et al.
attribution name: Guo et al.

Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants
type: item
type: AcademicArticle
description: Pathogen accumulation after introduction is unavoidable for exotic plants over a long period of time. Therefore, it is important to understand whether plant invasion promotes novel pathogen emergence and increases the risk of pathogen movement among agricultural, horticultural, and wild native plants. In this study, we used multiple gene analysis to characterize the species composition of 104 isolates of Alternaria obtained from the invasive plant Ageratina adenophora and native plants from Yunnan, Hubei, Guizhou, Sichuan, and Guangxi in China. Phylogenetically, these strains were from A. alternata (88.5%), A. gossypina (10.6%) and A. steviae (0.9%). There was a high amount of sharing between strains associated with A. adenophora and with local plants. Pathogenicity tests indicated that most of these Alternaria strains are generalists; the isolates with a wider host range were more virulent to the plant. Woody plants were more resistant to these strains than herbaceous plants and vines. However, the invasive plant A. adenophora was highly sensitive to these strains. Our data are valuable for understanding how A. adenophora invasion impacts the Alternaria species composition of the native plant and whether A. adenophora invasion causes potential disease risks in invaded ecosystems.
format: application/pdf
format: text/html
creator: Yu-Xuan Li
creator: Xing-Fan Dong
creator: Ai-Ling Yang
creator: Han-Bo Zhang
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.13012
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Pathogen accumulation after introduction is unavoidable for exotic plants over a long period of time. Therefore, it is important to understand whether plant invasion promotes novel pathogen emergence and increases the risk of pathogen movement among agricultural, horticultural, and wild native plants. In this study, we used multiple gene analysis to characterize the species composition of 104 isolates of Alternaria obtained from the invasive plant Ageratina adenophora and native plants from Yunnan, Hubei, Guizhou, Sichuan, and Guangxi in China. Phylogenetically, these strains were from A. alternata (88.5%), A. gossypina (10.6%) and A. steviae (0.9%). There was a high amount of sharing between strains associated with A. adenophora and with local plants. Pathogenicity tests indicated that most of these Alternaria strains are generalists; the isolates with a wider host range were more virulent to the plant. Woody plants were more resistant to these strains than herbaceous plants and vines. However, the invasive plant A. adenophora was highly sensitive to these strains. Our data are valuable for understanding how A. adenophora invasion impacts the Alternaria species composition of the native plant and whether A. adenophora invasion causes potential disease risks in invaded ecosystems.
bibliographic citation: Li et al. (2022) Diversity and pathogenicity of Alternaria species associated with the invasive plant Ageratina adenophora and local plants. PeerJ 10:e13012 https://doi.org/10.7717/peerj.13012
date submitted: 2021-10-26
date accepted: 2022-02-04
issued: 2022-02-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yu-Xuan
author list: Agent
  family name: Dong
  given name: Xing-Fan
author list: Agent
  family name: Yang
  given name: Ai-Ling
author list: Agent
  family name: Zhang
  given name: Han-Bo
doi: 10.7717/peerj.13012
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-28
copyright: © 2022 Li et al.
attribution name: Li et al.

Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.
type: item
type: AcademicArticle
description: The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant’s adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.
format: application/pdf
format: text/html
creator: Bin-Jie Gu
creator: Yi-Kai Tong
creator: You-Yi Wang
creator: Mei-Li Zhang
creator: Guang-Jing Ma
creator: Xiao-Qin Wu
creator: Jian-Feng Zhang
creator: Fan Xu
creator: Jun Li
creator: Feng Ren
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12882
publisher: PeerJ Inc.
rights: © 2022 Gu et al.
abstract: The MYB-CC family is a subtype within the MYB superfamily. This family contains an MYB domain and a predicted coiled-coil (CC) domain. Several MYB-CC transcription factors are involved in the plant’s adaptability to low phosphate (Pi) stress. We identified 30, 34, and 55 MYB-CC genes in Brassica rapa, Brassica oleracea, and Brassica napus, respectively. The MYB-CC genes were divided into nine groups based on phylogenetic analysis. The analysis of the chromosome distribution and gene structure revealed that most MYB-CC genes retained the same relative position on the chromosomes and had similar gene structures during allotetraploidy. Evolutionary analysis showed that the ancestral whole-genome triplication (WGT) and the recent allopolyploidy are critical for the expansion of the MYB-CC gene family. The expression patterns of MYB-CC genes were found to be diverse in different tissues of the three Brassica species. Furthermore, the gene expression analysis under low Pi stress revealed that MYB-CC genes may be related to low Pi stress responses. These results may increase our understanding of MYB-CC gene family diversification and provide the basis for further analysis of the specific functions of MYB-CC genes in Brassica species.
bibliographic citation: Gu et al. (2022) Genome-wide evolution and expression analysis of the MYB-CC gene family in Brassica spp.. PeerJ 10:e12882 https://doi.org/10.7717/peerj.12882
date submitted: 2021-06-27
date accepted: 2022-01-13
issued: 2022-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gu
  given name: Bin-Jie
author list: Agent
  family name: Tong
  given name: Yi-Kai
author list: Agent
  family name: Wang
  given name: You-Yi
author list: Agent
  family name: Zhang
  given name: Mei-Li
author list: Agent
  family name: Ma
  given name: Guang-Jing
author list: Agent
  family name: Wu
  given name: Xiao-Qin
author list: Agent
  family name: Zhang
  given name: Jian-Feng
author list: Agent
  family name: Xu
  given name: Fan
author list: Agent
  family name: Li
  given name: Jun
author list: Agent
  family name: Ren
  given name: Feng
doi: 10.7717/peerj.12882
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-25
copyright: © 2022 Gu et al.
attribution name: Gu et al.

Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury
type: item
type: AcademicArticle
description: MicroRNAs (miRNAs or miRs) are non-coding RNAs that contribute to pathological processes of various kidney diseases. Renal function injury represents a final common outcome of congenital obstructive nephropathy and has attracted a great deal of attention. However the molecular mechanisms are still not fully established. In this study, we compared transcriptome sequencing data of miRNAs of renal tissues from congenital hydronephrosis children with or without renal functional injury, in order to better understand whether microRNAs could play important roles in renal functional injury after ureteropelvic junction obstruction. A total of 22 microRNAs with significant changes in their expression were identified. Five microRNAs were up-regulated and 17 microRNAs were down-regulated in the renal tissues of the hydronephrosis patients with renal function injury compared with those without renal function injury. MicroRNA target genes were predicted by three major online miRNA target prediction algorithms, and all these mRNAs were used to perform the gene ontology analysis and Kyoto Encyclopedia of Gene and Genomes pathway analysis. Then, twelve candidate human and rat homologous miRNAs were selected for validation using RT-qPCR in vitro and in vivo; only miR-187-3p had a trend identical to that detected by the sequencing results among the human tissues, in vivo and in vitro experimental models. In addition, we found that the change of miR-187-3p in vivo was consistent with results in vitro models and showed a decrease trend in time dependence. These results provided a detailed catalog of candidate miRNAs to investigate their regulatory role in renal injury of congenital hydronephrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.
format: application/pdf
format: text/html
creator: Ge Liu
creator: Xin Liu
creator: Yi Yang
subject: Bioinformatics
subject: Cell Biology
subject: Nephrology
subject: Pediatrics
subject: Urology
description: doi:10.7717/peerj.12962
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: MicroRNAs (miRNAs or miRs) are non-coding RNAs that contribute to pathological processes of various kidney diseases. Renal function injury represents a final common outcome of congenital obstructive nephropathy and has attracted a great deal of attention. However the molecular mechanisms are still not fully established. In this study, we compared transcriptome sequencing data of miRNAs of renal tissues from congenital hydronephrosis children with or without renal functional injury, in order to better understand whether microRNAs could play important roles in renal functional injury after ureteropelvic junction obstruction. A total of 22 microRNAs with significant changes in their expression were identified. Five microRNAs were up-regulated and 17 microRNAs were down-regulated in the renal tissues of the hydronephrosis patients with renal function injury compared with those without renal function injury. MicroRNA target genes were predicted by three major online miRNA target prediction algorithms, and all these mRNAs were used to perform the gene ontology analysis and Kyoto Encyclopedia of Gene and Genomes pathway analysis. Then, twelve candidate human and rat homologous miRNAs were selected for validation using RT-qPCR in vitro and in vivo; only miR-187-3p had a trend identical to that detected by the sequencing results among the human tissues, in vivo and in vitro experimental models. In addition, we found that the change of miR-187-3p in vivo was consistent with results in vitro models and showed a decrease trend in time dependence. These results provided a detailed catalog of candidate miRNAs to investigate their regulatory role in renal injury of congenital hydronephrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.
bibliographic citation: Liu et al. (2022) Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury. PeerJ 10:e12962 https://doi.org/10.7717/peerj.12962
date submitted: 2021-03-25
date accepted: 2022-01-27
issued: 2022-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Ge
author list: Agent
  family name: Liu
  given name: Xin
author list: Agent
  family name: Yang
  given name: Yi
doi: 10.7717/peerj.12962
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-25
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Applications and limitations of current markerless motion capture methods for clinical gait biomechanics
type: item
type: AcademicArticle
description: Background Markerless motion capture has the potential to perform movement analysis with reduced data collection and processing time compared to marker-based methods. This technology is now starting to be applied for clinical and rehabilitation applications and therefore it is crucial that users of these systems understand both their potential and limitations. This literature review aims to provide a comprehensive overview of the current state of markerless motion capture for both single camera and multi-camera systems. Additionally, this review explores how practical applications of markerless technology are being used in clinical and rehabilitation settings, and examines the future challenges and directions markerless research must explore to facilitate full integration of this technology within clinical biomechanics. Methodology A scoping review is needed to examine this emerging broad body of literature and determine where gaps in knowledge exist, this is key to developing motion capture methods that are cost effective and practically relevant to clinicians, coaches and researchers around the world. Literature searches were performed to examine studies that report accuracy of markerless motion capture methods, explore current practical applications of markerless motion capture methods in clinical biomechanics and identify gaps in our knowledge that are relevant to future developments in this area. Results Markerless methods increase motion capture data versatility, enabling datasets to be re-analyzed using updated pose estimation algorithms and may even provide clinicians with the capability to collect data while patients are wearing normal clothing. While markerless temporospatial measures generally appear to be equivalent to marker-based motion capture, joint center locations and joint angles are not yet sufficiently accurate for clinical applications. Pose estimation algorithms are approaching similar error rates of marker-based motion capture, however, witho…
format: application/pdf
format: text/html
creator: Logan Wade
creator: Laurie Needham
creator: Polly McGuigan
creator: James Bilzon
subject: Data Mining and Machine Learning
subject: Biomechanics
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.12995
publisher: PeerJ Inc.
rights: © 2022 Wade et al.
abstract: Background Markerless motion capture has the potential to perform movement analysis with reduced data collection and processing time compared to marker-based methods. This technology is now starting to be applied for clinical and rehabilitation applications and therefore it is crucial that users of these systems understand both their potential and limitations. This literature review aims to provide a comprehensive overview of the current state of markerless motion capture for both single camera and multi-camera systems. Additionally, this review explores how practical applications of markerless technology are being used in clinical and rehabilitation settings, and examines the future challenges and directions markerless research must explore to facilitate full integration of this technology within clinical biomechanics. Methodology A scoping review is needed to examine this emerging broad body of literature and determine where gaps in knowledge exist, this is key to developing motion capture methods that are cost effective and practically relevant to clinicians, coaches and researchers around the world. Literature searches were performed to examine studies that report accuracy of markerless motion capture methods, explore current practical applications of markerless motion capture methods in clinical biomechanics and identify gaps in our knowledge that are relevant to future developments in this area. Results Markerless methods increase motion capture data versatility, enabling datasets to be re-analyzed using updated pose estimation algorithms and may even provide clinicians with the capability to collect data while patients are wearing normal clothing. While markerless temporospatial measures generally appear to be equivalent to marker-based motion capture, joint center locations and joint angles are not yet sufficiently accurate for clinical applications. Pose estimation algorithms are approaching similar error rates of marker-based motion capture, however, witho…
bibliographic citation: Wade et al. (2022) Applications and limitations of current markerless motion capture methods for clinical gait biomechanics. PeerJ 10:e12995 https://doi.org/10.7717/peerj.12995
date submitted: 2021-12-03
date accepted: 2022-02-02
issued: 2022-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wade
  given name: Logan
author list: Agent
  family name: Needham
  given name: Laurie
author list: Agent
  family name: McGuigan
  given name: Polly
author list: Agent
  family name: Bilzon
  given name: James
doi: 10.7717/peerj.12995
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-25
copyright: ©2022 Wade et al.
attribution name: Wade et al.

Profiles of anemia in adolescent students with sports club membership in an outpatient clinic setting: a retrospective study
type: item
type: AcademicArticle
description: Background Anemia is a common health issue among adolescents. Anemic conditions could affect physical performance; however, the actual profiles of anemia in adolescent students in sports clubs have not been well documented. Methods We conducted a retrospective chart review of individuals aged 13–22 years who belonged to sports clubs in schools and visited an outpatient clinic between August 1, 2016, and August 31, 2020. The medical and laboratory records, including serum levels of ferritin, folate, vitamin B12, and creatinine kinase at their first visit were assessed. Results A total of 485 individuals (231 male (48%) and 254 female (52%) patients) were eligible for the study. The most common club activity was track and field (n = 171 (35%)). The overall prevalence of the World Health Organization-defined anemia was 16.5% (95% CI [13.1–20.4]; 9.0% [5.4–13.8] and 23.1% [17.8–29.2] in males and females, respectively) after excluding pre-treated individuals. Hypoferritinemia and elevation of serum creatinine kinase levels were identified as independent contributors to anemia in both sexes (odds ratios: 13.2 (95% CI [4.2–41.1]), p < 0.001 and 14.7 (95% CI [1.8–118.4]), p = 0.012, respectively for males; odds ratios: 6.6 (95% CI [1.3–13.9]), p < 0.001 and 2.7 (95% CI [1.4–5.5]), p = 0.004, respectively for females). Discussion Anemia is prevalent in both male and female adolescent students in sports clubs. Iron deficiency and excessive training indicated by elevated creatinine kinase levels may contribute to the risk of anemia. Physicians should assess the amount of exercise, and not merely iron storage, in clinical practice.
format: application/pdf
format: text/html
creator: Kana Yamamoto
creator: Morihito Takita
creator: Masahiro Kami
creator: Masaharu Tsubokura
creator: Tetsuya Tanimoto
creator: Toshio Kitamura
creator: Yoshinobu Takemoto
subject: Hematology
subject: Pediatrics
subject: Sports Medicine
description: doi:10.7717/peerj.13004
publisher: PeerJ Inc.
rights: © 2022 Yamamoto et al.
abstract: Background Anemia is a common health issue among adolescents. Anemic conditions could affect physical performance; however, the actual profiles of anemia in adolescent students in sports clubs have not been well documented. Methods We conducted a retrospective chart review of individuals aged 13–22 years who belonged to sports clubs in schools and visited an outpatient clinic between August 1, 2016, and August 31, 2020. The medical and laboratory records, including serum levels of ferritin, folate, vitamin B12, and creatinine kinase at their first visit were assessed. Results A total of 485 individuals (231 male (48%) and 254 female (52%) patients) were eligible for the study. The most common club activity was track and field (n = 171 (35%)). The overall prevalence of the World Health Organization-defined anemia was 16.5% (95% CI [13.1–20.4]; 9.0% [5.4–13.8] and 23.1% [17.8–29.2] in males and females, respectively) after excluding pre-treated individuals. Hypoferritinemia and elevation of serum creatinine kinase levels were identified as independent contributors to anemia in both sexes (odds ratios: 13.2 (95% CI [4.2–41.1]), p < 0.001 and 14.7 (95% CI [1.8–118.4]), p = 0.012, respectively for males; odds ratios: 6.6 (95% CI [1.3–13.9]), p < 0.001 and 2.7 (95% CI [1.4–5.5]), p = 0.004, respectively for females). Discussion Anemia is prevalent in both male and female adolescent students in sports clubs. Iron deficiency and excessive training indicated by elevated creatinine kinase levels may contribute to the risk of anemia. Physicians should assess the amount of exercise, and not merely iron storage, in clinical practice.
bibliographic citation: Yamamoto et al. (2022) Profiles of anemia in adolescent students with sports club membership in an outpatient clinic setting: a retrospective study. PeerJ 10:e13004 https://doi.org/10.7717/peerj.13004
date submitted: 2021-10-19
date accepted: 2022-02-03
issued: 2022-02-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yamamoto
  given name: Kana
author list: Agent
  family name: Takita
  given name: Morihito
author list: Agent
  family name: Kami
  given name: Masahiro
author list: Agent
  family name: Tsubokura
  given name: Masaharu
author list: Agent
  family name: Tanimoto
  given name: Tetsuya
author list: Agent
  family name: Kitamura
  given name: Toshio
author list: Agent
  family name: Takemoto
  given name: Yoshinobu
doi: 10.7717/peerj.13004
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-25
copyright: © 2022 Yamamoto et al.
attribution name: Yamamoto et al.

Effects of long-term nitrogen & phosphorus fertilization on soil microbial, bacterial and fungi respiration and their temperature sensitivity on the Qinghai-Tibet Plateau
type: item
type: AcademicArticle
description: Background The microbial decomposition of soil organic carbon (SOC) is a major source of carbon loss, especially in ecologically fragile regions (e.g., the Tibetan Plateau), which are also affected by global warming and anthropogenic activities (e.g., fertilization). The inherent differences between bacteria and fungi indicate that they are likely to play distinct roles in the above processes. However, there still have been no reports on that, which is restricting our knowledge about the mechanisms underlying SOC decomposition. Methods A long-term nitrogen (N) and phosphorus (P) addition field experiment was conducted to assess their effects on soil microbial, fungal, and bacterial respiration (RM, RF, and RB, respectively) and temperature sensitivity (Q10; at 15 °C, 25 °C, and 35 °C) using cycloheximide and streptomycin to inhibit the growth of fungi and bacteria. Results We found that N suppressed RM and RF at all temperatures, but RB was only suppressed at 15 °C, regardless of the addition of P. The addition of N significantly decreased the ratio of RF/RM at 35 °C, and the combined NP treatment increased the Q10 of RB but not that of RF. Results of the redundancy analysis showed that variations in soil respiration were linked with NO3−-N formation, while the variations in Q10 were linked with SOC complexity. Long-term N addition suppressed RM by the formation of NO3−-N, and this was mediated by fungi rather than bacteria. The contribution of fungi toward SOC decomposition was weakened by N addition and increasing temperatures. Combined NP addition increased the Q10 of RB due to increased SOC complexity. The present study emphasizes the importance of fungi and the soil environment in SOC decomposition. It also highlights that the role of bacteria and SOC quality will be important in the future due to global warming and increasing N deposition.
format: application/pdf
format: text/html
creator: Kelu Chen
creator: Huakun Zhou
creator: Yang Wu
creator: Ziwen Zhao
creator: Yuanze Li
creator: Leilei Qiao
creator: Guobin Liu
creator: Sha Xue
subject: Ecology
subject: Soil Science
subject: Climate Change Biology
subject: Biogeochemistry
description: doi:10.7717/peerj.12851
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Background The microbial decomposition of soil organic carbon (SOC) is a major source of carbon loss, especially in ecologically fragile regions (e.g., the Tibetan Plateau), which are also affected by global warming and anthropogenic activities (e.g., fertilization). The inherent differences between bacteria and fungi indicate that they are likely to play distinct roles in the above processes. However, there still have been no reports on that, which is restricting our knowledge about the mechanisms underlying SOC decomposition. Methods A long-term nitrogen (N) and phosphorus (P) addition field experiment was conducted to assess their effects on soil microbial, fungal, and bacterial respiration (RM, RF, and RB, respectively) and temperature sensitivity (Q10; at 15 °C, 25 °C, and 35 °C) using cycloheximide and streptomycin to inhibit the growth of fungi and bacteria. Results We found that N suppressed RM and RF at all temperatures, but RB was only suppressed at 15 °C, regardless of the addition of P. The addition of N significantly decreased the ratio of RF/RM at 35 °C, and the combined NP treatment increased the Q10 of RB but not that of RF. Results of the redundancy analysis showed that variations in soil respiration were linked with NO3−-N formation, while the variations in Q10 were linked with SOC complexity. Long-term N addition suppressed RM by the formation of NO3−-N, and this was mediated by fungi rather than bacteria. The contribution of fungi toward SOC decomposition was weakened by N addition and increasing temperatures. Combined NP addition increased the Q10 of RB due to increased SOC complexity. The present study emphasizes the importance of fungi and the soil environment in SOC decomposition. It also highlights that the role of bacteria and SOC quality will be important in the future due to global warming and increasing N deposition.
bibliographic citation: Chen et al. (2022) Effects of long-term nitrogen & phosphorus fertilization on soil microbial, bacterial and fungi respiration and their temperature sensitivity on the Qinghai-Tibet Plateau. PeerJ 10:e12851 https://doi.org/10.7717/peerj.12851
date submitted: 2021-09-27
date accepted: 2022-01-07
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Kelu
author list: Agent
  family name: Zhou
  given name: Huakun
author list: Agent
  family name: Wu
  given name: Yang
author list: Agent
  family name: Zhao
  given name: Ziwen
author list: Agent
  family name: Li
  given name: Yuanze
author list: Agent
  family name: Qiao
  given name: Leilei
author list: Agent
  family name: Liu
  given name: Guobin
author list: Agent
  family name: Xue
  given name: Sha
doi: 10.7717/peerj.12851
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: ©2022 Chen et al.
attribution name: Chen et al.

Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives
type: item
type: AcademicArticle
description: The need for comprehensive and effective coral restoration projects, as part of a broader conservation management strategy, is accelerating in the face of coral reef ecosystem decline. This study aims to expand the currently limited knowledge base for restoration techniques in the Maldives by testing the performance of mid-water rope nurseries in a lagoon and a reef habitat. We examined whether different coral farming habitats impacted fragment survival, health and growth of two coral genera and how the occurrence of mutualistic fauna, predation and disease influenced coral rearing success. Two nurseries were stocked with a total of 448 Pocillopora verrucosa and 96 Acropora spp. fragments, divided into different groups (four Pocillopora groups: lagoon nursery at 5 m; reef nursery at 5, 10 and 15 m; two Acropora groups: lagoon nursery at 5 m and reef nursery at 5 m). Eight fragment replicates from the same donor colony (Pocillopora genets: N = 14, Acropora genets N = 6) were used in each group and monitored for one year. Our results show that fragment survival was high in both farming habitats (>90%), with P. verrucosa surviving significantly better in the lagoon and Acropora spp. surviving and growing significantly faster in the reef nursery. P. verrucosa growth rates were similar between reef and lagoon habitat. Different rearing depths in the reef nursery had no impact on the survival of P. verrucosa but coral growth decreased considerably with depth, reducing fragments’ ecological volume augmentation and growth rates by almost half from 5 to 15 m depth. Further, higher fish predation rates on fragments were recorded on the reef, which did not impact overall nursery performance. Mutualistic fauna, which correlated positively with fragment survival, was more frequently observed in the lagoon nursery. The occurrence of disease was noted in both habitats, even though implications for fragment health were more severe in the lagoon. Overall, our study demonstrates that…
format: application/pdf
format: text/html
creator: Inga Dehnert
creator: Luca Saponari
creator: Paolo Galli
creator: Simone Montano
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.12874
publisher: PeerJ Inc.
rights: © 2022 Dehnert et al.
abstract: The need for comprehensive and effective coral restoration projects, as part of a broader conservation management strategy, is accelerating in the face of coral reef ecosystem decline. This study aims to expand the currently limited knowledge base for restoration techniques in the Maldives by testing the performance of mid-water rope nurseries in a lagoon and a reef habitat. We examined whether different coral farming habitats impacted fragment survival, health and growth of two coral genera and how the occurrence of mutualistic fauna, predation and disease influenced coral rearing success. Two nurseries were stocked with a total of 448 Pocillopora verrucosa and 96 Acropora spp. fragments, divided into different groups (four Pocillopora groups: lagoon nursery at 5 m; reef nursery at 5, 10 and 15 m; two Acropora groups: lagoon nursery at 5 m and reef nursery at 5 m). Eight fragment replicates from the same donor colony (Pocillopora genets: N = 14, Acropora genets N = 6) were used in each group and monitored for one year. Our results show that fragment survival was high in both farming habitats (>90%), with P. verrucosa surviving significantly better in the lagoon and Acropora spp. surviving and growing significantly faster in the reef nursery. P. verrucosa growth rates were similar between reef and lagoon habitat. Different rearing depths in the reef nursery had no impact on the survival of P. verrucosa but coral growth decreased considerably with depth, reducing fragments’ ecological volume augmentation and growth rates by almost half from 5 to 15 m depth. Further, higher fish predation rates on fragments were recorded on the reef, which did not impact overall nursery performance. Mutualistic fauna, which correlated positively with fragment survival, was more frequently observed in the lagoon nursery. The occurrence of disease was noted in both habitats, even though implications for fragment health were more severe in the lagoon. Overall, our study demonstrates that…
bibliographic citation: Dehnert et al. (2022) Comparing different farming habitats for mid-water rope nurseries to advance coral restoration efforts in the Maldives. PeerJ 10:e12874 https://doi.org/10.7717/peerj.12874
date submitted: 2021-09-01
date accepted: 2022-01-11
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dehnert
  given name: Inga
author list: Agent
  family name: Saponari
  given name: Luca
author list: Agent
  family name: Galli
  given name: Paolo
author list: Agent
  family name: Montano
  given name: Simone
doi: 10.7717/peerj.12874
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: ©2022 Dehnert et al.
attribution name: Dehnert et al.

Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes
type: item
type: AcademicArticle
description: Background Wind, an important abiotic stress factor, affects forests in coastal areas, causes tree damage and timber loss. Methods Two genotypes of Eucalyptus camaldulensis-strong wind-resistant CA5 and weak wind-resistant C037 were used for RNA-seq analysis to screen for candidate wind-resistance genes and transcription factors (TFs) by comparing the transcriptome analysis of the two varieties in response to wind stress. Results It showed that 7061 differentially expressed unigenes could be annotated including 4,110 up-regulated unigenes and 2,951 down-regulated unigenes. Gene Ontology (GO) analysis revealed that six cellulose pathways were involved in response to wind stress. The unigenes in phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways were found to be differentially expressed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, 37 differentially expressed genes were functionally annotated to be involved in the secondary metabolism of phenylalanine (ko00940). Seventy-eight TFs related to the regulating cellulose and lignin synthesis were expressed differently from the various treatments. The expressions of C3H, POX, MYB, NAC, Gene008307, and Gene011799 were significantly upregulated in CA5. Overall, the main response of Eucalyptus to wind stress was associated with cell wall biosynthesis; key genes of cellulose and lignin biosynthesis pathways and related TFs were involved in the tree response to wind stress.
format: application/pdf
format: text/html
creator: Xiuhua Shang
creator: Peijian Zhang
creator: Guo Liu
creator: Ni Zhan
creator: Zhihua Wu
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12954
publisher: PeerJ Inc.
rights: © 2022 Shang et al.
abstract: Background Wind, an important abiotic stress factor, affects forests in coastal areas, causes tree damage and timber loss. Methods Two genotypes of Eucalyptus camaldulensis-strong wind-resistant CA5 and weak wind-resistant C037 were used for RNA-seq analysis to screen for candidate wind-resistance genes and transcription factors (TFs) by comparing the transcriptome analysis of the two varieties in response to wind stress. Results It showed that 7061 differentially expressed unigenes could be annotated including 4,110 up-regulated unigenes and 2,951 down-regulated unigenes. Gene Ontology (GO) analysis revealed that six cellulose pathways were involved in response to wind stress. The unigenes in phenylpropanoid biosynthesis, phenylalanine metabolism, and flavonoid biosynthesis pathways were found to be differentially expressed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Moreover, 37 differentially expressed genes were functionally annotated to be involved in the secondary metabolism of phenylalanine (ko00940). Seventy-eight TFs related to the regulating cellulose and lignin synthesis were expressed differently from the various treatments. The expressions of C3H, POX, MYB, NAC, Gene008307, and Gene011799 were significantly upregulated in CA5. Overall, the main response of Eucalyptus to wind stress was associated with cell wall biosynthesis; key genes of cellulose and lignin biosynthesis pathways and related TFs were involved in the tree response to wind stress.
bibliographic citation: Shang et al. (2022) Comparative transcriptomics analysis of contrasting varieties of Eucalyptus camaldulensis reveals wind resistance genes. PeerJ 10:e12954 https://doi.org/10.7717/peerj.12954
date submitted: 2021-08-04
date accepted: 2022-01-27
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shang
  given name: Xiuhua
author list: Agent
  family name: Zhang
  given name: Peijian
author list: Agent
  family name: Liu
  given name: Guo
author list: Agent
  family name: Zhan
  given name: Ni
author list: Agent
  family name: Wu
  given name: Zhihua
doi: 10.7717/peerj.12954
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: ©2022 Shang et al.
attribution name: Shang et al.

AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis
type: item
type: AcademicArticle
description: Ascorbic acid (AsA) is an important nutrient in celery, the conversion of D-mannose-1-P to GDP-D-mannose catalyzed by GDP-D-mannose pyrophosphorylase (GMPase) represents the first committed step in the biosynthesis of AsA. To clarify the function of the AgGMP gene of celery, the AgGMP gene was cloned from celery cv. ‘Jinnan Shiqin’ . It contains an open reading frame (ORF) with the length of 1,086 bp, encoding 361 amino acids. AgGMP protein was highly conserved among different plant species. Phylogenetic analysis demonstrated that the GMP proteins from celery and carrot belonged to the same branch. AgGMP protein was mainly composed of three α-helixes and certain random coils. No signal peptide was found in the AgGMP protein. The subcellular localization indicated that the AgGMP protein was located in the cytoplasm. The relative expression levels of AgGMP in ‘Jinnan Shiqin’ were significantly up-regulated at 2 h and 4 h under drought stress treatments. AsA contents in transgenic Arabidopsis lines hosting AgGMP gene were higher than that in wild type plants, and the root lengths were also longer in the MS medium containing 300 mM mannitol. The present study provides useful evidence for the functional involvement of AgGMP in regulating AsA accumulation and response to drought stress in celery.
format: application/pdf
format: text/html
creator: Yan-Hua Liu
creator: Hao Wang
creator: Jie-Xia Liu
creator: Sheng Shu
creator: Guo-Fei Tan
creator: Meng-Yao Li
creator: Ao-Qi Duan
creator: Hui Liu
creator: Ai-Sheng Xiong
subject: Genetics
subject: Molecular Biology
subject: Plant Science
subject: Infectious Diseases
description: doi:10.7717/peerj.12976
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Ascorbic acid (AsA) is an important nutrient in celery, the conversion of D-mannose-1-P to GDP-D-mannose catalyzed by GDP-D-mannose pyrophosphorylase (GMPase) represents the first committed step in the biosynthesis of AsA. To clarify the function of the AgGMP gene of celery, the AgGMP gene was cloned from celery cv. ‘Jinnan Shiqin’ . It contains an open reading frame (ORF) with the length of 1,086 bp, encoding 361 amino acids. AgGMP protein was highly conserved among different plant species. Phylogenetic analysis demonstrated that the GMP proteins from celery and carrot belonged to the same branch. AgGMP protein was mainly composed of three α-helixes and certain random coils. No signal peptide was found in the AgGMP protein. The subcellular localization indicated that the AgGMP protein was located in the cytoplasm. The relative expression levels of AgGMP in ‘Jinnan Shiqin’ were significantly up-regulated at 2 h and 4 h under drought stress treatments. AsA contents in transgenic Arabidopsis lines hosting AgGMP gene were higher than that in wild type plants, and the root lengths were also longer in the MS medium containing 300 mM mannitol. The present study provides useful evidence for the functional involvement of AgGMP in regulating AsA accumulation and response to drought stress in celery.
bibliographic citation: Liu et al. (2022) AgGMP encoding GDP-D-mannose pyrophosphorylase from celery enhanced the accumulation of ascorbic acid and resistance to drought stress in Arabidopsis. PeerJ 10:e12976 https://doi.org/10.7717/peerj.12976
date submitted: 2021-10-01
date accepted: 2022-01-31
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yan-Hua
author list: Agent
  family name: Wang
  given name: Hao
author list: Agent
  family name: Liu
  given name: Jie-Xia
author list: Agent
  family name: Shu
  given name: Sheng
author list: Agent
  family name: Tan
  given name: Guo-Fei
author list: Agent
  family name: Li
  given name: Meng-Yao
author list: Agent
  family name: Duan
  given name: Ao-Qi
author list: Agent
  family name: Liu
  given name: Hui
author list: Agent
  family name: Xiong
  given name: Ai-Sheng
doi: 10.7717/peerj.12976
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: © 2022 Liu et al.
attribution name: Liu et al.

Biomarkers of non-communicable chronic disease: an update on contemporary methods
type: item
type: AcademicArticle
description: Chronic diseases constitute a major global burden with significant impact on health systems, economies, and quality of life. Chronic diseases include a broad range of diseases that can be communicable or non-communicable. Chronic diseases are often associated with modifications of normal physiological levels of various analytes that are routinely measured in serum and other body fluids, as well as pathological findings, such as chronic inflammation, oxidative stress, and mitochondrial dysfunction. Identification of at-risk populations, early diagnosis, and prediction of prognosis play a major role in preventing or reducing the burden of chronic diseases. Biomarkers are tools that are used by health professionals to aid in the identification and management of chronic diseases. Biomarkers can be diagnostic, predictive, or prognostic. Several individual or grouped biomarkers have been used successfully in the diagnosis and prediction of certain chronic diseases, however, it is generally accepted that a more sophisticated approach to link and interpret various biomarkers involved in chronic disease is necessary to improve our current procedures. In order to ensure a comprehensive and unbiased coverage of the literature, first a primary frame of the manuscript (title, headings and subheadings) was drafted by the authors working on this paper. Second, based on the components drafted in the preliminary skeleton a comprehensive search of the literature was performed using the PubMed and Google Scholar search engines. Multiple keywords related to the topic were used. Out of screened papers, only 190 papers, which are the most relevant, and recent articles were selected to cover the topic in relation to etiological mechanisms of different chronic diseases, the most recently used biomarkers of chronic diseases and finally the advances in the applications of multivariate biomarkers of chronic diseases as statistical and clinically applied tool for the early diagnosis of chronic…
format: application/pdf
format: text/html
creator: Solaiman M. Al-hadlaq
creator: Hanan A. Balto
creator: Wail M. Hassan
creator: Najat A. Marraiki
creator: Afaf K. El-Ansary
subject: Cardiology
subject: Diabetes and Endocrinology
subject: Evidence Based Medicine
subject: Statistics
description: doi:10.7717/peerj.12977
publisher: PeerJ Inc.
rights: © 2022 Al-hadlaq et al.
abstract: Chronic diseases constitute a major global burden with significant impact on health systems, economies, and quality of life. Chronic diseases include a broad range of diseases that can be communicable or non-communicable. Chronic diseases are often associated with modifications of normal physiological levels of various analytes that are routinely measured in serum and other body fluids, as well as pathological findings, such as chronic inflammation, oxidative stress, and mitochondrial dysfunction. Identification of at-risk populations, early diagnosis, and prediction of prognosis play a major role in preventing or reducing the burden of chronic diseases. Biomarkers are tools that are used by health professionals to aid in the identification and management of chronic diseases. Biomarkers can be diagnostic, predictive, or prognostic. Several individual or grouped biomarkers have been used successfully in the diagnosis and prediction of certain chronic diseases, however, it is generally accepted that a more sophisticated approach to link and interpret various biomarkers involved in chronic disease is necessary to improve our current procedures. In order to ensure a comprehensive and unbiased coverage of the literature, first a primary frame of the manuscript (title, headings and subheadings) was drafted by the authors working on this paper. Second, based on the components drafted in the preliminary skeleton a comprehensive search of the literature was performed using the PubMed and Google Scholar search engines. Multiple keywords related to the topic were used. Out of screened papers, only 190 papers, which are the most relevant, and recent articles were selected to cover the topic in relation to etiological mechanisms of different chronic diseases, the most recently used biomarkers of chronic diseases and finally the advances in the applications of multivariate biomarkers of chronic diseases as statistical and clinically applied tool for the early diagnosis of chronic…
bibliographic citation: Al-hadlaq et al. (2022) Biomarkers of non-communicable chronic disease: an update on contemporary methods. PeerJ 10:e12977 https://doi.org/10.7717/peerj.12977
date submitted: 2021-07-15
date accepted: 2022-01-31
issued: 2022-02-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-hadlaq
  given name: Solaiman M.
author list: Agent
  family name: Balto
  given name: Hanan A.
author list: Agent
  family name: Hassan
  given name: Wail M.
author list: Agent
  family name: Marraiki
  given name: Najat A.
author list: Agent
  family name: El-Ansary
  given name: Afaf K.
doi: 10.7717/peerj.12977
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-24
copyright: ©2022 Al-hadlaq et al.
attribution name: Al-hadlaq et al.

Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard
type: item
type: AcademicArticle
description: High levels of within-individual variation (WIV) in reiterative components in plants such as leaves, flowers, and fruits have been shown to increase individual fitness by multiple mechanisms including mediating interactions with natural enemies. This relationship between WIV and fitness has been studied almost exclusively in plant systems. While animals do not exhibit conspicuous reiterative components, they have traits that can vary at the individual level such as erythrocyte size. It is currently unknown if WIV in animals can influence individual fitness by mediating the outcome of interactions with natural enemies as it has been shown in plants. To address this issue, we tested for a relationship between WIV in erythrocyte size, hemoparasite infection status, and body condition (a proxy for fitness) in a Caribbean anole lizard. We quantified the coefficient of variation of adult erythrocytes size in $n = 95$ infected and $n = 107$ non-infected lizards. We found higher degrees of erythrocyte size variation in infected lizards than in non-infected individuals. However, we found no significant relationship between infection status or erythrocyte size variation, and lizard body condition. These results suggest that higher WIV in erythrocyte size in infected lizards is not necessarily adaptive but likely a consequence of the host response to infection. Many hemoparasites destroy their host cells as part of their life cycle. To compensate, the host lizard may respond by increasing production of erythrocytes resulting in higher WIV. Our results emphasize the need to better understand the role of within-animal variation as a neglected driver or consequence of ecological and evolutionary interactions.
format: application/pdf
format: text/html
creator: Virnaliz Cruz
creator: Omar Cruz-Pantoja
creator: Raymond Tremblay
creator: Miguel Acevedo
subject: Ecology
subject: Parasitology
subject: Zoology
subject: Hematology
description: doi:10.7717/peerj.12761
publisher: PeerJ Inc.
rights: © 2022 Cruz et al.
abstract: High levels of within-individual variation (WIV) in reiterative components in plants such as leaves, flowers, and fruits have been shown to increase individual fitness by multiple mechanisms including mediating interactions with natural enemies. This relationship between WIV and fitness has been studied almost exclusively in plant systems. While animals do not exhibit conspicuous reiterative components, they have traits that can vary at the individual level such as erythrocyte size. It is currently unknown if WIV in animals can influence individual fitness by mediating the outcome of interactions with natural enemies as it has been shown in plants. To address this issue, we tested for a relationship between WIV in erythrocyte size, hemoparasite infection status, and body condition (a proxy for fitness) in a Caribbean anole lizard. We quantified the coefficient of variation of adult erythrocytes size in $n = 95$ infected and $n = 107$ non-infected lizards. We found higher degrees of erythrocyte size variation in infected lizards than in non-infected individuals. However, we found no significant relationship between infection status or erythrocyte size variation, and lizard body condition. These results suggest that higher WIV in erythrocyte size in infected lizards is not necessarily adaptive but likely a consequence of the host response to infection. Many hemoparasites destroy their host cells as part of their life cycle. To compensate, the host lizard may respond by increasing production of erythrocytes resulting in higher WIV. Our results emphasize the need to better understand the role of within-animal variation as a neglected driver or consequence of ecological and evolutionary interactions.
bibliographic citation: Cruz et al. (2022) Animal trait variation at the within-individual level: erythrocyte size variation and malaria infection in a tropical lizard. PeerJ 10:e12761 https://doi.org/10.7717/peerj.12761
date submitted: 2019-07-15
date accepted: 2021-12-16
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cruz
  given name: Virnaliz
author list: Agent
  family name: Cruz-Pantoja
  given name: Omar
author list: Agent
  family name: Tremblay
  given name: Raymond
author list: Agent
  family name: Acevedo
  given name: Miguel
doi: 10.7717/peerj.12761
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Cruz et al.
attribution name: Cruz et al.

Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy
type: item
type: AcademicArticle
description: Background Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species. Methods We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs. Results This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trape…
format: application/pdf
format: text/html
creator: Fernando Cortés-Carrasco
creator: Manuel Elías-Gutiérrez
creator: María del Socorro García-Madrigal
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12774
publisher: PeerJ Inc.
rights: © 2022 Cortés-Carrasco et al.
abstract: Background Holothuriophilus trapeziformis Nauck, 1880 is a holothurian-dweller pinnotherid crab representing one of the two species of the genus distributed along the Pacific coast of Mexico and Chile, respectively. While the parasitic ecological interaction with its host is well established, the morphology of the male remains unknown, and DNA information for the species is not available. Furthermore, the only morphological trait separating both species of the genus is subjective and corresponds to the presence or absence of a gap between the fingers of the chelae. Our goal is to complete and clarify the taxonomic status of H. trapeziformis and describe the male morphology with the use of the integrative taxonomy, providing additional characters to differentiate this species. Methods We collected new biological material in the Pacific coast of Mexico including the topotypes. We also reviewed material from national collections to integrate morphology (based on a complete and detailed description and illustration of the species using light microscopy), ecological data (based on the identification of the host and the place where it was located within the host), and the mtCOI gene information (commonly known as DNA barcode) to differentiate Holothuriophilus trapeziformis from other related crabs. Results This species presents marked sexual dimorphism only in the primary sexual characters. For the first time we describe morphological variability of traditionally stable characters. In addition to the gap between the fingers of the chelae, Holothuriophilus trapeziformis differs from H. pacificus (Poeppig, 1836) by their ornamentation, the shape of the male abdomen, and the gonopod. Cytocrome Oxidase 1 gene (COI) distance divergence was >3% between both Holothuriophilus species forming a clear clade. DNA barcoding indicates only one taxon, with a maximum divergence of 2.2%. All the specimens have the same Barcode Index Number (BIN; BOLD: ADE9974). All the hosts for H. trape…
bibliographic citation: Cortés-Carrasco et al. (2022) Holothuriophilus trapeziformis Nauck, 1880 (Decapoda: Pinnotheridae) from the Pacific coast of Mexico: taxonomic revision based on integrative taxonomy. PeerJ 10:e12774 https://doi.org/10.7717/peerj.12774
date submitted: 2021-02-19
date accepted: 2021-12-20
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cortés-Carrasco
  given name: Fernando
author list: Agent
  family name: Elías-Gutiérrez
  given name: Manuel
author list: Agent
  family name: García-Madrigal
  given name: María del Socorro
doi: 10.7717/peerj.12774
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: © 2022 Cortés-Carrasco et al.
attribution name: Cortés-Carrasco et al.

Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species
type: item
type: AcademicArticle
description: Background Population dynamics are driven by a number of biotic (e.g., density-dependence) and abiotic (e.g., climate) factors whose contribution can greatly vary across study systems (i.e., populations). Yet, the extent to which the contribution of these factors varies across populations and between species and whether spatial patterns can be identified has received little attention. Methods Here, we used a long-term (1982–2011), broad scale (182 sites distributed across metropolitan France) dataset to study spatial patterns in the population’s dynamics of three freshwater fish species presenting contrasted life-histories and patterns of elevation range shifts in recent decades. We used a hierarchical Bayesian approach together with an elasticity analysis to estimate the relative contribution of a set of biotic (e.g., strength of density dependence, recruitment rate) and abiotic (mean and variability of water temperature) factors affecting the site-specific dynamic of two different size classes (0+ and >0+ individuals) for the three species. We then tested whether the local contribution of each factor presented evidence for biogeographical patterns by confronting two non-mutually exclusive hypotheses: the “range-shift” hypothesis that predicts a gradient along elevation or latitude and the “abundant-center” hypothesis that predicts a gradient from the center to the edge of the species’ distributional range. Results Despite contrasted life-histories, the three species displayed similar large-scale patterns in population dynamics with a much stronger contribution of biotic factors over abiotic ones. Yet, the contribution of the different factors strongly varied within distributional ranges and followed distinct spatial patterns. Indeed, while abiotic factors mostly varied along elevation, biotic factors—which disproportionately contributed to population dynamics—varied along both elevation and latitude. Conclusions Overall while our results provide stronger support f…
format: application/pdf
format: text/html
creator: Mathieu Chevalier
creator: Pablo Tedesco
creator: Gael Grenouillet
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Ecology
subject: Freshwater Biology
subject: Population Biology
description: doi:10.7717/peerj.12857
publisher: PeerJ Inc.
rights: © 2022 Chevalier et al.
abstract: Background Population dynamics are driven by a number of biotic (e.g., density-dependence) and abiotic (e.g., climate) factors whose contribution can greatly vary across study systems (i.e., populations). Yet, the extent to which the contribution of these factors varies across populations and between species and whether spatial patterns can be identified has received little attention. Methods Here, we used a long-term (1982–2011), broad scale (182 sites distributed across metropolitan France) dataset to study spatial patterns in the population’s dynamics of three freshwater fish species presenting contrasted life-histories and patterns of elevation range shifts in recent decades. We used a hierarchical Bayesian approach together with an elasticity analysis to estimate the relative contribution of a set of biotic (e.g., strength of density dependence, recruitment rate) and abiotic (mean and variability of water temperature) factors affecting the site-specific dynamic of two different size classes (0+ and >0+ individuals) for the three species. We then tested whether the local contribution of each factor presented evidence for biogeographical patterns by confronting two non-mutually exclusive hypotheses: the “range-shift” hypothesis that predicts a gradient along elevation or latitude and the “abundant-center” hypothesis that predicts a gradient from the center to the edge of the species’ distributional range. Results Despite contrasted life-histories, the three species displayed similar large-scale patterns in population dynamics with a much stronger contribution of biotic factors over abiotic ones. Yet, the contribution of the different factors strongly varied within distributional ranges and followed distinct spatial patterns. Indeed, while abiotic factors mostly varied along elevation, biotic factors—which disproportionately contributed to population dynamics—varied along both elevation and latitude. Conclusions Overall while our results provide stronger support f…
bibliographic citation: Chevalier et al. (2022) Spatial patterns in the contribution of biotic and abiotic factors to the population dynamics of three freshwater fish species. PeerJ 10:e12857 https://doi.org/10.7717/peerj.12857
date submitted: 2021-07-15
date accepted: 2022-01-09
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chevalier
  given name: Mathieu
author list: Agent
  family name: Tedesco
  given name: Pablo
author list: Agent
  family name: Grenouillet
  given name: Gael
doi: 10.7717/peerj.12857
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Chevalier et al.
attribution name: Chevalier et al.

Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits
type: item
type: AcademicArticle
description: Background Animal models are significant for understanding human osteoarthritis (OA). This study compared the synovial fluid proteomics changes in surgical and chemical induced OA models. Methods Thirty rabbits either had anterior cruciate ligament transection (ACLT) procedure or injected intra-articularly with monosodium iodoacetate (MIA, 8 mg) into the right knee. The joints were anatomically assessed, and the synovial fluid proteins analyzed using two-dimensional polyacrylamide gel electrophoresis (2DGE) and MALDI TOF/TOF mass spectrometry analysis at 4, 8 and 12 weeks. The proteins’ upregulation and downregulation were compared with control healthy knees. Results Seven proteins (histidine-rich glycoprotein, beta-actin-like protein 2 isoform X1, retinol-binding protein-4, alpha-1-antiproteinase, gelsolin isoform, serotransferrin, immunoglobulin kappa-b4 chain-C-region) were significantly expressed by the surgical induction. They characterized cellular process (27%), organization of cellular components or biogenesis (27%), localization (27%) and biological regulation (18%), which related to synovitis, increased cellularity, and subsequently cartilage damage. Three proteins (apolipoprotein I-IV precursor, serpin peptidase inhibitor and haptoglobin precursor) were significantly modified by the chemical induction. They characterized stimulus responses (23%), immune responses (15%), biological regulations (15%), metabolism (15%), organization of cellular components or biogenesis (8%), cellular process (8%), biological adhesions (8%) and localization (8%), which related to chondrocytes glycolysis/death, neovascularization, subchondral bone necrosis/collapse and inflammation. Conclusions The surgical induced OA model showed a wider range of protein changes, which were most upregulated at week 12. The biological process proteins expressions showed the chemical induced joints had slower OA progression compared to surgical induced joints. The chemical induced OA joints sho…
format: application/pdf
format: text/html
creator: Sharifah Zakiah Syed Sulaiman
creator: Wei Miao Tan
creator: Rozanaliza Radzi
creator: Intan Nur Fatiha Shafie
creator: Mokrish Ajat
creator: Rozaihan Mansor
creator: Suhaila Mohamed
creator: Norasfaliza Rahmad
creator: Angela Min Hwei Ng
creator: Seng Fong Lau
subject: Biochemistry
subject: Molecular Biology
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.12897
publisher: PeerJ Inc.
rights: © 2022 Syed Sulaiman et al.
abstract: Background Animal models are significant for understanding human osteoarthritis (OA). This study compared the synovial fluid proteomics changes in surgical and chemical induced OA models. Methods Thirty rabbits either had anterior cruciate ligament transection (ACLT) procedure or injected intra-articularly with monosodium iodoacetate (MIA, 8 mg) into the right knee. The joints were anatomically assessed, and the synovial fluid proteins analyzed using two-dimensional polyacrylamide gel electrophoresis (2DGE) and MALDI TOF/TOF mass spectrometry analysis at 4, 8 and 12 weeks. The proteins’ upregulation and downregulation were compared with control healthy knees. Results Seven proteins (histidine-rich glycoprotein, beta-actin-like protein 2 isoform X1, retinol-binding protein-4, alpha-1-antiproteinase, gelsolin isoform, serotransferrin, immunoglobulin kappa-b4 chain-C-region) were significantly expressed by the surgical induction. They characterized cellular process (27%), organization of cellular components or biogenesis (27%), localization (27%) and biological regulation (18%), which related to synovitis, increased cellularity, and subsequently cartilage damage. Three proteins (apolipoprotein I-IV precursor, serpin peptidase inhibitor and haptoglobin precursor) were significantly modified by the chemical induction. They characterized stimulus responses (23%), immune responses (15%), biological regulations (15%), metabolism (15%), organization of cellular components or biogenesis (8%), cellular process (8%), biological adhesions (8%) and localization (8%), which related to chondrocytes glycolysis/death, neovascularization, subchondral bone necrosis/collapse and inflammation. Conclusions The surgical induced OA model showed a wider range of protein changes, which were most upregulated at week 12. The biological process proteins expressions showed the chemical induced joints had slower OA progression compared to surgical induced joints. The chemical induced OA joints sho…
bibliographic citation: Syed Sulaiman et al. (2022) Synovial fluid proteome profile of surgical versus chemical induced osteoarthritis in rabbits. PeerJ 10:e12897 https://doi.org/10.7717/peerj.12897
date submitted: 2021-06-04
date accepted: 2022-01-16
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Syed Sulaiman
  given name: Sharifah Zakiah
author list: Agent
  family name: Tan
  given name: Wei Miao
author list: Agent
  family name: Radzi
  given name: Rozanaliza
author list: Agent
  family name: Shafie
  given name: Intan Nur Fatiha
author list: Agent
  family name: Ajat
  given name: Mokrish
author list: Agent
  family name: Mansor
  given name: Rozaihan
author list: Agent
  family name: Mohamed
  given name: Suhaila
author list: Agent
  family name: Rahmad
  given name: Norasfaliza
author list: Agent
  family name: Ng
  given name: Angela Min Hwei
author list: Agent
  family name: Lau
  given name: Seng Fong
doi: 10.7717/peerj.12897
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Syed Sulaiman et al.
attribution name: Syed Sulaiman et al.

Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis
type: item
type: AcademicArticle
description: This study aimed to conduct a network meta-analysis (NMA) to compare the efficacy of brain natriuretic peptide (BNP) vs nicorandil for preventing contrast-induced nephropathy (CIN). Databases of Pubmed, Cochrane, Embase, Web of Science were searched by keywords for eligible studies of randomized controlled trials investigating different agents (BNP, nicorandil, nitroglycerin, intravenous saline) for preventing CIN. The outcomes included a change in serum creatinine level at 48 h and the incidence of CIN after percutaneous coronary intervention (PCI) or coronary angiography (CAG). A total of 13 studies with 3,462 patients were included. Compared with intravenous saline alone, except for nitroglycerin (odds ratio [OR]: 1.02, 95% CI [0.36–2.88]), the other drugs significantly reduced the CIN incidence with OR of 0.35 (95% CI [0.24–0.51]) for BNP, 0.52 (0.29, 0.94) for usual-dose nicorandil, 0.28 (0.19, 0.43) for double-dose nicorandil. BNP and double-dose nicorandil significantly decreased the change of serum creatinine (SCr) levels with mean difference (MD) of −6.98, (−10.01, −3.95) for BNP, −8.78, (−11.63, −5.93) for double-dose nicorandil. No significant differences were observed in the change of SCr levels for nitroglycerin (−4.97, [−11.46, 1.52]) and usual-dose nicorandil (−2.32, [−5.52, 0.89]) compared with intravenous saline alone. For double-dose nicorandil, the CIN incidence and the change of SCr level in group of 4–5 days treatment course were more than group of less than or equal to 24 h treatment course (OR of 1.48, [0.63–3.46] and MD of 2.48, [−1.96, 6.91]). In conclusion, BNP and double-dose nicorandil can have effects on preventing the incidence of CIN and double-dose nicorandil performed better than BNP. In double-dose nicorandil groups, a course of less than or equal to 24 h before and after procedure performed with better efficacy than a course of 4–5 days.
format: application/pdf
format: text/html
creator: Ziwei Mei
creator: Songmei Luo
creator: Peipei Chen
creator: Qiankun Zhang
creator: Limei Zhou
creator: Chaoyong Zhu
creator: Hong Zhu
creator: Lie Jin
subject: Biochemistry
subject: Diabetes and Endocrinology
subject: Nephrology
subject: Pharmacology
description: doi:10.7717/peerj.12975
publisher: PeerJ Inc.
rights: © 2022 Mei et al.
abstract: This study aimed to conduct a network meta-analysis (NMA) to compare the efficacy of brain natriuretic peptide (BNP) vs nicorandil for preventing contrast-induced nephropathy (CIN). Databases of Pubmed, Cochrane, Embase, Web of Science were searched by keywords for eligible studies of randomized controlled trials investigating different agents (BNP, nicorandil, nitroglycerin, intravenous saline) for preventing CIN. The outcomes included a change in serum creatinine level at 48 h and the incidence of CIN after percutaneous coronary intervention (PCI) or coronary angiography (CAG). A total of 13 studies with 3,462 patients were included. Compared with intravenous saline alone, except for nitroglycerin (odds ratio [OR]: 1.02, 95% CI [0.36–2.88]), the other drugs significantly reduced the CIN incidence with OR of 0.35 (95% CI [0.24–0.51]) for BNP, 0.52 (0.29, 0.94) for usual-dose nicorandil, 0.28 (0.19, 0.43) for double-dose nicorandil. BNP and double-dose nicorandil significantly decreased the change of serum creatinine (SCr) levels with mean difference (MD) of −6.98, (−10.01, −3.95) for BNP, −8.78, (−11.63, −5.93) for double-dose nicorandil. No significant differences were observed in the change of SCr levels for nitroglycerin (−4.97, [−11.46, 1.52]) and usual-dose nicorandil (−2.32, [−5.52, 0.89]) compared with intravenous saline alone. For double-dose nicorandil, the CIN incidence and the change of SCr level in group of 4–5 days treatment course were more than group of less than or equal to 24 h treatment course (OR of 1.48, [0.63–3.46] and MD of 2.48, [−1.96, 6.91]). In conclusion, BNP and double-dose nicorandil can have effects on preventing the incidence of CIN and double-dose nicorandil performed better than BNP. In double-dose nicorandil groups, a course of less than or equal to 24 h before and after procedure performed with better efficacy than a course of 4–5 days.
bibliographic citation: Mei et al. (2022) Efficacy of brain natriuretic peptide vs. nicorandil in preventing contrast-induced nephropathy: a network meta-analysis. PeerJ 10:e12975 https://doi.org/10.7717/peerj.12975
date submitted: 2021-11-23
date accepted: 2022-01-31
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mei
  given name: Ziwei
author list: Agent
  family name: Luo
  given name: Songmei
author list: Agent
  family name: Chen
  given name: Peipei
author list: Agent
  family name: Zhang
  given name: Qiankun
author list: Agent
  family name: Zhou
  given name: Limei
author list: Agent
  family name: Zhu
  given name: Chaoyong
author list: Agent
  family name: Zhu
  given name: Hong
author list: Agent
  family name: Jin
  given name: Lie
doi: 10.7717/peerj.12975
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Mei et al.
attribution name: Mei et al.

Disentangling bias for non-destructive insect metabarcoding
type: item
type: AcademicArticle
description: A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
format: application/pdf
format: text/html
creator: Francesco Martoni
creator: Alexander M. Piper
creator: Brendan C. Rodoni
creator: Mark J. Blacket
subject: Bioinformatics
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.12981
publisher: PeerJ Inc.
rights: © 2022 Martoni et al.
abstract: A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
bibliographic citation: Martoni et al. (2022) Disentangling bias for non-destructive insect metabarcoding. PeerJ 10:e12981 https://doi.org/10.7717/peerj.12981
date submitted: 2021-10-01
date accepted: 2022-02-01
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martoni
  given name: Francesco
author list: Agent
  family name: Piper
  given name: Alexander M.
author list: Agent
  family name: Rodoni
  given name: Brendan C.
author list: Agent
  family name: Blacket
  given name: Mark J.
doi: 10.7717/peerj.12981
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: © 2022 Martoni et al.
attribution name: Martoni et al.

Microbial biogeography of the wombat gastrointestinal tract
type: item
type: AcademicArticle
description: Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region—the putative site of primary plant fermentation in wombats—are distinct from the distal colon, and that faecal sample…
format: application/pdf
format: text/html
creator: Raphael Eisenhofer
creator: Erin D’Agnese
creator: David Taggart
creator: Scott Carver
creator: Beth Penrose
subject: Biodiversity
subject: Biogeography
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.12982
publisher: PeerJ Inc.
rights: © 2022 Eisenhofer et al.
abstract: Most herbivorous mammals have symbiotic microbes living in their gastrointestinal tracts that help with harvesting energy from recalcitrant plant fibre. The bulk of research into these microorganisms has focused on samples collected from faeces, representing the distal region of the gastrointestinal (GI) tract. However, the GI tract in herbivorous mammals is typically long and complex, containing different regions with distinct physico-chemical properties that can structure resident microbial communities. Little work has been done to document GI microbial communities of herbivorous animals at these sites. In this study, we use 16S rRNA gene sequencing to characterize the microbial biogeography along the GI tract in two species of wombats. Specifically, we survey the microbes along four major gut regions (stomach, small intestine, proximal colon, distal colon) in a single bare-nosed wombat (Vombatus ursinus) and a single southern hairy-nosed wombat (Lasiorhinus latifrons). Our preliminary results show that GI microbial communities of wombats are structured by GI region. For both wombat individuals, we observed a trend of increasing microbial diversity from stomach to distal colon. The microbial composition in the first proximal colon region was more similar between wombat species than the corresponding distal colon region in the same species. We found several microbial genera that were differentially abundant between the first proximal colon (putative site for primary plant fermentation) and distal colon regions (which resemble faecal samples). Surprisingly, only 10.6% (98) and 18.8% (206) of amplicon sequence variants (ASVs) were shared between the first proximal colon region and the distal colon region for the bare-nosed and southern hairy-nosed wombat, respectively. These results suggest that microbial communities in the first proximal colon region—the putative site of primary plant fermentation in wombats—are distinct from the distal colon, and that faecal sample…
bibliographic citation: Eisenhofer et al. (2022) Microbial biogeography of the wombat gastrointestinal tract. PeerJ 10:e12982 https://doi.org/10.7717/peerj.12982
date submitted: 2021-09-15
date accepted: 2022-02-01
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eisenhofer
  given name: Raphael
author list: Agent
  family name: D’Agnese
  given name: Erin
author list: Agent
  family name: Taggart
  given name: David
author list: Agent
  family name: Carver
  given name: Scott
author list: Agent
  family name: Penrose
  given name: Beth
doi: 10.7717/peerj.12982
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: ©2022 Eisenhofer et al.
attribution name: Eisenhofer et al.

A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift
type: item
type: AcademicArticle
description: Cerebral blood flow (CBF) monitoring is of great significance for treating and preventing strokes. However, there has not been a fully accepted method targeting continuous assessment in clinical practice. In this work, we built a noninvasive continuous assessment system for cerebral blood flow pulsation (CBFP) that is based on magnetic induction phase shift (MIPS) technology and designed a physical model of the middle cerebral artery (MCA). Physical experiments were carried out through different simulations of CBF states. Four healthy volunteers were enrolled to perform the MIPS and ECG synchronously monitoring trials. Then, the components of MIPS related to the blood supply level and CBFP were investigated by signal analysis in time and frequency domain, wavelet decomposition and band-pass filtering. The results show that the time-domain baseline of MIPS increases with blood supply level. A pulse signal was identified in the spectrum (0.2–2 Hz in 200–2,000 ml/h groups, respectively) of MIPS when the simulated blood flow rate was not zero. The pulsation frequency with different simulated blood flow rates is the same as the squeezing frequency of the feeding pump. Similar to pulse waves, the MIPS signals on four healthy volunteers all had periodic change trends with obvious peaks and valleys. Its frequency is close to that of the ECG signal and there is a certain time delay between them. These results indicate that the CBFP component can effectively be extracted from MIPS, through which different blood supply levels can be distinguished. This method has the potential to become a new solution for non-invasive and comprehensive monitoring of CBFP.
format: application/pdf
format: text/html
creator: Lingxi Zeng
creator: Gen Li
creator: Maoting Zhang
creator: Rui Zhu
creator: Jingbo Chen
creator: Mingyan Li
creator: Shengtong Yin
creator: Zelin Bai
creator: Wei Zhuang
creator: Jian Sun
subject: Bioengineering
subject: Biophysics
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.13002
publisher: PeerJ Inc.
rights: © 2022 Zeng et al.
abstract: Cerebral blood flow (CBF) monitoring is of great significance for treating and preventing strokes. However, there has not been a fully accepted method targeting continuous assessment in clinical practice. In this work, we built a noninvasive continuous assessment system for cerebral blood flow pulsation (CBFP) that is based on magnetic induction phase shift (MIPS) technology and designed a physical model of the middle cerebral artery (MCA). Physical experiments were carried out through different simulations of CBF states. Four healthy volunteers were enrolled to perform the MIPS and ECG synchronously monitoring trials. Then, the components of MIPS related to the blood supply level and CBFP were investigated by signal analysis in time and frequency domain, wavelet decomposition and band-pass filtering. The results show that the time-domain baseline of MIPS increases with blood supply level. A pulse signal was identified in the spectrum (0.2–2 Hz in 200–2,000 ml/h groups, respectively) of MIPS when the simulated blood flow rate was not zero. The pulsation frequency with different simulated blood flow rates is the same as the squeezing frequency of the feeding pump. Similar to pulse waves, the MIPS signals on four healthy volunteers all had periodic change trends with obvious peaks and valleys. Its frequency is close to that of the ECG signal and there is a certain time delay between them. These results indicate that the CBFP component can effectively be extracted from MIPS, through which different blood supply levels can be distinguished. This method has the potential to become a new solution for non-invasive and comprehensive monitoring of CBFP.
bibliographic citation: Zeng et al. (2022) A noninvasive and comprehensive method for continuous assessment of cerebral blood flow pulsation based on magnetic induction phase shift. PeerJ 10:e13002 https://doi.org/10.7717/peerj.13002
date submitted: 2021-11-08
date accepted: 2022-02-03
issued: 2022-02-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zeng
  given name: Lingxi
author list: Agent
  family name: Li
  given name: Gen
author list: Agent
  family name: Zhang
  given name: Maoting
author list: Agent
  family name: Zhu
  given name: Rui
author list: Agent
  family name: Chen
  given name: Jingbo
author list: Agent
  family name: Li
  given name: Mingyan
author list: Agent
  family name: Yin
  given name: Shengtong
author list: Agent
  family name: Bai
  given name: Zelin
author list: Agent
  family name: Zhuang
  given name: Wei
author list: Agent
  family name: Sun
  given name: Jian
doi: 10.7717/peerj.13002
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-23
copyright: © 2022 Zeng et al.
attribution name: Zeng et al.

Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum
type: item
type: AcademicArticle
description: Fusarium oxysporum f. sp. cubense (FOC4) is a pathogen of banana fusarium wilt, which is a serious problem that has plagued the tropical banana industry for many years. The pathogenic mechanism is complex and unclear, so the prevention and control in agricultural production applications is ineffective. SNP-D4, an artificial peptide aptamer, was identified and specifically inhibited FOC4. To evaluate the efficacy of SNP-D4, FoC4 spores were treated with purified SNP-D4 to calculate the germination and fungicide rates. Damage of FOC4 spores was observed by staining with propidium iodide (PI). Eight proteins of FOC4 were identified to have high affinity for SNP-D4 by a pull-down method combined with Q-Exactive mass spectrometry. Of these eight proteins, A0A5C6SPC6, the aldehyde dehydrogenase of FOC4, was selected as an example to scrutinize the interaction sites with SNP-D4. Molecular docking revealed that Thr66 on the peptide loop of SNP-D4 bound with Tyr437 near the catalytic center of A0A5C6SPC6. Subsequently 42 spore proteins which exhibited associations with the eight proteins were retrieved for protein-protein interaction analysis, demonstrating that SNP-D4 interfered with pathways including ‘translation’, ‘folding, sorting and degradation’, ‘transcription’, ‘signal transduction’ and ‘cell growth and death’, eventually causing the inhibition of growth of FOC4. This study not only investigated the possible pathogenic mechanism of FOC4, but also provided a potential antifungal agent SNP-D4 for use in the control of banana wilt disease.
format: application/pdf
format: text/html
creator: Junjun Huang
creator: Dan Wang
creator: Hong Li
creator: Yanqiong Tang
creator: Xiang Ma
creator: Hongqian Tang
creator: Min Lin
creator: Zhu Liu
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.12756
publisher: PeerJ Inc.
rights: © 2022 Huang et al.
abstract: Fusarium oxysporum f. sp. cubense (FOC4) is a pathogen of banana fusarium wilt, which is a serious problem that has plagued the tropical banana industry for many years. The pathogenic mechanism is complex and unclear, so the prevention and control in agricultural production applications is ineffective. SNP-D4, an artificial peptide aptamer, was identified and specifically inhibited FOC4. To evaluate the efficacy of SNP-D4, FoC4 spores were treated with purified SNP-D4 to calculate the germination and fungicide rates. Damage of FOC4 spores was observed by staining with propidium iodide (PI). Eight proteins of FOC4 were identified to have high affinity for SNP-D4 by a pull-down method combined with Q-Exactive mass spectrometry. Of these eight proteins, A0A5C6SPC6, the aldehyde dehydrogenase of FOC4, was selected as an example to scrutinize the interaction sites with SNP-D4. Molecular docking revealed that Thr66 on the peptide loop of SNP-D4 bound with Tyr437 near the catalytic center of A0A5C6SPC6. Subsequently 42 spore proteins which exhibited associations with the eight proteins were retrieved for protein-protein interaction analysis, demonstrating that SNP-D4 interfered with pathways including ‘translation’, ‘folding, sorting and degradation’, ‘transcription’, ‘signal transduction’ and ‘cell growth and death’, eventually causing the inhibition of growth of FOC4. This study not only investigated the possible pathogenic mechanism of FOC4, but also provided a potential antifungal agent SNP-D4 for use in the control of banana wilt disease.
bibliographic citation: Huang et al. (2022) Antifungal activity of an artificial peptide aptamer SNP-D4 against Fusarium oxysporum. PeerJ 10:e12756 https://doi.org/10.7717/peerj.12756
date submitted: 2021-08-30
date accepted: 2021-12-16
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Junjun
author list: Agent
  family name: Wang
  given name: Dan
author list: Agent
  family name: Li
  given name: Hong
author list: Agent
  family name: Tang
  given name: Yanqiong
author list: Agent
  family name: Ma
  given name: Xiang
author list: Agent
  family name: Tang
  given name: Hongqian
author list: Agent
  family name: Lin
  given name: Min
author list: Agent
  family name: Liu
  given name: Zhu
doi: 10.7717/peerj.12756
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Huang et al.
attribution name: Huang et al.

Estimation of Coregonus ussuriensis age, growth, and maturation in China’s Amur River
type: item
type: AcademicArticle
description: This study examined the age, growth, and maturation of 1,064 Coregonus ussuriensis individuals that were collected monthly from the middle section of the Amur River, China between 2016 and 2018. The fork length (FL) ranged from 14.9 to 49.1 cm for males and 21.5 to 58.8 cm for females, and the body weight (BW) ranged from 72.6 to 1,348.7 g for males and 107.9 to 2,854.9 g for females. The relationship of BW and FL was expressed as: BW♂ = 0.0324 × FL2.708; BW♀ = 0.014 × FL2.963. The sample ages ranged from 2 to 8 years for males and 2 to 9 years for females. We used the von Bertalanffy function based on otolith reading and observed FL data to simulate Coregonus ussuriensis growth, which has been suggested to be similar to that of other Salmonidae fishes. No significant difference in growth was determined between males and females. The monthly gonad somatic index (GSI) value ranged from 0.16% to 1.69% for males and from 0.73% to 16.15% for females, with a peak in November. Additionally, the reproductive staging suggested that the Coregonus ussuriensis spawning season was mainly in November and December. The size at maturity (FL50%) for males and females was 34.9 cm and 37.9 cm respectively, and the corresponding age (T50%) was 4.5 and 5.1, respectively. This study provides basic information for understanding the biological characteristics of Coregonus ussuriensis and should aid in the assessment and management of fishery resources.
format: application/pdf
format: text/html
creator: Jilong Wang
creator: Wei Liu
creator: Peilun Li
creator: Fujiang Tang
creator: Wanqiao Lu
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12817
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: This study examined the age, growth, and maturation of 1,064 Coregonus ussuriensis individuals that were collected monthly from the middle section of the Amur River, China between 2016 and 2018. The fork length (FL) ranged from 14.9 to 49.1 cm for males and 21.5 to 58.8 cm for females, and the body weight (BW) ranged from 72.6 to 1,348.7 g for males and 107.9 to 2,854.9 g for females. The relationship of BW and FL was expressed as: BW♂ = 0.0324 × FL2.708; BW♀ = 0.014 × FL2.963. The sample ages ranged from 2 to 8 years for males and 2 to 9 years for females. We used the von Bertalanffy function based on otolith reading and observed FL data to simulate Coregonus ussuriensis growth, which has been suggested to be similar to that of other Salmonidae fishes. No significant difference in growth was determined between males and females. The monthly gonad somatic index (GSI) value ranged from 0.16% to 1.69% for males and from 0.73% to 16.15% for females, with a peak in November. Additionally, the reproductive staging suggested that the Coregonus ussuriensis spawning season was mainly in November and December. The size at maturity (FL50%) for males and females was 34.9 cm and 37.9 cm respectively, and the corresponding age (T50%) was 4.5 and 5.1, respectively. This study provides basic information for understanding the biological characteristics of Coregonus ussuriensis and should aid in the assessment and management of fishery resources.
bibliographic citation: Wang et al. (2022) Estimation of Coregonus ussuriensis age, growth, and maturation in China’s Amur River. PeerJ 10:e12817 https://doi.org/10.7717/peerj.12817
date submitted: 2020-12-13
date accepted: 2021-12-29
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Jilong
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Li
  given name: Peilun
author list: Agent
  family name: Tang
  given name: Fujiang
author list: Agent
  family name: Lu
  given name: Wanqiao
doi: 10.7717/peerj.12817
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Wang et al.
attribution name: Wang et al.

A retrospective study on molecular epidemiology trends of carbapenem resistant Enterobacteriaceae in a teaching hospital in Malaysia
type: item
type: AcademicArticle
description: Background Carbapenem resistant Enterobacteriaceae (CRE) has rapidly disseminated worldwide and has become a global threat to the healthcare system due to its resistance towards “last line” antibiotics. This study aimed to investigate the prevalence of CRE and the resistance mechanism as well as the risk factors associated with in-hospital mortality. Methods A total of 168 CRE strains isolated from a tertiary teaching hospital from 2014–2015 were included in this study. The presence of carbapenemase genes and minimum inhibitory concentration of imipenem, meropenem and colistin were investigated. All carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) strains were characterised by PFGE. The risk factors of patients infected by CRE associated with in-hospital mortality were determined statistically. Results The predominant CRE species isolated was K. pneumoniae. The carbapenemases detected were blaOXA-48, blaOXA-232, blaVIM and blaNDM of which blaOXA-48 was the predominant carbapenemase detected among 168 CRE strains. A total of 40 CRE strains harboured two different carbapenemase genes. A total of seven clusters and 48 pulsotypes were identified among 140 CRKp strains. A predominant pulsotype responsible for the transmission from 2014 to 2015 was identified. Univariate statistical analysis identified that the period between CRE isolation and start of appropriate therapy of more than 3 days was statistically associated with in-hospital mortality.
format: application/pdf
format: text/html
creator: Zhi Xian Kong
creator: Rina N. Karunakaran
creator: Kartini Abdul Jabar
creator: Sasheela Ponnampalavanar
creator: Chun Wie Chong
creator: Cindy Shuan Ju Teh
subject: Microbiology
subject: Molecular Biology
subject: Epidemiology
description: doi:10.7717/peerj.12830
publisher: PeerJ Inc.
rights: © 2022 Kong et al.
abstract: Background Carbapenem resistant Enterobacteriaceae (CRE) has rapidly disseminated worldwide and has become a global threat to the healthcare system due to its resistance towards “last line” antibiotics. This study aimed to investigate the prevalence of CRE and the resistance mechanism as well as the risk factors associated with in-hospital mortality. Methods A total of 168 CRE strains isolated from a tertiary teaching hospital from 2014–2015 were included in this study. The presence of carbapenemase genes and minimum inhibitory concentration of imipenem, meropenem and colistin were investigated. All carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) strains were characterised by PFGE. The risk factors of patients infected by CRE associated with in-hospital mortality were determined statistically. Results The predominant CRE species isolated was K. pneumoniae. The carbapenemases detected were blaOXA-48, blaOXA-232, blaVIM and blaNDM of which blaOXA-48 was the predominant carbapenemase detected among 168 CRE strains. A total of 40 CRE strains harboured two different carbapenemase genes. A total of seven clusters and 48 pulsotypes were identified among 140 CRKp strains. A predominant pulsotype responsible for the transmission from 2014 to 2015 was identified. Univariate statistical analysis identified that the period between CRE isolation and start of appropriate therapy of more than 3 days was statistically associated with in-hospital mortality.
bibliographic citation: Kong et al. (2022) A retrospective study on molecular epidemiology trends of carbapenem resistant Enterobacteriaceae in a teaching hospital in Malaysia. PeerJ 10:e12830 https://doi.org/10.7717/peerj.12830
date submitted: 2021-06-02
date accepted: 2022-01-04
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Zhi Xian
author list: Agent
  family name: N. Karunakaran
  given name: Rina
author list: Agent
  family name: Abdul Jabar
  given name: Kartini
author list: Agent
  family name: Ponnampalavanar
  given name: Sasheela
author list: Agent
  family name: Chong
  given name: Chun Wie
author list: Agent
  family name: Teh
  given name: Cindy Shuan Ju
doi: 10.7717/peerj.12830
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Kong et al.
attribution name: Kong et al.

Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands
type: item
type: AcademicArticle
description: Background Urbanization and global warming are generating ecological degradation and land pattern alteration problems in natural wetlands. These changes are greatly affecting the ecological services of wetlands. Therefore, there is an urgent need to explore the relationship between pollutants and land-use type for wetland restoration purposes. Zaozhadian Lake is a freshwater wetland in the North China Plain, which is facing degradation and land-use types changes. An experiment for analyzing soil pollutants was conducted in three land-use types of farmland, lake, and ditch in the Zaozhadian Lake. The aims of this study were to identify the distribution, pollution degree, and sources of pollutants in different land-use types, and to explore the influence of land-use type changes on contamination. Methods In this study, surface sediments (0–10 cm) of three land types (farmland, lake, and ditch) in Zaozhadian Lake were collected, and heavy metals (Cu, Ni, Zn, Pb, Cd, Cr, Hg), As, total nitrogen (TN), total phosphorus (TP) and organic matter (OM) were determined. Kriging interpolation was used to visualize the pollutants distribution. The pollution degree of TN and TP was evaluated by the Nemerow pollution index. The pollution of heavy metals and As was evaluated by the geological accumulation index (Igeo) and the potential ecological risk index (RI). Then, dual hierarchical clustering analysis and the principal component analysis were performed to further analyze the impact of land type changes on pollutants. Results The heavy metal contents in the farmland were higher than other areas, while the TN (3.71 ± 1.03 g kg-1) and OM (57.17 ± 15.16 g kg−1) in lake sediments were higher than that in other regions. Farmland, lake, and ditches had low ecological risks, with RI values of 84.21, 71.34, and 50.78, respectively. The primary heavy metal pollutants are Pb, Cu, and Ni. Furthermore, Cu, As, Ni, Pb, and Zn were primarily derived from agriculture pollution, the source of C…
format: application/pdf
format: text/html
creator: Yangyang Han
creator: Hongjie Wang
creator: Guangming Zhang
creator: Shengqi Zhang
creator: Xingchun Liu
creator: Ling Liu
subject: Soil Science
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.12885
publisher: PeerJ Inc.
rights: © 2022 Han et al.
abstract: Background Urbanization and global warming are generating ecological degradation and land pattern alteration problems in natural wetlands. These changes are greatly affecting the ecological services of wetlands. Therefore, there is an urgent need to explore the relationship between pollutants and land-use type for wetland restoration purposes. Zaozhadian Lake is a freshwater wetland in the North China Plain, which is facing degradation and land-use types changes. An experiment for analyzing soil pollutants was conducted in three land-use types of farmland, lake, and ditch in the Zaozhadian Lake. The aims of this study were to identify the distribution, pollution degree, and sources of pollutants in different land-use types, and to explore the influence of land-use type changes on contamination. Methods In this study, surface sediments (0–10 cm) of three land types (farmland, lake, and ditch) in Zaozhadian Lake were collected, and heavy metals (Cu, Ni, Zn, Pb, Cd, Cr, Hg), As, total nitrogen (TN), total phosphorus (TP) and organic matter (OM) were determined. Kriging interpolation was used to visualize the pollutants distribution. The pollution degree of TN and TP was evaluated by the Nemerow pollution index. The pollution of heavy metals and As was evaluated by the geological accumulation index (Igeo) and the potential ecological risk index (RI). Then, dual hierarchical clustering analysis and the principal component analysis were performed to further analyze the impact of land type changes on pollutants. Results The heavy metal contents in the farmland were higher than other areas, while the TN (3.71 ± 1.03 g kg-1) and OM (57.17 ± 15.16 g kg−1) in lake sediments were higher than that in other regions. Farmland, lake, and ditches had low ecological risks, with RI values of 84.21, 71.34, and 50.78, respectively. The primary heavy metal pollutants are Pb, Cu, and Ni. Furthermore, Cu, As, Ni, Pb, and Zn were primarily derived from agriculture pollution, the source of C…
bibliographic citation: Han et al. (2022) Distribution, ecological risk assessment and source identification of pollutants in soils of different land-use types in degraded wetlands. PeerJ 10:e12885 https://doi.org/10.7717/peerj.12885
date submitted: 2021-09-16
date accepted: 2022-01-14
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Yangyang
author list: Agent
  family name: Wang
  given name: Hongjie
author list: Agent
  family name: Zhang
  given name: Guangming
author list: Agent
  family name: Zhang
  given name: Shengqi
author list: Agent
  family name: Liu
  given name: Xingchun
author list: Agent
  family name: Liu
  given name: Ling
doi: 10.7717/peerj.12885
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Han et al.
attribution name: Han et al.

Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia
type: item
type: AcademicArticle
description: Background Investigating the land use and land cover (LULC) dynamics and the status of traditional agroforestry practices provide important data for policymakers. The main objective of this study was to assess the LULC dynamics and traditional agroforestry practices among smallholder farmers across the two agro-ecological zones in Wonchi District of Ethiopia. Methods Landsat images were acquired from Earth Explorer, and changes in LULC were quantified with three Landsat sensors in the three time-series (1985, 2001, and 2019). Supervised classification with maximum likelihood technique was employed using ERDAS Imagine and ArcGIS. A ground survey was conducted with 100 key informants who were selected from 10 sites using a purposive sampling method. The collected data were subjected to direct matrix ranking, use-value analysis of most important multipurpose plant species, and semi-structured interviews were conducted for qualitative analysis. Results In total, 103 agroforestry plant species belonging to 44 families were identified in Wonchi District, of which 74 were indigenous including seven endemic and 29 exotic species. The highest species (13) were recorded in the Fabaceae family. About 61% of species were reported in the midland agro-ecological zone. A mixed farming system was the most frequently (56%) reported source of income. The results of LULC changes from 1985 to 2019 showed that the agroforestry cover increased from 31.1% to 34.9% and settlement including road construction increased from 12.5% to 31.6% of the total area with an annual rate change of 0.3% and 2.7%, respectively. These changes corresponded with a decreasing trend of the forest, cropland, water body, and shrub at a rate of 4.7%, 1.3%, 0.8%, and 0.5%, respectively. The LULC changes were more pronounced in the highlands than in the midlands of Wonchi District. Expansion of settlement and tenure policy change are the main drivers for these changes in the area. The authors recommended that prote…
format: application/pdf
format: text/html
creator: Misganaw Meragiaw
creator: Zerihun Woldu
creator: Bal Ram Singh
subject: Biodiversity
subject: Conservation Biology
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12898
publisher: PeerJ Inc.
rights: © 2022 Meragiaw et al.
abstract: Background Investigating the land use and land cover (LULC) dynamics and the status of traditional agroforestry practices provide important data for policymakers. The main objective of this study was to assess the LULC dynamics and traditional agroforestry practices among smallholder farmers across the two agro-ecological zones in Wonchi District of Ethiopia. Methods Landsat images were acquired from Earth Explorer, and changes in LULC were quantified with three Landsat sensors in the three time-series (1985, 2001, and 2019). Supervised classification with maximum likelihood technique was employed using ERDAS Imagine and ArcGIS. A ground survey was conducted with 100 key informants who were selected from 10 sites using a purposive sampling method. The collected data were subjected to direct matrix ranking, use-value analysis of most important multipurpose plant species, and semi-structured interviews were conducted for qualitative analysis. Results In total, 103 agroforestry plant species belonging to 44 families were identified in Wonchi District, of which 74 were indigenous including seven endemic and 29 exotic species. The highest species (13) were recorded in the Fabaceae family. About 61% of species were reported in the midland agro-ecological zone. A mixed farming system was the most frequently (56%) reported source of income. The results of LULC changes from 1985 to 2019 showed that the agroforestry cover increased from 31.1% to 34.9% and settlement including road construction increased from 12.5% to 31.6% of the total area with an annual rate change of 0.3% and 2.7%, respectively. These changes corresponded with a decreasing trend of the forest, cropland, water body, and shrub at a rate of 4.7%, 1.3%, 0.8%, and 0.5%, respectively. The LULC changes were more pronounced in the highlands than in the midlands of Wonchi District. Expansion of settlement and tenure policy change are the main drivers for these changes in the area. The authors recommended that prote…
bibliographic citation: Meragiaw et al. (2022) Land use and land cover dynamics and traditional agroforestry practices in Wonchi District, Ethiopia. PeerJ 10:e12898 https://doi.org/10.7717/peerj.12898
date submitted: 2021-10-29
date accepted: 2022-01-16
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meragiaw
  given name: Misganaw
author list: Agent
  family name: Woldu
  given name: Zerihun
author list: Agent
  family name: Singh
  given name: Bal Ram
doi: 10.7717/peerj.12898
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Meragiaw et al.
attribution name: Meragiaw et al.

Methodological approaches for estimating populations of the endangered dhole Cuon alpinus
type: item
type: AcademicArticle
description: Large carnivores are important for maintaining ecosystem integrity and attract much research and conservation interest. For most carnivore species, estimating population density or abundance is challenging because they do not have unique markings for individual identification. This hinders status assessments for many threatened species, and calls for testing new methodological approaches. We examined past efforts to assess the population status of the endangered dhole (Cuon alpinus), and explored the application of a suite of recently developed models for estimating their populations using camera-trap data from India’s Western Ghats. We compared the performance of Site-Based Abundance (SBA), Space-to-Event (STE), and Time-to-Event (TTE) models against current knowledge of their population size in the area. We also applied two of these models (TTE and STE) to the co-occurring leopard (Panthera pardus), for which density estimates were available from Spatially Explicit Capture–Recapture (SECR) models, so as to simultaneously validate the accuracy of estimates for one marked and one unmarked species. Our review of literature (n = 38) showed that most assessments of dhole populations involved crude indices (relative abundance index; RAI) or estimates of occupancy and area of suitable habitat; very few studies attempted to estimate populations. Based on empirical data from our field surveys, the TTE and SBA models overestimated dhole population size beyond ecologically plausible limits, but the STE model produced reliable estimates for both the species. Our findings suggest that it is difficult to estimate population sizes of unmarked species when model assumptions are not fully met and data are sparse, which are commonplace for most ecological surveys in the tropics. Based on our assessment, we propose that practitioners who have access to photo-encounter data on dholes across Asia test old and new analytical approaches to increase the overall knowledge-base on the spec…
format: application/pdf
format: text/html
creator: Girish A. Punjabi
creator: Linnea Worsøe Havmøller
creator: Rasmus Worsøe Havmøller
creator: Dusit Ngoprasert
creator: Arjun Srivathsa
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.12905
publisher: PeerJ Inc.
rights: © 2022 Punjabi et al.
abstract: Large carnivores are important for maintaining ecosystem integrity and attract much research and conservation interest. For most carnivore species, estimating population density or abundance is challenging because they do not have unique markings for individual identification. This hinders status assessments for many threatened species, and calls for testing new methodological approaches. We examined past efforts to assess the population status of the endangered dhole (Cuon alpinus), and explored the application of a suite of recently developed models for estimating their populations using camera-trap data from India’s Western Ghats. We compared the performance of Site-Based Abundance (SBA), Space-to-Event (STE), and Time-to-Event (TTE) models against current knowledge of their population size in the area. We also applied two of these models (TTE and STE) to the co-occurring leopard (Panthera pardus), for which density estimates were available from Spatially Explicit Capture–Recapture (SECR) models, so as to simultaneously validate the accuracy of estimates for one marked and one unmarked species. Our review of literature (n = 38) showed that most assessments of dhole populations involved crude indices (relative abundance index; RAI) or estimates of occupancy and area of suitable habitat; very few studies attempted to estimate populations. Based on empirical data from our field surveys, the TTE and SBA models overestimated dhole population size beyond ecologically plausible limits, but the STE model produced reliable estimates for both the species. Our findings suggest that it is difficult to estimate population sizes of unmarked species when model assumptions are not fully met and data are sparse, which are commonplace for most ecological surveys in the tropics. Based on our assessment, we propose that practitioners who have access to photo-encounter data on dholes across Asia test old and new analytical approaches to increase the overall knowledge-base on the spec…
bibliographic citation: Punjabi et al. (2022) Methodological approaches for estimating populations of the endangered dhole Cuon alpinus. PeerJ 10:e12905 https://doi.org/10.7717/peerj.12905
date submitted: 2021-11-03
date accepted: 2022-01-17
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Punjabi
  given name: Girish A.
author list: Agent
  family name: Havmøller
  given name: Linnea Worsøe
author list: Agent
  family name: Havmøller
  given name: Rasmus Worsøe
author list: Agent
  family name: Ngoprasert
  given name: Dusit
author list: Agent
  family name: Srivathsa
  given name: Arjun
doi: 10.7717/peerj.12905
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Punjabi et al.
attribution name: Punjabi et al.

SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.
type: item
type: AcademicArticle
description: Background Pogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil. Methods To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads. Results In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” …
format: application/pdf
format: text/html
creator: Hongyi Zhang
creator: Wenjing Deng
creator: Changhua Lu
creator: Mengling He
creator: Hanjing Yan
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12940
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Pogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil. Methods To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads. Results In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” …
bibliographic citation: Zhang et al. (2022) SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.. PeerJ 10:e12940 https://doi.org/10.7717/peerj.12940
date submitted: 2021-06-04
date accepted: 2022-01-24
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hongyi
author list: Agent
  family name: Deng
  given name: Wenjing
author list: Agent
  family name: Lu
  given name: Changhua
author list: Agent
  family name: He
  given name: Mengling
author list: Agent
  family name: Yan
  given name: Hanjing
doi: 10.7717/peerj.12940
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study
type: item
type: AcademicArticle
description: Background In the United States, state-level policies requiring vaccination of school-going children constitute a critical strategy for improving vaccination coverage. However, policies allowing vaccination exemptions have also been implemented and contribute to reductions in vaccination coverage and potential increases in the burden of vaccine-preventable diseases. Understanding the geographic disparities in the distribution of vaccination exemptions and identifying high risk areas is necessary for guiding resource allocation and public health control strategies. This study investigated geographic disparities in vaccination exemptions as well as socioeconomic and demographic predictors of vaccination exemptions in Florida. Methods Vaccination exemption data were obtained from the Florida Department of Health’s Florida HealthCHARTS web interface. Spatial patterns in geographic distribution of total and non-medical vaccination exemptions were assessed using county-level choropleth maps. Negative binomial models were used to identify significant predictors of county-level risks of both total and non-medical vaccination exemptions. Results Total exemptions varied from 0 to 30.2 per 10,000 people. Nine counties had exemption risks in the top two classes (10.4–15.9 and 15.9–30.2 exemptions per 10,000 people). These counties were distributed in five distinct areas: Western Panhandle, central northern area, central, South-eastern coastal area, and the southern coastal border of the state. Non-medical exemptions varied from 0 to 10.4 per 10,000 people. Fifteen counties had exemption risks in the top two classes (3.7–5.6 and 5.6–10.4 exemptions per 10,000 people), and were located in six distinct areas: Western and Central Panhandle, Northeastern, Central-eastern coastal area, Central-western coastal area, and the South-western coastal border of the state. Predictors of high risk of total vaccination exemptions were high density of primary care providers (p < 0.001), high me…
format: application/pdf
format: text/html
creator: Corinne B. Tandy
creator: Agricola Odoi
subject: Epidemiology
subject: Immunology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.12973
publisher: PeerJ Inc.
rights: © 2022 Tandy and Odoi
abstract: Background In the United States, state-level policies requiring vaccination of school-going children constitute a critical strategy for improving vaccination coverage. However, policies allowing vaccination exemptions have also been implemented and contribute to reductions in vaccination coverage and potential increases in the burden of vaccine-preventable diseases. Understanding the geographic disparities in the distribution of vaccination exemptions and identifying high risk areas is necessary for guiding resource allocation and public health control strategies. This study investigated geographic disparities in vaccination exemptions as well as socioeconomic and demographic predictors of vaccination exemptions in Florida. Methods Vaccination exemption data were obtained from the Florida Department of Health’s Florida HealthCHARTS web interface. Spatial patterns in geographic distribution of total and non-medical vaccination exemptions were assessed using county-level choropleth maps. Negative binomial models were used to identify significant predictors of county-level risks of both total and non-medical vaccination exemptions. Results Total exemptions varied from 0 to 30.2 per 10,000 people. Nine counties had exemption risks in the top two classes (10.4–15.9 and 15.9–30.2 exemptions per 10,000 people). These counties were distributed in five distinct areas: Western Panhandle, central northern area, central, South-eastern coastal area, and the southern coastal border of the state. Non-medical exemptions varied from 0 to 10.4 per 10,000 people. Fifteen counties had exemption risks in the top two classes (3.7–5.6 and 5.6–10.4 exemptions per 10,000 people), and were located in six distinct areas: Western and Central Panhandle, Northeastern, Central-eastern coastal area, Central-western coastal area, and the South-western coastal border of the state. Predictors of high risk of total vaccination exemptions were high density of primary care providers (p < 0.001), high me…
bibliographic citation: Tandy et al. (2022) Geographic disparities and predictors of vaccination exemptions in Florida: a retrospective study. PeerJ 10:e12973 https://doi.org/10.7717/peerj.12973
date submitted: 2021-09-07
date accepted: 2022-01-31
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tandy
  given name: Corinne B.
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.12973
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Tandy and Odoi
attribution name: Tandy and Odoi

Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition
type: item
type: AcademicArticle
description: Background Oral squamous cell carcinoma (OSCC), the most common type of primary malignant tumor in the oral cavity, is a lethal disease with high recurrence and mortality rates. Butyrate, a metabolite produced by periodontal pathogens, has been linked to oral diseases. The purpose of this study was to evaluate the effect of sodium butyrate (NaB) on the proliferation, migration, and invasion of OSCC cells in vitro and to explore the potential mechanism. Methods Two OSCC cell lines (HSC-4 and SCC-9) were treated with NaB at different concentrations. The cell proliferation was assayed by CCK-8, ethylene deoxyuridine (EdU), and flow cytometry. Wound healing and transwell assay were performed to detect cell migration and invasion. Changes in epithelial-mesenchymal transition (EMT) markers, including E-cadherin, Vimentin, and SNAI1, were evaluated by quantitative real-time PCR (qRT-PCR), western blot, and immunofluorescent staining. The expression levels of matrix metalloproteinases (MMPs) were analyzed by qRT-PCR and gelatin zymography. Results Our results showed that NaB inhibited the proliferation of OSCC cells and induced cell cycle arrest at G1 phase, but NaB significantly enhanced cell migration and invasion compared with the control group. Further mechanistic investigation demonstrated that NaB induced EMT by increasing the expression of Vimentin and SNAI1, decreasing the expression of membrane-bound E-cadherin, and correspondingly promoting E-cadherin translocation from the membrane to the cytoplasm. In addition, the overexpression of MMP1/2/9/13 was closely related to NaB treatment. Conclusions Our study conclude that butyrate may promote the migration and invasion of OSCC cells by inducing EMT. These findings indicate that butyrate may contribute to OSCC metastasis.
format: application/pdf
format: text/html
creator: Wenli Zang
creator: Junchao Liu
creator: Fengxue Geng
creator: Dongjuan Liu
creator: Shuwei Zhang
creator: Yuchao Li
creator: Yaping Pan
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Oncology
subject: Otorhinolaryngology
description: doi:10.7717/peerj.12991
publisher: PeerJ Inc.
rights: © 2022 Zang et al.
abstract: Background Oral squamous cell carcinoma (OSCC), the most common type of primary malignant tumor in the oral cavity, is a lethal disease with high recurrence and mortality rates. Butyrate, a metabolite produced by periodontal pathogens, has been linked to oral diseases. The purpose of this study was to evaluate the effect of sodium butyrate (NaB) on the proliferation, migration, and invasion of OSCC cells in vitro and to explore the potential mechanism. Methods Two OSCC cell lines (HSC-4 and SCC-9) were treated with NaB at different concentrations. The cell proliferation was assayed by CCK-8, ethylene deoxyuridine (EdU), and flow cytometry. Wound healing and transwell assay were performed to detect cell migration and invasion. Changes in epithelial-mesenchymal transition (EMT) markers, including E-cadherin, Vimentin, and SNAI1, were evaluated by quantitative real-time PCR (qRT-PCR), western blot, and immunofluorescent staining. The expression levels of matrix metalloproteinases (MMPs) were analyzed by qRT-PCR and gelatin zymography. Results Our results showed that NaB inhibited the proliferation of OSCC cells and induced cell cycle arrest at G1 phase, but NaB significantly enhanced cell migration and invasion compared with the control group. Further mechanistic investigation demonstrated that NaB induced EMT by increasing the expression of Vimentin and SNAI1, decreasing the expression of membrane-bound E-cadherin, and correspondingly promoting E-cadherin translocation from the membrane to the cytoplasm. In addition, the overexpression of MMP1/2/9/13 was closely related to NaB treatment. Conclusions Our study conclude that butyrate may promote the migration and invasion of OSCC cells by inducing EMT. These findings indicate that butyrate may contribute to OSCC metastasis.
bibliographic citation: Zang et al. (2022) Butyrate promotes oral squamous cell carcinoma cells migration, invasion and epithelial-mesenchymal transition. PeerJ 10:e12991 https://doi.org/10.7717/peerj.12991
date submitted: 2021-08-19
date accepted: 2022-02-02
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zang
  given name: Wenli
author list: Agent
  family name: Liu
  given name: Junchao
author list: Agent
  family name: Geng
  given name: Fengxue
author list: Agent
  family name: Liu
  given name: Dongjuan
author list: Agent
  family name: Zhang
  given name: Shuwei
author list: Agent
  family name: Li
  given name: Yuchao
author list: Agent
  family name: Pan
  given name: Yaping
doi: 10.7717/peerj.12991
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: © 2022 Zang et al.
attribution name: Zang et al.

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish
type: item
type: AcademicArticle
description: The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.
format: application/pdf
format: text/html
creator: Lasse Nyholm
creator: Iñaki Odriozola
creator: Garazi Martin Bideguren
creator: Ostaizka Aizpurua
creator: Antton Alberdi
subject: Aquaculture, Fisheries and Fish Science
subject: Mathematical Biology
subject: Microbiology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.12992
publisher: PeerJ Inc.
rights: © 2022 Nyholm et al.
abstract: The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.
bibliographic citation: Nyholm et al. (2022) Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish. PeerJ 10:e12992 https://doi.org/10.7717/peerj.12992
date submitted: 2021-11-11
date accepted: 2022-02-02
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nyholm
  given name: Lasse
author list: Agent
  family name: Odriozola
  given name: Iñaki
author list: Agent
  family name: Martin Bideguren
  given name: Garazi
author list: Agent
  family name: Aizpurua
  given name: Ostaizka
author list: Agent
  family name: Alberdi
  given name: Antton
doi: 10.7717/peerj.12992
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Nyholm et al.
attribution name: Nyholm et al.

Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans)
type: item
type: AcademicArticle
description: Toads release toxic dry secretions from glands in their skin. Toxin possesses a wide range of biological effects, but little is known about its specific gene expression pattern and regulatory mechanisms. The Asiatic toad (Bufo gargarizans) is widely used to produce toxin. Here, we explored the gene expression of 30 tissue samples from three different skin sites (parotoid gland, dorsal skin, and abdomen skin) of B. gargarizans. After de novo assembly, 783,130 unigenes with an average length of 489 bp (N50 = 556 bp) were obtained. A total of 9,248 significant differentially expressed genes (DEGs) were detected. There were 8,819 DEGs between the parotoid gland and abdomen skin and 1,299 DEGs between the dorsal skin and abdomen skin, while only 1,283 DEGs were obtained between the parotoid gland and dorsal skin. Through enrichment analysis, it was found that the detected differential gene expressions corresponded to the different functions of different skin sites. Our key findings were the genetic expression of toxin secretion, the protection function of skin, and the related genes such as HSD3B, Cyp2c, and CAT, LGALS9. In conclusion, we provide useful transcript resources to study the gene expression and gene function of B. gargarizans and other amphibians. The detected DEGs between different sites of the skin provided better insights into the genetic mechanisms of toxin secretion and the protection function of skin for amphibians.
format: application/pdf
format: text/html
creator: Yue Lan
creator: Lewei He
creator: Xue Dong
creator: Ruixiang Tang
creator: Wanyu Li
creator: Jiao Wang
creator: Lei Wang
creator: Bisong Yue
creator: Megan Price
creator: Tao Guo
creator: Zhenxin Fan
subject: Bioinformatics
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12993
publisher: PeerJ Inc.
rights: © 2022 Lan et al.
abstract: Toads release toxic dry secretions from glands in their skin. Toxin possesses a wide range of biological effects, but little is known about its specific gene expression pattern and regulatory mechanisms. The Asiatic toad (Bufo gargarizans) is widely used to produce toxin. Here, we explored the gene expression of 30 tissue samples from three different skin sites (parotoid gland, dorsal skin, and abdomen skin) of B. gargarizans. After de novo assembly, 783,130 unigenes with an average length of 489 bp (N50 = 556 bp) were obtained. A total of 9,248 significant differentially expressed genes (DEGs) were detected. There were 8,819 DEGs between the parotoid gland and abdomen skin and 1,299 DEGs between the dorsal skin and abdomen skin, while only 1,283 DEGs were obtained between the parotoid gland and dorsal skin. Through enrichment analysis, it was found that the detected differential gene expressions corresponded to the different functions of different skin sites. Our key findings were the genetic expression of toxin secretion, the protection function of skin, and the related genes such as HSD3B, Cyp2c, and CAT, LGALS9. In conclusion, we provide useful transcript resources to study the gene expression and gene function of B. gargarizans and other amphibians. The detected DEGs between different sites of the skin provided better insights into the genetic mechanisms of toxin secretion and the protection function of skin for amphibians.
bibliographic citation: Lan et al. (2022) Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans). PeerJ 10:e12993 https://doi.org/10.7717/peerj.12993
date submitted: 2021-07-27
date accepted: 2022-02-02
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lan
  given name: Yue
author list: Agent
  family name: He
  given name: Lewei
author list: Agent
  family name: Dong
  given name: Xue
author list: Agent
  family name: Tang
  given name: Ruixiang
author list: Agent
  family name: Li
  given name: Wanyu
author list: Agent
  family name: Wang
  given name: Jiao
author list: Agent
  family name: Wang
  given name: Lei
author list: Agent
  family name: Yue
  given name: Bisong
author list: Agent
  family name: Price
  given name: Megan
author list: Agent
  family name: Guo
  given name: Tao
author list: Agent
  family name: Fan
  given name: Zhenxin
doi: 10.7717/peerj.12993
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Lan et al.
attribution name: Lan et al.

Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow
type: item
type: AcademicArticle
description: Objective The purpose of the present study was to determine the effects of starch sugar by-product (SSB) feeding on the rumen in-vitro digestibility, in situ disappearance rate, and lactating dairy cow. Methods To determine the rumen in vitro digestibility, 50 mL of the buffer-rumen fluid mixture was dispensed into a 125 mL serum bottle containing 0.5 g of dry matter (DM) of substrates. Nitrogen gas (N2, 99.9% pure) was flushed into the serum bottles and three replications were incubated at 0, 2, 4, 8, 16, 24, and 48 h. To determine the in-situ disappearance rate, SSB was incubated for 0, 2, 4, 8, 16, 24, and 48 hours in nylon bags (5 × 10 cm, 45*m pore size) placed within the ventral sac of two cannulated Holstein cows.. A total of sixteen Holstein Friesian cows (60.5 ± 20.4 months old, 706.8 ± 3.4 kg initial body wieght) fed experimental diets during the experimental periods. The treatments were basal diet (control) and 3.0% DM of SSB, with the diet formulated according to national research council (NRC) nutrient requirements of dairy cattle guideline. An experiment was conducted with a randomized block design for six weeks based on body weight. Results Soluble fraction (fraction a) of DM and crude protein (CP) was 28.99 and 11.92%DM, fraction b of DM and CP was 44.63 and 31.61% DM, and c value of DM and CP was 26.38 and 56.47%DM. As an increase SSB level in total mixed ration (TMR), there was a decrease in gas production at 0, 16, and 48 h (p < 0.05). As an increase SSB level in TMR, there was a decrease in acetate to propionate ratio at 8, 16, 24, and 48 h (p < 0.05). Dry matter intake, milk production, and milk composition did not differ between the treatments. All blood profile contents did not differ between treatments. Conclusion A diet containing 3.0% SSB could be fed to ruminants without adverse effects on rumen fermentation.
format: application/pdf
format: text/html
creator: Yongjun Choi
creator: Suhun Kim
creator: Sangrak Lee
creator: Youngjun Na
subject: Agricultural Science
subject: Biochemistry
subject: Veterinary Medicine
description: doi:10.7717/peerj.12998
publisher: PeerJ Inc.
rights: © 2022 Choi et al.
abstract: Objective The purpose of the present study was to determine the effects of starch sugar by-product (SSB) feeding on the rumen in-vitro digestibility, in situ disappearance rate, and lactating dairy cow. Methods To determine the rumen in vitro digestibility, 50 mL of the buffer-rumen fluid mixture was dispensed into a 125 mL serum bottle containing 0.5 g of dry matter (DM) of substrates. Nitrogen gas (N2, 99.9% pure) was flushed into the serum bottles and three replications were incubated at 0, 2, 4, 8, 16, 24, and 48 h. To determine the in-situ disappearance rate, SSB was incubated for 0, 2, 4, 8, 16, 24, and 48 hours in nylon bags (5 × 10 cm, 45*m pore size) placed within the ventral sac of two cannulated Holstein cows.. A total of sixteen Holstein Friesian cows (60.5 ± 20.4 months old, 706.8 ± 3.4 kg initial body wieght) fed experimental diets during the experimental periods. The treatments were basal diet (control) and 3.0% DM of SSB, with the diet formulated according to national research council (NRC) nutrient requirements of dairy cattle guideline. An experiment was conducted with a randomized block design for six weeks based on body weight. Results Soluble fraction (fraction a) of DM and crude protein (CP) was 28.99 and 11.92%DM, fraction b of DM and CP was 44.63 and 31.61% DM, and c value of DM and CP was 26.38 and 56.47%DM. As an increase SSB level in total mixed ration (TMR), there was a decrease in gas production at 0, 16, and 48 h (p < 0.05). As an increase SSB level in TMR, there was a decrease in acetate to propionate ratio at 8, 16, 24, and 48 h (p < 0.05). Dry matter intake, milk production, and milk composition did not differ between the treatments. All blood profile contents did not differ between treatments. Conclusion A diet containing 3.0% SSB could be fed to ruminants without adverse effects on rumen fermentation.
bibliographic citation: Choi et al. (2022) Effects of starch sugar by-product on rumen in vitro digestibility, in situ disappearance rate, and milking productivity of the lactating dairy cow. PeerJ 10:e12998 https://doi.org/10.7717/peerj.12998
date submitted: 2021-10-20
date accepted: 2022-02-02
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Yongjun
author list: Agent
  family name: Kim
  given name: Suhun
author list: Agent
  family name: Lee
  given name: Sangrak
author list: Agent
  family name: Na
  given name: Youngjun
doi: 10.7717/peerj.12998
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Choi et al.
attribution name: Choi et al.

Functional network motifs defined through integration of protein-protein and genetic interactions
type: item
type: AcademicArticle
description: Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.
format: application/pdf
format: text/html
creator: Amruta Sahoo
creator: Sebastian Pechmann
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Data Science
description: doi:10.7717/peerj.13016
publisher: PeerJ Inc.
rights: © 2022 Sahoo and Pechmann
abstract: Cells are enticingly complex systems. The identification of feedback regulation is critically important for understanding this complexity. Network motifs defined as small graphlets that occur more frequently than expected by chance have revolutionized our understanding of feedback circuits in cellular networks. However, with their definition solely based on statistical over-representation, network motifs often lack biological context, which limits their usefulness. Here, we define functional network motifs (FNMs) through the systematic integration of genetic interaction data that directly inform on functional relationships between genes and encoded proteins. Occurring two orders of magnitude less frequently than conventional network motifs, we found FNMs significantly enriched in genes known to be functionally related. Moreover, our comprehensive analyses of FNMs in yeast showed that they are powerful at capturing both known and putative novel regulatory interactions, thus suggesting a promising strategy towards the systematic identification of feedback regulation in biological networks. Many FNMs appeared as excellent candidates for the prioritization of follow-up biochemical characterization, which is a recurring bottleneck in the targeting of complex diseases. More generally, our work highlights a fruitful avenue for integrating and harnessing genomic network data.
bibliographic citation: Sahoo et al. (2022) Functional network motifs defined through integration of protein-protein and genetic interactions. PeerJ 10:e13016 https://doi.org/10.7717/peerj.13016
date submitted: 2021-11-11
date accepted: 2022-02-06
issued: 2022-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sahoo
  given name: Amruta
author list: Agent
  family name: Pechmann
  given name: Sebastian
doi: 10.7717/peerj.13016
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-22
copyright: ©2022 Sahoo and Pechmann
attribution name: Sahoo and Pechmann

Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat
type: item
type: AcademicArticle
description: Shrimp aquaculture has been accomplished with breeding and nursing of shrimp in an artificial environment to fulfill the increasing demand of shrimp consumption worldwide. However, the microbial diseases appear as a serious problem in this industry. The study was designed to identify the diverse bacteria from shrimp PL (post-larvae) nurseries and to profile antibiotic resistance patterns. The rearing water (raw seawater, treated and outlet water) and shrimp PL were collected from eight nurseries of south-west Bangladesh. Using selective agar plates, thirty representative isolates were selected for 16S rRNA gene sequencing, antibiotic susceptibility test and MAR index calculation. Representative isolates were identified as Aeromonas caviae, Pseudomonas monteilii, Shewanella algae, Vibrio alginolyticus, V. brasiliensis, V. natriegens, V. parahaemolyticus, V. shilonii, V. xuii, Zobellella denitrificans which are Gram-negative, and Bacillus licheniformis and B. pumilus which are Gram-positive. Notably, six strains identified as Acinetobacter venetianus might be a concern of risk for shrimp industry. The antibiotic resistance pattern reveals that the strain YWO8-97 (identified as P. monteilii) was resistant to all twelve antibiotics. Ceftazidime was the most powerful antibiotic since most of the studied strains were sensitive against it. The six strains of A. venetianus showed multiple antibiotic resistance patterns. MAR index were ranged from 0.08 to 1.0, and values of 26 isolates were more than 0.2 which means prior high exposure to the antibiotics. From the present study, it can be concluded that shrimp PL nurseries in southern part of Bangladesh are getting contaminated with antibiotic resistant pathogenic bacteria.
format: application/pdf
format: text/html
creator: Abdullah Yasin
creator: Mst. Khadiza Begum
creator: Md. Mostavi Enan Eshik
creator: Nusrat Jahan Punom
creator: Shawon Ahmmed
creator: Mohammad Shamsur Rahman
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
description: doi:10.7717/peerj.12808
publisher: PeerJ Inc.
rights: © 2022 Yasin et al.
abstract: Shrimp aquaculture has been accomplished with breeding and nursing of shrimp in an artificial environment to fulfill the increasing demand of shrimp consumption worldwide. However, the microbial diseases appear as a serious problem in this industry. The study was designed to identify the diverse bacteria from shrimp PL (post-larvae) nurseries and to profile antibiotic resistance patterns. The rearing water (raw seawater, treated and outlet water) and shrimp PL were collected from eight nurseries of south-west Bangladesh. Using selective agar plates, thirty representative isolates were selected for 16S rRNA gene sequencing, antibiotic susceptibility test and MAR index calculation. Representative isolates were identified as Aeromonas caviae, Pseudomonas monteilii, Shewanella algae, Vibrio alginolyticus, V. brasiliensis, V. natriegens, V. parahaemolyticus, V. shilonii, V. xuii, Zobellella denitrificans which are Gram-negative, and Bacillus licheniformis and B. pumilus which are Gram-positive. Notably, six strains identified as Acinetobacter venetianus might be a concern of risk for shrimp industry. The antibiotic resistance pattern reveals that the strain YWO8-97 (identified as P. monteilii) was resistant to all twelve antibiotics. Ceftazidime was the most powerful antibiotic since most of the studied strains were sensitive against it. The six strains of A. venetianus showed multiple antibiotic resistance patterns. MAR index were ranged from 0.08 to 1.0, and values of 26 isolates were more than 0.2 which means prior high exposure to the antibiotics. From the present study, it can be concluded that shrimp PL nurseries in southern part of Bangladesh are getting contaminated with antibiotic resistant pathogenic bacteria.
bibliographic citation: Yasin et al. (2022) Molecular identification and antibiotic resistance patterns of diverse bacteria associated with shrimp PL nurseries of Bangladesh: suspecting Acinetobacter venetianus as future threat. PeerJ 10:e12808 https://doi.org/10.7717/peerj.12808
date submitted: 2021-08-04
date accepted: 2021-12-27
issued: 2022-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yasin
  given name: Abdullah
author list: Agent
  family name: Begum
  given name: Mst. Khadiza
author list: Agent
  family name: Eshik
  given name: Md. Mostavi Enan
author list: Agent
  family name: Punom
  given name: Nusrat Jahan
author list: Agent
  family name: Ahmmed
  given name: Shawon
author list: Agent
  family name: Rahman
  given name: Mohammad Shamsur
doi: 10.7717/peerj.12808
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-21
copyright: © 2022 Yasin et al.
attribution name: Yasin et al.

Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1
type: item
type: AcademicArticle
description: Inorganic and synthetic flocculants are widely investigated for removing harmful microalgae, such as Microcystis aeruginosa. However, their toxicity and non-biodegradability are shortcomings. Bioflocculants based on extracellular polysaccharides have attracted much attention as alternative flocculants. However, its high production cost is a limiting factor for applying bioflocculants. Here, we investigate the potential of the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1, as a novel flocculant on M. aeruginosa cells. The removal efficiency of M. aeruginosa cells by the dead cells was measured by mixing and shaking both components in a buffer with 5 mM CaCl2 in different incubation times and concentrations of the dead cells. After that, the minimum effective concentration of CaCl2 was determined. The combination effect of FeCl3 and the dead cells on the removal efficiency was tested. The structure of cell aggregates consisted of the dead cells and M. aeruginosa cells were also observed using a scanning electron microscope. The maximum removal efficiency (75.39%) was reached within 3 min in the presence of CaCl2 when 5 mg/ml of the dead cells (wet cells) were added. The optimal concentration of CaCl2 was 5 mM. The combination of the dead cells and a low concentration of FeCl3 (10 mg/L) with 5 mM of CaCl2 significantly improved the removal efficiency by about 1.2 times (P < 0.05). This result indicates that the combination usage of the dead cells can reduce the use of FeCl3. These results indicated that the dead cells could potentially be a novel biolfocculant to remove M. aeruginosa cells.
format: application/pdf
format: text/html
creator: Go Furusawa
creator: Koji Iwamoto
subject: Bioengineering
subject: Microbiology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12867
publisher: PeerJ Inc.
rights: © 2022 Furusawa and Iwamoto
abstract: Inorganic and synthetic flocculants are widely investigated for removing harmful microalgae, such as Microcystis aeruginosa. However, their toxicity and non-biodegradability are shortcomings. Bioflocculants based on extracellular polysaccharides have attracted much attention as alternative flocculants. However, its high production cost is a limiting factor for applying bioflocculants. Here, we investigate the potential of the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1, as a novel flocculant on M. aeruginosa cells. The removal efficiency of M. aeruginosa cells by the dead cells was measured by mixing and shaking both components in a buffer with 5 mM CaCl2 in different incubation times and concentrations of the dead cells. After that, the minimum effective concentration of CaCl2 was determined. The combination effect of FeCl3 and the dead cells on the removal efficiency was tested. The structure of cell aggregates consisted of the dead cells and M. aeruginosa cells were also observed using a scanning electron microscope. The maximum removal efficiency (75.39%) was reached within 3 min in the presence of CaCl2 when 5 mg/ml of the dead cells (wet cells) were added. The optimal concentration of CaCl2 was 5 mM. The combination of the dead cells and a low concentration of FeCl3 (10 mg/L) with 5 mM of CaCl2 significantly improved the removal efficiency by about 1.2 times (P < 0.05). This result indicates that the combination usage of the dead cells can reduce the use of FeCl3. These results indicated that the dead cells could potentially be a novel biolfocculant to remove M. aeruginosa cells.
bibliographic citation: Furusawa et al. (2022) Removal of Microcystis aeruginosa cells using the dead cells of a marine filamentous bacterium, Aureispira sp. CCB-QB1. PeerJ 10:e12867 https://doi.org/10.7717/peerj.12867
date submitted: 2021-10-22
date accepted: 2022-01-10
issued: 2022-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Furusawa
  given name: Go
author list: Agent
  family name: Iwamoto
  given name: Koji
doi: 10.7717/peerj.12867
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-21
copyright: ©2022 Furusawa and Iwamoto
attribution name: Furusawa and Iwamoto

Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.)
type: item
type: AcademicArticle
description: Laccase, as a copper-containing polyphenol oxidase, primarily functions in the process of lignin, anthocyanin biosynthesis, and various abiotic/biotic stresses. In this study, forty-eight laccase members were identified in the eggplant genome. Only forty-two laccase genes from eggplant (SmLACs) were anchored unevenly in 12 chromosomes, the other six SmLACs were mapped on unanchored scaffolds. Phylogenetic analysis indicated that only twenty-five SmLACs were divided into six different groups on the basis of groups reported in Arabidopsis. Gene structure analysis revealed that the number of exons ranged from one to 13. Motif analysis revealed that SmLACs included six conserved motifs. In aspects of gene duplication analysis, twenty-one SmLACs were collinear with LAC genes from Arabidopsis, tomato or rice. Cis-regulatory elements analysis indicated many SmLACs may be involved in eggplant morphogenesis, flavonoid biosynthesis, diverse stresses and growth/development processes. Expression analysis further confirmed that a few SmLACs may function in vegetative and reproductive organs at different developmental stages and also in response to one or multiple stresses. This study would help to further understand and enrich the physiological function of the SmLAC gene family in eggplant, and may provide high-quality genetic resources for eggplant genetics and breeding.
format: application/pdf
format: text/html
creator: Faxiang Wan
creator: Linqing Zhang
creator: Mengying Tan
creator: Xiaohua Wang
creator: Guang-Long Wang
creator: Mengru Qi
creator: Bingxin Liu
creator: Jun Gao
creator: Yu Pan
creator: Yongqing Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12922
publisher: PeerJ Inc.
rights: © 2022 Wan et al.
abstract: Laccase, as a copper-containing polyphenol oxidase, primarily functions in the process of lignin, anthocyanin biosynthesis, and various abiotic/biotic stresses. In this study, forty-eight laccase members were identified in the eggplant genome. Only forty-two laccase genes from eggplant (SmLACs) were anchored unevenly in 12 chromosomes, the other six SmLACs were mapped on unanchored scaffolds. Phylogenetic analysis indicated that only twenty-five SmLACs were divided into six different groups on the basis of groups reported in Arabidopsis. Gene structure analysis revealed that the number of exons ranged from one to 13. Motif analysis revealed that SmLACs included six conserved motifs. In aspects of gene duplication analysis, twenty-one SmLACs were collinear with LAC genes from Arabidopsis, tomato or rice. Cis-regulatory elements analysis indicated many SmLACs may be involved in eggplant morphogenesis, flavonoid biosynthesis, diverse stresses and growth/development processes. Expression analysis further confirmed that a few SmLACs may function in vegetative and reproductive organs at different developmental stages and also in response to one or multiple stresses. This study would help to further understand and enrich the physiological function of the SmLAC gene family in eggplant, and may provide high-quality genetic resources for eggplant genetics and breeding.
bibliographic citation: Wan et al. (2022) Genome-wide identification and characterization of laccase family members in eggplant (Solanum melongena L.). PeerJ 10:e12922 https://doi.org/10.7717/peerj.12922
date submitted: 2021-04-23
date accepted: 2022-01-20
issued: 2022-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Faxiang
author list: Agent
  family name: Zhang
  given name: Linqing
author list: Agent
  family name: Tan
  given name: Mengying
author list: Agent
  family name: Wang
  given name: Xiaohua
author list: Agent
  family name: Wang
  given name: Guang-Long
author list: Agent
  family name: Qi
  given name: Mengru
author list: Agent
  family name: Liu
  given name: Bingxin
author list: Agent
  family name: Gao
  given name: Jun
author list: Agent
  family name: Pan
  given name: Yu
author list: Agent
  family name: Wang
  given name: Yongqing
doi: 10.7717/peerj.12922
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-21
copyright: © 2022 Wan et al.
attribution name: Wan et al.

Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations
type: item
type: AcademicArticle
description: Background Fuji is a vital apple cultivar, and has been propagated clonally for nearly a century. The chloroplast genome variation of Fuji apples in China has not been investigated. Methods This study used next-generation high-throughput sequencing and bioinformatics to compare and analyze the chloroplast genome of 24 Red Fuji varieties from nine regions in China. Results The results showed that the 24 chloroplast genomes were highly conserved in genome size, structure, and organization. The length of the genomes ranged from 160,063 to 160,070 bp, and the GC content was 36.6%. Each of the 24 chloroplast genomes encoded 131 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of repeat sequence detection were consistent; the most common sequence was forward repeats (53.1%), and the least common sequence was complementary repeats (4.1%). The chloroplast genome sequence of Red Fuji was highly conserved. Two indels were detected, but the PI value was 0, and there were no SNP loci. The chloroplast genome variation rate of Red Fuji was low.
format: application/pdf
format: text/html
creator: Haoyu Miao
creator: Jinbo Bao
creator: Xueli Li
creator: Zhijie Ding
creator: Xinmin Tian
subject: Agricultural Science
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12927
publisher: PeerJ Inc.
rights: © 2022 Miao et al.
abstract: Background Fuji is a vital apple cultivar, and has been propagated clonally for nearly a century. The chloroplast genome variation of Fuji apples in China has not been investigated. Methods This study used next-generation high-throughput sequencing and bioinformatics to compare and analyze the chloroplast genome of 24 Red Fuji varieties from nine regions in China. Results The results showed that the 24 chloroplast genomes were highly conserved in genome size, structure, and organization. The length of the genomes ranged from 160,063 to 160,070 bp, and the GC content was 36.6%. Each of the 24 chloroplast genomes encoded 131 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The results of repeat sequence detection were consistent; the most common sequence was forward repeats (53.1%), and the least common sequence was complementary repeats (4.1%). The chloroplast genome sequence of Red Fuji was highly conserved. Two indels were detected, but the PI value was 0, and there were no SNP loci. The chloroplast genome variation rate of Red Fuji was low.
bibliographic citation: Miao et al. (2022) Comparative analyses of chloroplast genomes in ‘Red Fuji’ apples: low rate of chloroplast genome mutations. PeerJ 10:e12927 https://doi.org/10.7717/peerj.12927
date submitted: 2021-10-18
date accepted: 2022-01-20
issued: 2022-02-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miao
  given name: Haoyu
author list: Agent
  family name: Bao
  given name: Jinbo
author list: Agent
  family name: Li
  given name: Xueli
author list: Agent
  family name: Ding
  given name: Zhijie
author list: Agent
  family name: Tian
  given name: Xinmin
doi: 10.7717/peerj.12927
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-21
copyright: ©2022 Miao et al.
attribution name: Miao et al.

Drivers of phenotypic divergence in a Mesoamerican highland bird
type: item
type: AcademicArticle
description: Animals derive their coloration from a variety of pigments as well as non-pigmentary structural features. One of the most widespread types of pigments are carotenoids, which are used by all invertebrate taxa and most vertebrate orders to generate red, pink, orange and yellow coloration. Despite their widespread use by diverse animal groups, animals obligately obtain carotenoid pigments from diet. Carotenoid-based coloration is therefore modulated by evolutionary and ecological processes that affect the acquisition and deposition of these pigments into tegumentary structures. The Flame-colored Tanager (Piranga bidentata) is a highland songbird in the cardinal family (Cardinalidae) that is distributed from Mexican sierras through Central America up to western Panama. While female plumage throughout its entire range is predominantly yellow, males exhibit a noticeable split in ventral plumage color, which is bright orange on the West slope and the Tres Marias Islands and blood red in Eastern Mexico and Central America. We used Multiple Regression on Matrices (MRM) to evaluate the relative contributions of geographic distance, climate and genetic distance on color divergence and body differences between geographically disjunct populations. We found that differentiation in carotenoid plumage coloration was mainly explained by rainfall differences between disjunct populations, whereas body size differences was best explained by variation in the annual mean temperature and temperature of coldest quarter. These results indicate that climate is a strong driver of phenotypic divergence in Piranga bidentata.
format: application/pdf
format: text/html
creator: Sahid M. Robles-Bello
creator: Melisa Vázquez-López
creator: Sandra M. Ramírez-Barrera
creator: Alondra K. Terrones-Ramírez
creator: Blanca E. Hernández-Baños
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12901
publisher: PeerJ Inc.
rights: © 2022 Robles-Bello et al.
abstract: Animals derive their coloration from a variety of pigments as well as non-pigmentary structural features. One of the most widespread types of pigments are carotenoids, which are used by all invertebrate taxa and most vertebrate orders to generate red, pink, orange and yellow coloration. Despite their widespread use by diverse animal groups, animals obligately obtain carotenoid pigments from diet. Carotenoid-based coloration is therefore modulated by evolutionary and ecological processes that affect the acquisition and deposition of these pigments into tegumentary structures. The Flame-colored Tanager (Piranga bidentata) is a highland songbird in the cardinal family (Cardinalidae) that is distributed from Mexican sierras through Central America up to western Panama. While female plumage throughout its entire range is predominantly yellow, males exhibit a noticeable split in ventral plumage color, which is bright orange on the West slope and the Tres Marias Islands and blood red in Eastern Mexico and Central America. We used Multiple Regression on Matrices (MRM) to evaluate the relative contributions of geographic distance, climate and genetic distance on color divergence and body differences between geographically disjunct populations. We found that differentiation in carotenoid plumage coloration was mainly explained by rainfall differences between disjunct populations, whereas body size differences was best explained by variation in the annual mean temperature and temperature of coldest quarter. These results indicate that climate is a strong driver of phenotypic divergence in Piranga bidentata.
bibliographic citation: Robles-Bello et al. (2022) Drivers of phenotypic divergence in a Mesoamerican highland bird. PeerJ 10:e12901 https://doi.org/10.7717/peerj.12901
date submitted: 2021-09-01
date accepted: 2022-01-17
issued: 2022-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Robles-Bello
  given name: Sahid M.
author list: Agent
  family name: Vázquez-López
  given name: Melisa
author list: Agent
  family name: Ramírez-Barrera
  given name: Sandra M.
author list: Agent
  family name: Terrones-Ramírez
  given name: Alondra K.
author list: Agent
  family name: Hernández-Baños
  given name: Blanca E.
doi: 10.7717/peerj.12901
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-18
copyright: ©2022 Robles-Bello et al.
attribution name: Robles-Bello et al.

Climate in Africa sequentially shapes spring passage of Willow Warbler Phylloscopus trochilus across the Baltic coast
type: item
type: AcademicArticle
description: Background Many migrant birds have been returning to Europe earlier in spring since the 1980s. This has been attributed mostly to an earlier onset of spring in Europe, but we found the timing of Willow Warblers’ passage to be influenced by climate indices for Africa as much as those for Europe. Willow Warblers’ spring passage through northern Europe involves populations from different wintering quarters in Africa. We therefore expected that migration timing in the early, middle and late periods of spring would be influenced sequentially by climate indices operating in different parts of the winter range. Methods Using data from daily mistnetting in 1 April–15 May over 1982–2017 at Bukowo (Poland, Baltic Sea coast), we derived an Annual Anomaly (AA, in days) of Willow Warbler spring migration. We decomposed this anomaly into three main periods (1–26 April, 27 April–5 May, 6–15 May); one-third of migrants in each period. We modelled three sequential time series of spring passage using calendar year and 15 large-scale climate indices averaged over the months of Willow Warblers’ life stages in the year preceding spring migration as explanatory variables in multiple regression models. Nine climate variables were selected in the best models. We used these nine explanatory variables and calculated their partial correlations in models for nine overlapping sub-periods of AA. The pattern of relationships between AA in these nine sub-periods of spring and the nine climate variables indicated how spring passage had responded to the climate. We recommend this method for the study of birds’ phenological responses to climate change. Results The Southern Oscillation Index and Indian Ocean Dipole in Aug–Oct showed large partial correlations early in the passage, then faded in importance. For the Sahel Precipitation Index (PSAH) and Sahel Temperature Anomaly (TSAH) in Aug–Oct partial correlations occurred early then peaked in mid-passage; for PSAH (Nov–March) correlations peaked at t…
format: application/pdf
format: text/html
creator: Magdalena Remisiewicz
creator: Les G. Underhill
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.12964
publisher: PeerJ Inc.
rights: © 2022 Remisiewicz and Underhill
abstract: Background Many migrant birds have been returning to Europe earlier in spring since the 1980s. This has been attributed mostly to an earlier onset of spring in Europe, but we found the timing of Willow Warblers’ passage to be influenced by climate indices for Africa as much as those for Europe. Willow Warblers’ spring passage through northern Europe involves populations from different wintering quarters in Africa. We therefore expected that migration timing in the early, middle and late periods of spring would be influenced sequentially by climate indices operating in different parts of the winter range. Methods Using data from daily mistnetting in 1 April–15 May over 1982–2017 at Bukowo (Poland, Baltic Sea coast), we derived an Annual Anomaly (AA, in days) of Willow Warbler spring migration. We decomposed this anomaly into three main periods (1–26 April, 27 April–5 May, 6–15 May); one-third of migrants in each period. We modelled three sequential time series of spring passage using calendar year and 15 large-scale climate indices averaged over the months of Willow Warblers’ life stages in the year preceding spring migration as explanatory variables in multiple regression models. Nine climate variables were selected in the best models. We used these nine explanatory variables and calculated their partial correlations in models for nine overlapping sub-periods of AA. The pattern of relationships between AA in these nine sub-periods of spring and the nine climate variables indicated how spring passage had responded to the climate. We recommend this method for the study of birds’ phenological responses to climate change. Results The Southern Oscillation Index and Indian Ocean Dipole in Aug–Oct showed large partial correlations early in the passage, then faded in importance. For the Sahel Precipitation Index (PSAH) and Sahel Temperature Anomaly (TSAH) in Aug–Oct partial correlations occurred early then peaked in mid-passage; for PSAH (Nov–March) correlations peaked at t…
bibliographic citation: Remisiewicz et al. (2022) Climate in Africa sequentially shapes spring passage of Willow Warbler Phylloscopus trochilus across the Baltic coast. PeerJ 10:e12964 https://doi.org/10.7717/peerj.12964
date submitted: 2021-03-12
date accepted: 2022-01-28
issued: 2022-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Remisiewicz
  given name: Magdalena
author list: Agent
  family name: Underhill
  given name: Les G.
doi: 10.7717/peerj.12964
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-18
copyright: © 2022 Remisiewicz and Underhill
attribution name: Remisiewicz and Underhill

Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [Setaria italica (L.) P. Beauv.] varieties with different panicle types
type: item
type: AcademicArticle
description: Grain filling affects grain weight and quality and is among the most critical factors in determining the yield and quality of cereal crops. Though hybrids have larger panicles and numerous spikelets with a larger sink capacity than conventional varieties, data on the grain filling commonalities and differences between foxtail millet varieties with different panicle types remain sparse. In this study, we found that “Zhang Gu 13” (ZG, large panicle) exhibits a significantly higher panicle weight than “Yu Gu 18” (YG, conventional panicle) at the early stage of grain filling, but the weight of YG increased rapidly and gradually overtook ZG during the middle stages. A temporal expression pattern analysis demonstrated that the genes involved in photosynthesis, metabolic pathways, and phenylpropanoid biosynthesis were downregulated, while those related to peroxisome function, purine metabolism, and zeatin biosynthesis were upregulated during grain filling in both varieties. A total of 6,832 differentially expressed genes (DEGs) were identified in both varieties, with the majority identified at the early and late stages. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further revealed that the upregulated DEGs in YG were associated with gibberellin (GA) biosynthesis, ATP-binding cassette (ABC) transporters, and plant hormone signal transduction. Photosynthesis-related DEGs, such as photosystem and antenna proteins, were significantly upregulated in ZG. This study provides preliminary insights into the differences in gene expression and molecular mechanisms of grain filling between ZG and YG in the North China summer-sowing region.
format: application/pdf
format: text/html
creator: Hui Song
creator: Tao Wang
creator: Long Li
creator: Lu Xing
creator: Hui fang Xie
creator: Bai li Feng
creator: Jin rong Liu
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12968
publisher: PeerJ Inc.
rights: © 2022 Song et al.
abstract: Grain filling affects grain weight and quality and is among the most critical factors in determining the yield and quality of cereal crops. Though hybrids have larger panicles and numerous spikelets with a larger sink capacity than conventional varieties, data on the grain filling commonalities and differences between foxtail millet varieties with different panicle types remain sparse. In this study, we found that “Zhang Gu 13” (ZG, large panicle) exhibits a significantly higher panicle weight than “Yu Gu 18” (YG, conventional panicle) at the early stage of grain filling, but the weight of YG increased rapidly and gradually overtook ZG during the middle stages. A temporal expression pattern analysis demonstrated that the genes involved in photosynthesis, metabolic pathways, and phenylpropanoid biosynthesis were downregulated, while those related to peroxisome function, purine metabolism, and zeatin biosynthesis were upregulated during grain filling in both varieties. A total of 6,832 differentially expressed genes (DEGs) were identified in both varieties, with the majority identified at the early and late stages. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis further revealed that the upregulated DEGs in YG were associated with gibberellin (GA) biosynthesis, ATP-binding cassette (ABC) transporters, and plant hormone signal transduction. Photosynthesis-related DEGs, such as photosystem and antenna proteins, were significantly upregulated in ZG. This study provides preliminary insights into the differences in gene expression and molecular mechanisms of grain filling between ZG and YG in the North China summer-sowing region.
bibliographic citation: Song et al. (2022) Comparative transcriptome analysis provides insights into grain filling commonalities and differences between foxtail millet [Setaria italica (L.) P. Beauv.] varieties with different panicle types. PeerJ 10:e12968 https://doi.org/10.7717/peerj.12968
date submitted: 2021-05-24
date accepted: 2022-01-28
issued: 2022-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Hui
author list: Agent
  family name: Wang
  given name: Tao
author list: Agent
  family name: Li
  given name: Long
author list: Agent
  family name: Xing
  given name: Lu
author list: Agent
  family name: Xie
  given name: Hui fang
author list: Agent
  family name: Feng
  given name: Bai li
author list: Agent
  family name: Liu
  given name: Jin rong
doi: 10.7717/peerj.12968
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-18
copyright: © 2022 Song et al.
attribution name: Song et al.

A neuronal theta band signature of error monitoring during integration of facial expression cues
type: item
type: AcademicArticle
description: Error monitoring is the metacognitive process by which we are able to detect and signal our errors once a response has been made. Monitoring when the outcome of our actions deviates from the intended goal is crucial for behavior, learning, and the development of higher-order social skills. Here, we explored the neuronal substrates of error monitoring during the integration of facial expression cues using electroencephalography (EEG). Our goal was to investigate the signatures of error monitoring before and after a response execution dependent on the integration of facial cues. We followed the hypothesis of midfrontal theta as a robust neuronal marker of error monitoring since it has been consistently described as a mechanism to signal the need for cognitive control. Also, we hypothesized that EEG frequency-domain components might bring advantage to study error monitoring in complex scenarios as it carries information from locked and non-phase-locked signals. A challenging go/no-go saccadic paradigm was applied to elicit errors: integration of facial emotional signals and gaze direction was required to solve it. EEG data were acquired from twenty healthy participants and analyzed at the level of theta band activity during response preparation and execution. Although theta modulation has been consistently demonstrated during error monitoring, it is still unclear how early it starts to occur. We found theta power differences at midfrontal channels between correct and error trials. Theta was higher immediately after erroneous responses. Moreover, before response initiation we observed the opposite: lower theta preceding errors. These results suggest theta band activity not only as an index of error monitoring, which is needed to enhance cognitive control, but also as a requisite for success. This study adds to previous evidence for the role of theta band in error monitoring processes by revealing error-related patterns even before response execution in complex tasks, an…
format: application/pdf
format: text/html
creator: Camila Dias
creator: Diana Costa
creator: Teresa Sousa
creator: João Castelhano
creator: Verónica Figueiredo
creator: Andreia C. Pereira
creator: Miguel Castelo-Branco
subject: Neuroscience
subject: Psychiatry and Psychology
subject: Translational Medicine
description: doi:10.7717/peerj.12627
publisher: PeerJ Inc.
rights: © 2022 Dias et al.
abstract: Error monitoring is the metacognitive process by which we are able to detect and signal our errors once a response has been made. Monitoring when the outcome of our actions deviates from the intended goal is crucial for behavior, learning, and the development of higher-order social skills. Here, we explored the neuronal substrates of error monitoring during the integration of facial expression cues using electroencephalography (EEG). Our goal was to investigate the signatures of error monitoring before and after a response execution dependent on the integration of facial cues. We followed the hypothesis of midfrontal theta as a robust neuronal marker of error monitoring since it has been consistently described as a mechanism to signal the need for cognitive control. Also, we hypothesized that EEG frequency-domain components might bring advantage to study error monitoring in complex scenarios as it carries information from locked and non-phase-locked signals. A challenging go/no-go saccadic paradigm was applied to elicit errors: integration of facial emotional signals and gaze direction was required to solve it. EEG data were acquired from twenty healthy participants and analyzed at the level of theta band activity during response preparation and execution. Although theta modulation has been consistently demonstrated during error monitoring, it is still unclear how early it starts to occur. We found theta power differences at midfrontal channels between correct and error trials. Theta was higher immediately after erroneous responses. Moreover, before response initiation we observed the opposite: lower theta preceding errors. These results suggest theta band activity not only as an index of error monitoring, which is needed to enhance cognitive control, but also as a requisite for success. This study adds to previous evidence for the role of theta band in error monitoring processes by revealing error-related patterns even before response execution in complex tasks, an…
bibliographic citation: Dias et al. (2022) A neuronal theta band signature of error monitoring during integration of facial expression cues. PeerJ 10:e12627 https://doi.org/10.7717/peerj.12627
date submitted: 2021-07-19
date accepted: 2021-11-21
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dias
  given name: Camila
author list: Agent
  family name: Costa
  given name: Diana
author list: Agent
  family name: Sousa
  given name: Teresa
author list: Agent
  family name: Castelhano
  given name: João
author list: Agent
  family name: Figueiredo
  given name: Verónica
author list: Agent
  family name: Pereira
  given name: Andreia C.
author list: Agent
  family name: Castelo-Branco
  given name: Miguel
doi: 10.7717/peerj.12627
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: ©2022 Dias et al.
attribution name: Dias et al.

Deciphering the Heteropterys pannosa species complex (Malpighiaceae)
type: item
type: AcademicArticle
description: We describe three new species of Malpighiaceae that are endemic to central Brazil and related to the Heteropterys pannosa complex, a group of xylopodiferous, unbranched subshrubs with fruit in mericarps that have a strongly reduced or no dorsal wing. Heteropterys tocantinensis is more common in eastern Tocantins State and on the border with Bahia State, and there are a few records from Mato Grosso State. Heteropterys veadeirensis is restricted to northern Goiás State and H. walteri has a wider distribution, occurring in some municipalities in northern Goiás and southern Tocantins. Additionally, we also provide detailed redescriptions of H. pannosa and H. rosmarinifolia, the two previously known species in this complex. All species are considered Endangered (EN) based on IUCN criteria, especially due to the low area of occupancy. Illustrations, distribution maps, and information about phenology and habitat are also provided for all taxa.
format: application/pdf
format: text/html
creator: André M. Amorim
creator: Lucas C. Marinho
creator: Augusto Francener
subject: Biodiversity
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.12937
publisher: PeerJ Inc.
rights: © 2022 Amorim et al.
abstract: We describe three new species of Malpighiaceae that are endemic to central Brazil and related to the Heteropterys pannosa complex, a group of xylopodiferous, unbranched subshrubs with fruit in mericarps that have a strongly reduced or no dorsal wing. Heteropterys tocantinensis is more common in eastern Tocantins State and on the border with Bahia State, and there are a few records from Mato Grosso State. Heteropterys veadeirensis is restricted to northern Goiás State and H. walteri has a wider distribution, occurring in some municipalities in northern Goiás and southern Tocantins. Additionally, we also provide detailed redescriptions of H. pannosa and H. rosmarinifolia, the two previously known species in this complex. All species are considered Endangered (EN) based on IUCN criteria, especially due to the low area of occupancy. Illustrations, distribution maps, and information about phenology and habitat are also provided for all taxa.
bibliographic citation: Amorim et al. (2022) Deciphering the Heteropterys pannosa species complex (Malpighiaceae). PeerJ 10:e12937 https://doi.org/10.7717/peerj.12937
date submitted: 2021-10-21
date accepted: 2022-01-24
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amorim
  given name: André M.
author list: Agent
  family name: Marinho
  given name: Lucas C.
author list: Agent
  family name: Francener
  given name: Augusto
doi: 10.7717/peerj.12937
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: © 2022 Amorim et al.
attribution name: Amorim et al.

Characterizing the suckling behavior by video and 3D-accelerometry in humpback whale calves on a breeding ground
type: item
type: AcademicArticle
description: Getting maternal milk through nursing is vital for all newborn mammals. Despite its importance, nursing has been poorly documented in humpback whales (Megaptera novaeangliae). Nursing is difficult to observe underwater without disturbing the whales and is usually impossible to observe from a ship. We attempted to observe nursing from the calf’s perspective by placing CATS cam tags on three humpback whale calves in the Sainte Marie channel, Madagascar, Indian Ocean, during the breeding seasons. CATS cam tags are animal-borne multi-sensor tags equipped with a video camera, a hydrophone, and several auxiliary sensors (including a 3-axis accelerometer, a 3-axis magnetometer, and a depth sensor). The use of multi-sensor tags minimized potential disturbance from human presence. A total of 10.52 h of video recordings were collected with the corresponding auxiliary data. Video recordings were manually analyzed and correlated with the auxiliary data, allowing us to extract different kinematic features including the depth rate, speed, Fluke Stroke Rate (FSR), Overall Body Dynamic Acceleration (ODBA), pitch, roll, and roll rate. We found that suckling events lasted 18.8 ± 8.8 s on average (N = 34) and were performed mostly during dives. Suckling events represented 1.7% of the total observation time. During suckling, the calves were visually estimated to be at a 30–45° pitch angle relative to the midline of their mother’s body and were always observed rolling either to the right or to the left. In our auxiliary dataset, we confirmed that suckling behavior was primarily characterized by a high average absolute roll and additionally we also found that it was likely characterized by a high average FSR and a low average speed. Kinematic features were used for supervised machine learning in order to subsequently detect suckling behavior automatically. Our study is a proof of method on which future investigations can build upon. It opens new opportunities for further investigation of…
format: application/pdf
format: text/html
creator: Maevatiana N. Ratsimbazafindranahaka
creator: Chloé Huetz
creator: Aristide Andrianarimisa
creator: Joy S. Reidenberg
creator: Anjara Saloma
creator: Olivier Adam
creator: Isabelle Charrier
subject: Animal Behavior
subject: Marine Biology
subject: Zoology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.12945
publisher: PeerJ Inc.
rights: © 2022 Ratsimbazafindranahaka et al.
abstract: Getting maternal milk through nursing is vital for all newborn mammals. Despite its importance, nursing has been poorly documented in humpback whales (Megaptera novaeangliae). Nursing is difficult to observe underwater without disturbing the whales and is usually impossible to observe from a ship. We attempted to observe nursing from the calf’s perspective by placing CATS cam tags on three humpback whale calves in the Sainte Marie channel, Madagascar, Indian Ocean, during the breeding seasons. CATS cam tags are animal-borne multi-sensor tags equipped with a video camera, a hydrophone, and several auxiliary sensors (including a 3-axis accelerometer, a 3-axis magnetometer, and a depth sensor). The use of multi-sensor tags minimized potential disturbance from human presence. A total of 10.52 h of video recordings were collected with the corresponding auxiliary data. Video recordings were manually analyzed and correlated with the auxiliary data, allowing us to extract different kinematic features including the depth rate, speed, Fluke Stroke Rate (FSR), Overall Body Dynamic Acceleration (ODBA), pitch, roll, and roll rate. We found that suckling events lasted 18.8 ± 8.8 s on average (N = 34) and were performed mostly during dives. Suckling events represented 1.7% of the total observation time. During suckling, the calves were visually estimated to be at a 30–45° pitch angle relative to the midline of their mother’s body and were always observed rolling either to the right or to the left. In our auxiliary dataset, we confirmed that suckling behavior was primarily characterized by a high average absolute roll and additionally we also found that it was likely characterized by a high average FSR and a low average speed. Kinematic features were used for supervised machine learning in order to subsequently detect suckling behavior automatically. Our study is a proof of method on which future investigations can build upon. It opens new opportunities for further investigation of…
bibliographic citation: Ratsimbazafindranahaka et al. (2022) Characterizing the suckling behavior by video and 3D-accelerometry in humpback whale calves on a breeding ground. PeerJ 10:e12945 https://doi.org/10.7717/peerj.12945
date submitted: 2021-10-08
date accepted: 2022-01-25
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ratsimbazafindranahaka
  given name: Maevatiana N.
author list: Agent
  family name: Huetz
  given name: Chloé
author list: Agent
  family name: Andrianarimisa
  given name: Aristide
author list: Agent
  family name: Reidenberg
  given name: Joy S.
author list: Agent
  family name: Saloma
  given name: Anjara
author list: Agent
  family name: Adam
  given name: Olivier
author list: Agent
  family name: Charrier
  given name: Isabelle
doi: 10.7717/peerj.12945
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: ©2022 Ratsimbazafindranahaka et al.
attribution name: Ratsimbazafindranahaka et al.

Sarcopenia is not associated with inspiratory muscle strength but with expiratory muscle strength among older adults requiring long-term care/support
type: item
type: AcademicArticle
description: Background Recently, the concept of respiratory sarcopenia has been advocated, but evidence is lacking regarding which respiratory parameters are appropriate indicators. Therefore, we investigated the association between sarcopenia, respiratory function, and respiratory muscle strength to identify the most appropriate parameters for respiratory sarcopenia. Methods We included 124 older adults (67 men, 57 women; average age 77.2 ± 8.3 years) requiring long-term care/support who underwent Day Care for rehabilitation. Handgrip strength, usual gait speed, and skeletal muscle mass were measured using bioelectrical impedance analysis. Participants were then diagnosed with sarcopenia using the algorithm of the Asian Working Group for Sarcopenia 2019. Parameters of respiratory function (forced vital capacity, forced expiratory volume in one second [FEV1.0], FEV1.0%, and peak expiratory flow rate) and respiratory muscle strength (maximal expiratory pressure [MEP] and maximal inspiratory pressure) were also measured according to American Thoracic Society guidelines. Respiratory parameters significantly related to sarcopenia were identified using binomial logistic regression and receiver operating characteristic analyses. Results Seventy-seven participants were classified as having sarcopenia. Binomial logistic regression analysis showed that MEP was the only respiratory parameter significantly associated with sarcopenia. The cut-off MEP value for predicting sarcopenia was 47.0 cmH20 for men and 40.9 cmH20 for women. Conclusions The most appropriate parameter for assessing respiratory sarcopenia may be MEP, which is an indicator of expiratory muscle strength, rather than FVC, MIP, or PEFR, as suggested in previous studies. Measuring MEP is simpler than measuring respiratory function parameters. Moreover, it is expected to have clinical applications such as respiratory sarcopenia screening.
format: application/pdf
format: text/html
creator: Yohei Sawaya
creator: Takahiro Shiba
creator: Masahiro Ishizaka
creator: Tamaki Hirose
creator: Ryo Sato
creator: Akira Kubo
creator: Tomohiko Urano
subject: Geriatrics
subject: Nursing
subject: Nutrition
subject: Rehabilitation
description: doi:10.7717/peerj.12958
publisher: PeerJ Inc.
rights: © 2022 Sawaya et al.
abstract: Background Recently, the concept of respiratory sarcopenia has been advocated, but evidence is lacking regarding which respiratory parameters are appropriate indicators. Therefore, we investigated the association between sarcopenia, respiratory function, and respiratory muscle strength to identify the most appropriate parameters for respiratory sarcopenia. Methods We included 124 older adults (67 men, 57 women; average age 77.2 ± 8.3 years) requiring long-term care/support who underwent Day Care for rehabilitation. Handgrip strength, usual gait speed, and skeletal muscle mass were measured using bioelectrical impedance analysis. Participants were then diagnosed with sarcopenia using the algorithm of the Asian Working Group for Sarcopenia 2019. Parameters of respiratory function (forced vital capacity, forced expiratory volume in one second [FEV1.0], FEV1.0%, and peak expiratory flow rate) and respiratory muscle strength (maximal expiratory pressure [MEP] and maximal inspiratory pressure) were also measured according to American Thoracic Society guidelines. Respiratory parameters significantly related to sarcopenia were identified using binomial logistic regression and receiver operating characteristic analyses. Results Seventy-seven participants were classified as having sarcopenia. Binomial logistic regression analysis showed that MEP was the only respiratory parameter significantly associated with sarcopenia. The cut-off MEP value for predicting sarcopenia was 47.0 cmH20 for men and 40.9 cmH20 for women. Conclusions The most appropriate parameter for assessing respiratory sarcopenia may be MEP, which is an indicator of expiratory muscle strength, rather than FVC, MIP, or PEFR, as suggested in previous studies. Measuring MEP is simpler than measuring respiratory function parameters. Moreover, it is expected to have clinical applications such as respiratory sarcopenia screening.
bibliographic citation: Sawaya et al. (2022) Sarcopenia is not associated with inspiratory muscle strength but with expiratory muscle strength among older adults requiring long-term care/support. PeerJ 10:e12958 https://doi.org/10.7717/peerj.12958
date submitted: 2021-09-27
date accepted: 2022-01-27
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sawaya
  given name: Yohei
author list: Agent
  family name: Shiba
  given name: Takahiro
author list: Agent
  family name: Ishizaka
  given name: Masahiro
author list: Agent
  family name: Hirose
  given name: Tamaki
author list: Agent
  family name: Sato
  given name: Ryo
author list: Agent
  family name: Kubo
  given name: Akira
author list: Agent
  family name: Urano
  given name: Tomohiko
doi: 10.7717/peerj.12958
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: © 2022 Sawaya et al.
attribution name: Sawaya et al.

Prevalence of iron deficiency anemia in Brazilian women of childbearing age: a systematic review with meta-analysis
type: item
type: AcademicArticle
description: Background Iron deficiency anemia (IDA) is among the most common micronutrient deficiencies in women of childbearing age and may affect children’s development. Brazil has several national programs to tackle this condition, such as food fortification and supplementation for pregnant women, but IDA prevalence in this population has not been systematically reviewed. We sought to determine the prevalence of IDA in Brazilian women of childbearing age through a systematic review with metanalysis. Methodology A protocol was previously published on the PROSPERO platform under the code CRD42020200960. A panel of the National Council for Scientific and Technological Development (CNPq) approved the protocol of this study under the public call number 26/2019. The main databases searched were MEDLINE, Web of Science, Scopus, Lilacs, and SciELO. In gray literature, the Brazilian Digital Library of Theses and Dissertations and the annals of the Brazilian Congress of Epidemiology and the Brazilian Congress of Public Health were accessed. The search strategy involved terms related to the condition (IDA) and the age group of the population of interest (teenagers and adults). Studies that had assessed the prevalence of IDA in Brazilian women of childbearing age (10–49 years) were included. Three independent reviewers read all titles and abstracts and extracted data from the included studies. Random effects meta-analyses using the Freeman-Tukey arcsine transformation were carried out with prevalence data, and meta-regression was conducted to test for subgroup differences. The quality of the studies was assessed using the Newcastle-Ottawa Scale. Results From 21,210 unique records screened, 237 full-texts were retrieved, of which 91 were included in the qualitative synthesis, and 83 were included in the meta-analysis. The overall IDA prevalence was 25% (95% CI [23–28], 83 studies). The subgroup of studies that used random sampling showed a prevalence of 22% (95% CI [17–27], 22 studies), …
format: application/pdf
format: text/html
creator: Mateus Macena
creator: Dafiny Praxedes
creator: Ana Debora De Oliveira
creator: Déborah Paula
creator: Maykon Barros
creator: André Silva Júnior
creator: Witiane Araújo
creator: Isabele Pureza
creator: Ingrid Sofia de Melo
creator: Nassib Bueno
subject: Global Health
subject: Nutrition
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.12959
publisher: PeerJ Inc.
rights: © 2022 Macena et al.
abstract: Background Iron deficiency anemia (IDA) is among the most common micronutrient deficiencies in women of childbearing age and may affect children’s development. Brazil has several national programs to tackle this condition, such as food fortification and supplementation for pregnant women, but IDA prevalence in this population has not been systematically reviewed. We sought to determine the prevalence of IDA in Brazilian women of childbearing age through a systematic review with metanalysis. Methodology A protocol was previously published on the PROSPERO platform under the code CRD42020200960. A panel of the National Council for Scientific and Technological Development (CNPq) approved the protocol of this study under the public call number 26/2019. The main databases searched were MEDLINE, Web of Science, Scopus, Lilacs, and SciELO. In gray literature, the Brazilian Digital Library of Theses and Dissertations and the annals of the Brazilian Congress of Epidemiology and the Brazilian Congress of Public Health were accessed. The search strategy involved terms related to the condition (IDA) and the age group of the population of interest (teenagers and adults). Studies that had assessed the prevalence of IDA in Brazilian women of childbearing age (10–49 years) were included. Three independent reviewers read all titles and abstracts and extracted data from the included studies. Random effects meta-analyses using the Freeman-Tukey arcsine transformation were carried out with prevalence data, and meta-regression was conducted to test for subgroup differences. The quality of the studies was assessed using the Newcastle-Ottawa Scale. Results From 21,210 unique records screened, 237 full-texts were retrieved, of which 91 were included in the qualitative synthesis, and 83 were included in the meta-analysis. The overall IDA prevalence was 25% (95% CI [23–28], 83 studies). The subgroup of studies that used random sampling showed a prevalence of 22% (95% CI [17–27], 22 studies), …
bibliographic citation: Macena et al. (2022) Prevalence of iron deficiency anemia in Brazilian women of childbearing age: a systematic review with meta-analysis. PeerJ 10:e12959 https://doi.org/10.7717/peerj.12959
date submitted: 2021-10-29
date accepted: 2022-01-27
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Macena
  given name: Mateus
author list: Agent
  family name: Praxedes
  given name: Dafiny
author list: Agent
  family name: De Oliveira
  given name: Ana Debora
author list: Agent
  family name: Paula
  given name: Déborah
author list: Agent
  family name: Barros
  given name: Maykon
author list: Agent
  family name: Silva Júnior
  given name: André
author list: Agent
  family name: Araújo
  given name: Witiane
author list: Agent
  family name: Pureza
  given name: Isabele
author list: Agent
  family name: de Melo
  given name: Ingrid Sofia
author list: Agent
  family name: Bueno
  given name: Nassib
doi: 10.7717/peerj.12959
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: © 2022 Macena et al.
attribution name: Macena et al.

PCAtest: testing the statistical significance of Principal Component Analysis in R
type: item
type: AcademicArticle
description: Principal Component Analysis (PCA) is one of the most broadly used statistical methods for the ordination and dimensionality-reduction of multivariate datasets across many scientific disciplines. Trivial PCs can be estimated from data sets without any correlational structure among the original variables, and traditional criteria for selecting non-trivial PC axes are difficult to implement, partially subjective or based on ad hoc thresholds. PCAtest is an R package that implements permutation-based statistical tests to evaluate the overall significance of a PCA, the significance of each PC axis, and of contributions of each observed variable to the significant axes. Based on simulation and empirical results, I encourage R users to routinely apply PCAtest to test the significance of their PCA before proceeding with the direct interpretation of PC axes and/or the utilization of PC scores in subsequent evolutionary and ecological analyses.
format: application/pdf
format: text/html
creator: Arley Camargo
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.12967
publisher: PeerJ Inc.
rights: © 2022 Camargo
abstract: Principal Component Analysis (PCA) is one of the most broadly used statistical methods for the ordination and dimensionality-reduction of multivariate datasets across many scientific disciplines. Trivial PCs can be estimated from data sets without any correlational structure among the original variables, and traditional criteria for selecting non-trivial PC axes are difficult to implement, partially subjective or based on ad hoc thresholds. PCAtest is an R package that implements permutation-based statistical tests to evaluate the overall significance of a PCA, the significance of each PC axis, and of contributions of each observed variable to the significant axes. Based on simulation and empirical results, I encourage R users to routinely apply PCAtest to test the significance of their PCA before proceeding with the direct interpretation of PC axes and/or the utilization of PC scores in subsequent evolutionary and ecological analyses.
bibliographic citation: Camargo (2022) PCAtest: testing the statistical significance of Principal Component Analysis in R. PeerJ 10:e12967 https://doi.org/10.7717/peerj.12967
date submitted: 2021-08-19
date accepted: 2022-01-28
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Camargo
  given name: Arley
doi: 10.7717/peerj.12967
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: © 2022 Camargo
attribution name: Camargo

Molecular characterization and expression profiling of transformer 2 and fruitless-like homologs in the black tiger shrimp, Penaeus monodon
type: item
type: AcademicArticle
description: Transformer 2 (tra 2) and fruitless (fru) genes have been proven to play a key role in sex determination pathways in many Arthropods, including insects and crustaceans. In this study, a paralog of P. monodon tra 2 (Pmtra 2), P. monodon ovarian associated transformer 2 (PmOvtra 2) and 2 isoforms of P. monodon fruitless-like gene (Pmfru-1 and Pmfru-2) were identified and characterized. The full cDNA sequence of PmOvtra 2 consisted of 1,774 bp with the longest open reading frame (ORF) of 744 bp encoding for 247 amino acids. The PmOvtra 2 exhibited a predicted RNA-recognition motif (RRM) domain and two arginine-serine (RS) regions, suggesting its function in RNA splicing. The full cDNA sequence of Pmfru-1 consisted of 1,306 bp with 1,182 bp ORF encoding for 393 amino acids, whereas the full cDNA sequence of Pmfru-2 consisted of 1,858 bp with 1,437 bp ORF encoding 478 amino acids. The deduced amino acid sequences of Pmfru-1 and Pmfru-2 exhibited highly conserved domains of Fru proteins, including Broad-complex, Tramtrack and Bric-a-brac (BTB), and zinc finger (ZF) domains. In addition, Pmfru-1 and Pmfru-2 were suggestively originated from the same single genomic locus by genomic sequence analysis. Specifically, Pmfru pre-mRNA was alternatively spliced for Pmfru-1 and Pmfru-2 to include mutually exclusive exon 7 and exon 6, respectively. Temporal and spatial expression of PmOvtra 2, Pmfru-1, and Pmfru-2 were also investigated by qPCR. The results showed that all were expressed in early developmental stages with undifferentiated gonads starting from nauplius until postlarvae. The expression of PmOvtra 2 started at nauplius stage and gradually increased from mysis to postlarvae (PL) 1. However, the expression of Pmfru-1 was low at the nauplii stage and slightly increased from protozoea to PL5, whereas the expression of Pmfru-2 maintained a low level from nauplius to mysis and then gradually increased at the PL stages. Expressions of PmOvtra 2, Pmfru-1, and Pmfru-2 were dete…
format: application/pdf
format: text/html
creator: Prawporn Thaijongrak
creator: Charoonroj Chotwiwatthanakun
creator: Phaivit Laphyai
creator: Anuphap Prachumwat
creator: Thanapong Kruangkum
creator: Prasert Sobhon
creator: Rapeepun Vanichviriyakit
subject: Aquaculture, Fisheries and Fish Science
subject: Bioinformatics
subject: Developmental Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12980
publisher: PeerJ Inc.
rights: © 2022 Thaijongrak et al.
abstract: Transformer 2 (tra 2) and fruitless (fru) genes have been proven to play a key role in sex determination pathways in many Arthropods, including insects and crustaceans. In this study, a paralog of P. monodon tra 2 (Pmtra 2), P. monodon ovarian associated transformer 2 (PmOvtra 2) and 2 isoforms of P. monodon fruitless-like gene (Pmfru-1 and Pmfru-2) were identified and characterized. The full cDNA sequence of PmOvtra 2 consisted of 1,774 bp with the longest open reading frame (ORF) of 744 bp encoding for 247 amino acids. The PmOvtra 2 exhibited a predicted RNA-recognition motif (RRM) domain and two arginine-serine (RS) regions, suggesting its function in RNA splicing. The full cDNA sequence of Pmfru-1 consisted of 1,306 bp with 1,182 bp ORF encoding for 393 amino acids, whereas the full cDNA sequence of Pmfru-2 consisted of 1,858 bp with 1,437 bp ORF encoding 478 amino acids. The deduced amino acid sequences of Pmfru-1 and Pmfru-2 exhibited highly conserved domains of Fru proteins, including Broad-complex, Tramtrack and Bric-a-brac (BTB), and zinc finger (ZF) domains. In addition, Pmfru-1 and Pmfru-2 were suggestively originated from the same single genomic locus by genomic sequence analysis. Specifically, Pmfru pre-mRNA was alternatively spliced for Pmfru-1 and Pmfru-2 to include mutually exclusive exon 7 and exon 6, respectively. Temporal and spatial expression of PmOvtra 2, Pmfru-1, and Pmfru-2 were also investigated by qPCR. The results showed that all were expressed in early developmental stages with undifferentiated gonads starting from nauplius until postlarvae. The expression of PmOvtra 2 started at nauplius stage and gradually increased from mysis to postlarvae (PL) 1. However, the expression of Pmfru-1 was low at the nauplii stage and slightly increased from protozoea to PL5, whereas the expression of Pmfru-2 maintained a low level from nauplius to mysis and then gradually increased at the PL stages. Expressions of PmOvtra 2, Pmfru-1, and Pmfru-2 were dete…
bibliographic citation: Thaijongrak et al. (2022) Molecular characterization and expression profiling of transformer 2 and fruitless-like homologs in the black tiger shrimp, Penaeus monodon. PeerJ 10:e12980 https://doi.org/10.7717/peerj.12980
date submitted: 2021-05-11
date accepted: 2022-01-31
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thaijongrak
  given name: Prawporn
author list: Agent
  family name: Chotwiwatthanakun
  given name: Charoonroj
author list: Agent
  family name: Laphyai
  given name: Phaivit
author list: Agent
  family name: Prachumwat
  given name: Anuphap
author list: Agent
  family name: Kruangkum
  given name: Thanapong
author list: Agent
  family name: Sobhon
  given name: Prasert
author list: Agent
  family name: Vanichviriyakit
  given name: Rapeepun
doi: 10.7717/peerj.12980
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: ©2022 Thaijongrak et al.
attribution name: Thaijongrak et al.

The relationships between toad behaviour, antipredator defences, and spatial and sexual variation in predation pressure
type: item
type: AcademicArticle
description: Background Animal behaviour is under strong selection. Selection on behaviour, however, might not act in isolation from other fitness-related traits. Since predators represent outstanding selective forces, animal behaviour could covary with antipredator defences, such that individuals better suited against predators could afford facing the costs of riskier behaviours. Moreover, not all individuals undergo equivalent degrees of predation pressure, which can vary across sexes or habitats. Individuals under lower predation pressure might also exhibit riskier behaviours. Methods In this work, I tested these hypotheses on natterjack toads (Epidalea calamita). Specifically, I gauged activity time, exploratory behaviour and boldness in standard laboratory conditions, and assessed whether they correlated with body size and antipredator strategies, namely sprint speed, parotoid gland area and parotoid gland colour contrast. Additionally, I compared these traits between sexes and individuals from an agrosystem and pine grove, since there is evidence that males and agrosystem individuals are subjected to greater predation pressure. Results Sprint speed as well as parotoid gland contrast and size appeared unrelated to the behavioural traits studied. In turn, body mass was negatively related to activity time, boldness and exploration. This trend is consistent with the fact that larger toads could be more detectable to their predators, which are mostly gape unconstrained and could easily consume them. As predicted, females exhibited riskier behaviours. Nonetheless, agrosystem toads did not differ from pine grove toads in the behavioural traits measured, despite being under stronger predation pressure.
format: application/pdf
format: text/html
creator: Francisco Javier Zamora-Camacho
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.12985
publisher: PeerJ Inc.
rights: © 2022 Zamora-Camacho
abstract: Background Animal behaviour is under strong selection. Selection on behaviour, however, might not act in isolation from other fitness-related traits. Since predators represent outstanding selective forces, animal behaviour could covary with antipredator defences, such that individuals better suited against predators could afford facing the costs of riskier behaviours. Moreover, not all individuals undergo equivalent degrees of predation pressure, which can vary across sexes or habitats. Individuals under lower predation pressure might also exhibit riskier behaviours. Methods In this work, I tested these hypotheses on natterjack toads (Epidalea calamita). Specifically, I gauged activity time, exploratory behaviour and boldness in standard laboratory conditions, and assessed whether they correlated with body size and antipredator strategies, namely sprint speed, parotoid gland area and parotoid gland colour contrast. Additionally, I compared these traits between sexes and individuals from an agrosystem and pine grove, since there is evidence that males and agrosystem individuals are subjected to greater predation pressure. Results Sprint speed as well as parotoid gland contrast and size appeared unrelated to the behavioural traits studied. In turn, body mass was negatively related to activity time, boldness and exploration. This trend is consistent with the fact that larger toads could be more detectable to their predators, which are mostly gape unconstrained and could easily consume them. As predicted, females exhibited riskier behaviours. Nonetheless, agrosystem toads did not differ from pine grove toads in the behavioural traits measured, despite being under stronger predation pressure.
bibliographic citation: Zamora-Camacho (2022) The relationships between toad behaviour, antipredator defences, and spatial and sexual variation in predation pressure. PeerJ 10:e12985 https://doi.org/10.7717/peerj.12985
date submitted: 2021-12-23
date accepted: 2022-02-01
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zamora-Camacho
  given name: Francisco Javier
doi: 10.7717/peerj.12985
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: © 2022 Zamora-Camacho
attribution name: Zamora-Camacho

Measurement of dispersion of PM 2.5 in Thailand using confidence intervals for the coefficient of variation of an inverse Gaussian distribution
type: item
type: AcademicArticle
description: Air pollution is a growing concern for the general public in Thailand with PM 2.5 (particulate matter ≤ 2.5 µm) having the greatest impact on health. The inverse Gaussian (IG) distribution is used for examining the frequency of high concentration events and has often been applied to analyze pollution data, with the coefficient of variation (CV) being used to calculate the quantitative difference in PM 2.5 concentrations. Herein, we propose confidence intervals for the CV of an IG distribution based on the generalized confidence interval (GCI), the adjusted generalized confidence interval (AGCI), the bootstrap percentile confidence interval (BPCI), the fiducial confidence interval (FCI), and the fiducial highest posterior density confidence interval (F-HPDCI). The performance of the proposed confidence intervals was evaluated by using their coverage probabilities and average lengths from various scenarios via Monte Carlo simulations. The simulation results indicate that the coverage probabilities of the AGCI and FCI methods were higher than or close to the nominal level in all of test case scenarios. Moreover, FCI outperformed the others for small sample sizes by achieving the shortest average length. The efficacies of the confidence intervals were demonstrated by using PM 2.5 data from the Din Daeng and Bang Khun Thian districts in Bangkok, Thailand.
format: application/pdf
format: text/html
creator: Wasana Chankham
creator: Sa-Aat Niwitpong
creator: Suparat Niwitpong
subject: Statistics
subject: Computational Science
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.12988
publisher: PeerJ Inc.
rights: © 2022 Chankham et al.
abstract: Air pollution is a growing concern for the general public in Thailand with PM 2.5 (particulate matter ≤ 2.5 µm) having the greatest impact on health. The inverse Gaussian (IG) distribution is used for examining the frequency of high concentration events and has often been applied to analyze pollution data, with the coefficient of variation (CV) being used to calculate the quantitative difference in PM 2.5 concentrations. Herein, we propose confidence intervals for the CV of an IG distribution based on the generalized confidence interval (GCI), the adjusted generalized confidence interval (AGCI), the bootstrap percentile confidence interval (BPCI), the fiducial confidence interval (FCI), and the fiducial highest posterior density confidence interval (F-HPDCI). The performance of the proposed confidence intervals was evaluated by using their coverage probabilities and average lengths from various scenarios via Monte Carlo simulations. The simulation results indicate that the coverage probabilities of the AGCI and FCI methods were higher than or close to the nominal level in all of test case scenarios. Moreover, FCI outperformed the others for small sample sizes by achieving the shortest average length. The efficacies of the confidence intervals were demonstrated by using PM 2.5 data from the Din Daeng and Bang Khun Thian districts in Bangkok, Thailand.
bibliographic citation: Chankham et al. (2022) Measurement of dispersion of PM 2.5 in Thailand using confidence intervals for the coefficient of variation of an inverse Gaussian distribution. PeerJ 10:e12988 https://doi.org/10.7717/peerj.12988
date submitted: 2021-10-22
date accepted: 2022-02-01
issued: 2022-02-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chankham
  given name: Wasana
author list: Agent
  family name: Niwitpong
  given name: Sa-Aat
author list: Agent
  family name: Niwitpong
  given name: Suparat
doi: 10.7717/peerj.12988
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-17
copyright: ©2022 Chankham et al.
attribution name: Chankham et al.

Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe
type: item
type: AcademicArticle
description: Background After implementing of the “Grain-for-Green” project, Caragana korshinskii Kom. has been widely planted in China’s arid regions. Although natural restoration grassland and artificial Caragana plantations measures have long been focuses in carbon research, the combined influence of natural restoration grassland and artificial Caragana plantation measures on aggregate stability and the aggregate-associated organic carbon (OC) remains unclear. Method We selected natural grassland (NG) and three different densities of Caragana plantations (high planting density, HG; middle planting density, MD; low planting density, LD) on desert steppe. The soil aggregate distribution and stability index such as fractal dimension (D), mean weight diameter (MWD), geometric mean diameter (GMD), percentage of aggregation destruction (PAD), as well as aggregate-associated OC concentration and stock were measured. Results Results shows that the soil aggregates were primarily macroaggregates (>2 mm) and mesoaggregates (0.25–2 mm) under dry sieving while microaggregates (<0.25 mm) were preponderant under wet sieving (more than 57%). Overall, compared with Caragana plantations, the MWD (4.43 and 4.51 mm) and GMD (1.72 and 1.83 mm) were both highest in two soil layers under the NG and the D (2.77 and 2.71) was lowest. Compared with the NG, the aggregate-associated OC stocks in the 0–40 cm depths in the LD, MD, and HD decreased by 41.54%, 46.93%, and 42.03%, respectively. SOC stock was mainly concentrated in the soil aggregate with sizes of >2 mm and <0.25 mm. These results suggested that natural grassland restoration measures could improve the soil aggregate stability and aggregate-associated OC concentration better than Caragana plantation restoration measures, which NG may be optimal for increasing carbon sequestration and stabilizing soil aggregates on desert steppe.
format: application/pdf
format: text/html
creator: Qi Lu
creator: Hongbin Ma
creator: Yao Zhou
creator: Roberto Calvelo-Pereira
creator: Yan Shen
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
subject: Biogeochemistry
description: doi:10.7717/peerj.12507
publisher: PeerJ Inc.
rights: © 2022 Lu et al.
abstract: Background After implementing of the “Grain-for-Green” project, Caragana korshinskii Kom. has been widely planted in China’s arid regions. Although natural restoration grassland and artificial Caragana plantations measures have long been focuses in carbon research, the combined influence of natural restoration grassland and artificial Caragana plantation measures on aggregate stability and the aggregate-associated organic carbon (OC) remains unclear. Method We selected natural grassland (NG) and three different densities of Caragana plantations (high planting density, HG; middle planting density, MD; low planting density, LD) on desert steppe. The soil aggregate distribution and stability index such as fractal dimension (D), mean weight diameter (MWD), geometric mean diameter (GMD), percentage of aggregation destruction (PAD), as well as aggregate-associated OC concentration and stock were measured. Results Results shows that the soil aggregates were primarily macroaggregates (>2 mm) and mesoaggregates (0.25–2 mm) under dry sieving while microaggregates (<0.25 mm) were preponderant under wet sieving (more than 57%). Overall, compared with Caragana plantations, the MWD (4.43 and 4.51 mm) and GMD (1.72 and 1.83 mm) were both highest in two soil layers under the NG and the D (2.77 and 2.71) was lowest. Compared with the NG, the aggregate-associated OC stocks in the 0–40 cm depths in the LD, MD, and HD decreased by 41.54%, 46.93%, and 42.03%, respectively. SOC stock was mainly concentrated in the soil aggregate with sizes of >2 mm and <0.25 mm. These results suggested that natural grassland restoration measures could improve the soil aggregate stability and aggregate-associated OC concentration better than Caragana plantation restoration measures, which NG may be optimal for increasing carbon sequestration and stabilizing soil aggregates on desert steppe.
bibliographic citation: Lu et al. (2022) Caragana korshinskii Kom. plantation reduced soil aggregate stability and aggregate-associated organic carbon on desert steppe. PeerJ 10:e12507 https://doi.org/10.7717/peerj.12507
date submitted: 2021-06-11
date accepted: 2021-10-26
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Qi
author list: Agent
  family name: Ma
  given name: Hongbin
author list: Agent
  family name: Zhou
  given name: Yao
author list: Agent
  family name: Calvelo-Pereira
  given name: Roberto
author list: Agent
  family name: Shen
  given name: Yan
doi: 10.7717/peerj.12507
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Lu et al.
attribution name: Lu et al.

Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets
type: item
type: AcademicArticle
description: Background Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets. Methods Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets. Results Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.
format: application/pdf
format: text/html
creator: Marcus Vinicius Canário Viana
creator: Rodrigo Profeta
creator: Janaína Canário Cerqueira
creator: Alice Rebecca Wattam
creator: Debmalya Barh
creator: Artur Silva
creator: Vasco Azevedo
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.12662
publisher: PeerJ Inc.
rights: © 2022 Canário Viana et al.
abstract: Background Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets. Methods Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets. Results Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.
bibliographic citation: Canário Viana et al. (2022) Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets. PeerJ 10:e12662 https://doi.org/10.7717/peerj.12662
date submitted: 2021-07-22
date accepted: 2021-11-30
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Canário Viana
  given name: Marcus Vinicius
author list: Agent
  family name: Profeta
  given name: Rodrigo
author list: Agent
  family name: Cerqueira
  given name: Janaína Canário
author list: Agent
  family name: Wattam
  given name: Alice Rebecca
author list: Agent
  family name: Barh
  given name: Debmalya
author list: Agent
  family name: Silva
  given name: Artur
author list: Agent
  family name: Azevedo
  given name: Vasco
doi: 10.7717/peerj.12662
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Canário Viana et al.
attribution name: Canário Viana et al.

Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs
type: item
type: AcademicArticle
description: Obesity is a multifactorial nutritional disorder highly prevalent in dogs, observed in developed and developing countries. It is estimated that over 40% of the canine population suffers from obesity, which manifests in an increased risk of chronic osteoarticular, metabolic, and cardiovascular diseases. The intestinal microbiome of obese animals shows increases in the abundance of certain members capable of extracting energy from complex polysaccharides. The objective of this study was to compare the composition and predicted function of the intestinal microbiome of Chilean obese and normal weight adult dogs. Twenty clinically healthy dogs were classified according to their body condition score (BCS) as obese (n = 10) or normal weight (n = 10). DNA was extracted from stool samples, followed by next-generation sequencing of the 16S rRNA V3–V4 region and bioinformatics analysis targeting microbiome composition and function. Significant differences were observed between these groups at the phylum level, with anincrease in Firmicutes and a decrease in Bacteroidetes in obese dogs. Microbiome compositions of these animals correlated with their BCS, and obese dogs showed enrichment in pathways related to transport, chemotaxis, and flagellar assembly. These results highlight the differences in the gut microbiome between normal weight and obese dogs and prompt further research to improve animal health by modulating the gut microbiome.
format: application/pdf
format: text/html
creator: Pamela Thomson
creator: Rodrigo Santibáñez
creator: Camila Rodríguez-Salas
creator: Carla Flores-Yañez
creator: Daniel Garrido
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.12695
publisher: PeerJ Inc.
rights: © 2022 Thomson et al.
abstract: Obesity is a multifactorial nutritional disorder highly prevalent in dogs, observed in developed and developing countries. It is estimated that over 40% of the canine population suffers from obesity, which manifests in an increased risk of chronic osteoarticular, metabolic, and cardiovascular diseases. The intestinal microbiome of obese animals shows increases in the abundance of certain members capable of extracting energy from complex polysaccharides. The objective of this study was to compare the composition and predicted function of the intestinal microbiome of Chilean obese and normal weight adult dogs. Twenty clinically healthy dogs were classified according to their body condition score (BCS) as obese (n = 10) or normal weight (n = 10). DNA was extracted from stool samples, followed by next-generation sequencing of the 16S rRNA V3–V4 region and bioinformatics analysis targeting microbiome composition and function. Significant differences were observed between these groups at the phylum level, with anincrease in Firmicutes and a decrease in Bacteroidetes in obese dogs. Microbiome compositions of these animals correlated with their BCS, and obese dogs showed enrichment in pathways related to transport, chemotaxis, and flagellar assembly. These results highlight the differences in the gut microbiome between normal weight and obese dogs and prompt further research to improve animal health by modulating the gut microbiome.
bibliographic citation: Thomson et al. (2022) Differences in the composition and predicted functions of the intestinal microbiome of obese and normal weight adult dogs. PeerJ 10:e12695 https://doi.org/10.7717/peerj.12695
date submitted: 2021-05-17
date accepted: 2021-12-06
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomson
  given name: Pamela
author list: Agent
  family name: Santibáñez
  given name: Rodrigo
author list: Agent
  family name: Rodríguez-Salas
  given name: Camila
author list: Agent
  family name: Flores-Yañez
  given name: Carla
author list: Agent
  family name: Garrido
  given name: Daniel
doi: 10.7717/peerj.12695
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Thomson et al.
attribution name: Thomson et al.

Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey
type: item
type: AcademicArticle
description: To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine intent in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP 1,000 (USD20) for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 (USD38).
format: application/pdf
format: text/html
creator: Alexandria Caple
creator: Arnie Dimaano
creator: Marc Martin Sagolili
creator: April Anne Uy
creator: Panjee Mariel Aguirre
creator: Dean Lotus Alano
creator: Giselle Sophia Camaya
creator: Brent John Ciriaco
creator: Princess Jerah Mae Clavo
creator: Dominic Cuyugan
creator: Cleinne Florence Geeseler Fermo
creator: Paul Jeremy Lanete
creator: Ardwayne Jurel La Torre
creator: Thomas Loteyro
creator: Raisa Mikaela Lua
creator: Nicole Gayle Manansala
creator: Raphael Willard Mosquito
creator: Alexa Octaviano
creator: Alexandra Erika Orfanel
creator: Gheyanna Merly Pascual
creator: Aubrey Joy Sale
creator: Sophia Lorraine Tendenilla
creator: Maria Sofia Lauren Trinidad
creator: Nicole Jan Trinidad
creator: Daphne Louise Verano
creator: Nicanor Austriaco
subject: Global Health
subject: Immunology
subject: Psychiatry and Psychology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.12887
publisher: PeerJ Inc.
rights: © 2022 Caple et al.
abstract: To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine intent in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP 1,000 (USD20) for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 (USD38).
bibliographic citation: Caple et al. (2022) Interrogating COVID-19 vaccine intent in the Philippines with a nationwide open-access online survey. PeerJ 10:e12887 https://doi.org/10.7717/peerj.12887
date submitted: 2021-09-20
date accepted: 2022-01-14
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Caple
  given name: Alexandria
author list: Agent
  family name: Dimaano
  given name: Arnie
author list: Agent
  family name: Sagolili
  given name: Marc Martin
author list: Agent
  family name: Uy
  given name: April Anne
author list: Agent
  family name: Aguirre
  given name: Panjee Mariel
author list: Agent
  family name: Alano
  given name: Dean Lotus
author list: Agent
  family name: Camaya
  given name: Giselle Sophia
author list: Agent
  family name: Ciriaco
  given name: Brent John
author list: Agent
  family name: Clavo
  given name: Princess Jerah Mae
author list: Agent
  family name: Cuyugan
  given name: Dominic
author list: Agent
  family name: Fermo
  given name: Cleinne Florence Geeseler
author list: Agent
  family name: Lanete
  given name: Paul Jeremy
author list: Agent
  family name: La Torre
  given name: Ardwayne Jurel
author list: Agent
  family name: Loteyro
  given name: Thomas
author list: Agent
  family name: Lua
  given name: Raisa Mikaela
author list: Agent
  family name: Manansala
  given name: Nicole Gayle
author list: Agent
  family name: Mosquito
  given name: Raphael Willard
author list: Agent
  family name: Octaviano
  given name: Alexa
author list: Agent
  family name: Orfanel
  given name: Alexandra Erika
author list: Agent
  family name: Pascual
  given name: Gheyanna Merly
author list: Agent
  family name: Sale
  given name: Aubrey Joy
author list: Agent
  family name: Tendenilla
  given name: Sophia Lorraine
author list: Agent
  family name: Trinidad
  given name: Maria Sofia Lauren
author list: Agent
  family name: Trinidad
  given name: Nicole Jan
author list: Agent
  family name: Verano
  given name: Daphne Louise
author list: Agent
  family name: Austriaco
  given name: Nicanor
doi: 10.7717/peerj.12887
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Caple et al.
attribution name: Caple et al.

Effect of interaction between occupational stress and polymorphisms of MTHFR gene and SELE gene on hypertension
type: item
type: AcademicArticle
description: Background Gene-environment interaction is related to the prevalence of hypertension, but the impact of genetic polymorphisms on hypertension may vary due to different geography and population. Objective To explore the impact of the interaction among occupational stress and MTHFR gene and SELE gene polymorphism on the prevalence of hypertension in Xinjiang oil workers. Methods A case-control study was conducted on 310 oil workers. In an oilfield base in Karamay City, Xinjiang, 155 hypertensive patients aged 18~60 years old with more than one year of service were selected as the case group, and 155 oil workers without hypertension were selected as the control group according to the 1:1 matching principle (matching conditions: the gender and shift were the same. The age is around 2 years old). The Occupational Stress Scale was used to evaluate the degree of occupational stress, PCR technique was used to detect MTHFR and SELE gene polymorphism, Logistic regression analysis was used to analyze the effects of gene and occupational stress on hypertension, and gene-gene and gene-environment interactions were analyzed by generalized multi-factor dimension reduction method. Results The G98T polymorphism of SELE gene (χ2 = 6.776, P = 0.034), the C677T (χ2 = 7.130, P = 0.028) and A1298C (χ2 = 12.036, P = 0.002) loci of MTHFR gene and the degree of occupational stress (χ2 = 11.921, P = 0.003) were significantly different between the case group and the control group. The genotypes GT at the G98T polymorphism of the SELE gene (OR = 2.151, 95% CI [1.227–3.375]), and the dominant model (AC/CC vs AA, OR = 1.925, 95% CI [1.613–3.816]); AC and CC at the A1298C polymorphism of the MTHFR gene (ORAC = 1.917, 95% CI [1.064–3.453]; ORCC = 2.233, 95% CI [1.082–4.609]), the additive model (CC vs AA, OR = 2.497, 95% CI [1.277–4.883]) and the dominant model (AC/CC vs AA, OR = 2.012, 95% CI [1.200–3.373]); at the C677T polymorphism of the MTHFR gene CT and TT (ORCT = 1.913, 95% CI [1.085–3.375]…
format: application/pdf
format: text/html
creator: Fen Yang
creator: Ruiying Qiu
creator: Saimaitikari Abudoubari
creator: Ning Tao
creator: Hengqing An
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.12914
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background Gene-environment interaction is related to the prevalence of hypertension, but the impact of genetic polymorphisms on hypertension may vary due to different geography and population. Objective To explore the impact of the interaction among occupational stress and MTHFR gene and SELE gene polymorphism on the prevalence of hypertension in Xinjiang oil workers. Methods A case-control study was conducted on 310 oil workers. In an oilfield base in Karamay City, Xinjiang, 155 hypertensive patients aged 18~60 years old with more than one year of service were selected as the case group, and 155 oil workers without hypertension were selected as the control group according to the 1:1 matching principle (matching conditions: the gender and shift were the same. The age is around 2 years old). The Occupational Stress Scale was used to evaluate the degree of occupational stress, PCR technique was used to detect MTHFR and SELE gene polymorphism, Logistic regression analysis was used to analyze the effects of gene and occupational stress on hypertension, and gene-gene and gene-environment interactions were analyzed by generalized multi-factor dimension reduction method. Results The G98T polymorphism of SELE gene (χ2 = 6.776, P = 0.034), the C677T (χ2 = 7.130, P = 0.028) and A1298C (χ2 = 12.036, P = 0.002) loci of MTHFR gene and the degree of occupational stress (χ2 = 11.921, P = 0.003) were significantly different between the case group and the control group. The genotypes GT at the G98T polymorphism of the SELE gene (OR = 2.151, 95% CI [1.227–3.375]), and the dominant model (AC/CC vs AA, OR = 1.925, 95% CI [1.613–3.816]); AC and CC at the A1298C polymorphism of the MTHFR gene (ORAC = 1.917, 95% CI [1.064–3.453]; ORCC = 2.233, 95% CI [1.082–4.609]), the additive model (CC vs AA, OR = 2.497, 95% CI [1.277–4.883]) and the dominant model (AC/CC vs AA, OR = 2.012, 95% CI [1.200–3.373]); at the C677T polymorphism of the MTHFR gene CT and TT (ORCT = 1.913, 95% CI [1.085–3.375]…
bibliographic citation: Yang et al. (2022) Effect of interaction between occupational stress and polymorphisms of MTHFR gene and SELE gene on hypertension. PeerJ 10:e12914 https://doi.org/10.7717/peerj.12914
date submitted: 2021-08-31
date accepted: 2022-01-19
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Fen
author list: Agent
  family name: Qiu
  given name: Ruiying
author list: Agent
  family name: Abudoubari
  given name: Saimaitikari
author list: Agent
  family name: Tao
  given name: Ning
author list: Agent
  family name: An
  given name: Hengqing
doi: 10.7717/peerj.12914
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Yang et al.
attribution name: Yang et al.

Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China
type: item
type: AcademicArticle
description: Long-term and widespread cotton production in Xinjiang, China, has resulted in significant soil degradation, thereby leading to continuous cropping obstacles; cotton stalk biochar (CSB) addition may be an effective countermeasure to this issue, with effects that are felt immediately by root systems in direct contact with the soil. In this study, we assess the effects of different CSB application rates on soil nutrient contents, root morphology, and root physiology in two soil types commonly used for cotton production in the region. Compared with CK (no CSB addition), a 1% CSB addition increased total nitrogen (TN), available phosphorus (AP), and organic matter (OM) by 13.3%, 7.2%, and 50% in grey desert soil, respectively , and 36.5%, 19.9%, and 176.4%, respectively, in aeolian sandy soil. A 3% CSB addition increased TN, AP, and OM by 38.8%, 23.8%, and 208.1%, respectively, in grey desert soil, and 36%, 13%, and 183.2%, respectively, in aeolian sandy soil. Compared with the aeolian sandy soil, a 1% CSB addition increased TN, OM, and AP by 95%, 94.8%, and 33.3%, respectively, in the grey desert soil , while in the same soil 3% CSB addition increased TN, OM, and AP by 108%, 21.1%, and 73.9%, respectively. In the grey desert soil, compared with CK, a 1% CSB application increased the root length (RL) (34%), specific root length (SRL) (27.9%), and root volume (RV) (32.6%) during the bud stage, increased glutamine synthetase (GS) (13.9%) and nitrate reductase (NR) activities (237%), decreased the RV (34%) and average root diameter (ARD) (36.2%) during the harvesting stage. A 3% CSB addition increased the RL (44%), SRL (20%), and RV (41.2%) during the bud stage and decreased the RV (29%) and ARD (27%) during the harvesting stage. In the aeolian sandy soil, 1% CSB increased the RL (38.3%), SRL (73.7%), and RV (17%), while a 3% caused a greater increase in the RL (55%), SRL (89%), RV (28%), soluble sugar content (128%), and underground biomass (33.8%). Compared with the grey…
format: application/pdf
format: text/html
creator: Xiuxiu Dong
creator: Zhiyong Zhang
creator: Shaoming Wang
creator: Zihui Shen
creator: Xiaojiao Cheng
creator: Xinhua Lv
creator: Xiaozhen Pu
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Natural Resource Management
description: doi:10.7717/peerj.12928
publisher: PeerJ Inc.
rights: © 2022 Dong et al.
abstract: Long-term and widespread cotton production in Xinjiang, China, has resulted in significant soil degradation, thereby leading to continuous cropping obstacles; cotton stalk biochar (CSB) addition may be an effective countermeasure to this issue, with effects that are felt immediately by root systems in direct contact with the soil. In this study, we assess the effects of different CSB application rates on soil nutrient contents, root morphology, and root physiology in two soil types commonly used for cotton production in the region. Compared with CK (no CSB addition), a 1% CSB addition increased total nitrogen (TN), available phosphorus (AP), and organic matter (OM) by 13.3%, 7.2%, and 50% in grey desert soil, respectively , and 36.5%, 19.9%, and 176.4%, respectively, in aeolian sandy soil. A 3% CSB addition increased TN, AP, and OM by 38.8%, 23.8%, and 208.1%, respectively, in grey desert soil, and 36%, 13%, and 183.2%, respectively, in aeolian sandy soil. Compared with the aeolian sandy soil, a 1% CSB addition increased TN, OM, and AP by 95%, 94.8%, and 33.3%, respectively, in the grey desert soil , while in the same soil 3% CSB addition increased TN, OM, and AP by 108%, 21.1%, and 73.9%, respectively. In the grey desert soil, compared with CK, a 1% CSB application increased the root length (RL) (34%), specific root length (SRL) (27.9%), and root volume (RV) (32.6%) during the bud stage, increased glutamine synthetase (GS) (13.9%) and nitrate reductase (NR) activities (237%), decreased the RV (34%) and average root diameter (ARD) (36.2%) during the harvesting stage. A 3% CSB addition increased the RL (44%), SRL (20%), and RV (41.2%) during the bud stage and decreased the RV (29%) and ARD (27%) during the harvesting stage. In the aeolian sandy soil, 1% CSB increased the RL (38.3%), SRL (73.7%), and RV (17%), while a 3% caused a greater increase in the RL (55%), SRL (89%), RV (28%), soluble sugar content (128%), and underground biomass (33.8%). Compared with the grey…
bibliographic citation: Dong et al. (2022) Soil properties, root morphology and physiological responses to cotton stalk biochar addition in two continuous cropping cotton field soils from Xinjiang, China. PeerJ 10:e12928 https://doi.org/10.7717/peerj.12928
date submitted: 2021-09-06
date accepted: 2022-01-20
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Xiuxiu
author list: Agent
  family name: Zhang
  given name: Zhiyong
author list: Agent
  family name: Wang
  given name: Shaoming
author list: Agent
  family name: Shen
  given name: Zihui
author list: Agent
  family name: Cheng
  given name: Xiaojiao
author list: Agent
  family name: Lv
  given name: Xinhua
author list: Agent
  family name: Pu
  given name: Xiaozhen
doi: 10.7717/peerj.12928
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Dong et al.
attribution name: Dong et al.

New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea)
type: item
type: AcademicArticle
description: Piipironus grandis gen. et sp. nov. is described from Piip submarine volcano, the Bering Sea. Piipironus gen. nov. shows all main characters of Thalassironinae but differs from all known ironids in the form of the amphid (spiral vs pocket-like) and the simultaneous presence of precloacal papilliform supplements and tubular postcloacal organs. Pared tubular postcloacal organs have never been described before for the family Ironidae. The combination of papilliform precloacal supplements and the pair of tubular postcloacal organs described for Piipironus grandis gen. et sp. nov. is unique among nematodes. The study of the nematofauna of the Piip submarine volcano began quite recently, and Piipironus is the second new genus of nematodes described from here from one sample of bottom sediments. This can be taken as one of the examples of the hyper-high diversity of marine nematodes.
format: application/pdf
format: text/html
creator: Julia Zograf
creator: Vladimir Mordukhovich
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12946
publisher: PeerJ Inc.
rights: © 2022 Zograf and Mordukhovich
abstract: Piipironus grandis gen. et sp. nov. is described from Piip submarine volcano, the Bering Sea. Piipironus gen. nov. shows all main characters of Thalassironinae but differs from all known ironids in the form of the amphid (spiral vs pocket-like) and the simultaneous presence of precloacal papilliform supplements and tubular postcloacal organs. Pared tubular postcloacal organs have never been described before for the family Ironidae. The combination of papilliform precloacal supplements and the pair of tubular postcloacal organs described for Piipironus grandis gen. et sp. nov. is unique among nematodes. The study of the nematofauna of the Piip submarine volcano began quite recently, and Piipironus is the second new genus of nematodes described from here from one sample of bottom sediments. This can be taken as one of the examples of the hyper-high diversity of marine nematodes.
bibliographic citation: Zograf et al. (2022) New genus of Ironidae (Nematoda, Enoplida) from Piip volcano (the Bering Sea). PeerJ 10:e12946 https://doi.org/10.7717/peerj.12946
date submitted: 2021-11-19
date accepted: 2022-01-25
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zograf
  given name: Julia
author list: Agent
  family name: Mordukhovich
  given name: Vladimir
doi: 10.7717/peerj.12946
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: © 2022 Zograf and Mordukhovich
attribution name: Zograf and Mordukhovich

The impact of COVID-19 and control measures on public health in Thailand, 2020
type: item
type: AcademicArticle
description: Background The COVID-19 virus has been an emerging disease causing global outbreaks for over a year. In Thailand, transmission may be controlled by strict measures that could positively and negatively impact physical health and suicidal behavior. Methods The incidence of COVID-19 was retrieved from the Department of Disease Control (DDC). The impact of viral diseases was retrieved from the open-source of the DDC and King Chulalongkorn Memorial Hospital. The road accidents data were from the Thai Ministry of Transport. The suicidal behavior data were obtained from the Department of Mental Health. We compared data from the year 2019 with the pandemic COVID-19 outbreak period in 2020, before lockdown, during lockdown, easing, and new wave period using unpaired t-test and least-squares linear regression. We compared the impact of the outbreak on various data records in 2020 with corresponding non-outbreak from 2019. Results There was a significant decline in cases of influenza (p < 0.001) and norovirus (p = 0.01). However, there was no significant difference in RSV cases (p = 0.17). There was a dramatic increase in attempt to suicides and suicides (p < 0.001). There was no impact on roadside accidents and outpatient department visits. Discussion The extensive intervention measures during lockdown during the first wave positively impacted total cases for each period for acute respiratory and gastrointestinal tract diseases, car accidents, and injuries and negatively impacted indicators of suicidal behavior. The data support government policies that would be effective against the next outbreak by promoting the “new normal” lifestyle.
format: application/pdf
format: text/html
creator: Ritthideach Yorsaeng
creator: Nungruthai Suntronwong
creator: Ilada Thongpan
creator: Watchaporn Chuchaona
creator: Fajar Budi Lestari
creator: Siripat Pasittungkul
creator: Jiratchaya Puenpa
creator: Kamolthip Atsawawaranunt
creator: Chollasap Sharma
creator: Natthinee Sudhinaraset
creator: Anek Mungaomklang
creator: Rungrueng Kitphati
creator: Nasamon Wanlapakorn
creator: Yong Poovorawan
subject: Epidemiology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.12960
publisher: PeerJ Inc.
rights: © 2022 Yorsaeng et al.
abstract: Background The COVID-19 virus has been an emerging disease causing global outbreaks for over a year. In Thailand, transmission may be controlled by strict measures that could positively and negatively impact physical health and suicidal behavior. Methods The incidence of COVID-19 was retrieved from the Department of Disease Control (DDC). The impact of viral diseases was retrieved from the open-source of the DDC and King Chulalongkorn Memorial Hospital. The road accidents data were from the Thai Ministry of Transport. The suicidal behavior data were obtained from the Department of Mental Health. We compared data from the year 2019 with the pandemic COVID-19 outbreak period in 2020, before lockdown, during lockdown, easing, and new wave period using unpaired t-test and least-squares linear regression. We compared the impact of the outbreak on various data records in 2020 with corresponding non-outbreak from 2019. Results There was a significant decline in cases of influenza (p < 0.001) and norovirus (p = 0.01). However, there was no significant difference in RSV cases (p = 0.17). There was a dramatic increase in attempt to suicides and suicides (p < 0.001). There was no impact on roadside accidents and outpatient department visits. Discussion The extensive intervention measures during lockdown during the first wave positively impacted total cases for each period for acute respiratory and gastrointestinal tract diseases, car accidents, and injuries and negatively impacted indicators of suicidal behavior. The data support government policies that would be effective against the next outbreak by promoting the “new normal” lifestyle.
bibliographic citation: Yorsaeng et al. (2022) The impact of COVID-19 and control measures on public health in Thailand, 2020. PeerJ 10:e12960 https://doi.org/10.7717/peerj.12960
date submitted: 2021-08-27
date accepted: 2022-01-27
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yorsaeng
  given name: Ritthideach
author list: Agent
  family name: Suntronwong
  given name: Nungruthai
author list: Agent
  family name: Thongpan
  given name: Ilada
author list: Agent
  family name: Chuchaona
  given name: Watchaporn
author list: Agent
  family name: Lestari
  given name: Fajar Budi
author list: Agent
  family name: Pasittungkul
  given name: Siripat
author list: Agent
  family name: Puenpa
  given name: Jiratchaya
author list: Agent
  family name: Atsawawaranunt
  given name: Kamolthip
author list: Agent
  family name: Sharma
  given name: Chollasap
author list: Agent
  family name: Sudhinaraset
  given name: Natthinee
author list: Agent
  family name: Mungaomklang
  given name: Anek
author list: Agent
  family name: Kitphati
  given name: Rungrueng
author list: Agent
  family name: Wanlapakorn
  given name: Nasamon
author list: Agent
  family name: Poovorawan
  given name: Yong
doi: 10.7717/peerj.12960
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Yorsaeng et al.
attribution name: Yorsaeng et al.

In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury
type: item
type: AcademicArticle
description: Lipopolysaccharide (LPS) is a glycolipid component of the cell wall of Gram-negative bacteria, which induces multiple organ dysfunctions, eventually leading to septic shock and death. Arjunolic acid (AA) has been shown to have therapeutic benefits against various organ pathophysiologies, although its role in sepsis remains unclear. Here, we evaluated the effects of AA on LPS-induced free radical production and cardiotoxicity. Male albino mice were allocated to four groups: normal, 1.5 µg/30 g b.w. of LPS (LPS), 20 mg/kg b.w. AA with LPS (AA+LPS) and 20 mg/kg b.w. of AA (AA). Subsequently, blood and heart samples were harvested for biochemical and histopathological examinations. Pretreatment with AA attenuated LPS-induced increased serum levels of cardiac troponin I, lactate dehydrogenase and creatine kinase. In the meantime, AA pretreatment before LPS resulted in a significant increase in endogenous antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reduced glutathione) and a significant decrease in the level of lipid peroxidation product (malondialdehyde) in the heart as compared to the LPS group, while cardiac cytochrome c activity were significantly increased. In addition, in the AA-pretreated mice, C-reactive protein and proinflammatory cytokines (interlukin-1 and tumor necrosis factor-alpha) were significantly reduced, and anti-inflammatory cytokines (interleukin-4 and -10) were significantly increased in cardiac tissues as compared to the LPS-treated animals. Furthermore, prior administration of AA to LPS exposed mice led to a significant a significant decrease in heart caspase-3, -8, and -9 as compared to the LPS group. Interestingly, AA was also able to improve LPS-induced histopathological changes in the cardiomyocytes. In conclusion, these in vivo findings indicate that AA may be a promising cardioprotective agent against LPS-stimulated cardiotoxicity, at least in part, through upregulation of cardiac antioxidants, reduction of lipid …
format: application/pdf
format: text/html
creator: Hany Elsawy
creator: Mohammed Almalki
creator: Omar Elmenshawy
creator: Ashraf Abdel-Moneim
subject: Biochemistry
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.12986
publisher: PeerJ Inc.
rights: © 2022 Elsawy et al.
abstract: Lipopolysaccharide (LPS) is a glycolipid component of the cell wall of Gram-negative bacteria, which induces multiple organ dysfunctions, eventually leading to septic shock and death. Arjunolic acid (AA) has been shown to have therapeutic benefits against various organ pathophysiologies, although its role in sepsis remains unclear. Here, we evaluated the effects of AA on LPS-induced free radical production and cardiotoxicity. Male albino mice were allocated to four groups: normal, 1.5 µg/30 g b.w. of LPS (LPS), 20 mg/kg b.w. AA with LPS (AA+LPS) and 20 mg/kg b.w. of AA (AA). Subsequently, blood and heart samples were harvested for biochemical and histopathological examinations. Pretreatment with AA attenuated LPS-induced increased serum levels of cardiac troponin I, lactate dehydrogenase and creatine kinase. In the meantime, AA pretreatment before LPS resulted in a significant increase in endogenous antioxidants (superoxide dismutase, catalase, glutathione peroxidase and reduced glutathione) and a significant decrease in the level of lipid peroxidation product (malondialdehyde) in the heart as compared to the LPS group, while cardiac cytochrome c activity were significantly increased. In addition, in the AA-pretreated mice, C-reactive protein and proinflammatory cytokines (interlukin-1 and tumor necrosis factor-alpha) were significantly reduced, and anti-inflammatory cytokines (interleukin-4 and -10) were significantly increased in cardiac tissues as compared to the LPS-treated animals. Furthermore, prior administration of AA to LPS exposed mice led to a significant a significant decrease in heart caspase-3, -8, and -9 as compared to the LPS group. Interestingly, AA was also able to improve LPS-induced histopathological changes in the cardiomyocytes. In conclusion, these in vivo findings indicate that AA may be a promising cardioprotective agent against LPS-stimulated cardiotoxicity, at least in part, through upregulation of cardiac antioxidants, reduction of lipid …
bibliographic citation: Elsawy et al. (2022) In vivo evaluation of the protective effects of arjunolic acid against lipopolysaccharide-induced septic myocardial injury. PeerJ 10:e12986 https://doi.org/10.7717/peerj.12986
date submitted: 2021-11-08
date accepted: 2022-02-01
issued: 2022-02-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elsawy
  given name: Hany
author list: Agent
  family name: Almalki
  given name: Mohammed
author list: Agent
  family name: Elmenshawy
  given name: Omar
author list: Agent
  family name: Abdel-Moneim
  given name: Ashraf
doi: 10.7717/peerj.12986
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-16
copyright: ©2022 Elsawy et al.
attribution name: Elsawy et al.

A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)
type: item
type: AcademicArticle
description: To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.
format: application/pdf
format: text/html
creator: Gaurav Vaidya
creator: Nico Cellinese
creator: Hilmar Lapp
subject: Bioinformatics
subject: Evolutionary Studies
subject: Taxonomy
subject: Computational Science
subject: Data Science
description: doi:10.7717/peerj.12618
publisher: PeerJ Inc.
rights: © 2022 Vaidya et al.
abstract: To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.
bibliographic citation: Vaidya et al. (2022) A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx). PeerJ 10:e12618 https://doi.org/10.7717/peerj.12618
date submitted: 2021-03-23
date accepted: 2021-11-18
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vaidya
  given name: Gaurav
author list: Agent
  family name: Cellinese
  given name: Nico
author list: Agent
  family name: Lapp
  given name: Hilmar
doi: 10.7717/peerj.12618
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Vaidya et al.
attribution name: Vaidya et al.

Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?
type: item
type: AcademicArticle
description: Background The Oral Impacts on Daily Performances (OIDP) index asks the respondents to indicate both, the frequency and severity of the impact. However, it is not clear if the two scaling methods are correlated, and if using one scale is sufficient. The purpose of the study was to investigate the correlation between frequency and severity rating scales of the OIDP instrument, and whether only one of the rating scales can be used instead of both. Methods A battery of patient-reported outcome questionnaires were administered to a consecutive sample of adult dental patients from HealthPartners dental clinics in Minnesota (N = 2,115). Only those who responded to any of the OIDP items were included in the analysis for this study (N = 873). We assessed correlations between the frequency and severity scales for all OIDP items, and for the summary scores of the two OIDP response scales. We additionally fit a categorical structural equation model (SEM) (or an item factor analysis model) and examined the correlation between two latent variables (Frequency and Severity). Results The correlation estimates for all OIDP items were greater than 0.50, indicating large correlations between the frequency and severity scores for each OIDP item. The correlation estimate between the two summary scores was 0.85 (95% CI [0.82–0.86]). When we calculated the correlation coefficient using a latent variable model, the value increased to 0.96 (95% CI [0.93–1.00]). Conclusion Our study findings show that OIDP frequency and severity scores are highly correlated, which indicates the use of one scale only. Based on previous evidence, we recommend applying the frequency rating scale only in research and clinical settings.
format: application/pdf
format: text/html
creator: Swaha Pattanaik
creator: Mike T. John
creator: Seungwon Chung
creator: San Keller
subject: Dentistry
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12717
publisher: PeerJ Inc.
rights: © 2022 Pattanaik et al.
abstract: Background The Oral Impacts on Daily Performances (OIDP) index asks the respondents to indicate both, the frequency and severity of the impact. However, it is not clear if the two scaling methods are correlated, and if using one scale is sufficient. The purpose of the study was to investigate the correlation between frequency and severity rating scales of the OIDP instrument, and whether only one of the rating scales can be used instead of both. Methods A battery of patient-reported outcome questionnaires were administered to a consecutive sample of adult dental patients from HealthPartners dental clinics in Minnesota (N = 2,115). Only those who responded to any of the OIDP items were included in the analysis for this study (N = 873). We assessed correlations between the frequency and severity scales for all OIDP items, and for the summary scores of the two OIDP response scales. We additionally fit a categorical structural equation model (SEM) (or an item factor analysis model) and examined the correlation between two latent variables (Frequency and Severity). Results The correlation estimates for all OIDP items were greater than 0.50, indicating large correlations between the frequency and severity scores for each OIDP item. The correlation estimate between the two summary scores was 0.85 (95% CI [0.82–0.86]). When we calculated the correlation coefficient using a latent variable model, the value increased to 0.96 (95% CI [0.93–1.00]). Conclusion Our study findings show that OIDP frequency and severity scores are highly correlated, which indicates the use of one scale only. Based on previous evidence, we recommend applying the frequency rating scale only in research and clinical settings.
bibliographic citation: Pattanaik et al. (2022) Should the frequency, severity, or both response scales be used for multi-item dental patient-reported outcome measures?. PeerJ 10:e12717 https://doi.org/10.7717/peerj.12717
date submitted: 2021-10-11
date accepted: 2021-12-09
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pattanaik
  given name: Swaha
author list: Agent
  family name: John
  given name: Mike T.
author list: Agent
  family name: Chung
  given name: Seungwon
author list: Agent
  family name: Keller
  given name: San
doi: 10.7717/peerj.12717
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Pattanaik et al.
attribution name: Pattanaik et al.

Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure
type: item
type: AcademicArticle
description: Dogs and wolves both show attachment-like behaviors to their owners/caregivers, including exploring more in the presence of the owner/caregiver, and greeting the owner/caregiver more effusively after an absence. Concurrent choice studies can elucidate dogs’ and wolves’ relationship to their owners/caregivers by assessing their preference for the owner/caregiver compared to other stimuli. While previous research has used concurrent choice paradigms to evaluate dogs’ and wolves’ preference between humans giving social interaction or humans giving food, no research has explored their preferences for an owner/caregiver compared to food when the food is not delivered by a human. In the current study, we investigated whether dogs and hand-reared wolves preferred their owner/caregiver or food, unassociated with a human, when they had been equally deprived of each stimulus (at least 4 hours). Each canid experienced four trials; we measured first choice and time spent with each alternative. Dogs overall did not show a preference for the owner or food. Wolves, on the other hand, tended to show a preference for food in both measures. We observed a range of individual variation in both measures, although dogs showed more individual variation. The differences we observed between dogs and wolves align with prior research comparing wolf and dog behavior directed towards humans; however, the reasons for this differential responding could be due to a variety of factors beyond phylogeny.
format: application/pdf
format: text/html
creator: Lindsay Isernia
creator: Clive D.L. Wynne
creator: Leanna House
creator: Erica N. Feuerbacher
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.12834
publisher: PeerJ Inc.
rights: © 2022 Isernia et al.
abstract: Dogs and wolves both show attachment-like behaviors to their owners/caregivers, including exploring more in the presence of the owner/caregiver, and greeting the owner/caregiver more effusively after an absence. Concurrent choice studies can elucidate dogs’ and wolves’ relationship to their owners/caregivers by assessing their preference for the owner/caregiver compared to other stimuli. While previous research has used concurrent choice paradigms to evaluate dogs’ and wolves’ preference between humans giving social interaction or humans giving food, no research has explored their preferences for an owner/caregiver compared to food when the food is not delivered by a human. In the current study, we investigated whether dogs and hand-reared wolves preferred their owner/caregiver or food, unassociated with a human, when they had been equally deprived of each stimulus (at least 4 hours). Each canid experienced four trials; we measured first choice and time spent with each alternative. Dogs overall did not show a preference for the owner or food. Wolves, on the other hand, tended to show a preference for food in both measures. We observed a range of individual variation in both measures, although dogs showed more individual variation. The differences we observed between dogs and wolves align with prior research comparing wolf and dog behavior directed towards humans; however, the reasons for this differential responding could be due to a variety of factors beyond phylogeny.
bibliographic citation: Isernia et al. (2022) Dogs and wolves differ in their response allocation to their owner/caregiver or food in a concurrent choice procedure. PeerJ 10:e12834 https://doi.org/10.7717/peerj.12834
date submitted: 2020-09-28
date accepted: 2022-01-04
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Isernia
  given name: Lindsay
author list: Agent
  family name: Wynne
  given name: Clive D.L.
author list: Agent
  family name: House
  given name: Leanna
author list: Agent
  family name: Feuerbacher
  given name: Erica N.
doi: 10.7717/peerj.12834
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Isernia et al.
attribution name: Isernia et al.

https://peerj.com/articles/12872
type: item
type: AcademicArticle
title: From hair to liver: emerging application of hair follicle mesenchymal stem cell transplantation reverses liver cirrhosis by blocking the TGF-β/Smad signaling pathway to inhibit pathological HSC activation
description: Liver cirrhosis (LC) involves multiple systems throughout the body, and patients with LC often die of multiple organ failure. However, few drugs are useful to treat LC. Hair follicle mesenchymal stem cells (HF-MSCs) are derived from the dermal papilla and the bulge area of hair follicles and are pluripotent stem cells in the mesoderm with broad prospects in regenerative medicine. As an emerging seed cell type widely used in skin wound healing and plastic surgery, HF-MSCs show considerable prospects in the treatment of LC due to their proliferation and multidirectional differentiation capabilities. We established an LC model in C57BL/6J mice by administering carbon tetrachloride (CCl4) and injected HF-MSCs through the tail vein to explore the therapeutic effects and potential mechanisms of HF-MSCs on LC. Here, we found that HF-MSCs improved liver function and ameliorated the liver pathology of LC. Notably, PKH67-labeled HF-MSCs were detected in the injured liver and expressed the hepatocyte-specific markers cytokeratin 18 (CK18) and albumin (ALB). In addition, in contrast to that in the LC group, the α-SMA expression showed a decreasing trend in the treatment group in vitro and in vivo, indicating that the pathological activation of hepatic stellate cells (HSCs) was inhibited by HF-MSC treatment. Moreover, the levels of transforming growth factor β (TGF-β1) and p-Smad3, a signaling molecule downstream of TGF-β1, were increased in mice with LC, while HF-MSC treatment reversed these changes in vivo and in vitro. Based on these findings, HF-MSCs may reverse LC by blocking the TGF-β/Smad pathway and inhibiting the pathological activation of HSCs, which may provide evidence for the application of HF-MSCs to treat LC.
format: application/pdf
format: text/html
creator: Qi Liu
creator: Chengqian Lv
creator: Yanan Jiang
creator: Kunpeng Luo
creator: Yang Gao
creator: Jingyang Liu
creator: Xu Zhang
creator: Jan Mohammad Omar
creator: Shizhu Jin
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.12872
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Liver cirrhosis (LC) involves multiple systems throughout the body, and patients with LC often die of multiple organ failure. However, few drugs are useful to treat LC. Hair follicle mesenchymal stem cells (HF-MSCs) are derived from the dermal papilla and the bulge area of hair follicles and are pluripotent stem cells in the mesoderm with broad prospects in regenerative medicine. As an emerging seed cell type widely used in skin wound healing and plastic surgery, HF-MSCs show considerable prospects in the treatment of LC due to their proliferation and multidirectional differentiation capabilities. We established an LC model in C57BL/6J mice by administering carbon tetrachloride (CCl4) and injected HF-MSCs through the tail vein to explore the therapeutic effects and potential mechanisms of HF-MSCs on LC. Here, we found that HF-MSCs improved liver function and ameliorated the liver pathology of LC. Notably, PKH67-labeled HF-MSCs were detected in the injured liver and expressed the hepatocyte-specific markers cytokeratin 18 (CK18) and albumin (ALB). In addition, in contrast to that in the LC group, the α-SMA expression showed a decreasing trend in the treatment group in vitro and in vivo, indicating that the pathological activation of hepatic stellate cells (HSCs) was inhibited by HF-MSC treatment. Moreover, the levels of transforming growth factor β (TGF-β1) and p-Smad3, a signaling molecule downstream of TGF-β1, were increased in mice with LC, while HF-MSC treatment reversed these changes in vivo and in vitro. Based on these findings, HF-MSCs may reverse LC by blocking the TGF-β/Smad pathway and inhibiting the pathological activation of HSCs, which may provide evidence for the application of HF-MSCs to treat LC.
bibliographic citation: Liu et al. (2022) From hair to liver: emerging application of hair follicle mesenchymal stem cell transplantation reverses liver cirrhosis by blocking the TGF-β/Smad signaling pathway to inhibit pathological HSC activation. PeerJ 10:e12872 https://doi.org/10.7717/peerj.12872
date submitted: 2021-11-09
date accepted: 2022-01-11
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Qi
author list: Agent
  family name: Lv
  given name: Chengqian
author list: Agent
  family name: Jiang
  given name: Yanan
author list: Agent
  family name: Luo
  given name: Kunpeng
author list: Agent
  family name: Gao
  given name: Yang
author list: Agent
  family name: Liu
  given name: Jingyang
author list: Agent
  family name: Zhang
  given name: Xu
author list: Agent
  family name: Mohammad Omar
  given name: Jan
author list: Agent
  family name: Jin
  given name: Shizhu
doi: 10.7717/peerj.12872
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Liu et al.
attribution name: Liu et al.

New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans
type: item
type: AcademicArticle
description: We present new observations on Jullienella foetida Schlumberger, 1890, a giant agglutinated foraminifer with a leaf- or fan-like test reaching a maximum dimension of 14 cm, that is common on some parts of the west African continental shelf. The test wall comprises a smooth, outer veneer of small (<10 µm) mineral grains that overlies the much thicker inner layer, which has a porous structure and is composed of grains measuring several hundreds of microns in size. Micro-CT scans suggest that much of the test interior is filled with cytoplasm, while X-ray micrographs reveal an elaborate system of radiating internal partitions that probably serve to channel cytoplasmic flow and strengthen the test. Jullienella foetida resembles some xenophyophores (giant deep-sea foraminifera) in terms of test size and morphology, but lacks their distinctive internal organization; the similarities are therefore likely to be convergent. Based on micro-CT scan data, we calculated an individual cytoplasmic biomass of 3.65 mg wet weight for one specimen. When combined with literature records of seafloor coverage, this yielded an estimate of >7.0 g wet weight m−2 for the seafloor biomass of J. foetida in areas where it is particularly abundant. The relatively restricted distribution of this species off the north-west African coast at depths above 100 m is probably related to the elevated, upwelling-related surface productivity along this margin, which provides enough food to sustain this high biomass. This remarkable species appears to play an important, perhaps keystone, role in benthic ecosystems where it is abundant, providing the only common hard substrate on which sessile organisms can settle.
format: application/pdf
format: text/html
creator: Martin R. Langer
creator: Anna E. Weinmann
creator: Walid A. Makled
creator: Janine Könen
creator: Andrew J. Gooday
subject: Evolutionary Studies
subject: Marine Biology
subject: Paleontology
subject: Plant Science
description: doi:10.7717/peerj.12884
publisher: PeerJ Inc.
rights: © 2022 Langer et al.
abstract: We present new observations on Jullienella foetida Schlumberger, 1890, a giant agglutinated foraminifer with a leaf- or fan-like test reaching a maximum dimension of 14 cm, that is common on some parts of the west African continental shelf. The test wall comprises a smooth, outer veneer of small (<10 µm) mineral grains that overlies the much thicker inner layer, which has a porous structure and is composed of grains measuring several hundreds of microns in size. Micro-CT scans suggest that much of the test interior is filled with cytoplasm, while X-ray micrographs reveal an elaborate system of radiating internal partitions that probably serve to channel cytoplasmic flow and strengthen the test. Jullienella foetida resembles some xenophyophores (giant deep-sea foraminifera) in terms of test size and morphology, but lacks their distinctive internal organization; the similarities are therefore likely to be convergent. Based on micro-CT scan data, we calculated an individual cytoplasmic biomass of 3.65 mg wet weight for one specimen. When combined with literature records of seafloor coverage, this yielded an estimate of >7.0 g wet weight m−2 for the seafloor biomass of J. foetida in areas where it is particularly abundant. The relatively restricted distribution of this species off the north-west African coast at depths above 100 m is probably related to the elevated, upwelling-related surface productivity along this margin, which provides enough food to sustain this high biomass. This remarkable species appears to play an important, perhaps keystone, role in benthic ecosystems where it is abundant, providing the only common hard substrate on which sessile organisms can settle.
bibliographic citation: Langer et al. (2022) New observations on test architecture and construction of Jullienella foetida Schlumberger, 1890, the largest shallow-water agglutinated foraminifer in modern oceans. PeerJ 10:e12884 https://doi.org/10.7717/peerj.12884
date submitted: 2021-11-03
date accepted: 2022-01-13
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Langer
  given name: Martin R.
author list: Agent
  family name: Weinmann
  given name: Anna E.
author list: Agent
  family name: Makled
  given name: Walid A.
author list: Agent
  family name: Könen
  given name: Janine
author list: Agent
  family name: Gooday
  given name: Andrew J.
doi: 10.7717/peerj.12884
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: © 2022 Langer et al.
attribution name: Langer et al.

7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway
type: item
type: AcademicArticle
description: Background 7,8-dihydroxyflavone (7,8-DHF), a selective agonist of tropomyosin related kinase receptor B (TrkB), is known to exert protective effects in neurodegenerative diseases. However, the role of 7,8-DHF in TrkB signaling after ischemic stroke has remained elusive. Methods In the vitro model of ischemic stroke, we investigated the neuroprotective effect of 7,8-DHF through activation of TrkB signaling. Neurons subjected to oxygen and glucose deprivation/reperfusion were treated with the protein kinase inhibitor K252a and a knockdown of TrkB. Cell counting kit-8 (CCK-8) assay, Flow Cytometric Analysis (FACS), TdT-mediated dUTP nick end labeling (TUNEL) assay were conducted for measuring cell viability and numbers of apoptotic cells. And apoptosis-associated proteins were analyzed by Western blotting. Results Compared with the Control group, OGD/R group revealed lower cell viability by CCK-8 assay FACS and TUNEL assay showed increased rates of neuronal apoptosis. However, 7,8-DHF treatment increased cell viability and reduced neuronal apoptosis. Western blotting indicated upregulated Bax and cleaved caspase-3 and but downregulated Bcl-2 following OGD/R. Whereas 7,8-DHF treatment downregulated Bax and cleaved caspase-3 but upregulated Bcl-2. These changes were accompanied by a significant increase in the phosphorylation of TrkB and Akt following 7,8-DHF administration. However, the administration of K252a and knockdown of TrkB could alleviate those effects. Conclusion Our study demonstrates that activation of TrkB signaling by 7,8-DHF protects neurons against OGD/R injury via the TrkB/Akt pathway, which provides the evidence for the role of TrkB signaling in OGD-induced neuronal damage and may become a potential therapeutic target for ischemic stroke.
format: application/pdf
format: text/html
creator: Qinxiang Zhou
creator: Hao Tang
creator: Dingqun Bai
creator: Yuhan Kong
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
subject: Neurology
description: doi:10.7717/peerj.12886
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Background 7,8-dihydroxyflavone (7,8-DHF), a selective agonist of tropomyosin related kinase receptor B (TrkB), is known to exert protective effects in neurodegenerative diseases. However, the role of 7,8-DHF in TrkB signaling after ischemic stroke has remained elusive. Methods In the vitro model of ischemic stroke, we investigated the neuroprotective effect of 7,8-DHF through activation of TrkB signaling. Neurons subjected to oxygen and glucose deprivation/reperfusion were treated with the protein kinase inhibitor K252a and a knockdown of TrkB. Cell counting kit-8 (CCK-8) assay, Flow Cytometric Analysis (FACS), TdT-mediated dUTP nick end labeling (TUNEL) assay were conducted for measuring cell viability and numbers of apoptotic cells. And apoptosis-associated proteins were analyzed by Western blotting. Results Compared with the Control group, OGD/R group revealed lower cell viability by CCK-8 assay FACS and TUNEL assay showed increased rates of neuronal apoptosis. However, 7,8-DHF treatment increased cell viability and reduced neuronal apoptosis. Western blotting indicated upregulated Bax and cleaved caspase-3 and but downregulated Bcl-2 following OGD/R. Whereas 7,8-DHF treatment downregulated Bax and cleaved caspase-3 but upregulated Bcl-2. These changes were accompanied by a significant increase in the phosphorylation of TrkB and Akt following 7,8-DHF administration. However, the administration of K252a and knockdown of TrkB could alleviate those effects. Conclusion Our study demonstrates that activation of TrkB signaling by 7,8-DHF protects neurons against OGD/R injury via the TrkB/Akt pathway, which provides the evidence for the role of TrkB signaling in OGD-induced neuronal damage and may become a potential therapeutic target for ischemic stroke.
bibliographic citation: Zhou et al. (2022) 7,8-Dihydroxyflavone protects neurons against oxygen-glucose deprivation induced apoptosis and activates the TrkB/Akt pathway. PeerJ 10:e12886 https://doi.org/10.7717/peerj.12886
date submitted: 2021-09-27
date accepted: 2022-01-14
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Qinxiang
author list: Agent
  family name: Tang
  given name: Hao
author list: Agent
  family name: Bai
  given name: Dingqun
author list: Agent
  family name: Kong
  given name: Yuhan
doi: 10.7717/peerj.12886
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Zhou et al.
attribution name: Zhou et al.

Morphological characterization and sexual dimorphism of the antennal sensilla in Bactericera gobica Loginova (Hemiptera: Psyllidae)—a scanning and transmission electron microscopic study
type: item
type: AcademicArticle
description: Bactericera gobica is the major pest of Goji berry plants and causes severe damage. Psyllids mainly use the antennal sensilla to recognize olfactory cues necessary to find host plants and mates. However, the structure and function of the antenna and the antennal sensilla of B. gobica remains previously unexplored. Here, we identify the external and internal morphology of the antennal sensilla of B. gobica using both scanning electron microscopy (SEM) and transmission electron microscopy (TEM). We found seven types of sensilla on the filiform antennae, including apical setae (LAS, SAS), sensilla basiconica (SB1, SB2), sensilla campaniform (SCA), sensilla chaetica (ChS1, ChS2), cavity sensilla (CvS1, CvS2), antennal rhinaria (AR1, AR2), and sensilla trichodea (ST). Five of these sensilla types—apical setae, sensilla basiconica, sensilla chaetica, cavity sensilla, and antennal rhinaria—may have olfactory functions based on their porous surfaces and internal dendritic outer segments (DOS). We also found several differences between the two sexes of B. gobica in the sensilla array and internal structure. ChS and DOS in the protrusions of AR were more abundant in males than females. Altogether, we comprehensively revealed the fine structure and probable function of B. gobica antennae and identified differences in the distribution and structure between psyllid sexes. Our findings provide important insights for future studies on defining the olfactory function of psyllid antenna using electrophysiological methods.
format: application/pdf
format: text/html
creator: Yang Ge
creator: Olivia M. Smith
creator: Weilin Chen
creator: Pingping Liu
creator: Qingjun Yuan
creator: Chuanzhi Kang
creator: Tielin Wang
creator: Jiahui Sun
creator: Binbin Yan
creator: Xiaoli Liu
creator: Lanping Guo
subject: Agricultural Science
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.12888
publisher: PeerJ Inc.
rights: © 2022 Ge et al.
abstract: Bactericera gobica is the major pest of Goji berry plants and causes severe damage. Psyllids mainly use the antennal sensilla to recognize olfactory cues necessary to find host plants and mates. However, the structure and function of the antenna and the antennal sensilla of B. gobica remains previously unexplored. Here, we identify the external and internal morphology of the antennal sensilla of B. gobica using both scanning electron microscopy (SEM) and transmission electron microscopy (TEM). We found seven types of sensilla on the filiform antennae, including apical setae (LAS, SAS), sensilla basiconica (SB1, SB2), sensilla campaniform (SCA), sensilla chaetica (ChS1, ChS2), cavity sensilla (CvS1, CvS2), antennal rhinaria (AR1, AR2), and sensilla trichodea (ST). Five of these sensilla types—apical setae, sensilla basiconica, sensilla chaetica, cavity sensilla, and antennal rhinaria—may have olfactory functions based on their porous surfaces and internal dendritic outer segments (DOS). We also found several differences between the two sexes of B. gobica in the sensilla array and internal structure. ChS and DOS in the protrusions of AR were more abundant in males than females. Altogether, we comprehensively revealed the fine structure and probable function of B. gobica antennae and identified differences in the distribution and structure between psyllid sexes. Our findings provide important insights for future studies on defining the olfactory function of psyllid antenna using electrophysiological methods.
bibliographic citation: Ge et al. (2022) Morphological characterization and sexual dimorphism of the antennal sensilla in Bactericera gobica Loginova (Hemiptera: Psyllidae)—a scanning and transmission electron microscopic study. PeerJ 10:e12888 https://doi.org/10.7717/peerj.12888
date submitted: 2021-11-15
date accepted: 2022-01-14
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ge
  given name: Yang
author list: Agent
  family name: Smith
  given name: Olivia M.
author list: Agent
  family name: Chen
  given name: Weilin
author list: Agent
  family name: Liu
  given name: Pingping
author list: Agent
  family name: Yuan
  given name: Qingjun
author list: Agent
  family name: Kang
  given name: Chuanzhi
author list: Agent
  family name: Wang
  given name: Tielin
author list: Agent
  family name: Sun
  given name: Jiahui
author list: Agent
  family name: Yan
  given name: Binbin
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Guo
  given name: Lanping
doi: 10.7717/peerj.12888
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Ge et al.
attribution name: Ge et al.

The coalescent with replication-independent mutations
type: item
type: AcademicArticle
description: We develop the mathematical structure of the neutral coalescent with both replication-dependent and replication-independent mutations. This allows us to explain and quantify empirical results that explore differences in genetic diversity in bacterial cultures with different growth rates. We also derive an unbiased and consistent estimator for the replication-independent mutation rate that is based on a comparison of total single nucleotide polymorphism counts for two independent well-mixed cultures with different growth rates. In addition to explaining differences in genetic diversity between well-mixed cultures with different (but constant) growth rates, our coalescent also quantifies the effects of fluctuating growth rates—a situation that can be common in natural populations.
format: application/pdf
format: text/html
creator: Stephen M. Krone
creator: Beth M. Tuschhoff
subject: Genetics
subject: Mathematical Biology
subject: Microbiology
subject: Molecular Biology
subject: Population Biology
description: doi:10.7717/peerj.12926
publisher: PeerJ Inc.
rights: © 2022 Krone and Tuschhoff
abstract: We develop the mathematical structure of the neutral coalescent with both replication-dependent and replication-independent mutations. This allows us to explain and quantify empirical results that explore differences in genetic diversity in bacterial cultures with different growth rates. We also derive an unbiased and consistent estimator for the replication-independent mutation rate that is based on a comparison of total single nucleotide polymorphism counts for two independent well-mixed cultures with different growth rates. In addition to explaining differences in genetic diversity between well-mixed cultures with different (but constant) growth rates, our coalescent also quantifies the effects of fluctuating growth rates—a situation that can be common in natural populations.
bibliographic citation: Krone et al. (2022) The coalescent with replication-independent mutations. PeerJ 10:e12926 https://doi.org/10.7717/peerj.12926
date submitted: 2021-07-07
date accepted: 2022-01-20
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krone
  given name: Stephen M.
author list: Agent
  family name: Tuschhoff
  given name: Beth M.
doi: 10.7717/peerj.12926
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: © 2022 Krone and Tuschhoff
attribution name: Krone and Tuschhoff

Wei2GO: weighted sequence similarity-based protein function prediction
type: item
type: AcademicArticle
description: Background Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases. Methods This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations. Results Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes. Availability Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.
format: application/pdf
format: text/html
creator: Maarten J.M.F. Reijnders
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.12931
publisher: PeerJ Inc.
rights: © 2022 Reijnders
abstract: Background Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases. Methods This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations. Results Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes. Availability Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.
bibliographic citation: Reijnders (2022) Wei2GO: weighted sequence similarity-based protein function prediction. PeerJ 10:e12931 https://doi.org/10.7717/peerj.12931
date submitted: 2020-11-17
date accepted: 2022-01-21
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reijnders
  given name: Maarten J.M.F.
doi: 10.7717/peerj.12931
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: © 2022 Reijnders
attribution name: Reijnders

Human cytomegalovirus infection and its association with gestational diabetes mellitus during pregnancy
type: item
type: AcademicArticle
description: Background Infection is an important risk factor for gestational diabetes mellitus (GDM), while infection of human cytomegalovirus (HCMV) with GDM remains unclear and rarely reported. This study aimed to investigate the association of HCMV infection and serum inflammatory factor levels in pregnancy with GDM. Methods This prospective study included pregnant women who attended at Affiliated Hospital of Qingdao Hospital and Zibo Maternal and Child Health Hospital between December 2018 and August 2020. HCMV specific IgM and serum levels of inflammatory factors, including TNF-α, IL-6, and IL-1β, were analyzed. Results A total of 5,316 pregnant women were included (415 with GDM (107 with HCMV+GDM+ and 308 with HCMV-GDM+) and 4901 GDM-free (759 with HCMV+GDM- and 4142 with HCMV-GDM-)). The prevalence of GDM was 7.81%. The rate of activation of HCMV was 16.29%. Specifically, 107 and 759 women in the GDM and control group exhibited HCMV infection, with positive rates of25.78% and 15.48%, respectively (P < 0.01). TNF-α, IL-6, and IL-1β at 24–28 weeks of gestation were significantly higher in women with GDM and HCMV infection than inthe other groups (all P < 0.01). Multivariable analysis showed that HCMV positive (OR = 1.851; 95% CI [1.425–2.403]; P < 0.001), IL-6 (OR = 1.010; 95% CI [1.002–1.018]; P = 0.013), and IL-1β (OR = 1.410; 95% CI [1.348–1.474]; P < 0.001) were all significantly correlated with GDM. Conclusion This study suggests HCMV infection during pregnancy is an independent risk factor of GDM and could significantly increase its incidence. Further studies are needed to elucidate possible mechanisms underlying associations between HCMV infection and GDM.
format: application/pdf
format: text/html
creator: Yunyang Wang
creator: Xianjuan Zhang
creator: Xu Zheng
creator: Guanghui Song
creator: Lina Fang
creator: Yangang Wang
creator: Bin Wang
subject: Diabetes and Endocrinology
subject: Gynecology and Obstetrics
subject: Immunology
subject: Women’s Health
description: doi:10.7717/peerj.12934
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Infection is an important risk factor for gestational diabetes mellitus (GDM), while infection of human cytomegalovirus (HCMV) with GDM remains unclear and rarely reported. This study aimed to investigate the association of HCMV infection and serum inflammatory factor levels in pregnancy with GDM. Methods This prospective study included pregnant women who attended at Affiliated Hospital of Qingdao Hospital and Zibo Maternal and Child Health Hospital between December 2018 and August 2020. HCMV specific IgM and serum levels of inflammatory factors, including TNF-α, IL-6, and IL-1β, were analyzed. Results A total of 5,316 pregnant women were included (415 with GDM (107 with HCMV+GDM+ and 308 with HCMV-GDM+) and 4901 GDM-free (759 with HCMV+GDM- and 4142 with HCMV-GDM-)). The prevalence of GDM was 7.81%. The rate of activation of HCMV was 16.29%. Specifically, 107 and 759 women in the GDM and control group exhibited HCMV infection, with positive rates of25.78% and 15.48%, respectively (P < 0.01). TNF-α, IL-6, and IL-1β at 24–28 weeks of gestation were significantly higher in women with GDM and HCMV infection than inthe other groups (all P < 0.01). Multivariable analysis showed that HCMV positive (OR = 1.851; 95% CI [1.425–2.403]; P < 0.001), IL-6 (OR = 1.010; 95% CI [1.002–1.018]; P = 0.013), and IL-1β (OR = 1.410; 95% CI [1.348–1.474]; P < 0.001) were all significantly correlated with GDM. Conclusion This study suggests HCMV infection during pregnancy is an independent risk factor of GDM and could significantly increase its incidence. Further studies are needed to elucidate possible mechanisms underlying associations between HCMV infection and GDM.
bibliographic citation: Wang et al. (2022) Human cytomegalovirus infection and its association with gestational diabetes mellitus during pregnancy. PeerJ 10:e12934 https://doi.org/10.7717/peerj.12934
date submitted: 2021-10-15
date accepted: 2022-01-23
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yunyang
author list: Agent
  family name: Zhang
  given name: Xianjuan
author list: Agent
  family name: Zheng
  given name: Xu
author list: Agent
  family name: Song
  given name: Guanghui
author list: Agent
  family name: Fang
  given name: Lina
author list: Agent
  family name: Wang
  given name: Yangang
author list: Agent
  family name: Wang
  given name: Bin
doi: 10.7717/peerj.12934
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Exploring the mechanism of cordycepin combined with doxorubicin in treating glioblastoma based on network pharmacology and biological verification
type: item
type: AcademicArticle
description: Background Glioblastoma is the most common and fatal primary malignant tumor in the central nervous system, and the prognosis is poor. Currently, there are no effective treatments for glioblastoma. Cordycepin is a natural active substance with significant anticancer activity and doxorubicin is a broad-spectrum anticancer drug. Cordycepin administered with doxorubicin is a potential drug combination for the treatment of glioblastoma. However, the mechanism of action for this drug combination has not yet been elucidated. Aim of the study To explore the complex mechanism of cordycepin combined with doxorubicin against glioblastoma using network pharmacology and biological verification. Materials and methods We used an MTT assay, colony formation assay, and scratch healing to detect the growth, proliferation, and migration of LN-229, U251 and T98G cells. Putative targets and the potential mechanism of action for the drug combination in glioblastoma were obtained through online databases, network construction, and enrichment analyses. We verified the expression of EMT-related genes and identified important therapeutic targets by western blot. Results In this study, the combination of doxorubicin and cordycepin was found to significantly inhibit cell proliferation and migration and can induce apoptosis. These effects are better together than with either drug alone. The drug combination inhibited EMT by upregulating the expression of E-cadherin protein and downregulating the expression of N-cadherin, ZEB1, and Twist1 proteins. There were 71 potential targets for the drug combination in glioblastoma, and Kyoto Encyclopedia of Genes and Genome analysis suggested that the anticancer process may be mediated by proteoglycans in cancer, the tumor necrosis factor signaling pathway, microRNA in cancer, pathways in cancer, and other pathways. To study the molecular mechanism of anticancer activity, we detected the expression of target proteins with downregulated expression of NFKB1…
format: application/pdf
format: text/html
creator: Jing Chen
creator: Yuan-Dong Zhuang
creator: Qiang Zhang
creator: Shuang Liu
creator: Bing-Bo Zhuang
creator: Chun-Hua Wang
creator: Ri-Sheng Liang
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.12942
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Background Glioblastoma is the most common and fatal primary malignant tumor in the central nervous system, and the prognosis is poor. Currently, there are no effective treatments for glioblastoma. Cordycepin is a natural active substance with significant anticancer activity and doxorubicin is a broad-spectrum anticancer drug. Cordycepin administered with doxorubicin is a potential drug combination for the treatment of glioblastoma. However, the mechanism of action for this drug combination has not yet been elucidated. Aim of the study To explore the complex mechanism of cordycepin combined with doxorubicin against glioblastoma using network pharmacology and biological verification. Materials and methods We used an MTT assay, colony formation assay, and scratch healing to detect the growth, proliferation, and migration of LN-229, U251 and T98G cells. Putative targets and the potential mechanism of action for the drug combination in glioblastoma were obtained through online databases, network construction, and enrichment analyses. We verified the expression of EMT-related genes and identified important therapeutic targets by western blot. Results In this study, the combination of doxorubicin and cordycepin was found to significantly inhibit cell proliferation and migration and can induce apoptosis. These effects are better together than with either drug alone. The drug combination inhibited EMT by upregulating the expression of E-cadherin protein and downregulating the expression of N-cadherin, ZEB1, and Twist1 proteins. There were 71 potential targets for the drug combination in glioblastoma, and Kyoto Encyclopedia of Genes and Genome analysis suggested that the anticancer process may be mediated by proteoglycans in cancer, the tumor necrosis factor signaling pathway, microRNA in cancer, pathways in cancer, and other pathways. To study the molecular mechanism of anticancer activity, we detected the expression of target proteins with downregulated expression of NFKB1…
bibliographic citation: Chen et al. (2022) Exploring the mechanism of cordycepin combined with doxorubicin in treating glioblastoma based on network pharmacology and biological verification. PeerJ 10:e12942 https://doi.org/10.7717/peerj.12942
date submitted: 2021-08-18
date accepted: 2022-01-24
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Jing
author list: Agent
  family name: Zhuang
  given name: Yuan-Dong
author list: Agent
  family name: Zhang
  given name: Qiang
author list: Agent
  family name: Liu
  given name: Shuang
author list: Agent
  family name: Zhuang
  given name: Bing-Bo
author list: Agent
  family name: Wang
  given name: Chun-Hua
author list: Agent
  family name: Liang
  given name: Ri-Sheng
doi: 10.7717/peerj.12942
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: © 2022 Chen et al.
attribution name: Chen et al.

No evidence of conditioning of pupillary constriction despite overtraining
type: item
type: AcademicArticle
description: Eyeblink conditioning is the most popular paradigm for studying classical conditioning in humans. But the fact that eyelids are under voluntary control means it is ultimately impossible to ascertain whether a blink response is ‘conditioned’ or a timed ‘voluntary’ blink response. In contrast, the pupillary response is an autonomic response, not under voluntary control. By conditioning the pupillary response, one might avoid potential volition-related confounds. Several attempts have been made to condition the pupillary constriction and dilation responses, with the earliest published attempts dating back to the beginning of the 20th century. While a few early studies reported successful conditioning of pupillary constriction, later studies have failed to replicate this. The apparatus for recording pupil size, the type of stimuli used and the interval between the stimuli has varied in previous attempts—which may explain the inconsistent results. Moreover, measuring the pupil size used to be cumbersome compared with today when an eyetracker can continuously measure pupil size non-invasively. Here we used an eyetracker to test whether it is possible to condition the autonomic pupillary constriction response by pairing a tone (CS) and a light (US) with a 1s CS-US interval. Unlike in previous studies, our subjects went through multiple training sessions to ensure that any potential lack of conditioning would not be due to too little training. A total of 10 participants went through 2–12 conditioning sessions, each lasting approximately 20 min. One training session consisted of 75 paired, tone + light, trials and 25 randomly interspersed CS alone trials. The eyetracker (Tobii Pro Nano), continuously measured participants’ pupil size. To test statistically whether conditioning of the pupillary response occurred we compared the pupil size after the tone on the first session and the last session. The results showed a complete lack of evidence of conditioning. Though the pupil …
format: application/pdf
format: text/html
creator: Diederick C. Niehorster
creator: Stina Bengtsson
creator: Niklas Brodin
creator: Anders Rasmussen
subject: Neuroscience
subject: Ophthalmology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12948
publisher: PeerJ Inc.
rights: © 2022 Niehorster et al.
abstract: Eyeblink conditioning is the most popular paradigm for studying classical conditioning in humans. But the fact that eyelids are under voluntary control means it is ultimately impossible to ascertain whether a blink response is ‘conditioned’ or a timed ‘voluntary’ blink response. In contrast, the pupillary response is an autonomic response, not under voluntary control. By conditioning the pupillary response, one might avoid potential volition-related confounds. Several attempts have been made to condition the pupillary constriction and dilation responses, with the earliest published attempts dating back to the beginning of the 20th century. While a few early studies reported successful conditioning of pupillary constriction, later studies have failed to replicate this. The apparatus for recording pupil size, the type of stimuli used and the interval between the stimuli has varied in previous attempts—which may explain the inconsistent results. Moreover, measuring the pupil size used to be cumbersome compared with today when an eyetracker can continuously measure pupil size non-invasively. Here we used an eyetracker to test whether it is possible to condition the autonomic pupillary constriction response by pairing a tone (CS) and a light (US) with a 1s CS-US interval. Unlike in previous studies, our subjects went through multiple training sessions to ensure that any potential lack of conditioning would not be due to too little training. A total of 10 participants went through 2–12 conditioning sessions, each lasting approximately 20 min. One training session consisted of 75 paired, tone + light, trials and 25 randomly interspersed CS alone trials. The eyetracker (Tobii Pro Nano), continuously measured participants’ pupil size. To test statistically whether conditioning of the pupillary response occurred we compared the pupil size after the tone on the first session and the last session. The results showed a complete lack of evidence of conditioning. Though the pupil …
bibliographic citation: Niehorster et al. (2022) No evidence of conditioning of pupillary constriction despite overtraining. PeerJ 10:e12948 https://doi.org/10.7717/peerj.12948
date submitted: 2021-04-07
date accepted: 2022-01-25
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niehorster
  given name: Diederick C.
author list: Agent
  family name: Bengtsson
  given name: Stina
author list: Agent
  family name: Brodin
  given name: Niklas
author list: Agent
  family name: Rasmussen
  given name: Anders
doi: 10.7717/peerj.12948
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Niehorster et al.
attribution name: Niehorster et al.

Factors of balance determining the risk of falls in physically active women aged over 50 years
type: item
type: AcademicArticle
description: Background Balance disorders are believed to be one of the main reasons for falls in older adults. They are related to natural processes of ageing, resulting in deterioration of information integration and processing from the vestibular, somatosensory and visual systems. The consequence is an increased number of postural sways, which are some of balance factors. Balance control in static and dynamic activities is an essential element of daily functioning of older citizens. It seems that balance assessment is essential to determine the risk of falls, as well as to determine which factors of balance have greatest impact on the risk of falls. Methods The study involved physically active female students (n = 36, mean age 67,11 ± 5,35) of a University of the Third Age. We used the Balance System SD platform to assess their balance in four tests with eyes open and with eyes closed and to determine the risk of falls. We assessed the relationships between individual balance indices (overall stability index, anterior/posterior stability index, medial/lateral stability index) and the falls risk index. We also determined those factors which predicted the risk of falls the most. Results The studied subjects had low risk of falls for their age category. In most measurements there were relationships between the risk of falls and the size of sways in the coronal plane and the overall stability index. We also found that the overall stability index calculated in measurements with eyes closed predicted the risk of falls of the studied physically active females most accurately (R2 0.391 F(1.34)=23.475; <0.000). The subjects were physically active and their falls risk index was low - this allowed us to presume that there was a relationship between these two factors. Preventive programmes should include exercise performed with eyes closed, and tests conducted with eyes closed seem to be most sensitive in determining balance disorders in physically active women.
format: application/pdf
format: text/html
creator: Grzegorz Bednarczuk
creator: Izabela Rutkowska
subject: Geriatrics
subject: Women’s Health
subject: Biomechanics
description: doi:10.7717/peerj.12952
publisher: PeerJ Inc.
rights: © 2022 Bednarczuk and Rutkowska
abstract: Background Balance disorders are believed to be one of the main reasons for falls in older adults. They are related to natural processes of ageing, resulting in deterioration of information integration and processing from the vestibular, somatosensory and visual systems. The consequence is an increased number of postural sways, which are some of balance factors. Balance control in static and dynamic activities is an essential element of daily functioning of older citizens. It seems that balance assessment is essential to determine the risk of falls, as well as to determine which factors of balance have greatest impact on the risk of falls. Methods The study involved physically active female students (n = 36, mean age 67,11 ± 5,35) of a University of the Third Age. We used the Balance System SD platform to assess their balance in four tests with eyes open and with eyes closed and to determine the risk of falls. We assessed the relationships between individual balance indices (overall stability index, anterior/posterior stability index, medial/lateral stability index) and the falls risk index. We also determined those factors which predicted the risk of falls the most. Results The studied subjects had low risk of falls for their age category. In most measurements there were relationships between the risk of falls and the size of sways in the coronal plane and the overall stability index. We also found that the overall stability index calculated in measurements with eyes closed predicted the risk of falls of the studied physically active females most accurately (R2 0.391 F(1.34)=23.475; <0.000). The subjects were physically active and their falls risk index was low - this allowed us to presume that there was a relationship between these two factors. Preventive programmes should include exercise performed with eyes closed, and tests conducted with eyes closed seem to be most sensitive in determining balance disorders in physically active women.
bibliographic citation: Bednarczuk et al. (2022) Factors of balance determining the risk of falls in physically active women aged over 50 years. PeerJ 10:e12952 https://doi.org/10.7717/peerj.12952
date submitted: 2021-10-28
date accepted: 2022-01-26
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bednarczuk
  given name: Grzegorz
author list: Agent
  family name: Rutkowska
  given name: Izabela
doi: 10.7717/peerj.12952
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Bednarczuk and Rutkowska
attribution name: Bednarczuk and Rutkowska

Identification of novel prophage regions in Xenorhabdus nematophila genome and gene expression analysis during phage-like particle induction
type: item
type: AcademicArticle
description: Background Entomopathogenic Xenorhabdus bacteria are endosymbionts of Steinernema nematodes and together they form an insecticidal mutualistic association that infects a wide range of insect species. Xenorhabdus produce an arsenal of toxins and secondary metabolites that kill the insect host. In addition, they can induce the production of diverse phage particles. A few studies have focused on one integrated phage responsible for producing a phage tail-like bacteriocin, associated with an antimicrobial activity against other Xenorhabdus species. However, very little is known about the diversity of prophage regions in Xenorhabdus species. Methods In the present study, we identified several prophage regions in the genome of Xenorhabdus nematophila AN6/1. We performed a preliminary study on the relative expression of genes in these prophage regions. We also investigated some genes (not contained in prophage region) known to be involved in SOS bacterial response (recA and lexA) associated with mitomycin C and UV exposure. Results We described two integrated prophage regions (designated Xnp3 and Xnp4) not previously described in the genome of Xenorhabdus nematophila AN6/1. The Xnp3 prophage region appears very similar to complete Mu-like bacteriophage. These prophages regions are not unique to X. nematophila species, although they appear less conserved among Xenorhabdus species when compared to the previously described p1 prophage region. Our results showed that mitomycin C exposure induced an up-regulation of recA and lexA suggesting activation of SOS response. In addition, mitomycin C and UV exposure seems to lead to up-regulation of genes in three of the four integrated prophages regions.
format: application/pdf
format: text/html
creator: Emilie Lefoulon
creator: Natalie Campbell
creator: S. Patricia Stock
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.12956
publisher: PeerJ Inc.
rights: © 2022 Lefoulon et al.
abstract: Background Entomopathogenic Xenorhabdus bacteria are endosymbionts of Steinernema nematodes and together they form an insecticidal mutualistic association that infects a wide range of insect species. Xenorhabdus produce an arsenal of toxins and secondary metabolites that kill the insect host. In addition, they can induce the production of diverse phage particles. A few studies have focused on one integrated phage responsible for producing a phage tail-like bacteriocin, associated with an antimicrobial activity against other Xenorhabdus species. However, very little is known about the diversity of prophage regions in Xenorhabdus species. Methods In the present study, we identified several prophage regions in the genome of Xenorhabdus nematophila AN6/1. We performed a preliminary study on the relative expression of genes in these prophage regions. We also investigated some genes (not contained in prophage region) known to be involved in SOS bacterial response (recA and lexA) associated with mitomycin C and UV exposure. Results We described two integrated prophage regions (designated Xnp3 and Xnp4) not previously described in the genome of Xenorhabdus nematophila AN6/1. The Xnp3 prophage region appears very similar to complete Mu-like bacteriophage. These prophages regions are not unique to X. nematophila species, although they appear less conserved among Xenorhabdus species when compared to the previously described p1 prophage region. Our results showed that mitomycin C exposure induced an up-regulation of recA and lexA suggesting activation of SOS response. In addition, mitomycin C and UV exposure seems to lead to up-regulation of genes in three of the four integrated prophages regions.
bibliographic citation: Lefoulon et al. (2022) Identification of novel prophage regions in Xenorhabdus nematophila genome and gene expression analysis during phage-like particle induction. PeerJ 10:e12956 https://doi.org/10.7717/peerj.12956
date submitted: 2021-12-21
date accepted: 2022-01-27
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lefoulon
  given name: Emilie
author list: Agent
  family name: Campbell
  given name: Natalie
author list: Agent
  family name: Stock
  given name: S. Patricia
doi: 10.7717/peerj.12956
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: © 2022 Lefoulon et al.
attribution name: Lefoulon et al.

Validity and inter-rater reliability of ankle motion observed during a single leg squat
type: item
type: AcademicArticle
description: Background The single leg squat (SLS) test is a clinical functional test commonly used to evaluate clinically aberrant movement patterns of the knee. The SLS could be an interesting option to analyze ankle control in the frontal plane during dynamic load analysis. However, to date, there are no studies that have analyzed the associations between the increased subtalar joint pronation by navicular drop (ND) test and ankle control with single leg squat (SLSankle) using a three-point scale. The purpose of this study was to evaluate the reliability of a clinical observation method to assess and determine the relationship between navicular drop (ND) and ankle control on the SLSankle score. Methods A total of fifty-five healthy, physically active (31 females and 24 males) volunteers participated in this study. The degree of subtalar pronation was assessed through the ND test, and the ankle control was defined as the ankle displacement in the frontal plane during the SLS. Results We found good intra-rater and inter-rater agreement during SLSankle, with Kappa values from 0.731 to 0.750. The relationship between the SLSankle and ND was significant ; the Spearman’s rank correlation coefficient was 0.504 (p < 0.05). Conclusions The SLSankle score supplied the clinical practice with a reliable and valid alternative for quantifying foot mobility in comparison to the ND test.
format: application/pdf
format: text/html
creator: Paloma Guillén-Rogel
creator: Cristina San Emeterio
creator: Pedro J. Marín
subject: Biomechanics
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.12990
publisher: PeerJ Inc.
rights: © 2022 Guillén-Rogel et al.
abstract: Background The single leg squat (SLS) test is a clinical functional test commonly used to evaluate clinically aberrant movement patterns of the knee. The SLS could be an interesting option to analyze ankle control in the frontal plane during dynamic load analysis. However, to date, there are no studies that have analyzed the associations between the increased subtalar joint pronation by navicular drop (ND) test and ankle control with single leg squat (SLSankle) using a three-point scale. The purpose of this study was to evaluate the reliability of a clinical observation method to assess and determine the relationship between navicular drop (ND) and ankle control on the SLSankle score. Methods A total of fifty-five healthy, physically active (31 females and 24 males) volunteers participated in this study. The degree of subtalar pronation was assessed through the ND test, and the ankle control was defined as the ankle displacement in the frontal plane during the SLS. Results We found good intra-rater and inter-rater agreement during SLSankle, with Kappa values from 0.731 to 0.750. The relationship between the SLSankle and ND was significant ; the Spearman’s rank correlation coefficient was 0.504 (p < 0.05). Conclusions The SLSankle score supplied the clinical practice with a reliable and valid alternative for quantifying foot mobility in comparison to the ND test.
bibliographic citation: Guillén-Rogel et al. (2022) Validity and inter-rater reliability of ankle motion observed during a single leg squat. PeerJ 10:e12990 https://doi.org/10.7717/peerj.12990
date submitted: 2021-12-10
date accepted: 2022-02-02
issued: 2022-02-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guillén-Rogel
  given name: Paloma
author list: Agent
  family name: San Emeterio
  given name: Cristina
author list: Agent
  family name: Marín
  given name: Pedro J.
doi: 10.7717/peerj.12990
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-15
copyright: ©2022 Guillén-Rogel et al.
attribution name: Guillén-Rogel et al.

The shadow model: how and why small choices in spatially explicit species distribution models affect predictions
type: item
type: AcademicArticle
description: The use of species distribution models (SDMs) has rapidly increased over the last decade, driven largely by increasing observational evidence of distributional shifts of terrestrial and aquatic populations. These models permit, for example, the quantification of range shifts, the estimation of species co-occurrence, and the association of habitat to species distribution and abundance. The increasing complexity of contemporary SDMs presents new challenges—as the choices among modeling options increase, it is essential to understand how these choices affect model outcomes. Using a combination of original analysis and literature review, we synthesize the effects of three common model choices in semi-parametric predictive process species distribution modeling: model structure, spatial extent of the data, and spatial scale of predictions. To illustrate the effects of these choices, we develop a case study centered around sablefish (Anoplopoma fimbria) distribution on the west coast of the USA. The three modeling choices represent decisions necessary in virtually all ecological applications of these methods, and are important because the consequences of these choices impact derived quantities of interest (e.g., estimates of population size and their management implications). Truncating the spatial extent of data near the observed range edge, or using a model that is misspecified in terms of covariates and spatial and spatiotemporal fields, led to bias in population biomass trends and mean distribution compared to estimates from models using the full dataset and appropriate model structure. In some cases, these suboptimal modeling decisions may be unavoidable, but understanding the tradeoffs of these choices and impacts on predictions is critical. We illustrate how seemingly small model choices, often made out of necessity or simplicity, can affect scientific advice informing management decisions—potentially leading to erroneous conclusions about changes in abundance or di…
format: application/pdf
format: text/html
creator: Christian J. C. Commander
creator: Lewis A. K. Barnett
creator: Eric J. Ward
creator: Sean C. Anderson
creator: Timothy E. Essington
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.12783
publisher: PeerJ Inc.
rights: © 2022 Commander et al.
abstract: The use of species distribution models (SDMs) has rapidly increased over the last decade, driven largely by increasing observational evidence of distributional shifts of terrestrial and aquatic populations. These models permit, for example, the quantification of range shifts, the estimation of species co-occurrence, and the association of habitat to species distribution and abundance. The increasing complexity of contemporary SDMs presents new challenges—as the choices among modeling options increase, it is essential to understand how these choices affect model outcomes. Using a combination of original analysis and literature review, we synthesize the effects of three common model choices in semi-parametric predictive process species distribution modeling: model structure, spatial extent of the data, and spatial scale of predictions. To illustrate the effects of these choices, we develop a case study centered around sablefish (Anoplopoma fimbria) distribution on the west coast of the USA. The three modeling choices represent decisions necessary in virtually all ecological applications of these methods, and are important because the consequences of these choices impact derived quantities of interest (e.g., estimates of population size and their management implications). Truncating the spatial extent of data near the observed range edge, or using a model that is misspecified in terms of covariates and spatial and spatiotemporal fields, led to bias in population biomass trends and mean distribution compared to estimates from models using the full dataset and appropriate model structure. In some cases, these suboptimal modeling decisions may be unavoidable, but understanding the tradeoffs of these choices and impacts on predictions is critical. We illustrate how seemingly small model choices, often made out of necessity or simplicity, can affect scientific advice informing management decisions—potentially leading to erroneous conclusions about changes in abundance or di…
bibliographic citation: Commander et al. (2022) The shadow model: how and why small choices in spatially explicit species distribution models affect predictions. PeerJ 10:e12783 https://doi.org/10.7717/peerj.12783
date submitted: 2021-05-20
date accepted: 2021-12-21
issued: 2022-02-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Commander
  given name: Christian J. C.
author list: Agent
  family name: Barnett
  given name: Lewis A. K.
author list: Agent
  family name: Ward
  given name: Eric J.
author list: Agent
  family name: Anderson
  given name: Sean C.
author list: Agent
  family name: Essington
  given name: Timothy E.
doi: 10.7717/peerj.12783
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-14
copyright: © 2022 Commander et al.
attribution name: Commander et al.

Uptake of a plasticizer (di-n-butyl phthalate) impacts the biochemical and physiological responses of barley
type: item
type: AcademicArticle
description: Background DBP is one of the most commonly used plasticizers for imparting desirable properties to polymers. The introduction of phthalates is reported to have occurred in the late 1920s, and there has been a significant rise in their release into the environment in past decades due to a lack of covalent bonding with the parent matrix. Because of their numerous applications in day-to-day life, phthalates have become ubiquitous and also classified as endocrine disruptors. Hence, several studies have been conducted to investigate the phthalate-mediated toxicities in animals; however, plants have not been explored to the same amount. Methods Therefore, in the present study, the accumulation and translocation along with morpho-physiological perturbations in barley plants after 15, 30, 60, and 120 days of exposure to di-n-butyl phthalate (DBP) are investigated using standard protocols. Results The maximal accumulation and translocation of DBP in the roots and shoots of barley plants was observed after 60 days of exposure. The exposure of DBP from 15 to 120 days was recorded to decline all the morphological indices (i.e., dry weight, net primary productivity, seed number per spike, and seed weight) of barley plants. The pigments content declined under DBP treatment for all exposure durations except 120 days exposure. Carbohydrate content increased after 15–30 days of exposure afterward it was observed to be decreased under 60 and 120 days of exposure. The protein content was declined in DBP stressed plants for 15–120 days. Proline content was increased in all exposure durations and maximal percent increase was recorded in 120 days of exposure. MDA content showed an increase at earlier exposure durations then followed by a decline in long-term exposure. Hydrogen peroxide content increased at all exposure durations. There were significant alterations observed in the activities of all antioxidative enzymes in comparison to the control. Furthermore, DBP stressed plants after …
format: application/pdf
format: text/html
creator: Arpna Kumari
creator: Rajinder Kaur
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
subject: Ecotoxicology
description: doi:10.7717/peerj.12859
publisher: PeerJ Inc.
rights: © 2022 Kumari and Kaur
abstract: Background DBP is one of the most commonly used plasticizers for imparting desirable properties to polymers. The introduction of phthalates is reported to have occurred in the late 1920s, and there has been a significant rise in their release into the environment in past decades due to a lack of covalent bonding with the parent matrix. Because of their numerous applications in day-to-day life, phthalates have become ubiquitous and also classified as endocrine disruptors. Hence, several studies have been conducted to investigate the phthalate-mediated toxicities in animals; however, plants have not been explored to the same amount. Methods Therefore, in the present study, the accumulation and translocation along with morpho-physiological perturbations in barley plants after 15, 30, 60, and 120 days of exposure to di-n-butyl phthalate (DBP) are investigated using standard protocols. Results The maximal accumulation and translocation of DBP in the roots and shoots of barley plants was observed after 60 days of exposure. The exposure of DBP from 15 to 120 days was recorded to decline all the morphological indices (i.e., dry weight, net primary productivity, seed number per spike, and seed weight) of barley plants. The pigments content declined under DBP treatment for all exposure durations except 120 days exposure. Carbohydrate content increased after 15–30 days of exposure afterward it was observed to be decreased under 60 and 120 days of exposure. The protein content was declined in DBP stressed plants for 15–120 days. Proline content was increased in all exposure durations and maximal percent increase was recorded in 120 days of exposure. MDA content showed an increase at earlier exposure durations then followed by a decline in long-term exposure. Hydrogen peroxide content increased at all exposure durations. There were significant alterations observed in the activities of all antioxidative enzymes in comparison to the control. Furthermore, DBP stressed plants after …
bibliographic citation: Kumari et al. (2022) Uptake of a plasticizer (di-n-butyl phthalate) impacts the biochemical and physiological responses of barley. PeerJ 10:e12859 https://doi.org/10.7717/peerj.12859
date submitted: 2021-07-07
date accepted: 2022-01-09
issued: 2022-02-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kumari
  given name: Arpna
author list: Agent
  family name: Kaur
  given name: Rajinder
doi: 10.7717/peerj.12859
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-14
copyright: ©2022 Kumari and Kaur
attribution name: Kumari and Kaur

https://peerj.com/articles/12896
type: item
type: AcademicArticle
title: Assessment of the effects of storage temperature on fatty acid analysis using dried blood spot cards from managed southern white rhinoceroses (Ceratotherium simum simum): implications for field collection and nutritional care
description: Background Southern white rhinoceroses (Ceratotherium simum simum) are an endangered species in decline due to poaching and negative habitat changes. Conservation of the species has become increasingly important and a focus on better human management has become prevalent. One area of management that impacts southern white rhinoceroses is nutritional health monitoring, which is often conducted through blood analysis. Blood analysis conducted during field research can be difficult due to temperature, distance, and limited technological resources, so new methods of fast, and relatively stable blood collection are being pursued. One method that has been used in humans for many years is beginning to make its way into wildlife studies: the use of dried blood spot (DBS) cards. These cards are used as a tool to store single drops of whole blood on specialized filter paper and, once dried, can be used for nutritional biomarker analysis. An area of interest for southern white rhinoceroses and nutrition is monitoring fatty acid percentages for cardiovascular, immune, and reproductive health. The time and temperature limitations for storing blood fractions or liquid whole blood when analyzing fatty acids have been investigated, but few studies have performed storage studies on DBS cards colder than −20 °C or in non-human species. Methods In order to better understand the limitations of DBS cards and the impact of temperature on fatty acid DBS samples in long-term storage, triplicate samples from seven adult southern white rhinoceroses at the North Carolina Zoo were collected and subjected to three storage treatments (immediate, room temperature (23 °C), or frozen (−80 °C) for 1 year). Results Stearidonic (18:4w3) (Δ 0.3%), arachdic (20:0) (Δ 0.1%), eicosatetraenoic (20:4w3) (Δ 0.2%), and erucic acid (22:1w9) (Δ 0.1%) were in higher concentration in frozen than initial. Fatty acids in higher concentrations in the initial samples than frozen were myristic (14:0) (Δ 0.2%), mead (2…
format: application/pdf
format: text/html
creator: Jordan Wood
creator: Larry J. Minter
creator: Doug Bibus
creator: Troy N. Tollefson
creator: Kimberly Ange-van Heugten
subject: Biochemistry
subject: Biotechnology
subject: Veterinary Medicine
description: doi:10.7717/peerj.12896
publisher: PeerJ Inc.
rights: © 2022 Wood et al.
abstract: Background Southern white rhinoceroses (Ceratotherium simum simum) are an endangered species in decline due to poaching and negative habitat changes. Conservation of the species has become increasingly important and a focus on better human management has become prevalent. One area of management that impacts southern white rhinoceroses is nutritional health monitoring, which is often conducted through blood analysis. Blood analysis conducted during field research can be difficult due to temperature, distance, and limited technological resources, so new methods of fast, and relatively stable blood collection are being pursued. One method that has been used in humans for many years is beginning to make its way into wildlife studies: the use of dried blood spot (DBS) cards. These cards are used as a tool to store single drops of whole blood on specialized filter paper and, once dried, can be used for nutritional biomarker analysis. An area of interest for southern white rhinoceroses and nutrition is monitoring fatty acid percentages for cardiovascular, immune, and reproductive health. The time and temperature limitations for storing blood fractions or liquid whole blood when analyzing fatty acids have been investigated, but few studies have performed storage studies on DBS cards colder than −20 °C or in non-human species. Methods In order to better understand the limitations of DBS cards and the impact of temperature on fatty acid DBS samples in long-term storage, triplicate samples from seven adult southern white rhinoceroses at the North Carolina Zoo were collected and subjected to three storage treatments (immediate, room temperature (23 °C), or frozen (−80 °C) for 1 year). Results Stearidonic (18:4w3) (Δ 0.3%), arachdic (20:0) (Δ 0.1%), eicosatetraenoic (20:4w3) (Δ 0.2%), and erucic acid (22:1w9) (Δ 0.1%) were in higher concentration in frozen than initial. Fatty acids in higher concentrations in the initial samples than frozen were myristic (14:0) (Δ 0.2%), mead (2…
bibliographic citation: Wood et al. (2022) Assessment of the effects of storage temperature on fatty acid analysis using dried blood spot cards from managed southern white rhinoceroses (Ceratotherium simum simum): implications for field collection and nutritional care. PeerJ 10:e12896 https://doi.org/10.7717/peerj.12896
date submitted: 2021-10-28
date accepted: 2022-01-16
issued: 2022-02-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wood
  given name: Jordan
author list: Agent
  family name: Minter
  given name: Larry J.
author list: Agent
  family name: Bibus
  given name: Doug
author list: Agent
  family name: Tollefson
  given name: Troy N.
author list: Agent
  family name: Ange-van Heugten
  given name: Kimberly
doi: 10.7717/peerj.12896
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-14
copyright: © 2022 Wood et al.
attribution name: Wood et al.

Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes
type: item
type: AcademicArticle
description: We investigated the potential use and quantification of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA (Adenovirus and crAssphage) and RNA enteric viruses (Pepper mild mottle virus, Norovirus genogroups GI and GII, Rotavirus Astrovirus, and Sapovirus) as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantified in the extracted samples via quantitative PCR using TaqMan assays. Overall, the average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.1023 and 0.9921) than the average gene copies assessed in the effluents for DNA and RNA viruses and uidA in terms of both volume and biomass. A significant reduction (p-value ≤ 0.0438) of Adenovirus and Noroviruses genogroups GI and GII was observed in activated sludge samples compared with those for raw sewage per volume. Higher GCNs of enteric viruses were observed in dewatered sludge samples compared to liquid samples in terms of volume (g of sample) and biomass (ng of nucleic acids). Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA, indicating that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Viruses such as Noroviruses genogroups GI and GII, and Rotavirus were detected during colder months. Our results suggest that Adenov…
format: application/pdf
format: text/html
creator: Audrey Garcia
creator: Tri Le
creator: Paul Jankowski
creator: Kadir Yanaç
creator: Qiuyan Yuan
creator: Miguel I. Uyaguari-Diaz
subject: Microbiology
subject: Molecular Biology
subject: Virology
subject: Environmental Impacts
description: doi:10.7717/peerj.12957
publisher: PeerJ Inc.
rights: © 2022 Garcia et al.
abstract: We investigated the potential use and quantification of human enteric viruses in municipal wastewater samples of Winnipeg (Manitoba, Canada) as alternative indicators of contamination and evaluated the processing stages of the wastewater treatment plant. During the fall 2019 and winter 2020 seasons, samples of raw sewage, activated sludge, effluents, and biosolids (sludge cake) were collected from the North End Sewage Treatment Plant (NESTP), which is the largest wastewater treatment plant in the City of Winnipeg. DNA (Adenovirus and crAssphage) and RNA enteric viruses (Pepper mild mottle virus, Norovirus genogroups GI and GII, Rotavirus Astrovirus, and Sapovirus) as well as the uidA gene found in Escherichia coli were targeted in the samples collected from the NESTP. Total nucleic acids from each wastewater treatment sample were extracted using a commercial spin-column kit. Enteric viruses were quantified in the extracted samples via quantitative PCR using TaqMan assays. Overall, the average gene copies assessed in the raw sewage were not significantly different (p-values ranged between 0.1023 and 0.9921) than the average gene copies assessed in the effluents for DNA and RNA viruses and uidA in terms of both volume and biomass. A significant reduction (p-value ≤ 0.0438) of Adenovirus and Noroviruses genogroups GI and GII was observed in activated sludge samples compared with those for raw sewage per volume. Higher GCNs of enteric viruses were observed in dewatered sludge samples compared to liquid samples in terms of volume (g of sample) and biomass (ng of nucleic acids). Enteric viruses found in gene copy numbers were at least one order of magnitude higher than the E. coli marker uidA, indicating that enteric viruses may survive the wastewater treatment process and viral-like particles are being released into the aquatic environment. Viruses such as Noroviruses genogroups GI and GII, and Rotavirus were detected during colder months. Our results suggest that Adenov…
bibliographic citation: Garcia et al. (2022) Quantification of human enteric viruses as alternative indicators of fecal pollution to evaluate wastewater treatment processes. PeerJ 10:e12957 https://doi.org/10.7717/peerj.12957
date submitted: 2021-08-06
date accepted: 2022-01-27
issued: 2022-02-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia
  given name: Audrey
author list: Agent
  family name: Le
  given name: Tri
author list: Agent
  family name: Jankowski
  given name: Paul
author list: Agent
  family name: Yanaç
  given name: Kadir
author list: Agent
  family name: Yuan
  given name: Qiuyan
author list: Agent
  family name: Uyaguari-Diaz
  given name: Miguel I.
doi: 10.7717/peerj.12957
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-14
copyright: ©2022 Garcia et al.
attribution name: Garcia et al.

Defense mechanism responses to COVID-19
type: item
type: AcademicArticle
description: The COVID-19 pandemic has had a wide range of negative physical and mental impacts. This review begins with a theoretical explanation of the psychological defense mechanisms used to deal with the pandemic. It then discusses different categories of defense mechanisms and their roles in managing the impacts of psychological distress. The aim of this review is to highlight the various psychological defense mechanisms individuals use to deal with the pandemic and to discuss how adjustment mechanisms can protect individuals from internal and external threats by shielding the integrity of the ego (the mind) and helping individuals maintain their self-schema.
format: application/pdf
format: text/html
creator: Nouf Altwaijri
creator: Turki Abualait
creator: Mohammed Aljumaan
creator: Raidah Albaradie
creator: Zahid Arain
creator: Shahid Bashir
subject: Psychiatry and Psychology
subject: Mental Health
subject: COVID-19
description: doi:10.7717/peerj.12811
publisher: PeerJ Inc.
rights: © 2022 Altwaijri et al.
abstract: The COVID-19 pandemic has had a wide range of negative physical and mental impacts. This review begins with a theoretical explanation of the psychological defense mechanisms used to deal with the pandemic. It then discusses different categories of defense mechanisms and their roles in managing the impacts of psychological distress. The aim of this review is to highlight the various psychological defense mechanisms individuals use to deal with the pandemic and to discuss how adjustment mechanisms can protect individuals from internal and external threats by shielding the integrity of the ego (the mind) and helping individuals maintain their self-schema.
bibliographic citation: Altwaijri et al. (2022) Defense mechanism responses to COVID-19. PeerJ 10:e12811 https://doi.org/10.7717/peerj.12811
date submitted: 2021-10-11
date accepted: 2021-12-28
issued: 2022-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Altwaijri
  given name: Nouf
author list: Agent
  family name: Abualait
  given name: Turki
author list: Agent
  family name: Aljumaan
  given name: Mohammed
author list: Agent
  family name: Albaradie
  given name: Raidah
author list: Agent
  family name: Arain
  given name: Zahid
author list: Agent
  family name: Bashir
  given name: Shahid
doi: 10.7717/peerj.12811
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-11
copyright: ©2022 Altwaijri et al.
attribution name: Altwaijri et al.

A synergistic, global approach to revising the trypanorhynch tapeworm family Rhinoptericolidae (Trypanobatoida)
type: item
type: AcademicArticle
description: Since 2010, the trypanorhynch tapeworm family Rhinoptericolidae Carvajal & Campbell, 1975 has housed just two distinctive, monotypic genera (Rhinoptericola Carvajal & Campbell, 1975 and Nataliella Palm, 2010). However, global collections of tapeworms from sharks and rays over the last more than three decades brought to light the need for major revision of the family by suggesting a much greater species-level diversity for the nominal genus Rhinoptericola. Through synonymy and the description of new species, the number of species in the genus is increased from one to eight. A phylogenetic analysis of the D1–D3 gene region of 28S rRNA (28S), including seven of the now nine species of rhinoptericolids, and a broad sampling of the other Trypanobatoida is the first to recover a monophyletic Rhinoptericolidae. In addition to systematic revision, this study allowed for the first evaluation of the degree of intraspecific vs interspecific variation in 28S for adult trypanorhynchs across the various hosts and geographic localities from which they have been reported, suggesting a relatively consistent boundary for Rhinoptericola. It is further suggested that detailed scanning electron microscopy (SEM) images of both the basal and metabasal armatures greatly aid in the interpretation of hook arrangement and shape. A schematic to streamline determination of the tentacular surface presented in scanning electron micrographs and line drawings of trypanorhynchs is presented for species with both two and four bothria. In combination, these methodological refinements can now be used as a model to resolve issues of classification and non-monophyly within both major lineages of the Trypanorhyncha. As a result of the taxonomic work, Rhinoptericola megacantha Carvajal & Campbell, 1975 (previously only known from the American cownose ray from the Chesapeake Bay and the Ticon cownose ray from the Gulf of Mexico, Venezuela, and Brazil) is now known from an additional species of cownose ray a…
format: application/pdf
format: text/html
creator: Kaylee S. Herzog
creator: Kirsten Jensen
subject: Biodiversity
subject: Marine Biology
subject: Parasitology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12865
publisher: PeerJ Inc.
rights: © 2022 Herzog and Jensen
abstract: Since 2010, the trypanorhynch tapeworm family Rhinoptericolidae Carvajal & Campbell, 1975 has housed just two distinctive, monotypic genera (Rhinoptericola Carvajal & Campbell, 1975 and Nataliella Palm, 2010). However, global collections of tapeworms from sharks and rays over the last more than three decades brought to light the need for major revision of the family by suggesting a much greater species-level diversity for the nominal genus Rhinoptericola. Through synonymy and the description of new species, the number of species in the genus is increased from one to eight. A phylogenetic analysis of the D1–D3 gene region of 28S rRNA (28S), including seven of the now nine species of rhinoptericolids, and a broad sampling of the other Trypanobatoida is the first to recover a monophyletic Rhinoptericolidae. In addition to systematic revision, this study allowed for the first evaluation of the degree of intraspecific vs interspecific variation in 28S for adult trypanorhynchs across the various hosts and geographic localities from which they have been reported, suggesting a relatively consistent boundary for Rhinoptericola. It is further suggested that detailed scanning electron microscopy (SEM) images of both the basal and metabasal armatures greatly aid in the interpretation of hook arrangement and shape. A schematic to streamline determination of the tentacular surface presented in scanning electron micrographs and line drawings of trypanorhynchs is presented for species with both two and four bothria. In combination, these methodological refinements can now be used as a model to resolve issues of classification and non-monophyly within both major lineages of the Trypanorhyncha. As a result of the taxonomic work, Rhinoptericola megacantha Carvajal & Campbell, 1975 (previously only known from the American cownose ray from the Chesapeake Bay and the Ticon cownose ray from the Gulf of Mexico, Venezuela, and Brazil) is now known from an additional species of cownose ray a…
bibliographic citation: Herzog et al. (2022) A synergistic, global approach to revising the trypanorhynch tapeworm family Rhinoptericolidae (Trypanobatoida). PeerJ 10:e12865 https://doi.org/10.7717/peerj.12865
date submitted: 2021-09-20
date accepted: 2022-01-10
issued: 2022-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Herzog
  given name: Kaylee S.
author list: Agent
  family name: Jensen
  given name: Kirsten
doi: 10.7717/peerj.12865
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-11
copyright: © 2022 Herzog and Jensen
attribution name: Herzog and Jensen

Carbon isotope discrimination and the factors affecting it in a summer maize field under different tillage systems
type: item
type: AcademicArticle
description: Based on two years of field experiments, under different soil tillage methods and straw management practices, which included conventional tillage (CT), subsoiling (SS), rotary tillage (RT), and no-tillage (NT), combined with either straw return (S) or straw removal (0), we characterized the dynamic changes in Δ13C among three height layers [upper (U, 240 cm above the ground), middle (M, 120 cm above the ground), and lower (L, 30 cm above the ground)] of the summer maize canopy. The Δ13C, the factors affecting it, and the relationships between Δ13C and soil water content (SWC), the leaf area index (LAI), canopy microclimate, and the CO2 concentration were elucidated. The results indicated that the Δ13C of summer maize at the pre-filling stage was greater than that at the post-filling stage. Δ13C also varied at different heights, with the order of the Δ13C values being L > U > M. Among the different tillage methods, the Δ13C values were ordered SSS > CTS > RTS > NTS. SSS and NTS significantly increased the LAI; air temperature and relative humidity tended to gradually decrease with the increase in height of summer maize. Correlation analyses of the various influencing factors and Δ13C showed that SWC, LAI, air temperature, and CO2 concentration were all positively correlated with Δ13C, in which LAI and air temperature were significantly or extremely significantly positively correlated with Δ13C. In addition, we show that Δ13C can be used as a prediction index for summer maize yield, providing a theoretical basis for future yield research that may save precious time in summer maize breeding efforts.
format: application/pdf
format: text/html
creator: Jichao Cui
creator: Huifang Han
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.12891
publisher: PeerJ Inc.
rights: © 2022 Cui and Han
abstract: Based on two years of field experiments, under different soil tillage methods and straw management practices, which included conventional tillage (CT), subsoiling (SS), rotary tillage (RT), and no-tillage (NT), combined with either straw return (S) or straw removal (0), we characterized the dynamic changes in Δ13C among three height layers [upper (U, 240 cm above the ground), middle (M, 120 cm above the ground), and lower (L, 30 cm above the ground)] of the summer maize canopy. The Δ13C, the factors affecting it, and the relationships between Δ13C and soil water content (SWC), the leaf area index (LAI), canopy microclimate, and the CO2 concentration were elucidated. The results indicated that the Δ13C of summer maize at the pre-filling stage was greater than that at the post-filling stage. Δ13C also varied at different heights, with the order of the Δ13C values being L > U > M. Among the different tillage methods, the Δ13C values were ordered SSS > CTS > RTS > NTS. SSS and NTS significantly increased the LAI; air temperature and relative humidity tended to gradually decrease with the increase in height of summer maize. Correlation analyses of the various influencing factors and Δ13C showed that SWC, LAI, air temperature, and CO2 concentration were all positively correlated with Δ13C, in which LAI and air temperature were significantly or extremely significantly positively correlated with Δ13C. In addition, we show that Δ13C can be used as a prediction index for summer maize yield, providing a theoretical basis for future yield research that may save precious time in summer maize breeding efforts.
bibliographic citation: Cui et al. (2022) Carbon isotope discrimination and the factors affecting it in a summer maize field under different tillage systems. PeerJ 10:e12891 https://doi.org/10.7717/peerj.12891
date submitted: 2021-07-01
date accepted: 2022-01-14
issued: 2022-02-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cui
  given name: Jichao
author list: Agent
  family name: Han
  given name: Huifang
doi: 10.7717/peerj.12891
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-11
copyright: © 2022 Cui and Han
attribution name: Cui and Han

Genetic variability studies for tuber yield and yield attributes in Ethiopian released potato (Solanum tuberosum L.) varieties
type: item
type: AcademicArticle
description: Information on the extent of genetic variability and association among quantitative traits are vital for any crop improvement program and the development of suitable selection strategies. Limited research has been carried out thus far on potato genetic variability and trait association. This study on genetic variability and association among quantitative traits was conducted to assess the extent of genetic variability among yield and agronomic traits to identify superior varieties for the breeding program. To this effect, 20 improved varieties and a local cultivar were planted at two locations in central Ethiopia during the main cropping season of 2017/18 in a randomized complete block design using three replications. Analysis of variance of tuber yield and yield traits at each location and over locations, revealed the existence of highly significant (P < 0.01) differences among varieties in all agronomic and yield traits. Phenotypic coefficient of variation values ranged from 0.75% (specific gravity) to 32.22% (total starch yield) while the genotypic coefficient of variation values ranged between 0.70% (specific gravity) to 30.22% (total starch yield). Maximum difference between phenotypic and genotypic coefficient of variation values were noted for stem number, average tuber number, average tuber weight, number of leaves per plant and tuber yield. Hence, these traits are substantially influenced by the physiological status of the seed tuber at planting and by the environment, post emergence. Range of variability for most of the traits was high, indicating ample scope for selection and improvement in these traits. The estimated values for broad sense heritability and genetic advance, as percent of mean, ranged from 33.52% to 98.66% and 1.35% to 58.26%, respectively. All the traits had high heritability values, except average tuber number per hill, days to physiological maturity, average tuber weight and number of leaves per plant with moderate heritability values.
format: application/pdf
format: text/html
creator: Gebrehanna Lemma Tessema
creator: Ali Wassu Mohammed
creator: Desta Tesfaye Abebe
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.12860
publisher: PeerJ Inc.
rights: © 2022 Gebrehanna et al.
abstract: Information on the extent of genetic variability and association among quantitative traits are vital for any crop improvement program and the development of suitable selection strategies. Limited research has been carried out thus far on potato genetic variability and trait association. This study on genetic variability and association among quantitative traits was conducted to assess the extent of genetic variability among yield and agronomic traits to identify superior varieties for the breeding program. To this effect, 20 improved varieties and a local cultivar were planted at two locations in central Ethiopia during the main cropping season of 2017/18 in a randomized complete block design using three replications. Analysis of variance of tuber yield and yield traits at each location and over locations, revealed the existence of highly significant (P < 0.01) differences among varieties in all agronomic and yield traits. Phenotypic coefficient of variation values ranged from 0.75% (specific gravity) to 32.22% (total starch yield) while the genotypic coefficient of variation values ranged between 0.70% (specific gravity) to 30.22% (total starch yield). Maximum difference between phenotypic and genotypic coefficient of variation values were noted for stem number, average tuber number, average tuber weight, number of leaves per plant and tuber yield. Hence, these traits are substantially influenced by the physiological status of the seed tuber at planting and by the environment, post emergence. Range of variability for most of the traits was high, indicating ample scope for selection and improvement in these traits. The estimated values for broad sense heritability and genetic advance, as percent of mean, ranged from 33.52% to 98.66% and 1.35% to 58.26%, respectively. All the traits had high heritability values, except average tuber number per hill, days to physiological maturity, average tuber weight and number of leaves per plant with moderate heritability values.
bibliographic citation: Tessema et al. (2022) Genetic variability studies for tuber yield and yield attributes in Ethiopian released potato (Solanum tuberosum L.) varieties. PeerJ 10:e12860 https://doi.org/10.7717/peerj.12860
date submitted: 2020-06-11
date accepted: 2022-01-09
issued: 2022-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tessema
  given name: Gebrehanna Lemma
author list: Agent
  family name: Mohammed
  given name: Ali Wassu
author list: Agent
  family name: Abebe
  given name: Desta Tesfaye
doi: 10.7717/peerj.12860
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-10
copyright: © 2022 Gebrehanna et al.
attribution name: Gebrehanna et al.

Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem
type: item
type: AcademicArticle
description: Soil microbes are an essential component of terrestrial ecosystems and drive many biogeochemical processes throughout the soil profile. Prior field studies mainly focused on the vertical patterns of soil microbial communities, meaning their temporal dynamics have been largely neglected. In the present study, we investigated the vertical and temporal patterns of soil bacterial and archaeal communities in a wheat-soybean rotation agroecosystem at a depth of millions of sequences per sample. Our results revealed different vertical bacterial and archaeal richness patterns: bacterial richness was lowest in the deep soil layer and peaked in the surface or middle soil layer. In contrast, archaeal richness did not differ among soil layers. PERMANOVA analysis indicated that both bacterial and archaeal community compositions were significantly impacted by soil depth but unaffected by sampling time. Notably, the proportion of rare bacteria gradually decreased along with the soil profile. The rare bacterial community composition was the most important indicator for soil nutrient fertility index, as determined by random forest analysis. The soil prokaryotic co-occurrence networks of the surface and middle soil layers are more connected and harbored fewer negative links than that of the deep soil layer. Overall, our results highlighted soil depth as a more important determinant than temporal variation in shaping the soil prokaryotic community and interspecific interactions and revealed a potential role of rare taxa in soil biogeochemical function.
format: application/pdf
format: text/html
creator: Mika Yokota
creator: Yupeng Guan
creator: Yi Fan
creator: Ximei Zhang
creator: Wei Yang
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.12868
publisher: PeerJ Inc.
rights: © 2022 Yokota et al.
abstract: Soil microbes are an essential component of terrestrial ecosystems and drive many biogeochemical processes throughout the soil profile. Prior field studies mainly focused on the vertical patterns of soil microbial communities, meaning their temporal dynamics have been largely neglected. In the present study, we investigated the vertical and temporal patterns of soil bacterial and archaeal communities in a wheat-soybean rotation agroecosystem at a depth of millions of sequences per sample. Our results revealed different vertical bacterial and archaeal richness patterns: bacterial richness was lowest in the deep soil layer and peaked in the surface or middle soil layer. In contrast, archaeal richness did not differ among soil layers. PERMANOVA analysis indicated that both bacterial and archaeal community compositions were significantly impacted by soil depth but unaffected by sampling time. Notably, the proportion of rare bacteria gradually decreased along with the soil profile. The rare bacterial community composition was the most important indicator for soil nutrient fertility index, as determined by random forest analysis. The soil prokaryotic co-occurrence networks of the surface and middle soil layers are more connected and harbored fewer negative links than that of the deep soil layer. Overall, our results highlighted soil depth as a more important determinant than temporal variation in shaping the soil prokaryotic community and interspecific interactions and revealed a potential role of rare taxa in soil biogeochemical function.
bibliographic citation: Yokota et al. (2022) Vertical and temporal variations of soil bacterial and archaeal communities in wheat-soybean rotation agroecosystem. PeerJ 10:e12868 https://doi.org/10.7717/peerj.12868
date submitted: 2021-08-30
date accepted: 2022-01-10
issued: 2022-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yokota
  given name: Mika
author list: Agent
  family name: Guan
  given name: Yupeng
author list: Agent
  family name: Fan
  given name: Yi
author list: Agent
  family name: Zhang
  given name: Ximei
author list: Agent
  family name: Yang
  given name: Wei
doi: 10.7717/peerj.12868
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-10
copyright: ©2022 Yokota et al.
attribution name: Yokota et al.

Determinants of quality of life and well-being in cognitively unimpaired older adults: a systematic review
type: item
type: AcademicArticle
description: Objective It is important to know the psychological variables that are related to quality of life and well-being in healthy elderly people. The main objective of the present review is to analyse which factors, through psychological variables, are determinant on the adaptive processes that acquire relevance in the last stage of life. Data sources An electronic search was conducted in WOS, Science Direct, PsycARTICLES, Psychology Database and Psycinfo. Study selection The search terms used were derived from the combination of the following search string: ((“Emotional Factors” OR “Emotional Effects”) AND (“Emotional Intelligence” OR “Emotional Regulation”) AND (“Quality of Life” OR “Personal Satisfaction”) AND (“Healthy Old People” OR “Healthy Old Adults”) AND (“Healthy Aging” OR “Successful Aging”)). Data extraction 11th April 2021. Data synthesis In total, 13 articles were selected. Conclusions The articles showed the importance of social support, proactive coping strategies (emotional regulation) and emotional intelligence as key factors in the elderly population for their positive influence on variables such as quality of life and well-being. Prospero ID: CRD42021224789
format: application/pdf
format: text/html
creator: María Dolores Frías-Luque
creator: Abel Toledano-González
subject: Geriatrics
subject: Psychiatry and Psychology
subject: Rehabilitation
description: doi:10.7717/peerj.12900
publisher: PeerJ Inc.
rights: © 2022 Frías-Luque and Toledano-González
abstract: Objective It is important to know the psychological variables that are related to quality of life and well-being in healthy elderly people. The main objective of the present review is to analyse which factors, through psychological variables, are determinant on the adaptive processes that acquire relevance in the last stage of life. Data sources An electronic search was conducted in WOS, Science Direct, PsycARTICLES, Psychology Database and Psycinfo. Study selection The search terms used were derived from the combination of the following search string: ((“Emotional Factors” OR “Emotional Effects”) AND (“Emotional Intelligence” OR “Emotional Regulation”) AND (“Quality of Life” OR “Personal Satisfaction”) AND (“Healthy Old People” OR “Healthy Old Adults”) AND (“Healthy Aging” OR “Successful Aging”)). Data extraction 11th April 2021. Data synthesis In total, 13 articles were selected. Conclusions The articles showed the importance of social support, proactive coping strategies (emotional regulation) and emotional intelligence as key factors in the elderly population for their positive influence on variables such as quality of life and well-being. Prospero ID: CRD42021224789
bibliographic citation: Frías-Luque et al. (2022) Determinants of quality of life and well-being in cognitively unimpaired older adults: a systematic review. PeerJ 10:e12900 https://doi.org/10.7717/peerj.12900
date submitted: 2021-07-15
date accepted: 2022-01-17
issued: 2022-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frías-Luque
  given name: María Dolores
author list: Agent
  family name: Toledano-González
  given name: Abel
doi: 10.7717/peerj.12900
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-10
copyright: © 2022 Frías-Luque and Toledano-González
attribution name: Frías-Luque and Toledano-González

The effect of farmland on the surface water of the Aral Sea Region using Multi-source Satellite Data
type: item
type: AcademicArticle
description: Background The improper land utilization has brought tremendous pressure on the surface water of the Aral Sea Region in the past decades. It was seriously hindered for construction of the Green Silk Road Economic Belt by the fragile environment. Therefore, it is of great necessity for environmental protection and social development to monitor the change of surface water in the Aral Sea Region. Methods In this study, LandTrendr algorithm was used on Landsat time-series data to characterize the change in farmland on the Google Earth Engine platform. Based on multi-source data, the water area changes of the Aral Sea were extracted based on the Google Earth Engine, and the mean method was utilized to extract the changes in water level and water storage. Finally, a water-farmland coupling degree model was utilized to evaluate the impact of farmland changes on the surface water in the Aral Sea Region. Results As a result, the change of farmland is as follows: the farmland area of the Aral Sea Region has abandoned 3,129 km2 from 1987 to 2019, with overall accuracy of 85.3%. The farmland change had increased the drainage downstream of the Amu Darya River and the Syr Darya River. It has led area of the Aral Sea to decrease each year continuously. The area of the Aral Sea shrank by 1,606.36 km2 per year from 1987 to 2019. Furthermore, Aral Sea’s water level decreased by 0.13 m per year from 2003 to 2009. The amount of water storage in the Aral Sea Region also showed a downward trend from 2002 to 2016. There was a high-quality coupling coordination 0.903 relationship between surface water and farmland. It will increase the burden of water for people’s normal daily life by the water loss resources caused by abandoned farmland. This study emphasized threat of unreasonable farmland management to surface water of the Aral Sea Region. The findings contributed for decision makers to formulating effective reasonable policies to protect surface water and use land of the Aral Sea Regio…
format: application/pdf
format: text/html
creator: Jiancong Shi
creator: Qiaozhen Guo
creator: Shuang Zhao
creator: Yiting Su
creator: Yanqing Shi
subject: Agricultural Science
subject: Plant Science
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.12920
publisher: PeerJ Inc.
rights: © 2022 Shi et al.
abstract: Background The improper land utilization has brought tremendous pressure on the surface water of the Aral Sea Region in the past decades. It was seriously hindered for construction of the Green Silk Road Economic Belt by the fragile environment. Therefore, it is of great necessity for environmental protection and social development to monitor the change of surface water in the Aral Sea Region. Methods In this study, LandTrendr algorithm was used on Landsat time-series data to characterize the change in farmland on the Google Earth Engine platform. Based on multi-source data, the water area changes of the Aral Sea were extracted based on the Google Earth Engine, and the mean method was utilized to extract the changes in water level and water storage. Finally, a water-farmland coupling degree model was utilized to evaluate the impact of farmland changes on the surface water in the Aral Sea Region. Results As a result, the change of farmland is as follows: the farmland area of the Aral Sea Region has abandoned 3,129 km2 from 1987 to 2019, with overall accuracy of 85.3%. The farmland change had increased the drainage downstream of the Amu Darya River and the Syr Darya River. It has led area of the Aral Sea to decrease each year continuously. The area of the Aral Sea shrank by 1,606.36 km2 per year from 1987 to 2019. Furthermore, Aral Sea’s water level decreased by 0.13 m per year from 2003 to 2009. The amount of water storage in the Aral Sea Region also showed a downward trend from 2002 to 2016. There was a high-quality coupling coordination 0.903 relationship between surface water and farmland. It will increase the burden of water for people’s normal daily life by the water loss resources caused by abandoned farmland. This study emphasized threat of unreasonable farmland management to surface water of the Aral Sea Region. The findings contributed for decision makers to formulating effective reasonable policies to protect surface water and use land of the Aral Sea Regio…
bibliographic citation: Shi et al. (2022) The effect of farmland on the surface water of the Aral Sea Region using Multi-source Satellite Data. PeerJ 10:e12920 https://doi.org/10.7717/peerj.12920
date submitted: 2021-07-30
date accepted: 2022-01-20
issued: 2022-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Jiancong
author list: Agent
  family name: Guo
  given name: Qiaozhen
author list: Agent
  family name: Zhao
  given name: Shuang
author list: Agent
  family name: Su
  given name: Yiting
author list: Agent
  family name: Shi
  given name: Yanqing
doi: 10.7717/peerj.12920
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-10
copyright: © 2022 Shi et al.
attribution name: Shi et al.

Clinical predictors and electrodiagnostic characteristics in patients with Guillain-Barré syndrome with respiratory failure: a retrospective, matched case-control study
type: item
type: AcademicArticle
description: Background Respiratory failure is a common complication of Guillain-Barré syndrome (GBS). This study aimed to determine the clinical predictors and electrodiagnostic (EDx) characteristics in patients with Guillain-Barré syndrome (GBS) with respiratory failure. Methods The retrospective study included 29 confirmed GBS cases with respiratory failure and age- (±5 years) and sex-matched controls (1:1). The dependent t-test and McNemar–Bowker test were used to analyse the continuous and categorical data, respectively. In addition, a multiple logistic regression analysis was used to analyse the predictive factors for respiratory failure. Results Among both cases and controls, the majority were male (72.4%), and the average age was 50.9 years. The data showed that patients with respiratory failure had higher GBS disability scores, lower motor power (≤3) of the hip flexors and ankle dorsiflexors, and experienced facial and bulbar palsy. In the multivariate analysis, the significant predictive factors were bulbar palsy (AOR 10.4 [95% CI [2.6–41.4]) and motor power of hip flexors ≤ 3 (AOR 31.4 [95% CI [3.1–314.5]). Patients with respiratory failure had lower compound muscle action potential amplitude of the ulnar and tibial nerves. The median, ulnar, and tibial nerve conduction studies were more likely to reflect inexcitability. The GBS subtypes in GBS patients with and without respiratory failure were not significantly different. Conclusions Bulbar palsy and motor power of the hip flexors ≤ 3 were significant predictors for respiratory failure. The GBS subtypes in patients with and without respiratory failure were not significantly different.
format: application/pdf
format: text/html
creator: Kanchana Charoentanyarak
creator: Apiradee Singjam
creator: Jittima Saengsuwan
subject: Epidemiology
subject: Neurology
subject: Respiratory Medicine
description: doi:10.7717/peerj.12930
publisher: PeerJ Inc.
rights: © 2022 Charoentanyarak et al.
abstract: Background Respiratory failure is a common complication of Guillain-Barré syndrome (GBS). This study aimed to determine the clinical predictors and electrodiagnostic (EDx) characteristics in patients with Guillain-Barré syndrome (GBS) with respiratory failure. Methods The retrospective study included 29 confirmed GBS cases with respiratory failure and age- (±5 years) and sex-matched controls (1:1). The dependent t-test and McNemar–Bowker test were used to analyse the continuous and categorical data, respectively. In addition, a multiple logistic regression analysis was used to analyse the predictive factors for respiratory failure. Results Among both cases and controls, the majority were male (72.4%), and the average age was 50.9 years. The data showed that patients with respiratory failure had higher GBS disability scores, lower motor power (≤3) of the hip flexors and ankle dorsiflexors, and experienced facial and bulbar palsy. In the multivariate analysis, the significant predictive factors were bulbar palsy (AOR 10.4 [95% CI [2.6–41.4]) and motor power of hip flexors ≤ 3 (AOR 31.4 [95% CI [3.1–314.5]). Patients with respiratory failure had lower compound muscle action potential amplitude of the ulnar and tibial nerves. The median, ulnar, and tibial nerve conduction studies were more likely to reflect inexcitability. The GBS subtypes in GBS patients with and without respiratory failure were not significantly different. Conclusions Bulbar palsy and motor power of the hip flexors ≤ 3 were significant predictors for respiratory failure. The GBS subtypes in patients with and without respiratory failure were not significantly different.
bibliographic citation: Charoentanyarak et al. (2022) Clinical predictors and electrodiagnostic characteristics in patients with Guillain-Barré syndrome with respiratory failure: a retrospective, matched case-control study. PeerJ 10:e12930 https://doi.org/10.7717/peerj.12930
date submitted: 2021-09-30
date accepted: 2022-01-21
issued: 2022-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Charoentanyarak
  given name: Kanchana
author list: Agent
  family name: Singjam
  given name: Apiradee
author list: Agent
  family name: Saengsuwan
  given name: Jittima
doi: 10.7717/peerj.12930
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-10
copyright: ©2022 Charoentanyarak et al.
attribution name: Charoentanyarak et al.

Depletion of RIPK4 parallels higher malignancy potential in cutaneous squamous cell carcinoma
type: item
type: AcademicArticle
description: Background The RIPK4 (receptor-interacting protein kinase 4), a member of the RIPK family, acts as an important regulator of epidermal differentiation, cutaneous inflammation, and cutaneous wound repair. However, Until now, the role of RIPK4 in tumorigenesis remains elusive. There have been no studies exploring the effects of RIPK4 on the signaling pathway in cutaneous squamous cell carcinoma (SCC). It remains unknown whether RIPK4 expression, which can affect the degree of epidermal differentiation can also influence the radiosensitivity of skin SCC. It is urgent to fully elucidate the biological mechanism by which RIPK4 promotes carcinogenesis in skin SCC and determine whether RIPK4 expression levels predicts the sensitivity to radiotherapy in skin SCC. Methods Human skin SCC cell line, A431, was transfected with either small interfering RNAs (siRNAs) targeting RIPK4 (siR-RIPK4) or negative control siRNA (siR-NC). Western blotting was used to detect the expression of RIPK4 and Raf/MEK/ERK pathway-related proteins. The cells were irradiated using an X-ray irradiator at 6 MV with different radiation doses (0, 2, 6, and 10 Gy). Cell proliferation analysis, colony formation assay, transwell cell migration and invasion assay, cell cycle and apoptosis analysis were conducted to investigate the effect of RIPK4 silencing on skin SCC malignancy and radiosensitivity. Results RIPK4 protein expression was significantly decreased in the A431 cells transfected with siR-RIPK4, compared with the A431 cells transfected with siR-NC. RIPK4 silencing facilitated the proliferation, colony formation, migration, and invasion ability of A431 cell line, while cell cycle progression or cell apoptosis were not significantly influenced. In contrast with the previous literature, Raf/MEK/ERK pathway was not effected by RIPK4 knockdown in skin SCC. RIPK4 knockdown could not reverse the radiation resistance of A431 cells to irradiation in vitro. Conclusions In general, although depletion of RIPK…
format: application/pdf
format: text/html
creator: Jing Xu
creator: Dongping Wu
creator: Bicheng Zhang
creator: Chi Pan
creator: Yinglu Guo
creator: Qichun Wei
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.12932
publisher: PeerJ Inc.
rights: © 2022 Xu et al.
abstract: Background The RIPK4 (receptor-interacting protein kinase 4), a member of the RIPK family, acts as an important regulator of epidermal differentiation, cutaneous inflammation, and cutaneous wound repair. However, Until now, the role of RIPK4 in tumorigenesis remains elusive. There have been no studies exploring the effects of RIPK4 on the signaling pathway in cutaneous squamous cell carcinoma (SCC). It remains unknown whether RIPK4 expression, which can affect the degree of epidermal differentiation can also influence the radiosensitivity of skin SCC. It is urgent to fully elucidate the biological mechanism by which RIPK4 promotes carcinogenesis in skin SCC and determine whether RIPK4 expression levels predicts the sensitivity to radiotherapy in skin SCC. Methods Human skin SCC cell line, A431, was transfected with either small interfering RNAs (siRNAs) targeting RIPK4 (siR-RIPK4) or negative control siRNA (siR-NC). Western blotting was used to detect the expression of RIPK4 and Raf/MEK/ERK pathway-related proteins. The cells were irradiated using an X-ray irradiator at 6 MV with different radiation doses (0, 2, 6, and 10 Gy). Cell proliferation analysis, colony formation assay, transwell cell migration and invasion assay, cell cycle and apoptosis analysis were conducted to investigate the effect of RIPK4 silencing on skin SCC malignancy and radiosensitivity. Results RIPK4 protein expression was significantly decreased in the A431 cells transfected with siR-RIPK4, compared with the A431 cells transfected with siR-NC. RIPK4 silencing facilitated the proliferation, colony formation, migration, and invasion ability of A431 cell line, while cell cycle progression or cell apoptosis were not significantly influenced. In contrast with the previous literature, Raf/MEK/ERK pathway was not effected by RIPK4 knockdown in skin SCC. RIPK4 knockdown could not reverse the radiation resistance of A431 cells to irradiation in vitro. Conclusions In general, although depletion of RIPK…
bibliographic citation: Xu et al. (2022) Depletion of RIPK4 parallels higher malignancy potential in cutaneous squamous cell carcinoma. PeerJ 10:e12932 https://doi.org/10.7717/peerj.12932
date submitted: 2021-09-08
date accepted: 2022-01-23
issued: 2022-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Jing
author list: Agent
  family name: Wu
  given name: Dongping
author list: Agent
  family name: Zhang
  given name: Bicheng
author list: Agent
  family name: Pan
  given name: Chi
author list: Agent
  family name: Guo
  given name: Yinglu
author list: Agent
  family name: Wei
  given name: Qichun
doi: 10.7717/peerj.12932
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-10
copyright: © 2022 Xu et al.
attribution name: Xu et al.

Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum)
type: item
type: AcademicArticle
description: Serine hydroxymethyltransferase (SHMT) is one of the most important enzyme families in one-carbon metabolic pathway and photorespiration within plant cells. Recently studies reported the active roles of plant SHMTs in defending abiotic stresses. However, genome-scale analysis of SHMT in tomato is currently unknown. In this study, seven SHMT genes were identified in the tomato genome using a genome-wide search approach. In addition, their physicochemical properties, protein secondary structure, subcellular localization, gene structure, conserved motifs, phylogenetic and collinear relationships were analyzed. Our results demonstrated that tomato SHMT members were divided into two group and four subgroups, and they were conserved with the orthologs of other plants. Analysis of cis-acting elements showed that each of the SlSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Finally, qRT-PCR analysis indicated that SlSHMTs were expressed at different levels in different tissues, and they responded to UV, cold, heat, NaCl, H2O2, ABA and PEG treatments. These results provided definite evidence that SlSHMTs might involve in growth, development and stress responses in tomato, which laid a foundation for future functional studies of SlSHMTs.
format: application/pdf
format: text/html
creator: Zesheng Liu
creator: Xuejuan Pan
creator: Chunlei Wang
creator: Fahong Yun
creator: Dengjing Huang
creator: Yandong Yao
creator: Rong Gao
creator: Fujin Ye
creator: Xingjuan Liu
creator: Weibiao Liao
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12943
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Serine hydroxymethyltransferase (SHMT) is one of the most important enzyme families in one-carbon metabolic pathway and photorespiration within plant cells. Recently studies reported the active roles of plant SHMTs in defending abiotic stresses. However, genome-scale analysis of SHMT in tomato is currently unknown. In this study, seven SHMT genes were identified in the tomato genome using a genome-wide search approach. In addition, their physicochemical properties, protein secondary structure, subcellular localization, gene structure, conserved motifs, phylogenetic and collinear relationships were analyzed. Our results demonstrated that tomato SHMT members were divided into two group and four subgroups, and they were conserved with the orthologs of other plants. Analysis of cis-acting elements showed that each of the SlSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Finally, qRT-PCR analysis indicated that SlSHMTs were expressed at different levels in different tissues, and they responded to UV, cold, heat, NaCl, H2O2, ABA and PEG treatments. These results provided definite evidence that SlSHMTs might involve in growth, development and stress responses in tomato, which laid a foundation for future functional studies of SlSHMTs.
bibliographic citation: Liu et al. (2022) Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum). PeerJ 10:e12943 https://doi.org/10.7717/peerj.12943
date submitted: 2021-11-09
date accepted: 2022-01-24
issued: 2022-02-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Zesheng
author list: Agent
  family name: Pan
  given name: Xuejuan
author list: Agent
  family name: Wang
  given name: Chunlei
author list: Agent
  family name: Yun
  given name: Fahong
author list: Agent
  family name: Huang
  given name: Dengjing
author list: Agent
  family name: Yao
  given name: Yandong
author list: Agent
  family name: Gao
  given name: Rong
author list: Agent
  family name: Ye
  given name: Fujin
author list: Agent
  family name: Liu
  given name: Xingjuan
author list: Agent
  family name: Liao
  given name: Weibiao
doi: 10.7717/peerj.12943
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-10
copyright: ©2022 Liu et al.
attribution name: Liu et al.

A comparative study of bacterial diversity based on effects of three different shade shed types in the rhizosphere of Panax quiquefolium L.
type: item
type: AcademicArticle
description: Background Shading is an important factor affecting the cultivation of American ginseng, as it influences crop quality and yield. Rhizosphere microorganisms are also crucial for normal plant growth and development. However, whether different shade types significantly change American ginseng rhizosphere microorganisms is unknown. Methods This study evaluated the rhizosphere soils of American ginseng under traditional, high flag and high arch shade sheds. High-throughput 16S rRNA gene sequencing determined the change of rhizosphere bacterial communities. Results The microbial diversity in rhizosphere soils of American ginseng significantly changed under different shading conditions. The bacteria diversity was more abundant in the high arch shade than flat and traditional shades. Different bacterial genera, including Bradyrhizobium, Rhizobium, Sphingomonas, Streptomyces and Nitrospira, showed significantly different abundances. Different shading conditions changed the microbial metabolic function in the American ginseng rhizosphere soils. The three types of shade sheds had specific enriched functional groups. The abundance of ATP-binding cassette (ABC) transporters consistently increased in the bacterial microbiota. These results help understand the influence of shading systems on the rhizosphere microecology of American ginseng, and contribute to the American ginseng cultivation.
format: application/pdf
format: text/html
creator: Xianchang Wang
creator: Xu Guo
creator: Lijuan Hou
creator: Jiaohong Zhang
creator: Jing Hu
creator: Feng Zhang
creator: Jilei Mao
creator: Zhifen Wang
creator: Congjing Zhang
creator: Jinlong Han
creator: Yanwei Zhu
creator: Chao Liu
creator: Jinyue Sun
creator: Chenggang Shan
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.12807
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Shading is an important factor affecting the cultivation of American ginseng, as it influences crop quality and yield. Rhizosphere microorganisms are also crucial for normal plant growth and development. However, whether different shade types significantly change American ginseng rhizosphere microorganisms is unknown. Methods This study evaluated the rhizosphere soils of American ginseng under traditional, high flag and high arch shade sheds. High-throughput 16S rRNA gene sequencing determined the change of rhizosphere bacterial communities. Results The microbial diversity in rhizosphere soils of American ginseng significantly changed under different shading conditions. The bacteria diversity was more abundant in the high arch shade than flat and traditional shades. Different bacterial genera, including Bradyrhizobium, Rhizobium, Sphingomonas, Streptomyces and Nitrospira, showed significantly different abundances. Different shading conditions changed the microbial metabolic function in the American ginseng rhizosphere soils. The three types of shade sheds had specific enriched functional groups. The abundance of ATP-binding cassette (ABC) transporters consistently increased in the bacterial microbiota. These results help understand the influence of shading systems on the rhizosphere microecology of American ginseng, and contribute to the American ginseng cultivation.
bibliographic citation: Wang et al. (2022) A comparative study of bacterial diversity based on effects of three different shade shed types in the rhizosphere of Panax quiquefolium L.. PeerJ 10:e12807 https://doi.org/10.7717/peerj.12807
date submitted: 2021-01-11
date accepted: 2021-12-27
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xianchang
author list: Agent
  family name: Guo
  given name: Xu
author list: Agent
  family name: Hou
  given name: Lijuan
author list: Agent
  family name: Zhang
  given name: Jiaohong
author list: Agent
  family name: Hu
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Feng
author list: Agent
  family name: Mao
  given name: Jilei
author list: Agent
  family name: Wang
  given name: Zhifen
author list: Agent
  family name: Zhang
  given name: Congjing
author list: Agent
  family name: Han
  given name: Jinlong
author list: Agent
  family name: Zhu
  given name: Yanwei
author list: Agent
  family name: Liu
  given name: Chao
author list: Agent
  family name: Sun
  given name: Jinyue
author list: Agent
  family name: Shan
  given name: Chenggang
doi: 10.7717/peerj.12807
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Unraveling the hidden paleobiodiversity of the Middle Devonian (Emsian) crinoids (Crinoidea, Echinodermata) from Poland
type: item
type: AcademicArticle
description: Most previous publications on Devonian crinoids from the Holy Cross Mountains in Poland have concentrated on crinoid columns, and until now, little has been published about crinoid cups and calyxes. Herein, five crinoid taxa are described from an abundant occurrence of aboral cups and partial crowns from the Bukowa Góra Member (Emsian) in the Holy Cross Mountains of southern Poland. The following taxa are described: Bactrocrinites sp., Codiacrinus sevastopuloi sp. nov., Halocrinites geminatus (Bohatý, 2005), Halocrinites schlotheimii Steininger, 1831, and a single brachial plate from a flexible crinoid placed in Flexibilia incertae sedis. Simple discoid holdfasts are also present encrusted to cylindrical stromatoporoids. These taxa are the first crinoids described from the remains of partial crowns from Emsian strata of Poland.
format: application/pdf
format: text/html
creator: William I. Ausich
creator: Mariusz A. Salamon
creator: Bartosz J. Płachno
creator: Tomasz Brachaniec
creator: Wojciech Krawczyński
creator: Andrzej Boczarowski
creator: Karolina Paszcza
creator: Magdalena Łukowiak
creator: Przemysław Gorzelak
subject: Marine Biology
subject: Paleontology
description: doi:10.7717/peerj.12842
publisher: PeerJ Inc.
rights: © 2022 Ausich et al.
abstract: Most previous publications on Devonian crinoids from the Holy Cross Mountains in Poland have concentrated on crinoid columns, and until now, little has been published about crinoid cups and calyxes. Herein, five crinoid taxa are described from an abundant occurrence of aboral cups and partial crowns from the Bukowa Góra Member (Emsian) in the Holy Cross Mountains of southern Poland. The following taxa are described: Bactrocrinites sp., Codiacrinus sevastopuloi sp. nov., Halocrinites geminatus (Bohatý, 2005), Halocrinites schlotheimii Steininger, 1831, and a single brachial plate from a flexible crinoid placed in Flexibilia incertae sedis. Simple discoid holdfasts are also present encrusted to cylindrical stromatoporoids. These taxa are the first crinoids described from the remains of partial crowns from Emsian strata of Poland.
bibliographic citation: Ausich et al. (2022) Unraveling the hidden paleobiodiversity of the Middle Devonian (Emsian) crinoids (Crinoidea, Echinodermata) from Poland. PeerJ 10:e12842 https://doi.org/10.7717/peerj.12842
date submitted: 2021-12-13
date accepted: 2022-01-06
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ausich
  given name: William I.
author list: Agent
  family name: Salamon
  given name: Mariusz A.
author list: Agent
  family name: Płachno
  given name: Bartosz J.
author list: Agent
  family name: Brachaniec
  given name: Tomasz
author list: Agent
  family name: Krawczyński
  given name: Wojciech
author list: Agent
  family name: Boczarowski
  given name: Andrzej
author list: Agent
  family name: Paszcza
  given name: Karolina
author list: Agent
  family name: Łukowiak
  given name: Magdalena
author list: Agent
  family name: Gorzelak
  given name: Przemysław
doi: 10.7717/peerj.12842
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Ausich et al.
attribution name: Ausich et al.

Validation of a battery of inhibitory control tasks reveals a multifaceted structure in non-human primates
type: item
type: AcademicArticle
description: Inhibitory control, the ability to override an inappropriate prepotent response, is crucial in many aspects of everyday life. However, the various paradigms designed to measure inhibitory control often suffer from a lack of systematic validation and have yielded mixed results. Thus the nature of this ability remains unclear, is it a general construct or a family of distinct sub-components? Therefore, the aim of this study was first to demonstrate the content validity and the temporal repeatability of a battery of inhibitory control tasks. Then we wanted to assess the contextual consistency of performances between these tasks to better understand the structure of inhibitory control. We tested 21 rhesus macaques (Macaca mulatta, 12 males, nine females) in a battery of touchscreen tasks assessing three main components of inhibitory control: inhibition of a distraction (using a Distraction task), inhibition of an impulsive action (using a Go/No-go task) and inhibition of a cognitive set (using a Reversal learning task). All tasks were reliable and effective at measuring the inhibition of a prepotent response. However, while there was consistency of performance between the inhibition of a distraction and the inhibition of an action, representing a response-driven basic form of inhibition, this was not found for the inhibition of a cognitive set. We argue that the inhibition of a cognitive set is a more cognitively demanding form of inhibition. This study gives a new insight in the multifaceted structure of inhibitory control and highlights the importance of a systematic validation of cognitive tasks in animal cognition.
format: application/pdf
format: text/html
creator: Louise Loyant
creator: Bridget M. Waller
creator: Jérôme Micheletta
creator: Marine Joly
subject: Animal Behavior
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.12863
publisher: PeerJ Inc.
rights: © 2022 Loyant et al.
abstract: Inhibitory control, the ability to override an inappropriate prepotent response, is crucial in many aspects of everyday life. However, the various paradigms designed to measure inhibitory control often suffer from a lack of systematic validation and have yielded mixed results. Thus the nature of this ability remains unclear, is it a general construct or a family of distinct sub-components? Therefore, the aim of this study was first to demonstrate the content validity and the temporal repeatability of a battery of inhibitory control tasks. Then we wanted to assess the contextual consistency of performances between these tasks to better understand the structure of inhibitory control. We tested 21 rhesus macaques (Macaca mulatta, 12 males, nine females) in a battery of touchscreen tasks assessing three main components of inhibitory control: inhibition of a distraction (using a Distraction task), inhibition of an impulsive action (using a Go/No-go task) and inhibition of a cognitive set (using a Reversal learning task). All tasks were reliable and effective at measuring the inhibition of a prepotent response. However, while there was consistency of performance between the inhibition of a distraction and the inhibition of an action, representing a response-driven basic form of inhibition, this was not found for the inhibition of a cognitive set. We argue that the inhibition of a cognitive set is a more cognitively demanding form of inhibition. This study gives a new insight in the multifaceted structure of inhibitory control and highlights the importance of a systematic validation of cognitive tasks in animal cognition.
bibliographic citation: Loyant et al. (2022) Validation of a battery of inhibitory control tasks reveals a multifaceted structure in non-human primates. PeerJ 10:e12863 https://doi.org/10.7717/peerj.12863
date submitted: 2021-09-28
date accepted: 2022-01-09
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Loyant
  given name: Louise
author list: Agent
  family name: Waller
  given name: Bridget M.
author list: Agent
  family name: Micheletta
  given name: Jérôme
author list: Agent
  family name: Joly
  given name: Marine
doi: 10.7717/peerj.12863
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: © 2022 Loyant et al.
attribution name: Loyant et al.

Autophagy-related prognostic signature for survival prediction of triple negative breast cancer
type: item
type: AcademicArticle
description: Background Triple-negative breast cancer (TNBC) is a highly aggressive type of cancer with few available treatment methods. The aim of the current study was to provide a prognostic autophagy-related gene (ARG) model to predict the outcomes for TNBC patients using bioinformatic analysis. Methods mRNA expression data and its clinical information for TNBC samples obtained from The Cancer Genome Atlas (TCGA) and Metabric databases were extracted for bioinformatic analysis. Differentially expressed autophagy genes were identified using the Wilcoxon rank sum test in R software. ARGs were downloaded from the Human Autophagy Database. The Kaplan–Meier plotter was employed to determine the prognostic significance of the ARGs. The sample splitting method and Cox regression analysis were employed to establish the risk model and to demonstrate the association between the ARGs and the survival duration. The corresponding ARG-transcription factor interaction network was visualized using the Cytoscape software. Results A signature-based risk score model was established for eight genes (ITGA3, HSPA8, CTSD, ATG12, CLN3, ATG7, MAP1LC3C, and WIPI1) using the TCGA data and the model was validated with the GSE38959 and Metabric datasets, respectively. Patients with high risk scores had worse survival outcomes than those with low risk scores. Of note, amplification of ATG12 and reduction of WIPI were confirmed to be significantly correlated with the clinical stage of TNBC. Conclusion An eight-gene autophagic signature model was developed in this study to predict the survival risk for TNBC. The genes identified in the study may favor the design of target agents for autophagy control in advanced TNBC.
format: application/pdf
format: text/html
creator: Qiong Yang
creator: Kewang Sun
creator: Wenjie Xia
creator: Ying Li
creator: Miaochun Zhong
creator: Kefeng Lei
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.12878
publisher: PeerJ Inc.
rights: © 2022 Yang et al.
abstract: Background Triple-negative breast cancer (TNBC) is a highly aggressive type of cancer with few available treatment methods. The aim of the current study was to provide a prognostic autophagy-related gene (ARG) model to predict the outcomes for TNBC patients using bioinformatic analysis. Methods mRNA expression data and its clinical information for TNBC samples obtained from The Cancer Genome Atlas (TCGA) and Metabric databases were extracted for bioinformatic analysis. Differentially expressed autophagy genes were identified using the Wilcoxon rank sum test in R software. ARGs were downloaded from the Human Autophagy Database. The Kaplan–Meier plotter was employed to determine the prognostic significance of the ARGs. The sample splitting method and Cox regression analysis were employed to establish the risk model and to demonstrate the association between the ARGs and the survival duration. The corresponding ARG-transcription factor interaction network was visualized using the Cytoscape software. Results A signature-based risk score model was established for eight genes (ITGA3, HSPA8, CTSD, ATG12, CLN3, ATG7, MAP1LC3C, and WIPI1) using the TCGA data and the model was validated with the GSE38959 and Metabric datasets, respectively. Patients with high risk scores had worse survival outcomes than those with low risk scores. Of note, amplification of ATG12 and reduction of WIPI were confirmed to be significantly correlated with the clinical stage of TNBC. Conclusion An eight-gene autophagic signature model was developed in this study to predict the survival risk for TNBC. The genes identified in the study may favor the design of target agents for autophagy control in advanced TNBC.
bibliographic citation: Yang et al. (2022) Autophagy-related prognostic signature for survival prediction of triple negative breast cancer. PeerJ 10:e12878 https://doi.org/10.7717/peerj.12878
date submitted: 2020-05-14
date accepted: 2022-01-12
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Qiong
author list: Agent
  family name: Sun
  given name: Kewang
author list: Agent
  family name: Xia
  given name: Wenjie
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Zhong
  given name: Miaochun
author list: Agent
  family name: Lei
  given name: Kefeng
doi: 10.7717/peerj.12878
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Yang et al.
attribution name: Yang et al.

Comparative study on anatomical traits and gas exchange responses due to belowground hypoxic stress and thermal stress in three tropical seagrasses
type: item
type: AcademicArticle
description: Background The ability to maintain sufficient oxygen levels in the belowground tissues and the rhizosphere is crucial for the growth and survival of seagrasses in habitats with highly reduced sediment. Such ability varies depending on plant anatomical features and environmental conditions. Methods In the present study, we compared anatomical structures of roots, rhizomes and leaves of the tropical intertidal seagrasses, Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis, followed by an investigation of their gas exchange both in the belowground and aboveground tissues and photosynthetic electron transport rates (ETR) in response to experimental manipulations of O2 level (normoxia and root hypoxia) and temperature (30 °C and 40 °C). Results We found that C. rotundata and T. hemprichii displayed mostly comparable anatomical structures, whereas H. ovalis displayed various distinctive features, including leaf porosity, number and size of lacunae in roots and rhizomes and structure of radial O2 loss (ROL) barrier. H. ovalis also showed unique responses to root hypoxia and heat stress. Root hypoxia increased O2 release from belowground tissues and overall photosynthetic activity of H. ovalis but did not affect the other two seagrasses. More pronounced warming effects were detected in H. ovalis, measured as lower O2 release in the belowground tissues and overall photosynthetic capacity (O2 release and dissolved inorganic carbon uptake in the light and ETR). High temperature inhibited photosynthesis of C. rotundata and T. hemprichii but did not affect their O2 release in belowground tissues. Our data show that seagrasses inhabiting the same area respond differently to root hypoxia and temperature, possibly due to their differences in anatomical and physiological attributes. Halophila ovalis is highly dependent on photosynthesis and appears to be the most sensitive species with the highest tendency of O2 loss in hypoxic sediment. At the same time, its root oxidat…
format: application/pdf
format: text/html
creator: Sutthinut Soonthornkalump
creator: Yan Xiang Ow
creator: Chanida Saewong
creator: Pimchanok Buapet
subject: Marine Biology
subject: Plant Science
subject: Histology
subject: Biological Oceanography
description: doi:10.7717/peerj.12899
publisher: PeerJ Inc.
rights: © 2022 Soonthornkalump et al.
abstract: Background The ability to maintain sufficient oxygen levels in the belowground tissues and the rhizosphere is crucial for the growth and survival of seagrasses in habitats with highly reduced sediment. Such ability varies depending on plant anatomical features and environmental conditions. Methods In the present study, we compared anatomical structures of roots, rhizomes and leaves of the tropical intertidal seagrasses, Cymodocea rotundata, Thalassia hemprichii and Halophila ovalis, followed by an investigation of their gas exchange both in the belowground and aboveground tissues and photosynthetic electron transport rates (ETR) in response to experimental manipulations of O2 level (normoxia and root hypoxia) and temperature (30 °C and 40 °C). Results We found that C. rotundata and T. hemprichii displayed mostly comparable anatomical structures, whereas H. ovalis displayed various distinctive features, including leaf porosity, number and size of lacunae in roots and rhizomes and structure of radial O2 loss (ROL) barrier. H. ovalis also showed unique responses to root hypoxia and heat stress. Root hypoxia increased O2 release from belowground tissues and overall photosynthetic activity of H. ovalis but did not affect the other two seagrasses. More pronounced warming effects were detected in H. ovalis, measured as lower O2 release in the belowground tissues and overall photosynthetic capacity (O2 release and dissolved inorganic carbon uptake in the light and ETR). High temperature inhibited photosynthesis of C. rotundata and T. hemprichii but did not affect their O2 release in belowground tissues. Our data show that seagrasses inhabiting the same area respond differently to root hypoxia and temperature, possibly due to their differences in anatomical and physiological attributes. Halophila ovalis is highly dependent on photosynthesis and appears to be the most sensitive species with the highest tendency of O2 loss in hypoxic sediment. At the same time, its root oxidat…
bibliographic citation: Soonthornkalump et al. (2022) Comparative study on anatomical traits and gas exchange responses due to belowground hypoxic stress and thermal stress in three tropical seagrasses. PeerJ 10:e12899 https://doi.org/10.7717/peerj.12899
date submitted: 2021-10-01
date accepted: 2022-01-17
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soonthornkalump
  given name: Sutthinut
author list: Agent
  family name: Ow
  given name: Yan Xiang
author list: Agent
  family name: Saewong
  given name: Chanida
author list: Agent
  family name: Buapet
  given name: Pimchanok
doi: 10.7717/peerj.12899
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: © 2022 Soonthornkalump et al.
attribution name: Soonthornkalump et al.

Cyber-victimization and its association with depression among Vietnamese adolescents
type: item
type: AcademicArticle
description: Background Cyberbullying has become an alarming social issue, but little is known about its prevalence and consequences in many countries. This study investigated the prevalence of cyber-victimization and its association with depression among students in Ho Chi Minh City, Vietnam. Methods A cross-sectional study was conducted in 1,492 students from eight secondary schools and high schools in four urban and suburban areas. Multi-stage cluster sampling approach was used to recruit participants. Students participated in this study on a voluntary basis and completed a self-report questionnaire that included validated scales to measure their experience of cyber-bullying (Cyber Bullying Scale) and symptoms of depression (Center for Epidemiologic Studies–Depression Scale). Weighted logistic regression analysis was used to adjust for the cluster effect and sampling probability. Results Almost all (92.4%) students reported using the internet everyday and nearly 40% used internet for more than four hours per day. Cyber-victimization was identified in 36.5% of students and almost 25% experienced multiple types of cyber-victimization. Nearly half of students reported symptoms of depression. After adjusting for other covariates, students who experienced cyber-victimization were found to have 1.81 times (95% CI [1.42–2.30]) higher in odds of having symptoms of depression. Conclusions Cyber victimization and depression are both common in Vietnamese adolescents. Those who experienced cyber bullying have a higher likelihood of having symptoms of depression. These findings indicate an urgent need for interventions and policies targeting this emerging type of bullying in Vietnam and similar settings due to its potential harmful effects on adolescents’ health.
format: application/pdf
format: text/html
creator: Truc Thanh Thai
creator: Mai Huynh Thi Duong
creator: Duy Kim Vo
creator: Ngan Thien Thi Dang
creator: Quynh Ngoc Ho Huynh
creator: Huong Giang Nguyen Tran
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.12907
publisher: PeerJ Inc.
rights: © 2022 Thai et al.
abstract: Background Cyberbullying has become an alarming social issue, but little is known about its prevalence and consequences in many countries. This study investigated the prevalence of cyber-victimization and its association with depression among students in Ho Chi Minh City, Vietnam. Methods A cross-sectional study was conducted in 1,492 students from eight secondary schools and high schools in four urban and suburban areas. Multi-stage cluster sampling approach was used to recruit participants. Students participated in this study on a voluntary basis and completed a self-report questionnaire that included validated scales to measure their experience of cyber-bullying (Cyber Bullying Scale) and symptoms of depression (Center for Epidemiologic Studies–Depression Scale). Weighted logistic regression analysis was used to adjust for the cluster effect and sampling probability. Results Almost all (92.4%) students reported using the internet everyday and nearly 40% used internet for more than four hours per day. Cyber-victimization was identified in 36.5% of students and almost 25% experienced multiple types of cyber-victimization. Nearly half of students reported symptoms of depression. After adjusting for other covariates, students who experienced cyber-victimization were found to have 1.81 times (95% CI [1.42–2.30]) higher in odds of having symptoms of depression. Conclusions Cyber victimization and depression are both common in Vietnamese adolescents. Those who experienced cyber bullying have a higher likelihood of having symptoms of depression. These findings indicate an urgent need for interventions and policies targeting this emerging type of bullying in Vietnam and similar settings due to its potential harmful effects on adolescents’ health.
bibliographic citation: Thai et al. (2022) Cyber-victimization and its association with depression among Vietnamese adolescents. PeerJ 10:e12907 https://doi.org/10.7717/peerj.12907
date submitted: 2021-09-10
date accepted: 2022-01-18
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thai
  given name: Truc Thanh
author list: Agent
  family name: Duong
  given name: Mai Huynh Thi
author list: Agent
  family name: Vo
  given name: Duy Kim
author list: Agent
  family name: Dang
  given name: Ngan Thien Thi
author list: Agent
  family name: Huynh
  given name: Quynh Ngoc Ho
author list: Agent
  family name: Tran
  given name: Huong Giang Nguyen
doi: 10.7717/peerj.12907
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Thai et al.
attribution name: Thai et al.

https://peerj.com/articles/12913
type: item
type: AcademicArticle
title: On the Andean genus Leschenius (Coleoptera: Curculionidae: Entiminae): Updated phylogeny, with a new species from Ecuador, discovery of males, and larval description of the potato weevil Leschenius vulcanorum
description: The weevil genus Leschenius del Río (Curculionidae: Entiminae: Naupactini) is distributed in the northern Andes, in Colombia and Ecuador. Among its species, L. vulcanorum stands out as an important pest of potatoes in its parthenogenetic form, which is known as “tiroteador de la papa”. In this study, the adult male and the larval stage (first and mature larvae) of L. vulcanorun are described and illustrated for the first time. A description of the male of Leschenius bifurcatus is also provided. A new bisexual species was discovered, Leschenius ventrilingulatus sp. nov., and is described from Ecuador. An updated phylogenetic analysis was performed, including the new species, with results indicating a sister group relationship between L. ventrilingulatus and L. vulcanorum. They can be distinguished because the former is usually of smaller size and is covered by denser and thicker setae, has shorter antennae, a subcylindrical shape of the pronotum, shorter elytra (about 1.5×longer than wide at base), the female has ventrite 4 with a posterior rounded projection, and posterior margin of ventrite 5 subacute, not excavated. This paper also includes lectotype designations, a revised key to all known species of Leschenius, habitus photos of males and females, illustrations of genitalia, and a distribution map.
format: application/pdf
format: text/html
creator: María Guadalupe del Río
creator: Adriana E. Marvaldi
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12913
publisher: PeerJ Inc.
rights: © 2022 del Río and Marvaldi
abstract: The weevil genus Leschenius del Río (Curculionidae: Entiminae: Naupactini) is distributed in the northern Andes, in Colombia and Ecuador. Among its species, L. vulcanorum stands out as an important pest of potatoes in its parthenogenetic form, which is known as “tiroteador de la papa”. In this study, the adult male and the larval stage (first and mature larvae) of L. vulcanorun are described and illustrated for the first time. A description of the male of Leschenius bifurcatus is also provided. A new bisexual species was discovered, Leschenius ventrilingulatus sp. nov., and is described from Ecuador. An updated phylogenetic analysis was performed, including the new species, with results indicating a sister group relationship between L. ventrilingulatus and L. vulcanorum. They can be distinguished because the former is usually of smaller size and is covered by denser and thicker setae, has shorter antennae, a subcylindrical shape of the pronotum, shorter elytra (about 1.5×longer than wide at base), the female has ventrite 4 with a posterior rounded projection, and posterior margin of ventrite 5 subacute, not excavated. This paper also includes lectotype designations, a revised key to all known species of Leschenius, habitus photos of males and females, illustrations of genitalia, and a distribution map.
bibliographic citation: del Río et al. (2022) On the Andean genus Leschenius (Coleoptera: Curculionidae: Entiminae): Updated phylogeny, with a new species from Ecuador, discovery of males, and larval description of the potato weevil Leschenius vulcanorum. PeerJ 10:e12913 https://doi.org/10.7717/peerj.12913
date submitted: 2021-11-26
date accepted: 2022-01-19
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: del Río
  given name: María Guadalupe
author list: Agent
  family name: Marvaldi
  given name: Adriana E.
doi: 10.7717/peerj.12913
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 del Río and Marvaldi
attribution name: del Río and Marvaldi

Nontargeted and targeted metabolomics approaches reveal the key amino acid alterations involved in multiple myeloma
type: item
type: AcademicArticle
description: Purpose Multiple myeloma (MM), a kind of malignant neoplasm of clonal plasma cells in the bone marrow, is a refractory disease. Understanding the metabolism disorders and identification of metabolomics pathways as well as key metabolites will provide new insights for exploring diagnosis and therapeutic targets of MM. Methods We conducted nontargeted metabolomics analysis of MM patients and normal controls (NC) using ultra-high-performance liquid chromatography (UHPLC) combined with quadrupole time-of-flight mass spectrometry (Q-TOF-MS) in 40 cases of cohort 1 subjects. The targeted metabolomics analysis of amino acids using multiple reaction monitoring-mass spectrometry (MRM-MS) was also performed in 30 cases of cohort 1 and 30 cases of cohort 2 participants, to comprehensively investigate the metabolomics disorders of MM. Results The nontargeted metabolomics analysis in cohort 1 indicated that there was a significant metabolic signature change between MM patients and NC. The differential metabolites were mainly enriched in metabolic pathways related to amino acid metabolism, such as protein digestion and absorption, and biosynthesis of amino acids. Further, the targeted metabolomics analysis of amino acids in both cohort 1 and cohort 2 revealed differential metabolic profiling between MM patients and NC. We identified 12 and 14 amino acid metabolites with altered abundance in MM patients compared to NC subjects, in cohort 1 and cohort 2, respectively. Besides, key differential amino acid metabolites, such as choline, creatinine, leucine, tryptophan, and valine, may discriminate MM patients from NC. Moreover, the differential amino acid metabolites were associated with clinical indicators of MM patients. Conclusions Our findings indicate that amino acid metabolism disorders are involved in MM. The differential profiles reveal the potential utility of key amino acid metabolites as diagnostic biomarkers of MM. The alterations in metabolome, especially the amino acid m…
format: application/pdf
format: text/html
creator: Lingling Yue
creator: Pengyun Zeng
creator: Yanhong Li
creator: Ye Chai
creator: Chongyang Wu
creator: Bingren Gao
subject: Molecular Biology
subject: Oncology
subject: Orthopedics
subject: Pathology
subject: Metabolic Sciences
description: doi:10.7717/peerj.12918
publisher: PeerJ Inc.
rights: © 2022 Yue et al.
abstract: Purpose Multiple myeloma (MM), a kind of malignant neoplasm of clonal plasma cells in the bone marrow, is a refractory disease. Understanding the metabolism disorders and identification of metabolomics pathways as well as key metabolites will provide new insights for exploring diagnosis and therapeutic targets of MM. Methods We conducted nontargeted metabolomics analysis of MM patients and normal controls (NC) using ultra-high-performance liquid chromatography (UHPLC) combined with quadrupole time-of-flight mass spectrometry (Q-TOF-MS) in 40 cases of cohort 1 subjects. The targeted metabolomics analysis of amino acids using multiple reaction monitoring-mass spectrometry (MRM-MS) was also performed in 30 cases of cohort 1 and 30 cases of cohort 2 participants, to comprehensively investigate the metabolomics disorders of MM. Results The nontargeted metabolomics analysis in cohort 1 indicated that there was a significant metabolic signature change between MM patients and NC. The differential metabolites were mainly enriched in metabolic pathways related to amino acid metabolism, such as protein digestion and absorption, and biosynthesis of amino acids. Further, the targeted metabolomics analysis of amino acids in both cohort 1 and cohort 2 revealed differential metabolic profiling between MM patients and NC. We identified 12 and 14 amino acid metabolites with altered abundance in MM patients compared to NC subjects, in cohort 1 and cohort 2, respectively. Besides, key differential amino acid metabolites, such as choline, creatinine, leucine, tryptophan, and valine, may discriminate MM patients from NC. Moreover, the differential amino acid metabolites were associated with clinical indicators of MM patients. Conclusions Our findings indicate that amino acid metabolism disorders are involved in MM. The differential profiles reveal the potential utility of key amino acid metabolites as diagnostic biomarkers of MM. The alterations in metabolome, especially the amino acid m…
bibliographic citation: Yue et al. (2022) Nontargeted and targeted metabolomics approaches reveal the key amino acid alterations involved in multiple myeloma. PeerJ 10:e12918 https://doi.org/10.7717/peerj.12918
date submitted: 2021-07-05
date accepted: 2022-01-20
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yue
  given name: Lingling
author list: Agent
  family name: Zeng
  given name: Pengyun
author list: Agent
  family name: Li
  given name: Yanhong
author list: Agent
  family name: Chai
  given name: Ye
author list: Agent
  family name: Wu
  given name: Chongyang
author list: Agent
  family name: Gao
  given name: Bingren
doi: 10.7717/peerj.12918
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Yue et al.
attribution name: Yue et al.

External validation of five predictive models for postoperative cardiopulmonary morbidity in a Chinese population receiving lung resection
type: item
type: AcademicArticle
description: Background No postoperative cardiopulmonary morbidity models have been developed or validated in Chinese patients with lung resection. This study aims to externally validate five predictive models, including Eurolung models, the Brunelli model and the Age-adjusted Charlson Comorbidity Index, in a Chinese population. Methods Patients with lung cancer who underwent anatomic lung resection between 2018/09/01 and 2019/08/31 in our center were involved. Model discrimination was assessed by the area under the receiver operating characteristic curve. Model calibration was evaluated by the Hosmer–Lemeshow test. Calibration curves were plotted. Specificity, sensitivity, negative predictive value, positive predictive value and accuracy were calculated. Model updating was achieved by re-estimating the intercept and/or the slope of the linear predictor and re-estimating all coefficients. Results Among 1085 patients, 91 patients had postoperative cardiopulmonary complications defined by the European Society of Thoracic Surgeons. For original models, only parsimonious Eurolung1 had acceptable discrimination (area under the receiver operating characteristic curve = 0.688, 95% confidence interval 0.630–0.745) and calibration (p = 0.23 > 0.05) abilities simultaneously. Its sensitivity, specificity, positive predictive value, negative predictive value and accuracy were 0.700, 0.649, 0.153, 0.960 and 0.653, respectively. In the secondary analysis, increased pleural effusion (n = 94), which was nonchylous and nonpurulent, was labeled as a kind of postoperative complication. The area under the receiver operating characteristic curve of the models increased slightly, but all models were miscalibrated. The original Eurolung1 model had the highest discrimination ability but poor calibration, and thus it was updated by three methods. After model updating, new models showed good calibration and small improvements in discrimination. The discrimination ability was still merely acceptable. Conc…
format: application/pdf
format: text/html
creator: Guanghua Huang
creator: Lei Liu
creator: Luyi Wang
creator: Zhile Wang
creator: Zhaojian Wang
creator: Shanqing Li
subject: Oncology
subject: Respiratory Medicine
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.12936
publisher: PeerJ Inc.
rights: © 2022 Huang et al.
abstract: Background No postoperative cardiopulmonary morbidity models have been developed or validated in Chinese patients with lung resection. This study aims to externally validate five predictive models, including Eurolung models, the Brunelli model and the Age-adjusted Charlson Comorbidity Index, in a Chinese population. Methods Patients with lung cancer who underwent anatomic lung resection between 2018/09/01 and 2019/08/31 in our center were involved. Model discrimination was assessed by the area under the receiver operating characteristic curve. Model calibration was evaluated by the Hosmer–Lemeshow test. Calibration curves were plotted. Specificity, sensitivity, negative predictive value, positive predictive value and accuracy were calculated. Model updating was achieved by re-estimating the intercept and/or the slope of the linear predictor and re-estimating all coefficients. Results Among 1085 patients, 91 patients had postoperative cardiopulmonary complications defined by the European Society of Thoracic Surgeons. For original models, only parsimonious Eurolung1 had acceptable discrimination (area under the receiver operating characteristic curve = 0.688, 95% confidence interval 0.630–0.745) and calibration (p = 0.23 > 0.05) abilities simultaneously. Its sensitivity, specificity, positive predictive value, negative predictive value and accuracy were 0.700, 0.649, 0.153, 0.960 and 0.653, respectively. In the secondary analysis, increased pleural effusion (n = 94), which was nonchylous and nonpurulent, was labeled as a kind of postoperative complication. The area under the receiver operating characteristic curve of the models increased slightly, but all models were miscalibrated. The original Eurolung1 model had the highest discrimination ability but poor calibration, and thus it was updated by three methods. After model updating, new models showed good calibration and small improvements in discrimination. The discrimination ability was still merely acceptable. Conc…
bibliographic citation: Huang et al. (2022) External validation of five predictive models for postoperative cardiopulmonary morbidity in a Chinese population receiving lung resection. PeerJ 10:e12936 https://doi.org/10.7717/peerj.12936
date submitted: 2021-12-17
date accepted: 2022-01-23
issued: 2022-02-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Guanghua
author list: Agent
  family name: Liu
  given name: Lei
author list: Agent
  family name: Wang
  given name: Luyi
author list: Agent
  family name: Wang
  given name: Zhile
author list: Agent
  family name: Wang
  given name: Zhaojian
author list: Agent
  family name: Li
  given name: Shanqing
doi: 10.7717/peerj.12936
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-09
copyright: ©2022 Huang et al.
attribution name: Huang et al.

Description of a new and widely distributed species of Bathypathes (Cnidaria: Anthozoa: Antipatharia: Schizopathidae) previously misidentified as Bathypathes alternata Brook, 1889
type: item
type: AcademicArticle
description: For many years an undescribed species of the genus Bathypathes has been misidentified as Bathypathes alternata Brook, 1889 (a species currently re-assigned to the genus Alternatipathes). This new species is rather common at mid- and lower bathyal depths of the Pacific, Atlantic and Indian oceans, often in areas with high concentrations of commercially valuable cobalt-rich ferromanganese crusts, where it was observed in underwater photo and video transects to occur in high densities. Under the name B. alternata this species is recorded in several inventories and databases. There is an urgent need for a formal description of this misidentified and widely distributed species to avoid further confusion. The new species is superficially similar to A. alternata in having a monopodial corallum and simple, bilateral and alternately arranged pinnules. However, it differs from the former in that it has an upright corallum with a straight pinnulated part (vs. a horizontally bent pinnulated part), pinnules of uniform length and density (vs. decreasing regularly distally), and a constant distal angle formed by the pinnules and the stem along different parts of the corallum (vs. a decreasing distal angle near the top). The new species can therefore be easily distinguished from A. alternata in underwater imagery. We formally describe this new species in the genus Bathypathes and assign it the new name B. pseudoalternata. An extensive synonymy list with previous misidentified records is provided. To evaluate the distributional patterns of the new species we review the geographic distribution of antipatharians reported below 800 m. The majority of the hitherto described lower bathyal and abyssal species have been recorded from one biogeographic province; however, 20 species are known from more than two provinces, and only three species are widely distributed (>5 provinces), including the newly described Bathypathes pseudoalternata. Members of the family Schizopathidae, to which the …
format: application/pdf
format: text/html
creator: Tina N. Molodtsova
creator: Dennis M. Opresko
creator: Daniel Wagner
subject: Biodiversity
subject: Biogeography
subject: Marine Biology
subject: Taxonomy
subject: Biological Oceanography
description: doi:10.7717/peerj.12638
publisher: PeerJ Inc.
rights: © 2022 Molodtsova et al.
abstract: For many years an undescribed species of the genus Bathypathes has been misidentified as Bathypathes alternata Brook, 1889 (a species currently re-assigned to the genus Alternatipathes). This new species is rather common at mid- and lower bathyal depths of the Pacific, Atlantic and Indian oceans, often in areas with high concentrations of commercially valuable cobalt-rich ferromanganese crusts, where it was observed in underwater photo and video transects to occur in high densities. Under the name B. alternata this species is recorded in several inventories and databases. There is an urgent need for a formal description of this misidentified and widely distributed species to avoid further confusion. The new species is superficially similar to A. alternata in having a monopodial corallum and simple, bilateral and alternately arranged pinnules. However, it differs from the former in that it has an upright corallum with a straight pinnulated part (vs. a horizontally bent pinnulated part), pinnules of uniform length and density (vs. decreasing regularly distally), and a constant distal angle formed by the pinnules and the stem along different parts of the corallum (vs. a decreasing distal angle near the top). The new species can therefore be easily distinguished from A. alternata in underwater imagery. We formally describe this new species in the genus Bathypathes and assign it the new name B. pseudoalternata. An extensive synonymy list with previous misidentified records is provided. To evaluate the distributional patterns of the new species we review the geographic distribution of antipatharians reported below 800 m. The majority of the hitherto described lower bathyal and abyssal species have been recorded from one biogeographic province; however, 20 species are known from more than two provinces, and only three species are widely distributed (>5 provinces), including the newly described Bathypathes pseudoalternata. Members of the family Schizopathidae, to which the …
bibliographic citation: Molodtsova et al. (2022) Description of a new and widely distributed species of Bathypathes (Cnidaria: Anthozoa: Antipatharia: Schizopathidae) previously misidentified as Bathypathes alternata Brook, 1889. PeerJ 10:e12638 https://doi.org/10.7717/peerj.12638
date submitted: 2021-03-25
date accepted: 2021-11-24
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Molodtsova
  given name: Tina N.
author list: Agent
  family name: Opresko
  given name: Dennis M.
author list: Agent
  family name: Wagner
  given name: Daniel
doi: 10.7717/peerj.12638
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: © 2022 Molodtsova et al.
attribution name: Molodtsova et al.

A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus
type: item
type: AcademicArticle
description: A new species of Diasporus is described from the lowlands of southwestern Colombia. The new species exhibits a yellowish coloration in life, a character that it shares with other three species in the genus—Diasporus citrinobapheus, D. gularis, and D. tigrillo. The new species differs from all other congeners in having two chrome orange spots (=glandlike protrusions) on sacral region, smooth ventral skin, basal webbing between the toes, and distal papillae at tips of disc covers on fingers II–IV and toes II–IV. Further, the new species differs from all congeners by an uncorrected p-distance of > 5.56% of the 16S rRNA gene fragment examined. In addition to the new species described herein, we demonstrated that the possession of a yellowish coloration in life optimizes unambiguously as a synapomorphy of a clade within Diasporus, which may be recognized as the Diasporus diastema species group. We also discussed the phylogenetic significance of two morphological characters previously considered of systematic value in Diasporus, the occurrence of oval palmar tubercles (undivided) and longitudinal folds (of the vocal sacs) on the throat. On this basis, we demonstrated that these characters appear to be symplesiomorphies rather than synapomorphies of Diasporus. Regarding pointed disc covers (ungual flap) present in some species of Diasporus, we show that this character conflates various characters, involving variation in pad shape, dorsal outline of the disc (ungual flap), and dependence between discs of different digits. Finally, considering that phenotypic data are a valuable source of evidence in testing phylogenetic hypotheses of terraranan frogs, we encourage future research to incorporate phenotypic evidence into phylogenetic studies involved in the genus Diasporus.
format: application/pdf
format: text/html
creator: Jhon Jairo Ospina Sarria
creator: David Andrés Velásquez Trujillo
creator: Christian Oswaldo Castaño Saavedra
creator: Luis Fernando Castillo
creator: Wilmar Bolívar-García
subject: Biodiversity
subject: Evolutionary Studies
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12765
publisher: PeerJ Inc.
rights: © 2022 Ospina Sarria et al.
abstract: A new species of Diasporus is described from the lowlands of southwestern Colombia. The new species exhibits a yellowish coloration in life, a character that it shares with other three species in the genus—Diasporus citrinobapheus, D. gularis, and D. tigrillo. The new species differs from all other congeners in having two chrome orange spots (=glandlike protrusions) on sacral region, smooth ventral skin, basal webbing between the toes, and distal papillae at tips of disc covers on fingers II–IV and toes II–IV. Further, the new species differs from all congeners by an uncorrected p-distance of > 5.56% of the 16S rRNA gene fragment examined. In addition to the new species described herein, we demonstrated that the possession of a yellowish coloration in life optimizes unambiguously as a synapomorphy of a clade within Diasporus, which may be recognized as the Diasporus diastema species group. We also discussed the phylogenetic significance of two morphological characters previously considered of systematic value in Diasporus, the occurrence of oval palmar tubercles (undivided) and longitudinal folds (of the vocal sacs) on the throat. On this basis, we demonstrated that these characters appear to be symplesiomorphies rather than synapomorphies of Diasporus. Regarding pointed disc covers (ungual flap) present in some species of Diasporus, we show that this character conflates various characters, involving variation in pad shape, dorsal outline of the disc (ungual flap), and dependence between discs of different digits. Finally, considering that phenotypic data are a valuable source of evidence in testing phylogenetic hypotheses of terraranan frogs, we encourage future research to incorporate phenotypic evidence into phylogenetic studies involved in the genus Diasporus.
bibliographic citation: Ospina Sarria et al. (2022) A new golden species of Diasporus (Anura: Eleutherodactylidae) from southwestern Colombia, with evaluation of the phylogenetic significance of morphological characters in Diasporus. PeerJ 10:e12765 https://doi.org/10.7717/peerj.12765
date submitted: 2021-08-25
date accepted: 2021-12-17
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ospina Sarria
  given name: Jhon Jairo
author list: Agent
  family name: Velásquez Trujillo
  given name: David Andrés
author list: Agent
  family name: Castaño Saavedra
  given name: Christian Oswaldo
author list: Agent
  family name: Castillo
  given name: Luis Fernando
author list: Agent
  family name: Bolívar-García
  given name: Wilmar
doi: 10.7717/peerj.12765
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Ospina Sarria et al.
attribution name: Ospina Sarria et al.

Cathepsin S are involved in human carotid atherosclerotic disease progression, mainly by mediating phagosomes: bioinformatics and in vivo and vitro experiments
type: item
type: AcademicArticle
description: Background Atherosclerosis emerges as a result of multiple dynamic cell processes including endothelial damage, inflammatory and immune cell infiltration, foam cell formation, plaque rupture, and thrombosis. Animal experiments have indicated that cathepsins (CTSs) mediate the antigen transmission and inflammatory response involved in the atherosclerosis process, but the specific signal pathways and target cells of the CTSs involved in atherosclerosis are unknown. Methods We used the GEO query package to download the dataset GSE28829 from the Gene Expression Omnibus (GEO) and filtered the data to check the standardization of the samples through the box chart. We then used the ‘limma’ package to analyze between-group differences and selected the corresponding differentially expressed genes of CTSs from the protein-protein interaction (PPI) network constructed with the STRING database, and then visualized the CTS-target genes. The best matching pathway and target cells were verified by a male mouse ligation experiment, single-sample GSEA (ssGSEA) analysis, and vitro experiment. Results There were 275 differentially expressed genes (DEGs) selected from the GSE28829 dataset, and the DEGs were identified mainly in the PPI network; 58 core genes (APOE, CD74, CP, AIF1, etc.) target three selected CTS family members (CTSS, CTSB, and CTSC). After the enriched analysis, 15 CTS-target genes were markedly enriched in the phagosome signaling pathway. The mouse experiment results revealed that the percentages and numbers of monocytes and neutrophils and the number of CD68+ cells in CTSS deficiency (CatS−/−) group were lower than those in the wildtype (CatS+/+) group. CTSS mediating phagosome via macrophage were further verified by ssGSEA analysis and vitro experiment. Conclusions CTSS are the main target molecules in the CTS family that are involved in atherosclerosis. The molecule participate in the progression of atherosclerosis by mediating the phagosome via macrophage.
format: application/pdf
format: text/html
creator: Hailong Wang
creator: Haiying Jiang
creator: Xian Wu Cheng
subject: Bioinformatics
subject: Genetics
subject: Cardiology
description: doi:10.7717/peerj.12846
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Atherosclerosis emerges as a result of multiple dynamic cell processes including endothelial damage, inflammatory and immune cell infiltration, foam cell formation, plaque rupture, and thrombosis. Animal experiments have indicated that cathepsins (CTSs) mediate the antigen transmission and inflammatory response involved in the atherosclerosis process, but the specific signal pathways and target cells of the CTSs involved in atherosclerosis are unknown. Methods We used the GEO query package to download the dataset GSE28829 from the Gene Expression Omnibus (GEO) and filtered the data to check the standardization of the samples through the box chart. We then used the ‘limma’ package to analyze between-group differences and selected the corresponding differentially expressed genes of CTSs from the protein-protein interaction (PPI) network constructed with the STRING database, and then visualized the CTS-target genes. The best matching pathway and target cells were verified by a male mouse ligation experiment, single-sample GSEA (ssGSEA) analysis, and vitro experiment. Results There were 275 differentially expressed genes (DEGs) selected from the GSE28829 dataset, and the DEGs were identified mainly in the PPI network; 58 core genes (APOE, CD74, CP, AIF1, etc.) target three selected CTS family members (CTSS, CTSB, and CTSC). After the enriched analysis, 15 CTS-target genes were markedly enriched in the phagosome signaling pathway. The mouse experiment results revealed that the percentages and numbers of monocytes and neutrophils and the number of CD68+ cells in CTSS deficiency (CatS−/−) group were lower than those in the wildtype (CatS+/+) group. CTSS mediating phagosome via macrophage were further verified by ssGSEA analysis and vitro experiment. Conclusions CTSS are the main target molecules in the CTS family that are involved in atherosclerosis. The molecule participate in the progression of atherosclerosis by mediating the phagosome via macrophage.
bibliographic citation: Wang et al. (2022) Cathepsin S are involved in human carotid atherosclerotic disease progression, mainly by mediating phagosomes: bioinformatics and in vivo and vitro experiments. PeerJ 10:e12846 https://doi.org/10.7717/peerj.12846
date submitted: 2021-08-24
date accepted: 2022-01-07
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hailong
author list: Agent
  family name: Jiang
  given name: Haiying
author list: Agent
  family name: Cheng
  given name: Xian Wu
doi: 10.7717/peerj.12846
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Evaluating the therapeutic effect of tumor treating fields (TTFields) by monitoring the impedance across TTFields electrode arrays
type: item
type: AcademicArticle
description: Background Tumor Treating Fields (TTFields), are a novel, non-invasive tissue ablation technology for treatment of cancer. Tissue ablation is achieved through the continuous delivery of a narrow range of electromagnetic fields across a tumor, for a period of months. TTFields are designed to affect only cells that divide and to interfere with the cell division process. The therapy is monitored with MRI imaging, performed every couple of months. Current technology is unable to assess the treatment effectiveness in real time. Methods We propose that the effect of the treatment can be assessed, in real time, by continuously measuring the change in electrical impedance across the TTFields delivery electrode arrays. An in vitro anatomic skull experimental study, with brain and tumor mimics phantom tissues was conducted to confirm the potential value of the proposed monitoring system. Results Experiments show that measuring the change in the impedance amplitude between opposite TTFields electrode arrays, at a typical TTFields treatment frequency of (200 kHz), can detect changes in the tumor radius with a sensitivity that increases with the radius of the tumor. The study shows that TTFields electrode arrays can be used to assess the effectiveness of TTFields treatment on changes in the tumor dimensions in real time, throughout the treatement. This monitoring system may become a valuable addition to the TTFields cancer treatment technology. It could provide the means to continuously assess the effectiveness of the treatment, and thereby optimize the design of the treatment protocol.
format: application/pdf
format: text/html
creator: Xing Li
creator: Moshe Oziel
creator: Boris Rubinsky
subject: Biochemistry
subject: Bioengineering
subject: Biophysics
subject: Biotechnology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.12877
publisher: PeerJ Inc.
rights: © 2022 Li et al.
abstract: Background Tumor Treating Fields (TTFields), are a novel, non-invasive tissue ablation technology for treatment of cancer. Tissue ablation is achieved through the continuous delivery of a narrow range of electromagnetic fields across a tumor, for a period of months. TTFields are designed to affect only cells that divide and to interfere with the cell division process. The therapy is monitored with MRI imaging, performed every couple of months. Current technology is unable to assess the treatment effectiveness in real time. Methods We propose that the effect of the treatment can be assessed, in real time, by continuously measuring the change in electrical impedance across the TTFields delivery electrode arrays. An in vitro anatomic skull experimental study, with brain and tumor mimics phantom tissues was conducted to confirm the potential value of the proposed monitoring system. Results Experiments show that measuring the change in the impedance amplitude between opposite TTFields electrode arrays, at a typical TTFields treatment frequency of (200 kHz), can detect changes in the tumor radius with a sensitivity that increases with the radius of the tumor. The study shows that TTFields electrode arrays can be used to assess the effectiveness of TTFields treatment on changes in the tumor dimensions in real time, throughout the treatement. This monitoring system may become a valuable addition to the TTFields cancer treatment technology. It could provide the means to continuously assess the effectiveness of the treatment, and thereby optimize the design of the treatment protocol.
bibliographic citation: Li et al. (2022) Evaluating the therapeutic effect of tumor treating fields (TTFields) by monitoring the impedance across TTFields electrode arrays. PeerJ 10:e12877 https://doi.org/10.7717/peerj.12877
date submitted: 2021-09-24
date accepted: 2022-01-12
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xing
author list: Agent
  family name: Oziel
  given name: Moshe
author list: Agent
  family name: Rubinsky
  given name: Boris
doi: 10.7717/peerj.12877
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Li et al.
attribution name: Li et al.

Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense
type: item
type: AcademicArticle
description: Background Calcium dependent protein kinases (CDPKs) are a class of important calcium signal sensing response proteins, which play an important regulatory role in response to abiotic stress. However, researchers have not been excavated CDPKs’ role in drought in sea-island cotton(Gossypium barbadense L. ‘H7124’). Results Eighty-four CDPK genes have been identified in G. barbadense. These GbCDPK genes are unevenly distributed on 26 chromosomes, and segmental duplication is the significant way for the extension of CDPK family. Also, members within the same subfamily share a similar gene structure and motif composition. There are a large number of cis-elements involved in plant growth and response to stresses in the promoter regions of GbCDPKs. Additionally, these GbCDPKs show differential expression patterns in cotton tissues. The transcription levels of most genes were markedly altered in cotton under heat, cold, salt and PEG treatments, while the expressions of some GbCDPKs were induced in cotton under drought stress. Among these drought-induced genes, we selected GbCDPK32, GbCDPK68, GbCDPK74, GbCDPK80 and GbCDPK83 for further functional characterization by virus-induced gene silencing (VIGS) method. Conclusions In conclusion, the principal findings of this prospective study are that CDPKs were associated with drought. These findings provide a solid foundation for the development of future molecular mechanism in sea-island cotton.
format: application/pdf
format: text/html
creator: Guangzhen Shi
creator: Xinxia Zhu
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12883
publisher: PeerJ Inc.
rights: © 2022 Shi and Zhu
abstract: Background Calcium dependent protein kinases (CDPKs) are a class of important calcium signal sensing response proteins, which play an important regulatory role in response to abiotic stress. However, researchers have not been excavated CDPKs’ role in drought in sea-island cotton(Gossypium barbadense L. ‘H7124’). Results Eighty-four CDPK genes have been identified in G. barbadense. These GbCDPK genes are unevenly distributed on 26 chromosomes, and segmental duplication is the significant way for the extension of CDPK family. Also, members within the same subfamily share a similar gene structure and motif composition. There are a large number of cis-elements involved in plant growth and response to stresses in the promoter regions of GbCDPKs. Additionally, these GbCDPKs show differential expression patterns in cotton tissues. The transcription levels of most genes were markedly altered in cotton under heat, cold, salt and PEG treatments, while the expressions of some GbCDPKs were induced in cotton under drought stress. Among these drought-induced genes, we selected GbCDPK32, GbCDPK68, GbCDPK74, GbCDPK80 and GbCDPK83 for further functional characterization by virus-induced gene silencing (VIGS) method. Conclusions In conclusion, the principal findings of this prospective study are that CDPKs were associated with drought. These findings provide a solid foundation for the development of future molecular mechanism in sea-island cotton.
bibliographic citation: Shi et al. (2022) Genome-wide identification and functional characterization of CDPK gene family reveal their involvement in response to drought stress in Gossypium barbadense. PeerJ 10:e12883 https://doi.org/10.7717/peerj.12883
date submitted: 2021-11-04
date accepted: 2022-01-13
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Guangzhen
author list: Agent
  family name: Zhu
  given name: Xinxia
doi: 10.7717/peerj.12883
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Shi and Zhu
attribution name: Shi and Zhu

Occurrence of microplastics in edible aquatic insect Pantala sp. (Odonata: Libellulidae) from rice fields
type: item
type: AcademicArticle
description: Background Microplastic (MP) contamination has been discovered in aquatic systems throughout the world. They are well known as contaminants in aquatic species, but there is a gap in understanding about pathways of MP contamination into humans (i.e., through aquatic animals). The goal of this study is to assess MP contamination in an edible aquatic insect (Pantala sp.) living in rice fields. Methods A dragonfly larva, Pantala sp. (Odonata: Libellulidae), was tested for MPs. The study concentrated on three distinct anatomical compartments (whole body, gastrointestinal tract, and body without gastrointestinal tract), each of which was examined separately. For the physical identification and chemical analysis of MPs, a stereomicroscope and a Fourier transformed infrared spectroscope (FT-IR) were used, respectively. Results and Discussion The microplastics content was 121 in the whole body, 95 in the gastrointestinal tract, and 66 in the body without the gastrointestinal tract, with an average of 1.34 ± 1.11, 1.06 ± 0.77, and 0.73 ± 0.51 abundance/ individual, respectively. The most common MPs discovered during this study were fragments, followed by fibers and rods. The chemical analysis by FT-IR confirmed three different polymers, including polymethyl methacrylate (PMMA), polyethylene terephthalate (PET), and polypropylene (PP). There was no significant difference in MP abundances among the sample types (Kruskal-Wallis chi-squared = 2.774, df = 2, p = 0.250). The findings suggest that eating an edible aquatic insect (Odonata: Pantala sp.) could be one way for humans to ingest MPs.
format: application/pdf
format: text/html
creator: Witwisitpong Maneechan
creator: Taeng On Prommi
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Freshwater Biology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12902
publisher: PeerJ Inc.
rights: © 2022 Maneechan and Prommi
abstract: Background Microplastic (MP) contamination has been discovered in aquatic systems throughout the world. They are well known as contaminants in aquatic species, but there is a gap in understanding about pathways of MP contamination into humans (i.e., through aquatic animals). The goal of this study is to assess MP contamination in an edible aquatic insect (Pantala sp.) living in rice fields. Methods A dragonfly larva, Pantala sp. (Odonata: Libellulidae), was tested for MPs. The study concentrated on three distinct anatomical compartments (whole body, gastrointestinal tract, and body without gastrointestinal tract), each of which was examined separately. For the physical identification and chemical analysis of MPs, a stereomicroscope and a Fourier transformed infrared spectroscope (FT-IR) were used, respectively. Results and Discussion The microplastics content was 121 in the whole body, 95 in the gastrointestinal tract, and 66 in the body without the gastrointestinal tract, with an average of 1.34 ± 1.11, 1.06 ± 0.77, and 0.73 ± 0.51 abundance/ individual, respectively. The most common MPs discovered during this study were fragments, followed by fibers and rods. The chemical analysis by FT-IR confirmed three different polymers, including polymethyl methacrylate (PMMA), polyethylene terephthalate (PET), and polypropylene (PP). There was no significant difference in MP abundances among the sample types (Kruskal-Wallis chi-squared = 2.774, df = 2, p = 0.250). The findings suggest that eating an edible aquatic insect (Odonata: Pantala sp.) could be one way for humans to ingest MPs.
bibliographic citation: Maneechan et al. (2022) Occurrence of microplastics in edible aquatic insect Pantala sp. (Odonata: Libellulidae) from rice fields. PeerJ 10:e12902 https://doi.org/10.7717/peerj.12902
date submitted: 2021-10-13
date accepted: 2022-01-17
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maneechan
  given name: Witwisitpong
author list: Agent
  family name: Prommi
  given name: Taeng On
doi: 10.7717/peerj.12902
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Maneechan and Prommi
attribution name: Maneechan and Prommi

Detection of microplastics in Litopenaeus vannamei (Penaeidae) and Macrobrachium rosenbergii (Palaemonidae) in cultured pond
type: item
type: AcademicArticle
description: Background The presence of plastic particles in freshwater species is becoming a global concern owing to the potential impact on food security and human health. In this study, we investigated the presence microplastics (MPs) in two economically important freshwater species: the giant freshwater prawn (Macrobrachium rosenbergii) and the white leg shrimp (Litopenaeus vannamei) cultured in a polyculture pond in the central part of Thailand. Methods The gastrointestinal tract (GT) of 300 giant freshwater prawn (160 female and 140 male) and 150 white leg shrimp specimens were investigated for the presence of MPs. Results From the pooled samples, a total of 1,166 MP items were identified. Specifically, the GTs of female and male freshwater prawns and white leg shrimps contained an average of 33.31 ± 19.42, 33.43 ± 19.07, and 11.00 ± 4.60 MP items per individual, respectively. Further, their mean MP contents per g of gut material were 32.66 ± 5.10, 32.14 ± 4.85, and 10.28 ± 1.19 MP items, respectively. In the GT of these species, MPs with sizes in the range 500–1000 µm, were predominant, and white/transparent MPs were most prevalent (63.67%). Furthermore, regarding the morphotypes of the MPs, fibers, fragments, films, and spheres were frequently observed, with fibers shows predominance. Specifically, the proportions of fibers in the GTs of female Macrobrachium rosenbergii, male Macrobrachium rosenbergii, and Litopenaeus vannamei were 83.3, 79.91, and 46.06%, respectively. Four MP polymer types, polyethylene, polycaprolactone, polyvinyl alcohol, and acrylonitrile butadiene styrene, were also identified via FTIR spectroscopy, which further confirmed the presence of MPs in the GT of the freshwater-cultured species. Discussion Our findings indicated that consuming shrimps and prawns without first removing the MPs from their GTs is one of the mean by which humans get exposed to MPs. Thus, MPs in freshwater species can be passed down the food chain to humans.
format: application/pdf
format: text/html
creator: Thanya Reunura
creator: Taeng On Prommi
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Zoology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.12916
publisher: PeerJ Inc.
rights: © 2022 Reunura and Prommi
abstract: Background The presence of plastic particles in freshwater species is becoming a global concern owing to the potential impact on food security and human health. In this study, we investigated the presence microplastics (MPs) in two economically important freshwater species: the giant freshwater prawn (Macrobrachium rosenbergii) and the white leg shrimp (Litopenaeus vannamei) cultured in a polyculture pond in the central part of Thailand. Methods The gastrointestinal tract (GT) of 300 giant freshwater prawn (160 female and 140 male) and 150 white leg shrimp specimens were investigated for the presence of MPs. Results From the pooled samples, a total of 1,166 MP items were identified. Specifically, the GTs of female and male freshwater prawns and white leg shrimps contained an average of 33.31 ± 19.42, 33.43 ± 19.07, and 11.00 ± 4.60 MP items per individual, respectively. Further, their mean MP contents per g of gut material were 32.66 ± 5.10, 32.14 ± 4.85, and 10.28 ± 1.19 MP items, respectively. In the GT of these species, MPs with sizes in the range 500–1000 µm, were predominant, and white/transparent MPs were most prevalent (63.67%). Furthermore, regarding the morphotypes of the MPs, fibers, fragments, films, and spheres were frequently observed, with fibers shows predominance. Specifically, the proportions of fibers in the GTs of female Macrobrachium rosenbergii, male Macrobrachium rosenbergii, and Litopenaeus vannamei were 83.3, 79.91, and 46.06%, respectively. Four MP polymer types, polyethylene, polycaprolactone, polyvinyl alcohol, and acrylonitrile butadiene styrene, were also identified via FTIR spectroscopy, which further confirmed the presence of MPs in the GT of the freshwater-cultured species. Discussion Our findings indicated that consuming shrimps and prawns without first removing the MPs from their GTs is one of the mean by which humans get exposed to MPs. Thus, MPs in freshwater species can be passed down the food chain to humans.
bibliographic citation: Reunura et al. (2022) Detection of microplastics in Litopenaeus vannamei (Penaeidae) and Macrobrachium rosenbergii (Palaemonidae) in cultured pond. PeerJ 10:e12916 https://doi.org/10.7717/peerj.12916
date submitted: 2021-10-27
date accepted: 2022-01-20
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reunura
  given name: Thanya
author list: Agent
  family name: Prommi
  given name: Taeng On
doi: 10.7717/peerj.12916
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Reunura and Prommi
attribution name: Reunura and Prommi

Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease
type: item
type: AcademicArticle
description: The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main protease (Mpro) and a carefully selected dataset of 37,060 compounds comprising Mpro and antiviral protein-specific libraries. The compounds passed two-step docking filtration, starting with standard precision (SP) followed by extra precision (XP) runs. Fourteen compounds with the highest XP docking scores were examined by 20 ns molecular dynamics simulations (MDs). Based on backbone route mean square deviations (RMSD) and molecular mechanics/generalized Born surface area (MM/GBSA) binding energy, four drugs were selected for comprehensive MDs analysis at 100 ns. Results indicated that birinapant, atazanavir, and ritonavir potently bound and stabilized SARS-CoV-2 Mpro structure. Binding energies higher than −102 kcal/mol, RMSD values <0.22 nm, formation of several hydrogen bonds with Mpro, favourable electrostatic contributions, and low radii of gyration were among the estimated factors contributing to the strength of the binding of these three compounds with Mpro. The top two compounds, atazanavir and birinapant, were tested for their ability to prevent SARS-CoV-2 plaque formation. At 10 µM of birinapant concentration, antiviral tests against SARS-CoV-2 demonstrated a 37% reduction of virus multiplication. Antiviral assays demonstrated that birinapant has high anti-SARS-CoV-2 activity in the low micromolar range, with an IC50 value of 18 ± 3.6 µM. Therefore, birinapant is a candidate for further investigation to determine whether it is a feasible therapy option.
format: application/pdf
format: text/html
creator: Mahmoud Kandeel
creator: Jinsoo Kim
creator: Mahmoud Fayez
creator: Yukio Kitade
creator: Hyung-Joo Kwon
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
subject: Computational Science
description: doi:10.7717/peerj.12929
publisher: PeerJ Inc.
rights: © 2022 Kandeel et al.
abstract: The spread of SARS-CoV-2, the causative agent for COVID-19, has led to a global and deadly pandemic. To date, few drugs have been approved for treating SARS-CoV-2 infections. In this study, a structure-based approach was adopted using the SARS-CoV-2 main protease (Mpro) and a carefully selected dataset of 37,060 compounds comprising Mpro and antiviral protein-specific libraries. The compounds passed two-step docking filtration, starting with standard precision (SP) followed by extra precision (XP) runs. Fourteen compounds with the highest XP docking scores were examined by 20 ns molecular dynamics simulations (MDs). Based on backbone route mean square deviations (RMSD) and molecular mechanics/generalized Born surface area (MM/GBSA) binding energy, four drugs were selected for comprehensive MDs analysis at 100 ns. Results indicated that birinapant, atazanavir, and ritonavir potently bound and stabilized SARS-CoV-2 Mpro structure. Binding energies higher than −102 kcal/mol, RMSD values <0.22 nm, formation of several hydrogen bonds with Mpro, favourable electrostatic contributions, and low radii of gyration were among the estimated factors contributing to the strength of the binding of these three compounds with Mpro. The top two compounds, atazanavir and birinapant, were tested for their ability to prevent SARS-CoV-2 plaque formation. At 10 µM of birinapant concentration, antiviral tests against SARS-CoV-2 demonstrated a 37% reduction of virus multiplication. Antiviral assays demonstrated that birinapant has high anti-SARS-CoV-2 activity in the low micromolar range, with an IC50 value of 18 ± 3.6 µM. Therefore, birinapant is a candidate for further investigation to determine whether it is a feasible therapy option.
bibliographic citation: Kandeel et al. (2022) Antiviral drug discovery by targeting the SARS-CoV-2 polyprotein processing by inhibition of the main protease. PeerJ 10:e12929 https://doi.org/10.7717/peerj.12929
date submitted: 2021-09-16
date accepted: 2022-01-21
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kandeel
  given name: Mahmoud
author list: Agent
  family name: Kim
  given name: Jinsoo
author list: Agent
  family name: Fayez
  given name: Mahmoud
author list: Agent
  family name: Kitade
  given name: Yukio
author list: Agent
  family name: Kwon
  given name: Hyung-Joo
doi: 10.7717/peerj.12929
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Kandeel et al.
attribution name: Kandeel et al.

Characterization of the bark storage protein gene (JcBSP) family in the perennial woody plant Jatropha curcas and the function of JcBSP1 in Arabidopsis thaliana
type: item
type: AcademicArticle
description: Background Bark storage protein (BSP) plays an important role in seasonal nitrogen cycling in perennial deciduous trees. However, there is no report on the function of BSP in the perennial woody oil plant Jatropha curcas. Methods In this study, we identified six members of JcBSP gene family in J. curcas genome. The patterns, seasonal changes, and responses to nitrogen treatment in gene expression of JcBSPs were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Overexpression of JcBSP1 in transgenic Arabidopsis thaliana was driven by a constitutive cauliflower mosaic virus (CaMV) 35S RNA promoter. Results JcBSP members were found to be expressed in various tissues, except seeds. The seasonal changes in the total protein concentration and JcBSP1 expression in the stems of J. curcas were positively correlated, as both increased in autumn and winter and decreased in spring and summer. In addition, the JcBSP1 expression in J. curcas seedlings treated with different concentrations of an NH4NO3 solution was positively correlated with the NH4NO3 concentration and application duration. Furthermore, JcBSP1 overexpression in Arabidopsis resulted in a phenotype of enlarged rosette leaves, flowers, and seeds, and significantly increased the seed weight and yield in transgenic plants.
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format: text/html
creator: Ming-Jun Zhang
creator: Qiantang Fu
creator: Mao-Sheng Chen
creator: Huiying He
creator: Mingyong Tang
creator: Jun Ni
creator: Yan-Bin Tao
creator: Zeng-Fu Xu
subject: Molecular Biology
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.12938
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background Bark storage protein (BSP) plays an important role in seasonal nitrogen cycling in perennial deciduous trees. However, there is no report on the function of BSP in the perennial woody oil plant Jatropha curcas. Methods In this study, we identified six members of JcBSP gene family in J. curcas genome. The patterns, seasonal changes, and responses to nitrogen treatment in gene expression of JcBSPs were detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Overexpression of JcBSP1 in transgenic Arabidopsis thaliana was driven by a constitutive cauliflower mosaic virus (CaMV) 35S RNA promoter. Results JcBSP members were found to be expressed in various tissues, except seeds. The seasonal changes in the total protein concentration and JcBSP1 expression in the stems of J. curcas were positively correlated, as both increased in autumn and winter and decreased in spring and summer. In addition, the JcBSP1 expression in J. curcas seedlings treated with different concentrations of an NH4NO3 solution was positively correlated with the NH4NO3 concentration and application duration. Furthermore, JcBSP1 overexpression in Arabidopsis resulted in a phenotype of enlarged rosette leaves, flowers, and seeds, and significantly increased the seed weight and yield in transgenic plants.
bibliographic citation: Zhang et al. (2022) Characterization of the bark storage protein gene (JcBSP) family in the perennial woody plant Jatropha curcas and the function of JcBSP1 in Arabidopsis thaliana. PeerJ 10:e12938 https://doi.org/10.7717/peerj.12938
date submitted: 2021-11-10
date accepted: 2022-01-24
issued: 2022-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ming-Jun
author list: Agent
  family name: Fu
  given name: Qiantang
author list: Agent
  family name: Chen
  given name: Mao-Sheng
author list: Agent
  family name: He
  given name: Huiying
author list: Agent
  family name: Tang
  given name: Mingyong
author list: Agent
  family name: Ni
  given name: Jun
author list: Agent
  family name: Tao
  given name: Yan-Bin
author list: Agent
  family name: Xu
  given name: Zeng-Fu
doi: 10.7717/peerj.12938
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-08
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Cross-sectional study of chromosomal aberrations and immunologic factors in Iraqi couples with recurrent pregnancy loss
type: item
type: AcademicArticle
description: Background Parental chromosomal aberrations are important causes of recurrent pregnancy loss (RPL). Some immunological factors such as antiphospholipid antibodies and interleukin-6 (IL-6) also contribute to this complication. The aim of this study was to determine the frequency of chromosomal abnormalities and to evaluate some of the immunological factors in couples with RPL from different cities in Iraq. Methods This study was conducted on 25 couples (50 individuals) who had more than two first trimester abortions in the past and 25 healthy females as controls. Karyotyping was performed on peripheral blood of all participants. Anticardiolipin (IgG and IgM), antiphosopholipid (IgG and IgM), lupus anticoagulant, and IL-6 were assayed. Data were analyzed using appropriate statistical tests. Results Chromosomal abnormalities were found in 28.0% (n = 7/25) of RPL couples. Of these five (10.0%) were female and two (4.0%) were male. The types of structural abnormalities were as follows: 45, XX, t(21; 21); 45, XX, rob (14, 15); 46, XX, add (21) (p13); 46 XY, add (21)(p13); 46, XX, 21ps+; 46, XY, per inv (9) (p11q12) and 45, XX, t(13q, 13q). No chromosomal abnormalities were found in the control group. Also, no significant differences were found in the immunological parameters of the couples with RPL and the control group. Conclusion In this study, karyotyping revealed a high number of chromosomal abnormalities associated with the RPL in Iraqi couples. Since identification of genetic causes of miscarriage is important for genetic counseling and educating couples about the risk of future pregnancies, it is recommended that conventional karyotyping be investigated in patients with RPL.
format: application/pdf
format: text/html
creator: Doaa A. Khamees
creator: Mushtak T. S. Al-Ouqaili
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Andrology
subject: Gynecology and Obstetrics
description: doi:10.7717/peerj.12801
publisher: PeerJ Inc.
rights: © 2022 Khamees and Al-Ouqaili
abstract: Background Parental chromosomal aberrations are important causes of recurrent pregnancy loss (RPL). Some immunological factors such as antiphospholipid antibodies and interleukin-6 (IL-6) also contribute to this complication. The aim of this study was to determine the frequency of chromosomal abnormalities and to evaluate some of the immunological factors in couples with RPL from different cities in Iraq. Methods This study was conducted on 25 couples (50 individuals) who had more than two first trimester abortions in the past and 25 healthy females as controls. Karyotyping was performed on peripheral blood of all participants. Anticardiolipin (IgG and IgM), antiphosopholipid (IgG and IgM), lupus anticoagulant, and IL-6 were assayed. Data were analyzed using appropriate statistical tests. Results Chromosomal abnormalities were found in 28.0% (n = 7/25) of RPL couples. Of these five (10.0%) were female and two (4.0%) were male. The types of structural abnormalities were as follows: 45, XX, t(21; 21); 45, XX, rob (14, 15); 46, XX, add (21) (p13); 46 XY, add (21)(p13); 46, XX, 21ps+; 46, XY, per inv (9) (p11q12) and 45, XX, t(13q, 13q). No chromosomal abnormalities were found in the control group. Also, no significant differences were found in the immunological parameters of the couples with RPL and the control group. Conclusion In this study, karyotyping revealed a high number of chromosomal abnormalities associated with the RPL in Iraqi couples. Since identification of genetic causes of miscarriage is important for genetic counseling and educating couples about the risk of future pregnancies, it is recommended that conventional karyotyping be investigated in patients with RPL.
bibliographic citation: Khamees et al. (2022) Cross-sectional study of chromosomal aberrations and immunologic factors in Iraqi couples with recurrent pregnancy loss. PeerJ 10:e12801 https://doi.org/10.7717/peerj.12801
date submitted: 2021-10-25
date accepted: 2021-12-24
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khamees
  given name: Doaa A.
author list: Agent
  family name: Al-Ouqaili
  given name: Mushtak T. S.
doi: 10.7717/peerj.12801
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: © 2022 Khamees and Al-Ouqaili
attribution name: Khamees and Al-Ouqaili

Using virtual reality for anatomical landmark annotation in geometric morphometrics
type: item
type: AcademicArticle
description: To study the shape of objects using geometric morphometrics, landmarks are oftentimes collected digitally from a 3D scanned model. The expert may annotate landmarks using software that visualizes the 3D model on a flat screen, and interaction is achieved with a mouse and a keyboard. However, landmark annotation of a 3D model on a 2D display is a tedious process and potentially introduces error due to the perception and interaction limitations of the flat interface. In addition, digital landmark placement can be more time-consuming than direct annotation on the physical object using a tactile digitizer arm. Since virtual reality (VR) is designed to more closely resemble the real world, we present a VR prototype for annotating landmarks on 3D models. We study the impact of VR on annotation performance by comparing our VR prototype to Stratovan Checkpoint, a commonly used commercial desktop software. We use an experimental setup, where four operators placed six landmarks on six grey seal (Halichoerus grypus) skulls in six trials for both systems. This enables us to investigate multiple sources of measurement error. We analyse both for the configuration and for single landmarks. Our analysis shows that annotation in VR is a promising alternative to desktop annotation. We find that annotation precision is comparable between the two systems, with VR being significantly more precise for one of the landmarks. We do not find evidence that annotation in VR is faster than on the desktop, but it is accurate.
format: application/pdf
format: text/html
creator: Dolores Messer
creator: Michael Atchapero
creator: Mark B. Jensen
creator: Michelle S. Svendsen
creator: Anders Galatius
creator: Morten T. Olsen
creator: Jeppe R. Frisvad
creator: Vedrana A. Dahl
creator: Knut Conradsen
creator: Anders B. Dahl
creator: Andreas Bærentzen
subject: Zoology
subject: Data Science
description: doi:10.7717/peerj.12869
publisher: PeerJ Inc.
rights: © 2022 Messer et al.
abstract: To study the shape of objects using geometric morphometrics, landmarks are oftentimes collected digitally from a 3D scanned model. The expert may annotate landmarks using software that visualizes the 3D model on a flat screen, and interaction is achieved with a mouse and a keyboard. However, landmark annotation of a 3D model on a 2D display is a tedious process and potentially introduces error due to the perception and interaction limitations of the flat interface. In addition, digital landmark placement can be more time-consuming than direct annotation on the physical object using a tactile digitizer arm. Since virtual reality (VR) is designed to more closely resemble the real world, we present a VR prototype for annotating landmarks on 3D models. We study the impact of VR on annotation performance by comparing our VR prototype to Stratovan Checkpoint, a commonly used commercial desktop software. We use an experimental setup, where four operators placed six landmarks on six grey seal (Halichoerus grypus) skulls in six trials for both systems. This enables us to investigate multiple sources of measurement error. We analyse both for the configuration and for single landmarks. Our analysis shows that annotation in VR is a promising alternative to desktop annotation. We find that annotation precision is comparable between the two systems, with VR being significantly more precise for one of the landmarks. We do not find evidence that annotation in VR is faster than on the desktop, but it is accurate.
bibliographic citation: Messer et al. (2022) Using virtual reality for anatomical landmark annotation in geometric morphometrics. PeerJ 10:e12869 https://doi.org/10.7717/peerj.12869
date submitted: 2021-10-27
date accepted: 2022-01-10
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Messer
  given name: Dolores
author list: Agent
  family name: Atchapero
  given name: Michael
author list: Agent
  family name: Jensen
  given name: Mark B.
author list: Agent
  family name: Svendsen
  given name: Michelle S.
author list: Agent
  family name: Galatius
  given name: Anders
author list: Agent
  family name: Olsen
  given name: Morten T.
author list: Agent
  family name: Frisvad
  given name: Jeppe R.
author list: Agent
  family name: Dahl
  given name: Vedrana A.
author list: Agent
  family name: Conradsen
  given name: Knut
author list: Agent
  family name: Dahl
  given name: Anders B.
author list: Agent
  family name: Bærentzen
  given name: Andreas
doi: 10.7717/peerj.12869
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: © 2022 Messer et al.
attribution name: Messer et al.

Temperature and duration of exposure drive infection intensity with the amphibian pathogen Batrachochytrium dendrobatidis
type: item
type: AcademicArticle
description: The intensity of a pathogen infection plays a key role in determining how the host responds to infection. Hosts with high infections are more likely to transmit infection to others, and are may be more likely to experience progression from infection to disease symptoms, to being physiologically compromised by disease. Understanding how and why hosts exhibit variation in infection intensity therefore plays a major part in developing and implementing measures aimed at controlling infection spread, its effects, and its chance of persisting and circulating within a population of hosts. To track the relative importance of a number of variables in determining the level of infection intensity, we ran field-surveys at two breeding sites over a 12 month period using marked larvae of the common midwife toad (Alyes obstetricans) and their levels of infection with the amphibian pathogen Batrachochytrium dendrobatidis (Bd). At each sampling occasion we measured the density of larvae, the temperature of the water in the 48 h prior to sampling, the period of time the sampled individual had been in the water body, the developmental (Gosner) stage and the intensity of Bd infection of the individual. Overall our data suggest that the temperature and the duration of time spent in the water play a major role in determining the intensity of Bd infection within an individual host. However, although the duration of time spent in the water was clearly associated with infection intensity, the relationship was negative: larvae that had spent less than 3–6 months in the water had significantly higher infection intensities than those that had spent over 12 months, although this infection intensity peaked between 9 and 12 months. This could be due to animals with heavier infections developing more quickly, suffering increased mortality or, more likely, losing their mouthparts (the only part of anuran larvae that can be infected with Bd). Overall, our results identify drivers of infection intens…
format: application/pdf
format: text/html
creator: Jon Bielby
creator: Cristina Sausor
creator: Camino Monsalve-Carcaño
creator: Jaime Bosch
subject: Conservation Biology
subject: Ecology
subject: Parasitology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12889
publisher: PeerJ Inc.
rights: © 2022 Bielby et al.
abstract: The intensity of a pathogen infection plays a key role in determining how the host responds to infection. Hosts with high infections are more likely to transmit infection to others, and are may be more likely to experience progression from infection to disease symptoms, to being physiologically compromised by disease. Understanding how and why hosts exhibit variation in infection intensity therefore plays a major part in developing and implementing measures aimed at controlling infection spread, its effects, and its chance of persisting and circulating within a population of hosts. To track the relative importance of a number of variables in determining the level of infection intensity, we ran field-surveys at two breeding sites over a 12 month period using marked larvae of the common midwife toad (Alyes obstetricans) and their levels of infection with the amphibian pathogen Batrachochytrium dendrobatidis (Bd). At each sampling occasion we measured the density of larvae, the temperature of the water in the 48 h prior to sampling, the period of time the sampled individual had been in the water body, the developmental (Gosner) stage and the intensity of Bd infection of the individual. Overall our data suggest that the temperature and the duration of time spent in the water play a major role in determining the intensity of Bd infection within an individual host. However, although the duration of time spent in the water was clearly associated with infection intensity, the relationship was negative: larvae that had spent less than 3–6 months in the water had significantly higher infection intensities than those that had spent over 12 months, although this infection intensity peaked between 9 and 12 months. This could be due to animals with heavier infections developing more quickly, suffering increased mortality or, more likely, losing their mouthparts (the only part of anuran larvae that can be infected with Bd). Overall, our results identify drivers of infection intens…
bibliographic citation: Bielby et al. (2022) Temperature and duration of exposure drive infection intensity with the amphibian pathogen Batrachochytrium dendrobatidis. PeerJ 10:e12889 https://doi.org/10.7717/peerj.12889
date submitted: 2021-09-17
date accepted: 2022-01-14
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bielby
  given name: Jon
author list: Agent
  family name: Sausor
  given name: Cristina
author list: Agent
  family name: Monsalve-Carcaño
  given name: Camino
author list: Agent
  family name: Bosch
  given name: Jaime
doi: 10.7717/peerj.12889
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: © 2022 Bielby et al.
attribution name: Bielby et al.

Micropropagation of pokeweed (Phytolacca americana L.) and comparison of phenolic, flavonoid content, and antioxidant activity between pokeweed callus and other parts
type: item
type: AcademicArticle
description: Background Pokeweed (Phytolacca americana L.) is regarded as an invasive plant in many parts of the world but possesses therapeutic characteristics used for antitumor and rheumatism treatment. This study investigated the effects of auxins and four explants on pokeweed callus induction. The effects of cytokinins and combinations between cytokinins and NAA on shoot and root induction were also studied. TPC, TFC and antioxidant activity of calli were screened and compared with other pokeweed plant parts. Methods Four explants were used to induce callus using 2,4-D and IBA at 1, 2, 3 and 4 mg/l for each auxin. Direct shoot organogenesis from nodal explants was investigated using BAP, kinetin and TDZ (1, 2 and 4 mg/l for each cytokinin). Combined effects between cytokinins and NAA at 0.1, 0.2 and 0.3 mg/l were further simultaneously estimated with root induction. Calli derived from the leaves were compared with other plant parts for TPC, TFC and antioxidant activity using the Folin-Ciocalteu, AlCl3 colorimetric assay and DPPH assays, respectively. Results Results showed that MS medium containing 2 mg/l 2,4-D induced callus formation on leaf explants that provided highest fresh and dry weights. Three types of synthetic cytokinins as kinetin, TDZ and BAP were used for direct shoot organogenesis from pokeweed nodes. MS medium containing 2 mg/l kinetin was effective in stimulating normal shoots, with the largest number of shoots and leaves and the longest shoots. The combination between cytokinins and NAA showed no positive effect on shoot and root induction from pokeweed nodal explants. For TPC and TFC determination, pokeweed seeds and leaves possessed the highest phenolic and flavonoid contents, respectively. Highest phenolic content of pokeweed seeds led to lowest IC50 by DPPH assay. Phenolic content was higher than flavonoid content. Conclusion Results suggested promising conditions for callus induction. Leaf explants cultured on MS medium with 2 mg/l 2,4-D and nodal exp…
format: application/pdf
format: text/html
creator: Attachai Trunjaruen
creator: Prathan Luecha
creator: Worasitikulya Taratima
subject: Biochemistry
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.12892
publisher: PeerJ Inc.
rights: © 2022 Trunjaruen et al.
abstract: Background Pokeweed (Phytolacca americana L.) is regarded as an invasive plant in many parts of the world but possesses therapeutic characteristics used for antitumor and rheumatism treatment. This study investigated the effects of auxins and four explants on pokeweed callus induction. The effects of cytokinins and combinations between cytokinins and NAA on shoot and root induction were also studied. TPC, TFC and antioxidant activity of calli were screened and compared with other pokeweed plant parts. Methods Four explants were used to induce callus using 2,4-D and IBA at 1, 2, 3 and 4 mg/l for each auxin. Direct shoot organogenesis from nodal explants was investigated using BAP, kinetin and TDZ (1, 2 and 4 mg/l for each cytokinin). Combined effects between cytokinins and NAA at 0.1, 0.2 and 0.3 mg/l were further simultaneously estimated with root induction. Calli derived from the leaves were compared with other plant parts for TPC, TFC and antioxidant activity using the Folin-Ciocalteu, AlCl3 colorimetric assay and DPPH assays, respectively. Results Results showed that MS medium containing 2 mg/l 2,4-D induced callus formation on leaf explants that provided highest fresh and dry weights. Three types of synthetic cytokinins as kinetin, TDZ and BAP were used for direct shoot organogenesis from pokeweed nodes. MS medium containing 2 mg/l kinetin was effective in stimulating normal shoots, with the largest number of shoots and leaves and the longest shoots. The combination between cytokinins and NAA showed no positive effect on shoot and root induction from pokeweed nodal explants. For TPC and TFC determination, pokeweed seeds and leaves possessed the highest phenolic and flavonoid contents, respectively. Highest phenolic content of pokeweed seeds led to lowest IC50 by DPPH assay. Phenolic content was higher than flavonoid content. Conclusion Results suggested promising conditions for callus induction. Leaf explants cultured on MS medium with 2 mg/l 2,4-D and nodal exp…
bibliographic citation: Trunjaruen et al. (2022) Micropropagation of pokeweed (Phytolacca americana L.) and comparison of phenolic, flavonoid content, and antioxidant activity between pokeweed callus and other parts. PeerJ 10:e12892 https://doi.org/10.7717/peerj.12892
date submitted: 2021-09-20
date accepted: 2022-01-16
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trunjaruen
  given name: Attachai
author list: Agent
  family name: Luecha
  given name: Prathan
author list: Agent
  family name: Taratima
  given name: Worasitikulya
doi: 10.7717/peerj.12892
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: ©2022 Trunjaruen et al.
attribution name: Trunjaruen et al.

Effects of substituting soybean meal with corn on immune function and gene expression of gut TLR4 pathway of growing goats
type: item
type: AcademicArticle
description: Background Protein malnutrition remains a severe problem in ruminant production and can increase susceptibility to infection, especially during the growth stage. This study aimed to explore substituting soybean meal with corn on activation of the TLR pathway and potential impact on immune response bias towards Type 1 or Type 2 using growing female goats as experimental animals. Methods Twenty-four Xiangdong black goats (initial BW = 19.83 ± 0.53 kg, about 8 ± 0.3 months old) were selected and randomly divided into the corn-soybean meal basal diet group (CON, 10.77% protein) and replacing soybean meal with 100% of corn group (CRS, 5.52% protein). EDTA whole blood and serum samples were collected prior to slaughter for determinations of blood cell counts, anti-inflammatory cytokines and antibodies. The duodenum, jejunum, ileum and colon tissues were collected after formal trial to study the effect of CRS diet on the expression of TLR4 pathway. Results Our results showed CRS diet did not induce a significant change in immune function, as evidenced by the observations that white blood cell (WBC), neutrophil (Neu), lymphocyte (Lym), monocyte (Mon), eosinophil (Eos), interleukin-4 (IL-4), IL-5, IL-13, immunoglobin G (IgG), IgA, and IgM levels in serum were similar between the two groups. RT-PCR results showed the expression of tumor necrosis factor-α (TNF-α) (P < 0.01) and interferon-β (IFN-β) (P < 0.01) were up-regulated in the colon of goats in the CRS group. No differences in the expression of myeloid differentiation factor 88 (MyD88) adaptor-like protein (TIRAP), IL-1 receptor–associated kinase 1 (IRAK1), TNF receptor related factor 6 (TRAF6), NF-kappa B (NF-κB), mitogen-activated protein kinase 1 (MAPK1) or activator protein-1 (AP-1) in the TLR4/MyD88 dependent pathway were observed between the two groups for any of the tested tissue. However, the expression of NF-κB activator (TANK) binding kinase 1 (TBK1) in TLR4/MyD88 independent pathway was up-regulated in the du…
format: application/pdf
format: text/html
creator: Yan Cheng
creator: Chao Yang
creator: Wenxun Chen
creator: Qiongxian Yan
creator: Zhiliang Tan
creator: Zhixiong He
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.12910
publisher: PeerJ Inc.
rights: © 2022 Cheng et al.
abstract: Background Protein malnutrition remains a severe problem in ruminant production and can increase susceptibility to infection, especially during the growth stage. This study aimed to explore substituting soybean meal with corn on activation of the TLR pathway and potential impact on immune response bias towards Type 1 or Type 2 using growing female goats as experimental animals. Methods Twenty-four Xiangdong black goats (initial BW = 19.83 ± 0.53 kg, about 8 ± 0.3 months old) were selected and randomly divided into the corn-soybean meal basal diet group (CON, 10.77% protein) and replacing soybean meal with 100% of corn group (CRS, 5.52% protein). EDTA whole blood and serum samples were collected prior to slaughter for determinations of blood cell counts, anti-inflammatory cytokines and antibodies. The duodenum, jejunum, ileum and colon tissues were collected after formal trial to study the effect of CRS diet on the expression of TLR4 pathway. Results Our results showed CRS diet did not induce a significant change in immune function, as evidenced by the observations that white blood cell (WBC), neutrophil (Neu), lymphocyte (Lym), monocyte (Mon), eosinophil (Eos), interleukin-4 (IL-4), IL-5, IL-13, immunoglobin G (IgG), IgA, and IgM levels in serum were similar between the two groups. RT-PCR results showed the expression of tumor necrosis factor-α (TNF-α) (P < 0.01) and interferon-β (IFN-β) (P < 0.01) were up-regulated in the colon of goats in the CRS group. No differences in the expression of myeloid differentiation factor 88 (MyD88) adaptor-like protein (TIRAP), IL-1 receptor–associated kinase 1 (IRAK1), TNF receptor related factor 6 (TRAF6), NF-kappa B (NF-κB), mitogen-activated protein kinase 1 (MAPK1) or activator protein-1 (AP-1) in the TLR4/MyD88 dependent pathway were observed between the two groups for any of the tested tissue. However, the expression of NF-κB activator (TANK) binding kinase 1 (TBK1) in TLR4/MyD88 independent pathway was up-regulated in the du…
bibliographic citation: Cheng et al. (2022) Effects of substituting soybean meal with corn on immune function and gene expression of gut TLR4 pathway of growing goats. PeerJ 10:e12910 https://doi.org/10.7717/peerj.12910
date submitted: 2021-08-20
date accepted: 2022-01-19
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cheng
  given name: Yan
author list: Agent
  family name: Yang
  given name: Chao
author list: Agent
  family name: Chen
  given name: Wenxun
author list: Agent
  family name: Yan
  given name: Qiongxian
author list: Agent
  family name: Tan
  given name: Zhiliang
author list: Agent
  family name: He
  given name: Zhixiong
doi: 10.7717/peerj.12910
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: © 2022 Cheng et al.
attribution name: Cheng et al.

Antioxidant and anti-inflammatory activities of durian (Durio zibethinus Murr.) pulp, seed and peel flour
type: item
type: AcademicArticle
description: The unripe pulp, inner peel and seed of durian were used in this study. These are generally not considered edible and must be disposed of as waste. However, they are good sources of bioactive compounds. Flour extracts from the unripe pulp, inner peel, and seed of two durian (Durio zibethinus Murr.) varieties, namely, Monthong and Chanee, were analyzed chemically to determine their total phenolic content (TPC), antioxidant, and anti-inflammatory capacities. Chanee pulp (CPu) contained a higher TPC (5285.37 ± 517.65 mg GAE/g) than Monthong pulp (MPu), Monthong peel (MP), Monthong seed (MS), Chanee peel (CP) and Chanee seed (CS) (p = 0.0027, 0.0042, 0.0229, 0.0069 and 0.36), respectively. The antioxidant activity of each durian extract was determined against ABTS, nitric oxide, superoxide, hydroxyl, and metal ions. The results indicated that the pulp, inner peel and seed of these durian varieties had antioxidant capacities. Murine Raw 264.7 macrophages were used to determine the cytotoxicity of the flour extracts. The extract of CS flour had the lowest cytotoxicity followed by MP, CPu, CP, MPu and MS (p = 0.5926, 0.44, 0.3191, 0.1471 and 0.0014), respectively. The anti-inflammatory activity was tested by anti-nitric oxide (NO) production in lipopolysaccharide (LPS) stimulated cells by co-treating the Raw 264.7 cells with each durian flour extract and LPS. The extract of MP flour had the lowest IC50 against NO production, indicating the highest anti-NO production activity followed by CS, CPu, MPu, CP and MS (p = 0.7473, 0.0104, < 0.0001, 0.0002 and < 0.0001, respectively). The information obtained in this study is useful for researchers to explore more durian varieties in Southeast Asia to find bioactive compounds that might be novel nutraceuticals for antioxidant, anti-inflammation and therapeutic functional food.
format: application/pdf
format: text/html
creator: Narin Charoenphun
creator: Wiyada Kwanhian Klangbud
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Plant Science
subject: Evidence Based Medicine
description: doi:10.7717/peerj.12933
publisher: PeerJ Inc.
rights: © 2022 Charoenphun and Klangbud
abstract: The unripe pulp, inner peel and seed of durian were used in this study. These are generally not considered edible and must be disposed of as waste. However, they are good sources of bioactive compounds. Flour extracts from the unripe pulp, inner peel, and seed of two durian (Durio zibethinus Murr.) varieties, namely, Monthong and Chanee, were analyzed chemically to determine their total phenolic content (TPC), antioxidant, and anti-inflammatory capacities. Chanee pulp (CPu) contained a higher TPC (5285.37 ± 517.65 mg GAE/g) than Monthong pulp (MPu), Monthong peel (MP), Monthong seed (MS), Chanee peel (CP) and Chanee seed (CS) (p = 0.0027, 0.0042, 0.0229, 0.0069 and 0.36), respectively. The antioxidant activity of each durian extract was determined against ABTS, nitric oxide, superoxide, hydroxyl, and metal ions. The results indicated that the pulp, inner peel and seed of these durian varieties had antioxidant capacities. Murine Raw 264.7 macrophages were used to determine the cytotoxicity of the flour extracts. The extract of CS flour had the lowest cytotoxicity followed by MP, CPu, CP, MPu and MS (p = 0.5926, 0.44, 0.3191, 0.1471 and 0.0014), respectively. The anti-inflammatory activity was tested by anti-nitric oxide (NO) production in lipopolysaccharide (LPS) stimulated cells by co-treating the Raw 264.7 cells with each durian flour extract and LPS. The extract of MP flour had the lowest IC50 against NO production, indicating the highest anti-NO production activity followed by CS, CPu, MPu, CP and MS (p = 0.7473, 0.0104, < 0.0001, 0.0002 and < 0.0001, respectively). The information obtained in this study is useful for researchers to explore more durian varieties in Southeast Asia to find bioactive compounds that might be novel nutraceuticals for antioxidant, anti-inflammation and therapeutic functional food.
bibliographic citation: Charoenphun et al. (2022) Antioxidant and anti-inflammatory activities of durian (Durio zibethinus Murr.) pulp, seed and peel flour. PeerJ 10:e12933 https://doi.org/10.7717/peerj.12933
date submitted: 2021-07-16
date accepted: 2022-01-23
issued: 2022-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Charoenphun
  given name: Narin
author list: Agent
  family name: Klangbud
  given name: Wiyada Kwanhian
doi: 10.7717/peerj.12933
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-07
copyright: ©2022 Charoenphun and Klangbud
attribution name: Charoenphun and Klangbud

Assessing the impact of workaholism and work engagement on medical university employee stress and satisfaction levels
type: item
type: AcademicArticle
description: Background Workaholism (WH) is related with high mental trouble and physical objections, low employment and family fulfillment, and low occupation execution; however, work commitment is related with job and life satisfaction. This study aimed to assess the impact of WH and work engagement (WE) on medical university employee job stress and satisfaction. Methods This descriptive analytical study was conducted on workers employed in medical universities using validated questionnaires for data collection. The sample size was 330, from which 305 responded with completed questionnaire. The employees were the direct workers of different accessible medical universities in Karachi, Pakistan. The employee enrolment and distribution of the questionnaire was performed using non-probability convenient sampling. The Brief Job Questionnaire (BJQ), Dutch Work Addiction Scale (DUWAS) and Utrecht Work Engagement Scale (UWES) were used to assess the impact of job stress on job satisfaction and WE. The data was analyzed by applying descriptive statistics, Spearman correlation and regression analysis. A p-value of ≤ 0.05 was taken as significant. Results The study consisted of 117 (38.4%) male and 188 (61.6%) female participants; the mean age of participating employee was 28.50 ± 6.192. The mean score for WE was 3.78 ± 0.467, that of WH was 3.42 ± 0.559, for JS was 4.29 ± 0.400, whereas JSF was 3.10 ± 0.591. A positive correlation was observed between job stress, WH and WE. WH had a strong correlation with job stress and weak correlation with job satisfaction and performance. A significant difference was observed between WE and WH among males and females. Conclusions The study presented with a significant effect of job satisfaction with WH and WE with job stress. Hence, indicating the importance of social skills and WE with fellow employees to increase the work productivity and performance. However, in case of over work and WH, an increase of job stress is inevitable.
format: application/pdf
format: text/html
creator: Mahin Sarfaraz
creator: Shaur Sarfaraz
creator: Afsheen Maqsood
creator: Naseer Ahmed
creator: Fahim Vohra
creator: Tariq Abduljabbar
creator: Adel S. Abduljabbar
subject: Science and Medical Education
subject: Mental Health
description: doi:10.7717/peerj.12565
publisher: PeerJ Inc.
rights: © 2022 Sarfaraz et al.
abstract: Background Workaholism (WH) is related with high mental trouble and physical objections, low employment and family fulfillment, and low occupation execution; however, work commitment is related with job and life satisfaction. This study aimed to assess the impact of WH and work engagement (WE) on medical university employee job stress and satisfaction. Methods This descriptive analytical study was conducted on workers employed in medical universities using validated questionnaires for data collection. The sample size was 330, from which 305 responded with completed questionnaire. The employees were the direct workers of different accessible medical universities in Karachi, Pakistan. The employee enrolment and distribution of the questionnaire was performed using non-probability convenient sampling. The Brief Job Questionnaire (BJQ), Dutch Work Addiction Scale (DUWAS) and Utrecht Work Engagement Scale (UWES) were used to assess the impact of job stress on job satisfaction and WE. The data was analyzed by applying descriptive statistics, Spearman correlation and regression analysis. A p-value of ≤ 0.05 was taken as significant. Results The study consisted of 117 (38.4%) male and 188 (61.6%) female participants; the mean age of participating employee was 28.50 ± 6.192. The mean score for WE was 3.78 ± 0.467, that of WH was 3.42 ± 0.559, for JS was 4.29 ± 0.400, whereas JSF was 3.10 ± 0.591. A positive correlation was observed between job stress, WH and WE. WH had a strong correlation with job stress and weak correlation with job satisfaction and performance. A significant difference was observed between WE and WH among males and females. Conclusions The study presented with a significant effect of job satisfaction with WH and WE with job stress. Hence, indicating the importance of social skills and WE with fellow employees to increase the work productivity and performance. However, in case of over work and WH, an increase of job stress is inevitable.
bibliographic citation: Sarfaraz et al. (2022) Assessing the impact of workaholism and work engagement on medical university employee stress and satisfaction levels. PeerJ 10:e12565 https://doi.org/10.7717/peerj.12565
date submitted: 2021-09-07
date accepted: 2021-11-08
issued: 2022-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sarfaraz
  given name: Mahin
author list: Agent
  family name: Sarfaraz
  given name: Shaur
author list: Agent
  family name: Maqsood
  given name: Afsheen
author list: Agent
  family name: Ahmed
  given name: Naseer
author list: Agent
  family name: Vohra
  given name: Fahim
author list: Agent
  family name: Abduljabbar
  given name: Tariq
author list: Agent
  family name: Abduljabbar
  given name: Adel S.
doi: 10.7717/peerj.12565
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-04
copyright: © 2022 Sarfaraz et al.
attribution name: Sarfaraz et al.

Analysis of metabolites in young and mature Docynia delavayi (Franch.) Schneid leaves using UPLC-ESI-MS/MS
type: item
type: AcademicArticle
description: Docynia delavayi (Franch.) Schneid is a plant used both as food and traditional folk medicine. The leaves of D. delavayi are rich in polyphenols, plants with phenolic content are known to be extremely beneficial in terms of human nutrition. In the present study, we used metabolome technology (UPLC-ESI-MS/MS) to examine the young and mature D. delavayi leaves on metabolites changes, which were then analyzed and compared. As a result, 477 metabolites (including 111 flavonoids, 47 others (consisted of nine vitamin, 18 saccharides and alcohols, and 20 unassigned metabolites), 71 phenolic acids, 52 amino acids and derivatives, 18 alkaloids, 61 lipids, 24 terpenoids, 33 nucleotides and derivatives, 18 lignans and coumarins, 12 tannins, 30 organic acids) were identified, of which 281 differentially accumulated metabolites, including 146 up-regulated metabolites and 135 down-regulated metabolites. The result of clustering and PCA analyses showed that young and mature leaves were separated, which indicated that there was a great difference in metabolites between young and mature leaves. Meanwhile, we also found that both young and mature leaves displayed unique metabolites with important biological functions. KEGG enrichment analysis showed that 90 of the differential metabolites were mainly concentrated in 68 KEGG pathways. The result will greatly complement the existing knowledge on the D. delavayi leaves for lays a foundation for subsequent development and utilization.
format: application/pdf
format: text/html
creator: Xi Xia
creator: Can Chen
creator: Lin Yang
creator: Yuchang Wang
creator: Anan Duan
creator: Dawei Wang
subject: Agricultural Science
subject: Biochemistry
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12844
publisher: PeerJ Inc.
rights: © 2022 Xia et al.
abstract: Docynia delavayi (Franch.) Schneid is a plant used both as food and traditional folk medicine. The leaves of D. delavayi are rich in polyphenols, plants with phenolic content are known to be extremely beneficial in terms of human nutrition. In the present study, we used metabolome technology (UPLC-ESI-MS/MS) to examine the young and mature D. delavayi leaves on metabolites changes, which were then analyzed and compared. As a result, 477 metabolites (including 111 flavonoids, 47 others (consisted of nine vitamin, 18 saccharides and alcohols, and 20 unassigned metabolites), 71 phenolic acids, 52 amino acids and derivatives, 18 alkaloids, 61 lipids, 24 terpenoids, 33 nucleotides and derivatives, 18 lignans and coumarins, 12 tannins, 30 organic acids) were identified, of which 281 differentially accumulated metabolites, including 146 up-regulated metabolites and 135 down-regulated metabolites. The result of clustering and PCA analyses showed that young and mature leaves were separated, which indicated that there was a great difference in metabolites between young and mature leaves. Meanwhile, we also found that both young and mature leaves displayed unique metabolites with important biological functions. KEGG enrichment analysis showed that 90 of the differential metabolites were mainly concentrated in 68 KEGG pathways. The result will greatly complement the existing knowledge on the D. delavayi leaves for lays a foundation for subsequent development and utilization.
bibliographic citation: Xia et al. (2022) Analysis of metabolites in young and mature Docynia delavayi (Franch.) Schneid leaves using UPLC-ESI-MS/MS. PeerJ 10:e12844 https://doi.org/10.7717/peerj.12844
date submitted: 2021-10-05
date accepted: 2022-01-06
issued: 2022-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xia
  given name: Xi
author list: Agent
  family name: Chen
  given name: Can
author list: Agent
  family name: Yang
  given name: Lin
author list: Agent
  family name: Wang
  given name: Yuchang
author list: Agent
  family name: Duan
  given name: Anan
author list: Agent
  family name: Wang
  given name: Dawei
doi: 10.7717/peerj.12844
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-04
copyright: ©2022 Xia et al.
attribution name: Xia et al.

Interpretation of exercise-induced changes in human skeletal muscle mRNA expression depends on the timing of the post-exercise biopsies
type: item
type: AcademicArticle
description: Background Exercise elicits a range of adaptive responses in skeletal muscle, which include changes in mRNA expression. To better understand the health benefits of exercise training, it is important to investigate the underlying molecular mechanisms of skeletal muscle adaptation to exercise. However, most studies have assessed the molecular events at only a few time-points within a short time frame post-exercise, and the variations of gene expression kinetics have not been addressed systematically. Methods We assessed the mRNA expression of 23 gene isoforms implicated in the adaptive response to exercise at six time-points (0, 3, 9, 24, 48, and 72 h post exercise) over a 3-day period following a single session of high-intensity interval exercise. Results The temporal patterns of target gene expression were highly variable and the expression of mRNA transcripts detected was largely dependent on the timing of muscle sampling. The largest fold change in mRNA expression of each tested target gene was observed between 3 and 72 h post-exercise. Discussion and Conclusions Our findings highlight an important gap in knowledge regarding the molecular response to exercise, where the use of limited time-points within a short period post-exercise has led to an incomplete understanding of the molecular response to exercise. Muscle sampling timing for individual studies needs to be carefully chosen based on existing literature and preliminary analysis of the molecular targets of interest. We propose that a comprehensive time-course analysis on the exercise-induced transcriptional response in humans will significantly benefit the field of exercise molecular biology.
format: application/pdf
format: text/html
creator: Jujiao Kuang
creator: Cian McGinley
creator: Matthew J-C Lee
creator: Nicholas J. Saner
creator: Andrew Garnham
creator: David J. Bishop
subject: Biochemistry
subject: Molecular Biology
subject: Sports Medicine
description: doi:10.7717/peerj.12856
publisher: PeerJ Inc.
rights: © 2022 Kuang et al.
abstract: Background Exercise elicits a range of adaptive responses in skeletal muscle, which include changes in mRNA expression. To better understand the health benefits of exercise training, it is important to investigate the underlying molecular mechanisms of skeletal muscle adaptation to exercise. However, most studies have assessed the molecular events at only a few time-points within a short time frame post-exercise, and the variations of gene expression kinetics have not been addressed systematically. Methods We assessed the mRNA expression of 23 gene isoforms implicated in the adaptive response to exercise at six time-points (0, 3, 9, 24, 48, and 72 h post exercise) over a 3-day period following a single session of high-intensity interval exercise. Results The temporal patterns of target gene expression were highly variable and the expression of mRNA transcripts detected was largely dependent on the timing of muscle sampling. The largest fold change in mRNA expression of each tested target gene was observed between 3 and 72 h post-exercise. Discussion and Conclusions Our findings highlight an important gap in knowledge regarding the molecular response to exercise, where the use of limited time-points within a short period post-exercise has led to an incomplete understanding of the molecular response to exercise. Muscle sampling timing for individual studies needs to be carefully chosen based on existing literature and preliminary analysis of the molecular targets of interest. We propose that a comprehensive time-course analysis on the exercise-induced transcriptional response in humans will significantly benefit the field of exercise molecular biology.
bibliographic citation: Kuang et al. (2022) Interpretation of exercise-induced changes in human skeletal muscle mRNA expression depends on the timing of the post-exercise biopsies. PeerJ 10:e12856 https://doi.org/10.7717/peerj.12856
date submitted: 2021-08-12
date accepted: 2022-01-09
issued: 2022-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kuang
  given name: Jujiao
author list: Agent
  family name: McGinley
  given name: Cian
author list: Agent
  family name: Lee
  given name: Matthew J-C
author list: Agent
  family name: Saner
  given name: Nicholas J.
author list: Agent
  family name: Garnham
  given name: Andrew
author list: Agent
  family name: Bishop
  given name: David J.
doi: 10.7717/peerj.12856
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-04
copyright: © 2022 Kuang et al.
attribution name: Kuang et al.

Bayesian computation for the common coefficient of variation of delta-lognormal distributions with application to common rainfall dispersion in Thailand
type: item
type: AcademicArticle
description: Rainfall fluctuation makes precipitation and flood prediction difficult. The coefficient of variation can be used to measure rainfall dispersion to produce information for predicting future rainfall, thereby mitigating future disasters. Rainfall data usually consist of positive and true zero values that correspond to a delta-lognormal distribution. Therefore, the coefficient of variation of delta-lognormal distribution is appropriate to measure the rainfall dispersion more than lognormal distribution. In particular, the measurement of the dispersion of precipitation from several areas can be determined by measuring the common coefficient of variation in the rainfall from those areas together. Herein, we compose confidence intervals for the common coefficient of variation of delta-lognormal distributions by employing the fiducial generalized confidence interval, equal-tailed Bayesian credible intervals incorporating the independent Jeffreys or uniform priors, and the method of variance estimates recovery. A combination of the coverage probabilities and expected lengths of the proposed methods obtained via a Monte Carlo simulation study were used to compare their performances. The results show that the equal-tailed Bayesian based on the independent Jeffreys prior was suitable. In addition, it can be used the equal-tailed Bayesian based on the uniform prior as an alternative. The efficacies of the proposed confidence intervals are demonstrated via applying them to analyze daily rainfall datasets from Nan, Thailand.
format: application/pdf
format: text/html
creator: Noppadon Yosboonruang
creator: Sa-Aat Niwitpong
creator: Suparat Niwitpong
subject: Statistics
subject: Computational Science
subject: Natural Resource Management
subject: Ecohydrology
subject: Environmental Impacts
description: doi:10.7717/peerj.12858
publisher: PeerJ Inc.
rights: © 2022 Yosboonruang et al.
abstract: Rainfall fluctuation makes precipitation and flood prediction difficult. The coefficient of variation can be used to measure rainfall dispersion to produce information for predicting future rainfall, thereby mitigating future disasters. Rainfall data usually consist of positive and true zero values that correspond to a delta-lognormal distribution. Therefore, the coefficient of variation of delta-lognormal distribution is appropriate to measure the rainfall dispersion more than lognormal distribution. In particular, the measurement of the dispersion of precipitation from several areas can be determined by measuring the common coefficient of variation in the rainfall from those areas together. Herein, we compose confidence intervals for the common coefficient of variation of delta-lognormal distributions by employing the fiducial generalized confidence interval, equal-tailed Bayesian credible intervals incorporating the independent Jeffreys or uniform priors, and the method of variance estimates recovery. A combination of the coverage probabilities and expected lengths of the proposed methods obtained via a Monte Carlo simulation study were used to compare their performances. The results show that the equal-tailed Bayesian based on the independent Jeffreys prior was suitable. In addition, it can be used the equal-tailed Bayesian based on the uniform prior as an alternative. The efficacies of the proposed confidence intervals are demonstrated via applying them to analyze daily rainfall datasets from Nan, Thailand.
bibliographic citation: Yosboonruang et al. (2022) Bayesian computation for the common coefficient of variation of delta-lognormal distributions with application to common rainfall dispersion in Thailand. PeerJ 10:e12858 https://doi.org/10.7717/peerj.12858
date submitted: 2021-07-27
date accepted: 2022-01-09
issued: 2022-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yosboonruang
  given name: Noppadon
author list: Agent
  family name: Niwitpong
  given name: Sa-Aat
author list: Agent
  family name: Niwitpong
  given name: Suparat
doi: 10.7717/peerj.12858
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-04
copyright: © 2022 Yosboonruang et al.
attribution name: Yosboonruang et al.

Cytokinin and gibberellic acid-mediated waterlogging tolerance of mungbean (Vigna radiata L. Wilczek)
type: item
type: AcademicArticle
description: Background Mungbean (Vigna radiata L. Wilczek) is one of the most important pulse crops, well-known for its protein-rich seeds. Growth and productivity are severely undermined by waterlogging. Methods In this study, we aim to evaluate how two promising phytohormones, namely cytokinin (CK) and gibberellic acid (GA3), can improve waterlogging tolerance in mungbean by investigating key morphological, physiological, biochemical, and yield-related attributes. Results Our results showed that foliar application of CK and GA3 under 5-day of waterlogged conditions improved mungbean growth and biomass, which was associated with increased levels of photosynthetic rate and pigments. Waterlogged-induced accumulation of reactive oxygen species and the consequently elevated levels of malondialdehyde were considerably reduced by CK and GA3 treatments. Mungbean plants sprayed with either CK or GA3 suffered less oxidative stress due to the enhancement of total phenolics and flavonoids levels. Improvement in the contents of proline and total soluble sugars indicated a better osmotic adjustment following CK and GA3 treatments in waterlogged‐exposed plants. Most fundamentally, CK or GA3-sprayed waterlogged-stressed mungbean plants demonstrated better performance in the aforementioned parameters after the 15-day recovery period as compared to water-sprayed waterlogged-exposed plants. Our results also revealed that CK and GA3 treatments increased yield-associated features in the waterlogged-stressed plant. Here, both phytohormones are efficient in improving mungbean resistance to waterlogging. However, CK was found to be more effective. Overall, our findings suggested that CK or GA3 could be used for managing waterlogging-induced damage to mungbean and perhaps in other cash crops.
format: application/pdf
format: text/html
creator: M. Rafiqul Islam
creator: Md. Mezanur Rahman
creator: Mohammed Mohi-Ud-Din
creator: Munny Akter
creator: Erin Zaman
creator: Sanjida Sultana Keya
creator: Mehfuz Hasan
creator: Mirza Hasanuzzaman
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.12862
publisher: PeerJ Inc.
rights: © 2022 Islam et al.
abstract: Background Mungbean (Vigna radiata L. Wilczek) is one of the most important pulse crops, well-known for its protein-rich seeds. Growth and productivity are severely undermined by waterlogging. Methods In this study, we aim to evaluate how two promising phytohormones, namely cytokinin (CK) and gibberellic acid (GA3), can improve waterlogging tolerance in mungbean by investigating key morphological, physiological, biochemical, and yield-related attributes. Results Our results showed that foliar application of CK and GA3 under 5-day of waterlogged conditions improved mungbean growth and biomass, which was associated with increased levels of photosynthetic rate and pigments. Waterlogged-induced accumulation of reactive oxygen species and the consequently elevated levels of malondialdehyde were considerably reduced by CK and GA3 treatments. Mungbean plants sprayed with either CK or GA3 suffered less oxidative stress due to the enhancement of total phenolics and flavonoids levels. Improvement in the contents of proline and total soluble sugars indicated a better osmotic adjustment following CK and GA3 treatments in waterlogged‐exposed plants. Most fundamentally, CK or GA3-sprayed waterlogged-stressed mungbean plants demonstrated better performance in the aforementioned parameters after the 15-day recovery period as compared to water-sprayed waterlogged-exposed plants. Our results also revealed that CK and GA3 treatments increased yield-associated features in the waterlogged-stressed plant. Here, both phytohormones are efficient in improving mungbean resistance to waterlogging. However, CK was found to be more effective. Overall, our findings suggested that CK or GA3 could be used for managing waterlogging-induced damage to mungbean and perhaps in other cash crops.
bibliographic citation: Islam et al. (2022) Cytokinin and gibberellic acid-mediated waterlogging tolerance of mungbean (Vigna radiata L. Wilczek). PeerJ 10:e12862 https://doi.org/10.7717/peerj.12862
date submitted: 2021-08-23
date accepted: 2022-01-09
issued: 2022-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Islam
  given name: M. Rafiqul
author list: Agent
  family name: Rahman
  given name: Md. Mezanur
author list: Agent
  family name: Mohi-Ud-Din
  given name: Mohammed
author list: Agent
  family name: Akter
  given name: Munny
author list: Agent
  family name: Zaman
  given name: Erin
author list: Agent
  family name: Keya
  given name: Sanjida Sultana
author list: Agent
  family name: Hasan
  given name: Mehfuz
author list: Agent
  family name: Hasanuzzaman
  given name: Mirza
doi: 10.7717/peerj.12862
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-04
copyright: © 2022 Islam et al.
attribution name: Islam et al.

Involvement of TOB1 on autophagy in gastric cancer AGS cells via decreasing the activation of AKT/mTOR signaling pathway
type: item
type: AcademicArticle
description: Background We previously identified the tumor suppressor gene TOB1 as related to gastric cancer. The purpose of this study was to explore whether TOB1 induces autophagy through the AKT/mTOR signaling pathway in gastric cancer. Methods Western blotting was used to detect the protein levels of TOB1, LC3, AKT, mTOR, phosphorylated (p) AKT, and p-mTOR. A double fluorescent GFP-RFP-LC3 fusion protein was used to trace autophagy by laser confocal microscopy. Autophagosomes were observed by transmission electron microscopy. Results The conversion of LC3-I to LC3-II and the LC3-II/LC3-I ratio were significantly increased in AGS cells overexpressing TOB1 compared with control cells. Fluorescence imaging showed LC3 puncta at 48 h, and these puncta increased significantly at 72 h after TOB1 transfection compared with control tumor cells. The presence of autophagosomes in AGS cells was observed at 72 h after TOB1 transfection by transmission electron microscopy, and no autophagosomes were found in the control cells. Moreover, the levels of p-AKT and p -mTOR were lower in AGS cells than in control cancer cells. Conclusion Our results provide novel insight that TOB1 might suppress gastric cancer by inducing autophagy, possibly through decreasing phosphorylation and the subsequent activation of the AKT/mTOR signaling pathway.
format: application/pdf
format: text/html
creator: Dong Wang
creator: Yunlong Li
creator: Shuning Sui
creator: Mengdi Cai
creator: Kexian Dong
creator: Ping Wang
creator: Xiao Liang
creator: Songbin Fu
creator: Jingcui Yu
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.12904
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background We previously identified the tumor suppressor gene TOB1 as related to gastric cancer. The purpose of this study was to explore whether TOB1 induces autophagy through the AKT/mTOR signaling pathway in gastric cancer. Methods Western blotting was used to detect the protein levels of TOB1, LC3, AKT, mTOR, phosphorylated (p) AKT, and p-mTOR. A double fluorescent GFP-RFP-LC3 fusion protein was used to trace autophagy by laser confocal microscopy. Autophagosomes were observed by transmission electron microscopy. Results The conversion of LC3-I to LC3-II and the LC3-II/LC3-I ratio were significantly increased in AGS cells overexpressing TOB1 compared with control cells. Fluorescence imaging showed LC3 puncta at 48 h, and these puncta increased significantly at 72 h after TOB1 transfection compared with control tumor cells. The presence of autophagosomes in AGS cells was observed at 72 h after TOB1 transfection by transmission electron microscopy, and no autophagosomes were found in the control cells. Moreover, the levels of p-AKT and p -mTOR were lower in AGS cells than in control cancer cells. Conclusion Our results provide novel insight that TOB1 might suppress gastric cancer by inducing autophagy, possibly through decreasing phosphorylation and the subsequent activation of the AKT/mTOR signaling pathway.
bibliographic citation: Wang et al. (2022) Involvement of TOB1 on autophagy in gastric cancer AGS cells via decreasing the activation of AKT/mTOR signaling pathway. PeerJ 10:e12904 https://doi.org/10.7717/peerj.12904
date submitted: 2021-08-23
date accepted: 2022-01-17
issued: 2022-02-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Dong
author list: Agent
  family name: Li
  given name: Yunlong
author list: Agent
  family name: Sui
  given name: Shuning
author list: Agent
  family name: Cai
  given name: Mengdi
author list: Agent
  family name: Dong
  given name: Kexian
author list: Agent
  family name: Wang
  given name: Ping
author list: Agent
  family name: Liang
  given name: Xiao
author list: Agent
  family name: Fu
  given name: Songbin
author list: Agent
  family name: Yu
  given name: Jingcui
doi: 10.7717/peerj.12904
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-04
copyright: © 2022 Wang et al.
attribution name: Wang et al.

Testosterone and estradiol affect adolescent reinforcement learning
type: item
type: AcademicArticle
description: During adolescence, gonadal hormones influence brain maturation and behavior. The impact of 17β-estradiol and testosterone on reinforcement learning was previously investigated in adults, but studies with adolescents are rare. We tested 89 German male and female adolescents (mean age ± sd = 14.7 ± 1.9 years) to determine the extent 17β-estradiol and testosterone influenced reinforcement learning capacity in a response time adjustment task. Our data showed, that 17β-estradiol correlated with an enhanced ability to speed up responses for reward in both sexes, while the ability to wait for higher reward correlated with testosterone primary in males. This suggests that individual differences in reinforcement learning may be associated with variations in these hormones during adolescence, which may shift the balance between a more reward- and an avoidance-oriented learning style.
format: application/pdf
format: text/html
creator: Sina Kohne
creator: Esther K. Diekhof
subject: Developmental Biology
subject: Neuroscience
subject: Pediatrics
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12653
publisher: PeerJ Inc.
rights: © 2022 Kohne and Diekhof
abstract: During adolescence, gonadal hormones influence brain maturation and behavior. The impact of 17β-estradiol and testosterone on reinforcement learning was previously investigated in adults, but studies with adolescents are rare. We tested 89 German male and female adolescents (mean age ± sd = 14.7 ± 1.9 years) to determine the extent 17β-estradiol and testosterone influenced reinforcement learning capacity in a response time adjustment task. Our data showed, that 17β-estradiol correlated with an enhanced ability to speed up responses for reward in both sexes, while the ability to wait for higher reward correlated with testosterone primary in males. This suggests that individual differences in reinforcement learning may be associated with variations in these hormones during adolescence, which may shift the balance between a more reward- and an avoidance-oriented learning style.
bibliographic citation: Kohne et al. (2022) Testosterone and estradiol affect adolescent reinforcement learning. PeerJ 10:e12653 https://doi.org/10.7717/peerj.12653
date submitted: 2021-04-28
date accepted: 2021-11-29
issued: 2022-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kohne
  given name: Sina
author list: Agent
  family name: Diekhof
  given name: Esther K.
doi: 10.7717/peerj.12653
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-03
copyright: ©2022 Kohne and Diekhof
attribution name: Kohne and Diekhof

Functional mechanism of hsa-miR-128-3p in epithelial-mesenchymal transition of pancreatic cancer cells via ZEB1 regulation
type: item
type: AcademicArticle
description: Pancreatic cancer (PC) often correlates with high mortality due to late diagnosis, rapid metastasis, and resistance to chemotherapy. miR-128-3p has been validated as a tumor suppressor in PC. This study explored the functional mechanism of miR-128-3p in epithelial-mesenchymal transition (EMT) of PC cells. Four PC cancer cell lines with different degrees of malignancy and normal pancreatic cells were selected to detect expressions of hsa-miR-128-3p and ZEB1 by RT-qPCR and Western blot. miR-128-3p mimic or si-ZEB1 was delivered into PANC-1 cells and miR-128-3p inhibitor or oe-ZEB1 was delivered into AsPC-1 cells. Expressions of epithelial and mesenchymal markers were analyzed by Western blot and cell fluorescence staining. The binding relationship between miR-128-3p and ZEB1 was examined by bioinformatics analysis and dual-luciferase assay, and verified by RT-qPCR and Western blot. PC cell invasion and migration were assessed by Transwell assays. Generally, hsa-miR-128-3p was poorly-expressed in PC cells. However, it was relatively more expressed in AsPC-1 cells with epithelial phenotypes relative to PANC-1 cells with mesenchymal phenotype, whereas ZEB1 expression showed opposite tendencies. PANC-1 cells transfected with miR-128-3p mimic or si-ZEB1 showed upregulated E-cadherin and downregulated N-cadherin, and transformed from mesenchymal phenotypes to epithelial phenotypes, with decreased invasion and migration, while opposite results occurred in AsPC-1 cells transfected with miR-128-3p inhibitor or oe-ZEB1. miR-128-3p targeted ZEB1. oe-ZEB1 antagonized the inhibition of miR-128-3p mimic on PANC-1 cell EMT, invasion, and migration, while si-ZEB1 reversed the facilitation of miR-128-3p inhibitor in AsPC-1 cells. In conclusion, miR-128-3p inhibited PC cell EMT, invasion, and migration by targeting ZEB1.
format: application/pdf
format: text/html
creator: Tianying Zheng
creator: Wenfei Han
creator: Aijun Wang
creator: Yonggang Wang
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.12802
publisher: PeerJ Inc.
rights: © 2022 Zheng et al.
abstract: Pancreatic cancer (PC) often correlates with high mortality due to late diagnosis, rapid metastasis, and resistance to chemotherapy. miR-128-3p has been validated as a tumor suppressor in PC. This study explored the functional mechanism of miR-128-3p in epithelial-mesenchymal transition (EMT) of PC cells. Four PC cancer cell lines with different degrees of malignancy and normal pancreatic cells were selected to detect expressions of hsa-miR-128-3p and ZEB1 by RT-qPCR and Western blot. miR-128-3p mimic or si-ZEB1 was delivered into PANC-1 cells and miR-128-3p inhibitor or oe-ZEB1 was delivered into AsPC-1 cells. Expressions of epithelial and mesenchymal markers were analyzed by Western blot and cell fluorescence staining. The binding relationship between miR-128-3p and ZEB1 was examined by bioinformatics analysis and dual-luciferase assay, and verified by RT-qPCR and Western blot. PC cell invasion and migration were assessed by Transwell assays. Generally, hsa-miR-128-3p was poorly-expressed in PC cells. However, it was relatively more expressed in AsPC-1 cells with epithelial phenotypes relative to PANC-1 cells with mesenchymal phenotype, whereas ZEB1 expression showed opposite tendencies. PANC-1 cells transfected with miR-128-3p mimic or si-ZEB1 showed upregulated E-cadherin and downregulated N-cadherin, and transformed from mesenchymal phenotypes to epithelial phenotypes, with decreased invasion and migration, while opposite results occurred in AsPC-1 cells transfected with miR-128-3p inhibitor or oe-ZEB1. miR-128-3p targeted ZEB1. oe-ZEB1 antagonized the inhibition of miR-128-3p mimic on PANC-1 cell EMT, invasion, and migration, while si-ZEB1 reversed the facilitation of miR-128-3p inhibitor in AsPC-1 cells. In conclusion, miR-128-3p inhibited PC cell EMT, invasion, and migration by targeting ZEB1.
bibliographic citation: Zheng et al. (2022) Functional mechanism of hsa-miR-128-3p in epithelial-mesenchymal transition of pancreatic cancer cells via ZEB1 regulation. PeerJ 10:e12802 https://doi.org/10.7717/peerj.12802
date submitted: 2021-10-11
date accepted: 2021-12-25
issued: 2022-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Tianying
author list: Agent
  family name: Han
  given name: Wenfei
author list: Agent
  family name: Wang
  given name: Aijun
author list: Agent
  family name: Wang
  given name: Yonggang
doi: 10.7717/peerj.12802
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-03
copyright: ©2022 Zheng et al.
attribution name: Zheng et al.

Identification and expression profiles of the YABBY transcription factors in wheat
type: item
type: AcademicArticle
description: Background YABBY is a plant-specific transcription factor (TF) that belongs to the zinc finger protein superfamily and is composed of a C2–C2 domain at the N-terminus and a YABBY domain at the C-terminus. It plays a role in plant development and growth. Methods In this study, 20 YABBY TFs were identified in the wheat genome. Phylogenetic relationships, collinearity relationships, gene structures, conserved motifs, and expression patterns were analyzed. Results Twenty TaYABBY TFs were distributed unevenly on 15 chromosomes. Collinearity analysis showed that these genes have a close relationship with monocot plants. The phylogenetic tree of wheat YABBYs classified these TaYABBYs into FIL, YAB2, INO, and CRC clades. Gene structure and conserved motif analyses showed that they share similar components in the same clades. Expression profile analysis showed that many TaYABBY genes have high expression levels in leaf tissues and are regulated by abiotic stresses, especially salt stress. Our results provide a basis for further functional characterization of the YABBY gene family.
format: application/pdf
format: text/html
creator: Lidong Hao
creator: Jinshan Zhang
creator: Shubing Shi
creator: Peng Li
creator: Dandan Li
creator: Tianjiao Zhang
creator: Haibin Guo
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12855
publisher: PeerJ Inc.
rights: © 2022 Hao et al.
abstract: Background YABBY is a plant-specific transcription factor (TF) that belongs to the zinc finger protein superfamily and is composed of a C2–C2 domain at the N-terminus and a YABBY domain at the C-terminus. It plays a role in plant development and growth. Methods In this study, 20 YABBY TFs were identified in the wheat genome. Phylogenetic relationships, collinearity relationships, gene structures, conserved motifs, and expression patterns were analyzed. Results Twenty TaYABBY TFs were distributed unevenly on 15 chromosomes. Collinearity analysis showed that these genes have a close relationship with monocot plants. The phylogenetic tree of wheat YABBYs classified these TaYABBYs into FIL, YAB2, INO, and CRC clades. Gene structure and conserved motif analyses showed that they share similar components in the same clades. Expression profile analysis showed that many TaYABBY genes have high expression levels in leaf tissues and are regulated by abiotic stresses, especially salt stress. Our results provide a basis for further functional characterization of the YABBY gene family.
bibliographic citation: Hao et al. (2022) Identification and expression profiles of the YABBY transcription factors in wheat. PeerJ 10:e12855 https://doi.org/10.7717/peerj.12855
date submitted: 2021-11-01
date accepted: 2022-01-07
issued: 2022-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Lidong
author list: Agent
  family name: Zhang
  given name: Jinshan
author list: Agent
  family name: Shi
  given name: Shubing
author list: Agent
  family name: Li
  given name: Peng
author list: Agent
  family name: Li
  given name: Dandan
author list: Agent
  family name: Zhang
  given name: Tianjiao
author list: Agent
  family name: Guo
  given name: Haibin
doi: 10.7717/peerj.12855
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-03
copyright: © 2022 Hao et al.
attribution name: Hao et al.

Comparative transcriptomic analysis reveals potential mechanisms for high tolerance to submergence in arbor willows
type: item
type: AcademicArticle
description: Background Submergence threatens plant growth and survival by decreasing or eliminating oxygen supply. Uncovering the complex regulatory network underlying the tolerance of Salix to submergence and identifying the key regulators are important for molecular-assisted breeding of Salix. Methods In this study, we screened germplasm resources of arbor willows and discovered both submergence-tolerant and submergence-sensitive varieties. Then, by performing RNA-seq, we compared the differences between the transcriptomes of two varieties, i.e., the submergence-tolerant variety “Suliu 795” and the submergence-sensitive variety “Yanliu No. 1,” and the different submergence treatment time points to identify the potential mechanisms of submergence in Salix and the unique approaches by which the variety “Suliu 795” possessed a higher tolerance compared to “Yanliu No. 1”. Results A total of 22,790 differentially expressed genes were identified from 25 comparisons. Using gene ontology annotation and pathway enrichment analysis, the expression pattern of transcriptional factors, important players in hormone signaling, carbohydrate metabolism, and the anaerobic respiration pathway were found to differ significantly between the two varieties. The principal component analysis and qRT-PCR results verified the reliability of the RNA sequencing data. The results of further analysis indicated that “Suliu 795” had higher submergence tolerant activity than “Yanliu No. 1” because of three characteristics: (1) high sensitivity to the probable low oxygen stress and initiation of appropriate responding mechanisms in advance; (2) maintenance of energy homeostasis to prevent energy depletion under hypoxic stress; and (3) keep “quiescence” through fine-tuning the equilibrium between phytohormones GA, SA and ethylene.
format: application/pdf
format: text/html
creator: Yanhong Chen
creator: Jie Yang
creator: Hongyi Guo
creator: Yawen Du
creator: Guoyuan Liu
creator: Chunmei Yu
creator: Fei Zhong
creator: Bolin Lian
creator: Jian Zhang
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12881
publisher: PeerJ Inc.
rights: © 2022 Chen et al.
abstract: Background Submergence threatens plant growth and survival by decreasing or eliminating oxygen supply. Uncovering the complex regulatory network underlying the tolerance of Salix to submergence and identifying the key regulators are important for molecular-assisted breeding of Salix. Methods In this study, we screened germplasm resources of arbor willows and discovered both submergence-tolerant and submergence-sensitive varieties. Then, by performing RNA-seq, we compared the differences between the transcriptomes of two varieties, i.e., the submergence-tolerant variety “Suliu 795” and the submergence-sensitive variety “Yanliu No. 1,” and the different submergence treatment time points to identify the potential mechanisms of submergence in Salix and the unique approaches by which the variety “Suliu 795” possessed a higher tolerance compared to “Yanliu No. 1”. Results A total of 22,790 differentially expressed genes were identified from 25 comparisons. Using gene ontology annotation and pathway enrichment analysis, the expression pattern of transcriptional factors, important players in hormone signaling, carbohydrate metabolism, and the anaerobic respiration pathway were found to differ significantly between the two varieties. The principal component analysis and qRT-PCR results verified the reliability of the RNA sequencing data. The results of further analysis indicated that “Suliu 795” had higher submergence tolerant activity than “Yanliu No. 1” because of three characteristics: (1) high sensitivity to the probable low oxygen stress and initiation of appropriate responding mechanisms in advance; (2) maintenance of energy homeostasis to prevent energy depletion under hypoxic stress; and (3) keep “quiescence” through fine-tuning the equilibrium between phytohormones GA, SA and ethylene.
bibliographic citation: Chen et al. (2022) Comparative transcriptomic analysis reveals potential mechanisms for high tolerance to submergence in arbor willows. PeerJ 10:e12881 https://doi.org/10.7717/peerj.12881
date submitted: 2021-08-05
date accepted: 2022-01-13
issued: 2022-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Yanhong
author list: Agent
  family name: Yang
  given name: Jie
author list: Agent
  family name: Guo
  given name: Hongyi
author list: Agent
  family name: Du
  given name: Yawen
author list: Agent
  family name: Liu
  given name: Guoyuan
author list: Agent
  family name: Yu
  given name: Chunmei
author list: Agent
  family name: Zhong
  given name: Fei
author list: Agent
  family name: Lian
  given name: Bolin
author list: Agent
  family name: Zhang
  given name: Jian
doi: 10.7717/peerj.12881
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-03
copyright: © 2022 Chen et al.
attribution name: Chen et al.

Arbuscular mycorrhizal fungi improve the growth and performance in the seedlings of Leymus chinensis under alkali and drought stresses
type: item
type: AcademicArticle
description: Alkali and drought stresses are increasing severe environmental problems throughout the world, especially in the Songnen grassland of northern China. Leymus chinensis is the dominant grass species in the Songnen grassland of northern China and the most promising species for grassland restoration. Arbuscular mycorrhizal fungi (AMF) can colonize 80% of vascular plants, which can enhance the growth of host plants and provide extrinsic protection against abiotic stresses. However, little is known about the interaction effect of alkali and drought stresses on plant-AM symbionts. Here, seedlings of Leymus chinensis inoculated with or without mycorrhizae were cultivated in soil with 0, 100 or 200 mM NaHCO3 under 0, 5 or 10% (w/v) PEG treatment, and the changes in growth, osmotic adjustment substances and ions were measured. The results showed that the interaction of alkali and drought stresses caused greater seedling growth inhibition than either single alkali or drought stress due to ion toxicity and oxidative damage. Mycorrhizae could alleviate the growth inhibition of seedlings under alkali or drought stress. The interaction of alkali and drought stresses did not affect the alleviating effect of mycorrhizae on seedling growth but improved the osmotic regulation ability and ionic balance of the seedlings. Our results clearly show different effects of the interaction of alkali and drought stresses versus a single stress (alkali or drought) on plant development and provide new insights into the positive effect of arbuscular mycorrhizal fungi on host plants under such stress conditions.
format: application/pdf
format: text/html
creator: Yingnan Wang
creator: Jixiang Lin
creator: Fan Yang
creator: Shuang Tao
creator: Xiufeng Yan
creator: Zhiqiang Zhou
creator: Yuhong Zhang
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.12890
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Alkali and drought stresses are increasing severe environmental problems throughout the world, especially in the Songnen grassland of northern China. Leymus chinensis is the dominant grass species in the Songnen grassland of northern China and the most promising species for grassland restoration. Arbuscular mycorrhizal fungi (AMF) can colonize 80% of vascular plants, which can enhance the growth of host plants and provide extrinsic protection against abiotic stresses. However, little is known about the interaction effect of alkali and drought stresses on plant-AM symbionts. Here, seedlings of Leymus chinensis inoculated with or without mycorrhizae were cultivated in soil with 0, 100 or 200 mM NaHCO3 under 0, 5 or 10% (w/v) PEG treatment, and the changes in growth, osmotic adjustment substances and ions were measured. The results showed that the interaction of alkali and drought stresses caused greater seedling growth inhibition than either single alkali or drought stress due to ion toxicity and oxidative damage. Mycorrhizae could alleviate the growth inhibition of seedlings under alkali or drought stress. The interaction of alkali and drought stresses did not affect the alleviating effect of mycorrhizae on seedling growth but improved the osmotic regulation ability and ionic balance of the seedlings. Our results clearly show different effects of the interaction of alkali and drought stresses versus a single stress (alkali or drought) on plant development and provide new insights into the positive effect of arbuscular mycorrhizal fungi on host plants under such stress conditions.
bibliographic citation: Wang et al. (2022) Arbuscular mycorrhizal fungi improve the growth and performance in the seedlings of Leymus chinensis under alkali and drought stresses. PeerJ 10:e12890 https://doi.org/10.7717/peerj.12890
date submitted: 2021-10-14
date accepted: 2022-01-14
issued: 2022-02-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yingnan
author list: Agent
  family name: Lin
  given name: Jixiang
author list: Agent
  family name: Yang
  given name: Fan
author list: Agent
  family name: Tao
  given name: Shuang
author list: Agent
  family name: Yan
  given name: Xiufeng
author list: Agent
  family name: Zhou
  given name: Zhiqiang
author list: Agent
  family name: Zhang
  given name: Yuhong
doi: 10.7717/peerj.12890
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-03
copyright: ©2022 Wang et al.
attribution name: Wang et al.

Overexpression of the LcCUC2-like gene in Arabidopsis thaliana alters the cotyledon morphology and increases rosette leaf number
type: item
type: AcademicArticle
description: Background The unique ‘mandarin jacket’ leaf shape is the most famous trait of Liriodendron chinense and this characteristic gives L. chinense aesthetic and landscaping value. However, the underlying regulatory mechanism of genes involved in the leaf development of L. chinense has remained unclear. Methods Based on transcriptome data of leaves at different developmental stages from L. chinense, we identified differentially expression genes (DEGs) functioning in leaf development. A candidate gene named LcCUC2-like (LcCUC2L) had high similarity in sequence with Arabidopsis thaliana CUC2, and used for further research. We isolated the full-length LcCUC2L gene and its promoter from L. chinense. Subsequently, we analyzed the function of the LcCUC2L gene and its promoter activity via transformation into A. thaliana. Results In this study, we found that the LcCUC2L and AtCUC2 are homologous in sequence but not homologous in function. Unlike the role of AtCUC2 in leaf serration and SAM formation, the LcCUC2L mainly regulates cotyledon development and rosette leaf number. Histochemical β-glucuronidase (GUS) staining revealed that LcCUC2L was expressed in the cotyledons of A. thaliana seedlings, indicating that the LcCUC2L may play a role in cotyledon development. Ectopic expression of LcCUC2L resulted in long, narrow cotyledons without petioles, abnormal lamina epidermis cells and defective vascular tissue in cotyledons, and these results were consistent with the LcCUC2L expression pattern. Further analysis showed that overexpression of LcCUC2L also induced numerous rosette leaves. Also, LcCUC2L and other related genes showed a severe response in L. chinense by introducing exogenous auxin stimulation, partly revealed that LcCUC2L affects the leaf development by regulating the auxin content. Conclusions These results suggest that LcCUC2L may play a critical role in leaf development and morphogenesis in L. chinense, and our findings provide insight into the molecular mechanism…
format: application/pdf
format: text/html
creator: Shaoying Wen
creator: Jiayu Li
creator: Ziyuan Hao
creator: Lingmin Wei
creator: Jikai Ma
creator: Yaxian Zong
creator: Huogen Li
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12615
publisher: PeerJ Inc.
rights: © 2022 Wen et al.
abstract: Background The unique ‘mandarin jacket’ leaf shape is the most famous trait of Liriodendron chinense and this characteristic gives L. chinense aesthetic and landscaping value. However, the underlying regulatory mechanism of genes involved in the leaf development of L. chinense has remained unclear. Methods Based on transcriptome data of leaves at different developmental stages from L. chinense, we identified differentially expression genes (DEGs) functioning in leaf development. A candidate gene named LcCUC2-like (LcCUC2L) had high similarity in sequence with Arabidopsis thaliana CUC2, and used for further research. We isolated the full-length LcCUC2L gene and its promoter from L. chinense. Subsequently, we analyzed the function of the LcCUC2L gene and its promoter activity via transformation into A. thaliana. Results In this study, we found that the LcCUC2L and AtCUC2 are homologous in sequence but not homologous in function. Unlike the role of AtCUC2 in leaf serration and SAM formation, the LcCUC2L mainly regulates cotyledon development and rosette leaf number. Histochemical β-glucuronidase (GUS) staining revealed that LcCUC2L was expressed in the cotyledons of A. thaliana seedlings, indicating that the LcCUC2L may play a role in cotyledon development. Ectopic expression of LcCUC2L resulted in long, narrow cotyledons without petioles, abnormal lamina epidermis cells and defective vascular tissue in cotyledons, and these results were consistent with the LcCUC2L expression pattern. Further analysis showed that overexpression of LcCUC2L also induced numerous rosette leaves. Also, LcCUC2L and other related genes showed a severe response in L. chinense by introducing exogenous auxin stimulation, partly revealed that LcCUC2L affects the leaf development by regulating the auxin content. Conclusions These results suggest that LcCUC2L may play a critical role in leaf development and morphogenesis in L. chinense, and our findings provide insight into the molecular mechanism…
bibliographic citation: Wen et al. (2022) Overexpression of the LcCUC2-like gene in Arabidopsis thaliana alters the cotyledon morphology and increases rosette leaf number. PeerJ 10:e12615 https://doi.org/10.7717/peerj.12615
date submitted: 2021-02-26
date accepted: 2021-11-18
issued: 2022-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wen
  given name: Shaoying
author list: Agent
  family name: Li
  given name: Jiayu
author list: Agent
  family name: Hao
  given name: Ziyuan
author list: Agent
  family name: Wei
  given name: Lingmin
author list: Agent
  family name: Ma
  given name: Jikai
author list: Agent
  family name: Zong
  given name: Yaxian
author list: Agent
  family name: Li
  given name: Huogen
doi: 10.7717/peerj.12615
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-02
copyright: ©2022 Wen et al.
attribution name: Wen et al.

The effect of internet addiction and smartphone addiction on sleep quality among Turkish adolescents
type: item
type: AcademicArticle
description: Background: Sleep quality plays a principal role in the protection of health. There is an increasing number of studies in the literature demonstrating that internet addiction and smartphone addiction impair sleep quality. However, the number of studies on Turkish adolescents is very limited. Therefore, this study examined the effects of internet addiction and smartphone addiction on sleep quality among Turkish adolescents. Methods: Participants in this cross-sectional study were 910 adolescents aged 13–18 years. Data were collected with the Short Internet Addiction Test, Smartphone Addiction Scale, and Pittsburgh Sleep Quality Index. In addition, a questionnaire was used to gather information about the demographic, socioeconomic, and health-related characteristics. Pearson’s Chi-square test, Chi-square test for trend, Mann–Whitney U test, logistic regression analysis, and Spearman’s correlation analysis were used in the analysis. Results: The sleep quality of 58.7% of the adolescents was poor. Additionally, girls and adolescents ≥16 years old had poor sleep quality. Sleep quality deteriorated as perceived health status and perceived economic status of family deteriorated. Compared to participants with normal internet addiction scores, poor sleep quality was 1.83 (95% CI [1.22–2.74]) times higher in those with problematic internet addiction and 1.99 (95% CI [1.23–3.87]) times higher in those with pathological internet addiction. One point increase in Smartphone Addiction Scale total score increased poor sleep quality 1.01 (95% CI [1.00–1.02]) times. Sleep quality scale were positively correlated with the smartphone addiction and internet addiction. However, there was no positive correlation between habitual sleep efficiency subcomponent of sleep quality and smartphone addiction and internet addiction. Conclusions: Internet addiction and smartphone addiction were associated with poor sleep quality in adolescents. Older adolescents (≥16 years), gender (female), poor he…
format: application/pdf
format: text/html
creator: Ayla Acikgoz
creator: Burcu Acikgoz
creator: Osman Acikgoz
subject: Epidemiology
subject: Global Health
subject: Pediatrics
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.12876
publisher: PeerJ Inc.
rights: © 2022 Acikgoz et al.
abstract: Background: Sleep quality plays a principal role in the protection of health. There is an increasing number of studies in the literature demonstrating that internet addiction and smartphone addiction impair sleep quality. However, the number of studies on Turkish adolescents is very limited. Therefore, this study examined the effects of internet addiction and smartphone addiction on sleep quality among Turkish adolescents. Methods: Participants in this cross-sectional study were 910 adolescents aged 13–18 years. Data were collected with the Short Internet Addiction Test, Smartphone Addiction Scale, and Pittsburgh Sleep Quality Index. In addition, a questionnaire was used to gather information about the demographic, socioeconomic, and health-related characteristics. Pearson’s Chi-square test, Chi-square test for trend, Mann–Whitney U test, logistic regression analysis, and Spearman’s correlation analysis were used in the analysis. Results: The sleep quality of 58.7% of the adolescents was poor. Additionally, girls and adolescents ≥16 years old had poor sleep quality. Sleep quality deteriorated as perceived health status and perceived economic status of family deteriorated. Compared to participants with normal internet addiction scores, poor sleep quality was 1.83 (95% CI [1.22–2.74]) times higher in those with problematic internet addiction and 1.99 (95% CI [1.23–3.87]) times higher in those with pathological internet addiction. One point increase in Smartphone Addiction Scale total score increased poor sleep quality 1.01 (95% CI [1.00–1.02]) times. Sleep quality scale were positively correlated with the smartphone addiction and internet addiction. However, there was no positive correlation between habitual sleep efficiency subcomponent of sleep quality and smartphone addiction and internet addiction. Conclusions: Internet addiction and smartphone addiction were associated with poor sleep quality in adolescents. Older adolescents (≥16 years), gender (female), poor he…
bibliographic citation: Acikgoz et al. (2022) The effect of internet addiction and smartphone addiction on sleep quality among Turkish adolescents. PeerJ 10:e12876 https://doi.org/10.7717/peerj.12876
date submitted: 2021-08-23
date accepted: 2022-01-12
issued: 2022-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Acikgoz
  given name: Ayla
author list: Agent
  family name: Acikgoz
  given name: Burcu
author list: Agent
  family name: Acikgoz
  given name: Osman
doi: 10.7717/peerj.12876
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-02
copyright: © 2022 Acikgoz et al.
attribution name: Acikgoz et al.

Transcriptome analysis reveals the potential biological function of FSCN1 in HeLa cervical cancer cells
type: item
type: AcademicArticle
description: Fascin actin-bundling protein 1 (FSCN1), an actin-bundling protein associated with cell migration and invasion, is highly expressed in various tumor tissues. FSCN1 has also been reported to be a marker of increased invasive potential in cervical cancers. However, the functions of FSCN1 are still not fully understood in cervical cancers. Here, the gene expression profile of HeLa cells transfected with FSCN1 shRNA (shFSCN1) was compared with that of cells transfected with empty vector (shCtrl). The results showed that shFSCN1 extensively affected the transcription level of 5,043 genes in HeLa cells. In particular, Gene Ontology (GO) analysis showed that a large number of upregulated genes were annotated with terms including transcription regulation and DNA binding. The downregulated genes were enriched in some cancer pathways, including angiogenesis and cell adhesion. qPCR validation confirmed that FSCN1 knockdown significantly affected the expression of selected genes in HeLa cells either negatively or positively. Expression analysis in TCGA (The Cancer Genome Atlas) revealed that FSCN1 had negative correlations with several transcription factors and a positive correlation with an angiogenic factor (angiopoietin like 4, ANGPTL4) in cervical tumor tissue. In particular, validation by Western blotting showed that FSCN1 knockdown decreased the protein level of ANGPTL4. Our results demonstrated that FSCN1 is not only an actin-binding protein but also a transcriptional regulator and an angiogenic factor in cervical cancer. Thus, our study provides important insights for further study on the regulatory mechanism of FSCN1 in cervical cancer.
format: application/pdf
format: text/html
creator: Fengqin Guo
creator: Yanliang Liu
creator: Yanxiang Cheng
creator: Qifan Zhang
creator: Weili Quan
creator: Yaxun Wei
creator: Li Hong
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.12909
publisher: PeerJ Inc.
rights: © 2022 Guo et al.
abstract: Fascin actin-bundling protein 1 (FSCN1), an actin-bundling protein associated with cell migration and invasion, is highly expressed in various tumor tissues. FSCN1 has also been reported to be a marker of increased invasive potential in cervical cancers. However, the functions of FSCN1 are still not fully understood in cervical cancers. Here, the gene expression profile of HeLa cells transfected with FSCN1 shRNA (shFSCN1) was compared with that of cells transfected with empty vector (shCtrl). The results showed that shFSCN1 extensively affected the transcription level of 5,043 genes in HeLa cells. In particular, Gene Ontology (GO) analysis showed that a large number of upregulated genes were annotated with terms including transcription regulation and DNA binding. The downregulated genes were enriched in some cancer pathways, including angiogenesis and cell adhesion. qPCR validation confirmed that FSCN1 knockdown significantly affected the expression of selected genes in HeLa cells either negatively or positively. Expression analysis in TCGA (The Cancer Genome Atlas) revealed that FSCN1 had negative correlations with several transcription factors and a positive correlation with an angiogenic factor (angiopoietin like 4, ANGPTL4) in cervical tumor tissue. In particular, validation by Western blotting showed that FSCN1 knockdown decreased the protein level of ANGPTL4. Our results demonstrated that FSCN1 is not only an actin-binding protein but also a transcriptional regulator and an angiogenic factor in cervical cancer. Thus, our study provides important insights for further study on the regulatory mechanism of FSCN1 in cervical cancer.
bibliographic citation: Guo et al. (2022) Transcriptome analysis reveals the potential biological function of FSCN1 in HeLa cervical cancer cells. PeerJ 10:e12909 https://doi.org/10.7717/peerj.12909
date submitted: 2021-05-11
date accepted: 2022-01-19
issued: 2022-02-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Fengqin
author list: Agent
  family name: Liu
  given name: Yanliang
author list: Agent
  family name: Cheng
  given name: Yanxiang
author list: Agent
  family name: Zhang
  given name: Qifan
author list: Agent
  family name: Quan
  given name: Weili
author list: Agent
  family name: Wei
  given name: Yaxun
author list: Agent
  family name: Hong
  given name: Li
doi: 10.7717/peerj.12909
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-02
copyright: ©2022 Guo et al.
attribution name: Guo et al.

Spatial distribution and ecological risk assessment of heavy metals in karst soils from the Yinjiang County, Southwest China
type: item
type: AcademicArticle
description: Background Soil heavy metals (HMs) under different land-use types have diverse effects, which may trigger the ecological risk. To explore the potential sources of HMs in karst soils, the spatial distribution and geochemical behavior of HMs based on different land-use types are employed in this study. Methods Soil samples (n = 47) were collected in three suites of karst soil profiles from the secondary forest, abandoned cropland and shrubland in Yinjiang, Southwest China. The concentrations of Ni, Mn, Cr, Pb, Cd and Mo were determined to give a comprehensive understanding of the possible sources of these HMs and evaluate the potential ecological risk in Yinjiang County. Results The mean concentrations of HMs in all profiles followed the same order: Mn > Cr > Ni > Pb > Mo > Cd. Meanwhile, the concentrations of most HMs roughly increased with the depth. Additionally, the concentrations of HMs were mostly correlated with soil pH and SOC, rather than with clay and silt proportions. By contrast, with the enrichment factors (EF), geo-accumulation (Igeo) and potential ecological risk index (PERI) of HMs in soil under different land-use types, the results indicated that these HMs exhibited non-pollution (Igeo < 0) and no ecological risk (PERI < 30) to human health in soils of Yinjiang County. Conclusions The distribution of HMs is dominated by weathering in the karst area, and the effects of agricultural inputs on the enrichment of soil HMs in Yinjiang County are limited. This further state that the arrangement of the local agricultural structure is reasonable.
format: application/pdf
format: text/html
creator: Ruiyin Han
creator: Zhifang Xu
subject: Ecosystem Science
subject: Soil Science
subject: Ecotoxicology
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.12716
publisher: PeerJ Inc.
rights: © 2022 Han and Xu
abstract: Background Soil heavy metals (HMs) under different land-use types have diverse effects, which may trigger the ecological risk. To explore the potential sources of HMs in karst soils, the spatial distribution and geochemical behavior of HMs based on different land-use types are employed in this study. Methods Soil samples (n = 47) were collected in three suites of karst soil profiles from the secondary forest, abandoned cropland and shrubland in Yinjiang, Southwest China. The concentrations of Ni, Mn, Cr, Pb, Cd and Mo were determined to give a comprehensive understanding of the possible sources of these HMs and evaluate the potential ecological risk in Yinjiang County. Results The mean concentrations of HMs in all profiles followed the same order: Mn > Cr > Ni > Pb > Mo > Cd. Meanwhile, the concentrations of most HMs roughly increased with the depth. Additionally, the concentrations of HMs were mostly correlated with soil pH and SOC, rather than with clay and silt proportions. By contrast, with the enrichment factors (EF), geo-accumulation (Igeo) and potential ecological risk index (PERI) of HMs in soil under different land-use types, the results indicated that these HMs exhibited non-pollution (Igeo < 0) and no ecological risk (PERI < 30) to human health in soils of Yinjiang County. Conclusions The distribution of HMs is dominated by weathering in the karst area, and the effects of agricultural inputs on the enrichment of soil HMs in Yinjiang County are limited. This further state that the arrangement of the local agricultural structure is reasonable.
bibliographic citation: Han et al. (2022) Spatial distribution and ecological risk assessment of heavy metals in karst soils from the Yinjiang County, Southwest China. PeerJ 10:e12716 https://doi.org/10.7717/peerj.12716
date submitted: 2021-08-24
date accepted: 2021-12-09
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Ruiyin
author list: Agent
  family name: Xu
  given name: Zhifang
doi: 10.7717/peerj.12716
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: ©2022 Han and Xu
attribution name: Han and Xu

Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte
type: item
type: AcademicArticle
description: Background New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data. Methods Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium “black”, and the morphology of a species previously reported as Diversibipalium “blue”. Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species. Results The new species Humbertium covidum n. sp. (syn: Diversibipalium “black” of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium “blue” of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exc…
format: application/pdf
format: text/html
creator: Jean-Lou Justine
creator: Romain Gastineau
creator: Pierre Gros
creator: Delphine Gey
creator: Enrico Ruzzier
creator: Laurent Charles
creator: Leigh Winsor
subject: Biodiversity
subject: Conservation Biology
subject: Taxonomy
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.12725
publisher: PeerJ Inc.
rights: © 2022 Justine et al.
abstract: Background New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data. Methods Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium “black”, and the morphology of a species previously reported as Diversibipalium “blue”. Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species. Results The new species Humbertium covidum n. sp. (syn: Diversibipalium “black” of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium “blue” of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exc…
bibliographic citation: Justine et al. (2022) Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte. PeerJ 10:e12725 https://doi.org/10.7717/peerj.12725
date submitted: 2021-08-18
date accepted: 2021-12-10
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Justine
  given name: Jean-Lou
author list: Agent
  family name: Gastineau
  given name: Romain
author list: Agent
  family name: Gros
  given name: Pierre
author list: Agent
  family name: Gey
  given name: Delphine
author list: Agent
  family name: Ruzzier
  given name: Enrico
author list: Agent
  family name: Charles
  given name: Laurent
author list: Agent
  family name: Winsor
  given name: Leigh
doi: 10.7717/peerj.12725
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Justine et al.
attribution name: Justine et al.

Dispersal into the Qinghai–Tibet plateau: evidence from the genetic structure and demography of the alpine plant Triosteum pinnatifidum
type: item
type: AcademicArticle
description: Triosteum pinnatifidum Maxim., an alpine plant, is traditionally used for several medicinal purposes. Here, both chloroplast DNA sequences and nuclear low copy sequence markers were used to investigate the genetic diversity and population structure of T. pinnatifidum. Materials were collected from thirteen localities in the northeast Qinghai–Tibet Plateau (QTP) and adjacent highlands and advanced analytical toolkits were used to access their origin and range shifts. The results revealed a higher level of population differentiation based on chloroplast DNA (cpDNA) concatenated sequences compared with the nuclear DNA sequences (FST = 0.654 for cpDNA, FST = 0.398 for AT103), indicating that pollen flow was still extensive in T. pinnatifidum. A decline in haplotype variation was observed from the plateau edge and adjoining highlands toward the platform of the QTP. The hypothesis “dispersal into the QTP,” proposing that T. pinnatifidum experienced migration from the plateau edge and adjacent highlands to the platform, was supported. These results were in line with the hypothesis that multiple refugia exist on the plateau edge and adjacent highlands rather than on the plateau platform. Our unimodal mismatch distribution, star-like network supported a recent expansion in T. pinnatifidum.
format: application/pdf
format: text/html
creator: Hai Rui Liu
creator: Gulzar Khan
creator: Qingbo Gao
creator: Faqi Zhang
creator: Wenhui Liu
creator: Yingfang Wang
creator: Jie Fang
creator: Shilong Chen
creator: Sahib Gul Afridi
subject: Biodiversity
subject: Biogeography
subject: Genetics
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.12754
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: Triosteum pinnatifidum Maxim., an alpine plant, is traditionally used for several medicinal purposes. Here, both chloroplast DNA sequences and nuclear low copy sequence markers were used to investigate the genetic diversity and population structure of T. pinnatifidum. Materials were collected from thirteen localities in the northeast Qinghai–Tibet Plateau (QTP) and adjacent highlands and advanced analytical toolkits were used to access their origin and range shifts. The results revealed a higher level of population differentiation based on chloroplast DNA (cpDNA) concatenated sequences compared with the nuclear DNA sequences (FST = 0.654 for cpDNA, FST = 0.398 for AT103), indicating that pollen flow was still extensive in T. pinnatifidum. A decline in haplotype variation was observed from the plateau edge and adjoining highlands toward the platform of the QTP. The hypothesis “dispersal into the QTP,” proposing that T. pinnatifidum experienced migration from the plateau edge and adjacent highlands to the platform, was supported. These results were in line with the hypothesis that multiple refugia exist on the plateau edge and adjacent highlands rather than on the plateau platform. Our unimodal mismatch distribution, star-like network supported a recent expansion in T. pinnatifidum.
bibliographic citation: Liu et al. (2022) Dispersal into the Qinghai–Tibet plateau: evidence from the genetic structure and demography of the alpine plant Triosteum pinnatifidum. PeerJ 10:e12754 https://doi.org/10.7717/peerj.12754
date submitted: 2021-05-11
date accepted: 2021-12-15
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hai Rui
author list: Agent
  family name: Khan
  given name: Gulzar
author list: Agent
  family name: Gao
  given name: Qingbo
author list: Agent
  family name: Zhang
  given name: Faqi
author list: Agent
  family name: Liu
  given name: Wenhui
author list: Agent
  family name: Wang
  given name: Yingfang
author list: Agent
  family name: Fang
  given name: Jie
author list: Agent
  family name: Chen
  given name: Shilong
author list: Agent
  family name: Afridi
  given name: Sahib Gul
doi: 10.7717/peerj.12754
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: ©2022 Liu et al.
attribution name: Liu et al.

Pain threshold in selected trigger points of superficial muscles of the back in young adults
type: item
type: AcademicArticle
description: Background Monitoring of pain threshold is the basis for verification of the effectiveness of therapy or assessment of the patient’s condition. This study aimed to determine the pain threshold of selected superficial muscles of the back taking into account trigger point activity in young and healthy males and females, with the evaluation of intrarater reliability of algometric measurements. Material and methods The study examined 30 young adult participants (15 males and 15 females) aged 26.23 ± 3.21, and BMI of 23.80 ± 3.43. The Pain Test FPX Algometer (Wagner) was used for the study. Trigger points on the levator scapulae and trapezius muscles (superior and inferior portion) on both sides were examined. It was also verified whether the trigger points studied are active or inactive. Furthermore, an author’s survey questionnaire was used. Results Within the trigger points of the right (p = 0.04) and left (p = 0.02) superior trapezius muscle and the left (p = 0.04) levator scapulae muscle, the pain threshold values were higher in the male group. There was a statistically significantly higher number of active trigger points in the female group compared to that in the male group (2.49 ± 1.51 vs. 1.07 ± 1.16, respectively), p = 0.01. For all muscles tested, mean pain threshold values were significantly higher for inactive trigger points. A greater number of active trigger points is associated with lower pain thresholds at these points (left: the superior trapezius, r = −0.597, the inferior trapezius, r = −0.609; the levator scapulae, r = −0.746; right: the superior trapezius, r = −0.610, the inferior trapezius, r = −0.604; the levator scapulae, r = −0.747). The evaluation of the intrarater reliability showed excellent agreement between the first and second measurements, ICC > 0.987 for all examined trigger points. Conclusions (1) Women who reported pain more than once a week in the studied muscles showed a greater number of active trigger points. (2) A greater number of…
format: application/pdf
format: text/html
creator: Anna Katarzyna Cygańska
creator: Paweł Tomaszewski
creator: Anna Cabak
subject: Anesthesiology and Pain Management
subject: Drugs and Devices
subject: Kinesiology
subject: Orthopedics
subject: Public Health
description: doi:10.7717/peerj.12780
publisher: PeerJ Inc.
rights: © 2022 Cygańska et al.
abstract: Background Monitoring of pain threshold is the basis for verification of the effectiveness of therapy or assessment of the patient’s condition. This study aimed to determine the pain threshold of selected superficial muscles of the back taking into account trigger point activity in young and healthy males and females, with the evaluation of intrarater reliability of algometric measurements. Material and methods The study examined 30 young adult participants (15 males and 15 females) aged 26.23 ± 3.21, and BMI of 23.80 ± 3.43. The Pain Test FPX Algometer (Wagner) was used for the study. Trigger points on the levator scapulae and trapezius muscles (superior and inferior portion) on both sides were examined. It was also verified whether the trigger points studied are active or inactive. Furthermore, an author’s survey questionnaire was used. Results Within the trigger points of the right (p = 0.04) and left (p = 0.02) superior trapezius muscle and the left (p = 0.04) levator scapulae muscle, the pain threshold values were higher in the male group. There was a statistically significantly higher number of active trigger points in the female group compared to that in the male group (2.49 ± 1.51 vs. 1.07 ± 1.16, respectively), p = 0.01. For all muscles tested, mean pain threshold values were significantly higher for inactive trigger points. A greater number of active trigger points is associated with lower pain thresholds at these points (left: the superior trapezius, r = −0.597, the inferior trapezius, r = −0.609; the levator scapulae, r = −0.746; right: the superior trapezius, r = −0.610, the inferior trapezius, r = −0.604; the levator scapulae, r = −0.747). The evaluation of the intrarater reliability showed excellent agreement between the first and second measurements, ICC > 0.987 for all examined trigger points. Conclusions (1) Women who reported pain more than once a week in the studied muscles showed a greater number of active trigger points. (2) A greater number of…
bibliographic citation: Cygańska et al. (2022) Pain threshold in selected trigger points of superficial muscles of the back in young adults. PeerJ 10:e12780 https://doi.org/10.7717/peerj.12780
date submitted: 2021-06-27
date accepted: 2021-12-21
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cygańska
  given name: Anna Katarzyna
author list: Agent
  family name: Tomaszewski
  given name: Paweł
author list: Agent
  family name: Cabak
  given name: Anna
doi: 10.7717/peerj.12780
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Cygańska et al.
attribution name: Cygańska et al.

Characterization of habitat requirements of European fishing spiders
type: item
type: AcademicArticle
description: Wetlands are among the most threatened habitats in the world, and so are their species, which suffer habitat loss due to climate and land use changes. Freshwater species, and especially arthropods, receive comparatively little attention in conservation plans, and the goals to stop and reverse the destruction of wetlands published 25 years ago in a manifesto by the Union of Concerned Scientists have not been reached. In this study, we investigated the occurrence and habitat requirements at two spatial scales of two species of European fishing spiders Dolomedes, which rely heavily on declining wetland habitats in Sweden and southern Norway. We collected occurrence data for Dolomedes plantarius and Dolomedes fimbriatus, using a live-determination method. We modelled the placement of nursery webs to describe fine-scale habitat requirements related to vegetation and micro-climate. Using a machine learning approach, we described the habitat features for each species and for co-occurrence sites, thus providing insight into variables relevant for the presence and detectability of Dolomedes. Nursery placement is mostly dependent on proximity to water, presence of Carex sp. (Sedges) and crossing vegetation structures, and on humidity, while detection can be affected by weather conditions. Furthermore, co-occurrence sites were more similar to D. plantarius sites than to D. fimbriatus sites, whereby surrounding forest, water type and velocity, elevation and latitude were of importance for explaining which species of Dolomedes was present. Overall, habitat requirements were narrower for D. plantarius compared to D. fimbiratus.
format: application/pdf
format: text/html
creator: Lisa Dickel
creator: Jérémy Monsimet
creator: Denis Lafage
creator: Olivier Devineau
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.12806
publisher: PeerJ Inc.
rights: © 2022 Dickel et al.
abstract: Wetlands are among the most threatened habitats in the world, and so are their species, which suffer habitat loss due to climate and land use changes. Freshwater species, and especially arthropods, receive comparatively little attention in conservation plans, and the goals to stop and reverse the destruction of wetlands published 25 years ago in a manifesto by the Union of Concerned Scientists have not been reached. In this study, we investigated the occurrence and habitat requirements at two spatial scales of two species of European fishing spiders Dolomedes, which rely heavily on declining wetland habitats in Sweden and southern Norway. We collected occurrence data for Dolomedes plantarius and Dolomedes fimbriatus, using a live-determination method. We modelled the placement of nursery webs to describe fine-scale habitat requirements related to vegetation and micro-climate. Using a machine learning approach, we described the habitat features for each species and for co-occurrence sites, thus providing insight into variables relevant for the presence and detectability of Dolomedes. Nursery placement is mostly dependent on proximity to water, presence of Carex sp. (Sedges) and crossing vegetation structures, and on humidity, while detection can be affected by weather conditions. Furthermore, co-occurrence sites were more similar to D. plantarius sites than to D. fimbriatus sites, whereby surrounding forest, water type and velocity, elevation and latitude were of importance for explaining which species of Dolomedes was present. Overall, habitat requirements were narrower for D. plantarius compared to D. fimbiratus.
bibliographic citation: Dickel et al. (2022) Characterization of habitat requirements of European fishing spiders. PeerJ 10:e12806 https://doi.org/10.7717/peerj.12806
date submitted: 2021-08-26
date accepted: 2021-12-27
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dickel
  given name: Lisa
author list: Agent
  family name: Monsimet
  given name: Jérémy
author list: Agent
  family name: Lafage
  given name: Denis
author list: Agent
  family name: Devineau
  given name: Olivier
doi: 10.7717/peerj.12806
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Dickel et al.
attribution name: Dickel et al.

In leukemia, knock-down of the death inducer-obliterator gene would inhibit the proliferation of endothelial cells by inhibiting the expression of CDK6 and CCND1
type: item
type: AcademicArticle
description: Background Endothelial cells (ECs) are a critical component of the hematopoietic niche, and the cross-talk between ECs and leukemia was reported recently. This study aimed to determine the genes involved in the proliferation inhibition of endothelial cells in leukemia. Methods Human umbilical vein endothelial cells (HUVEC) were cultured alone or co-cultured with K562 cell lines. GeneChip assays were performed to identify the differentially expressed genes. The Celigo, MTT assay, and flow cytometric analysis were used to determine the effect of RNAi DIDO on cell growth and apoptosis. The differently expressed genes were verified by qRT-PCR (quantitative real-time PCR) and western-blot. Results In K562-HUVEC co-cultured cell lines, 323 down-regulated probes were identified and the extracellular signal-regulated kinase 5 (ERK5) signaling pathway was significantly inhibited. Among the down-regulated genes, the death inducer-obliterator gene (DIDO) is a part of the centrosome protein and may be involved in cell mitosis. As shown in the public data, leukemia patients with lower expression of DIDO showed a better overall survival (OS). The HUVEC cells were infected with shDIDO lentivirus, and reduced expression, inhibited proliferation, and increased apoptosis was observed in shDIDO cells. In addition, the expression of Cyclin-Dependent Kinase 6 (CDK6) and Cyclin D1 (CCND1) genes was inhibited in shDIDO cells. Finally, the public ChIP-seq data were used to analyze the regulators that bind with DIDO, and the H3K4me3 and PolII (RNA polymerase II) signals were found near the Exon1 and exon2 sites of DIDO. Conclusion The knock-down of DIDO will inhibit the proliferation of endothelial cells in the leukemia environment. The expression of DIDO may be regulated by H3K4me3 and the inhibition of DIDO may lead to the down-regulation of CDK6 and CCND1. However, how DIDO interacts with CDK6 and CCND1 requires further study.
format: application/pdf
format: text/html
creator: Honghua Cao
creator: Lilan Wang
creator: Chengkui Geng
creator: Man Yang
creator: Wenwen Mao
creator: Linlin Yang
creator: Yin Ma
creator: Ming He
creator: Yeying Zhou
creator: Lianqing Liu
creator: Xuejiao Hu
creator: Jingxing Yu
creator: Xiufen Shen
creator: Xuezhong Gu
creator: Liefen Yin
creator: Zhenglei Shen
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.12832
publisher: PeerJ Inc.
rights: © 2022 Cao et al.
abstract: Background Endothelial cells (ECs) are a critical component of the hematopoietic niche, and the cross-talk between ECs and leukemia was reported recently. This study aimed to determine the genes involved in the proliferation inhibition of endothelial cells in leukemia. Methods Human umbilical vein endothelial cells (HUVEC) were cultured alone or co-cultured with K562 cell lines. GeneChip assays were performed to identify the differentially expressed genes. The Celigo, MTT assay, and flow cytometric analysis were used to determine the effect of RNAi DIDO on cell growth and apoptosis. The differently expressed genes were verified by qRT-PCR (quantitative real-time PCR) and western-blot. Results In K562-HUVEC co-cultured cell lines, 323 down-regulated probes were identified and the extracellular signal-regulated kinase 5 (ERK5) signaling pathway was significantly inhibited. Among the down-regulated genes, the death inducer-obliterator gene (DIDO) is a part of the centrosome protein and may be involved in cell mitosis. As shown in the public data, leukemia patients with lower expression of DIDO showed a better overall survival (OS). The HUVEC cells were infected with shDIDO lentivirus, and reduced expression, inhibited proliferation, and increased apoptosis was observed in shDIDO cells. In addition, the expression of Cyclin-Dependent Kinase 6 (CDK6) and Cyclin D1 (CCND1) genes was inhibited in shDIDO cells. Finally, the public ChIP-seq data were used to analyze the regulators that bind with DIDO, and the H3K4me3 and PolII (RNA polymerase II) signals were found near the Exon1 and exon2 sites of DIDO. Conclusion The knock-down of DIDO will inhibit the proliferation of endothelial cells in the leukemia environment. The expression of DIDO may be regulated by H3K4me3 and the inhibition of DIDO may lead to the down-regulation of CDK6 and CCND1. However, how DIDO interacts with CDK6 and CCND1 requires further study.
bibliographic citation: Cao et al. (2022) In leukemia, knock-down of the death inducer-obliterator gene would inhibit the proliferation of endothelial cells by inhibiting the expression of CDK6 and CCND1. PeerJ 10:e12832 https://doi.org/10.7717/peerj.12832
date submitted: 2021-04-08
date accepted: 2022-01-04
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Honghua
author list: Agent
  family name: Wang
  given name: Lilan
author list: Agent
  family name: Geng
  given name: Chengkui
author list: Agent
  family name: Yang
  given name: Man
author list: Agent
  family name: Mao
  given name: Wenwen
author list: Agent
  family name: Yang
  given name: Linlin
author list: Agent
  family name: Ma
  given name: Yin
author list: Agent
  family name: He
  given name: Ming
author list: Agent
  family name: Zhou
  given name: Yeying
author list: Agent
  family name: Liu
  given name: Lianqing
author list: Agent
  family name: Hu
  given name: Xuejiao
author list: Agent
  family name: Yu
  given name: Jingxing
author list: Agent
  family name: Shen
  given name: Xiufen
author list: Agent
  family name: Gu
  given name: Xuezhong
author list: Agent
  family name: Yin
  given name: Liefen
author list: Agent
  family name: Shen
  given name: Zhenglei
doi: 10.7717/peerj.12832
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Cao et al.
attribution name: Cao et al.

Unearthing soil arthropod diversity through DNA metabarcoding
type: item
type: AcademicArticle
description: DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna–the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.
format: application/pdf
format: text/html
creator: Monica R. Young
creator: Paul D. N. Hebert
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.12845
publisher: PeerJ Inc.
rights: © 2022 Young and Hebert
abstract: DNA metabarcoding has the potential to greatly advance understanding of soil biodiversity, but this approach has seen limited application for the most abundant and species-rich group of soil fauna–the arthropods. This study begins to address this gap by comparing information on species composition recovered from metabarcoding two types of bulk samples (specimens, soil) from a temperate zone site and from bulk soil samples collected at eight sites in the Arctic. Analysis of 22 samples (3 specimen, 19 soil) revealed 410 arthropod OTUs belonging to 112 families, 25 orders, and nine classes. Studies at the temperate zone site revealed little overlap in species composition between soil and specimen samples, but more overlap at higher taxonomic levels (families, orders) and congruent patterns of α- and β-diversity. Expansion of soil analyses to the Arctic revealed locally rich, highly dissimilar, and spatially structured assemblages compatible with dispersal limited and environmentally driven assembly. The current study demonstrates that DNA metabarcoding of bulk soil enables rapid, large-scale assessments of soil arthropod diversity. However, deep sequence coverage is required to adequately capture the species present in these samples, and expansion of the DNA barcode reference library is necessary to improve taxonomic resolution of the sequences recovered through this approach.
bibliographic citation: Young et al. (2022) Unearthing soil arthropod diversity through DNA metabarcoding. PeerJ 10:e12845 https://doi.org/10.7717/peerj.12845
date submitted: 2021-09-24
date accepted: 2022-01-06
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Young
  given name: Monica R.
author list: Agent
  family name: Hebert
  given name: Paul D. N.
doi: 10.7717/peerj.12845
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: ©2022 Young and Hebert
attribution name: Young and Hebert

Adult bonobos show no prosociality in both prosocial choice task and group service paradigm
type: item
type: AcademicArticle
description: Previous studies reported contrasting conclusions concerning bonobo prosociality, which are likely due to differences in the experimental design, the social dynamics among subjects and characteristics of the subjects themselves. Two hypotheses have been proposed to explain the occurrence of prosociality in animals: the cooperative breeding hypothesis and the self-domestication hypothesis. While the former predicts low levels of prosociality in bonobos because they are non-cooperative breeders, the latter predicts high levels of prosociality because self-domestication has been proposed to select for high levels of tolerance in this species. Here, we presented a group of thirteen bonobos with two platform food-provisioning tasks: the prosocial choice task (PCT) and the group service paradigm (GSP). The latter has so far never been applied to bonobos. To allow for free choice of participation and partner, we implemented both tasks in a group setting. Like in previous PCT studies, bonobos did not choose the prosocial option more often when a group member could benefit vs not benefit. In the GSP, where food provisioning is costly, only subadult bonobos showed a limited amount of food provisioning, which was much lower than what was previously reported for chimpanzees. In both experiments, adult subjects were highly motivated to obtain rewards for themselves, suggesting that bonobos behaved indifferently to the gains of group members. We suggest that previous positive food-provisioning prosociality results in bonobos are mainly driven by the behaviour of subadult subjects. The lack of prosociality in this study corresponds to the hypothesis that proactive food provisioning co-occurs with cooperative breeding and suggests that proactive prosociality might not be part of the self-domestication syndrome in bonobos.
format: application/pdf
format: text/html
creator: Jonas Verspeek
creator: Edwin J. C. van Leeuwen
creator: Daan W. Laméris
creator: Nicky Staes
creator: Jeroen M. G. Stevens
subject: Animal Behavior
subject: Anthropology
subject: Environmental Sciences
subject: Zoology
description: doi:10.7717/peerj.12849
publisher: PeerJ Inc.
rights: © 2022 Verspeek et al.
abstract: Previous studies reported contrasting conclusions concerning bonobo prosociality, which are likely due to differences in the experimental design, the social dynamics among subjects and characteristics of the subjects themselves. Two hypotheses have been proposed to explain the occurrence of prosociality in animals: the cooperative breeding hypothesis and the self-domestication hypothesis. While the former predicts low levels of prosociality in bonobos because they are non-cooperative breeders, the latter predicts high levels of prosociality because self-domestication has been proposed to select for high levels of tolerance in this species. Here, we presented a group of thirteen bonobos with two platform food-provisioning tasks: the prosocial choice task (PCT) and the group service paradigm (GSP). The latter has so far never been applied to bonobos. To allow for free choice of participation and partner, we implemented both tasks in a group setting. Like in previous PCT studies, bonobos did not choose the prosocial option more often when a group member could benefit vs not benefit. In the GSP, where food provisioning is costly, only subadult bonobos showed a limited amount of food provisioning, which was much lower than what was previously reported for chimpanzees. In both experiments, adult subjects were highly motivated to obtain rewards for themselves, suggesting that bonobos behaved indifferently to the gains of group members. We suggest that previous positive food-provisioning prosociality results in bonobos are mainly driven by the behaviour of subadult subjects. The lack of prosociality in this study corresponds to the hypothesis that proactive food provisioning co-occurs with cooperative breeding and suggests that proactive prosociality might not be part of the self-domestication syndrome in bonobos.
bibliographic citation: Verspeek et al. (2022) Adult bonobos show no prosociality in both prosocial choice task and group service paradigm. PeerJ 10:e12849 https://doi.org/10.7717/peerj.12849
date submitted: 2021-09-07
date accepted: 2022-01-07
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Verspeek
  given name: Jonas
author list: Agent
  family name: van Leeuwen
  given name: Edwin J. C.
author list: Agent
  family name: Laméris
  given name: Daan W.
author list: Agent
  family name: Staes
  given name: Nicky
author list: Agent
  family name: Stevens
  given name: Jeroen M. G.
doi: 10.7717/peerj.12849
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Verspeek et al.
attribution name: Verspeek et al.

B-box containing protein 1 from Malus domestica (MdBBX1) is involved in the abiotic stress response
type: item
type: AcademicArticle
description: B-box proteins (BBXs), which act as transcription factors, mainly regulate photomorphogenesis. However, the molecular functions underlying the activity of plant BBXs in response to abiotic stress remain largely unclear. In this investigation, we found that a BBX from Malus domestica (MdBBX1) was involved in the response to various abiotic stresses. The expression of MdBBX1 was significantly upregulated in response to abiotic stresses and abscisic acid (ABA). Recombinant MdBBX1 increased stress tolerance in Escherichia coli cells. In addition, overexpression of MdBBX1 in Arabidopsis decreased sensitivity to exogenous ABA, resulting in a germination rate and root length that were greater and longer, respectively, than those of wild-type (WT) plants. Moreover, the expression of ABI5 was decreased in MdBBX1-overexpressing lines under ABA treatment. After salt and drought treatments, compared with the WT plants, the MdBBX1 transgenic plants displayed enhanced tolerance and had a higher survival rate. Furthermore, under salt stress, increased proline (PRO) contents, decreased levels of malondialdehyde (MDA), increased activity of antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX)) and decreased accumulation of reactive oxygen species (ROS) were observed in the MdBBX1-overexpressing plants. Overall, our results provide evidence that MdBBX1 might play a critical role in the regulation of abiotic stress tolerance by reducing the generation of ROS.
format: application/pdf
format: text/html
creator: Yaqing Dai
creator: Ying Lu
creator: Zhou Zhou
creator: Xiaoyun Wang
creator: Hongjuan Ge
creator: Qinghua Sun
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12852
publisher: PeerJ Inc.
rights: © 2022 Dai et al.
abstract: B-box proteins (BBXs), which act as transcription factors, mainly regulate photomorphogenesis. However, the molecular functions underlying the activity of plant BBXs in response to abiotic stress remain largely unclear. In this investigation, we found that a BBX from Malus domestica (MdBBX1) was involved in the response to various abiotic stresses. The expression of MdBBX1 was significantly upregulated in response to abiotic stresses and abscisic acid (ABA). Recombinant MdBBX1 increased stress tolerance in Escherichia coli cells. In addition, overexpression of MdBBX1 in Arabidopsis decreased sensitivity to exogenous ABA, resulting in a germination rate and root length that were greater and longer, respectively, than those of wild-type (WT) plants. Moreover, the expression of ABI5 was decreased in MdBBX1-overexpressing lines under ABA treatment. After salt and drought treatments, compared with the WT plants, the MdBBX1 transgenic plants displayed enhanced tolerance and had a higher survival rate. Furthermore, under salt stress, increased proline (PRO) contents, decreased levels of malondialdehyde (MDA), increased activity of antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX)) and decreased accumulation of reactive oxygen species (ROS) were observed in the MdBBX1-overexpressing plants. Overall, our results provide evidence that MdBBX1 might play a critical role in the regulation of abiotic stress tolerance by reducing the generation of ROS.
bibliographic citation: Dai et al. (2022) B-box containing protein 1 from Malus domestica (MdBBX1) is involved in the abiotic stress response. PeerJ 10:e12852 https://doi.org/10.7717/peerj.12852
date submitted: 2021-09-22
date accepted: 2022-01-07
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dai
  given name: Yaqing
author list: Agent
  family name: Lu
  given name: Ying
author list: Agent
  family name: Zhou
  given name: Zhou
author list: Agent
  family name: Wang
  given name: Xiaoyun
author list: Agent
  family name: Ge
  given name: Hongjuan
author list: Agent
  family name: Sun
  given name: Qinghua
doi: 10.7717/peerj.12852
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Dai et al.
attribution name: Dai et al.

Arbuscular mycorrhizal fungi increase crop yields by improving biomass under rainfed condition: a meta-analysis
type: item
type: AcademicArticle
description: Background Rainfed agriculture plays key role in ensuring food security and maintain ecological balance. Especially in developing areas, most grain food are produced rainfed agricultural ecosystem. Therefore, the increase of crop yields in rainfed agricultural ecosystem becomes vital as well as ensuring global food security. Methods The potential roles of arbuscular mycorrhizal fungi (AMF) in improving crop yields under rainfed condition were explored based on 546 pairs of observations published from 1950 to 2021. Results AMF inoculation increased 23.0% crop yields based on 13 popular crops under rainfed condition. Not only was crop biomass of shoot and root increased 24.2% and 29.6% by AMF inocula, respectively but also seed number and pod/fruit number per plant were enhanced markedly. Further, the effect of AMF on crop yields depended on different crop groups. AMF improved more yield of N-fixing crops than non-N-fixing crops. The effect of AMF changed between grain and non-grain crops with the effect size of 0.216 and 0.352, respectively. AMF inoculation enhances stress resistance and photosynthesis of host crop in rainfed agriculture. Conclusion AMF increased crop yields by enhancing shoot biomass due to the improvement of plant nutrition, photosynthesis, and stress resistance in rainfed field. Our findings provide a new view for understanding the sustainable productivity in rainfed agroecosystem, which enriched the theory of AMF functional diversity. This study provided a theoretical and technical way for sustainable production under rainfed agriculture.
format: application/pdf
format: text/html
creator: Shanwei Wu
creator: Zhaoyong Shi
creator: Xianni Chen
creator: Jiakai Gao
creator: Xugang Wang
subject: Agricultural Science
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.12861
publisher: PeerJ Inc.
rights: © 2022 Wu et al.
abstract: Background Rainfed agriculture plays key role in ensuring food security and maintain ecological balance. Especially in developing areas, most grain food are produced rainfed agricultural ecosystem. Therefore, the increase of crop yields in rainfed agricultural ecosystem becomes vital as well as ensuring global food security. Methods The potential roles of arbuscular mycorrhizal fungi (AMF) in improving crop yields under rainfed condition were explored based on 546 pairs of observations published from 1950 to 2021. Results AMF inoculation increased 23.0% crop yields based on 13 popular crops under rainfed condition. Not only was crop biomass of shoot and root increased 24.2% and 29.6% by AMF inocula, respectively but also seed number and pod/fruit number per plant were enhanced markedly. Further, the effect of AMF on crop yields depended on different crop groups. AMF improved more yield of N-fixing crops than non-N-fixing crops. The effect of AMF changed between grain and non-grain crops with the effect size of 0.216 and 0.352, respectively. AMF inoculation enhances stress resistance and photosynthesis of host crop in rainfed agriculture. Conclusion AMF increased crop yields by enhancing shoot biomass due to the improvement of plant nutrition, photosynthesis, and stress resistance in rainfed field. Our findings provide a new view for understanding the sustainable productivity in rainfed agroecosystem, which enriched the theory of AMF functional diversity. This study provided a theoretical and technical way for sustainable production under rainfed agriculture.
bibliographic citation: Wu et al. (2022) Arbuscular mycorrhizal fungi increase crop yields by improving biomass under rainfed condition: a meta-analysis. PeerJ 10:e12861 https://doi.org/10.7717/peerj.12861
date submitted: 2021-07-23
date accepted: 2022-01-09
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Shanwei
author list: Agent
  family name: Shi
  given name: Zhaoyong
author list: Agent
  family name: Chen
  given name: Xianni
author list: Agent
  family name: Gao
  given name: Jiakai
author list: Agent
  family name: Wang
  given name: Xugang
doi: 10.7717/peerj.12861
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Wu et al.
attribution name: Wu et al.

C. elegans as an in vivo model system for the phenotypic drug discovery for treating paraquat poisoning
type: item
type: AcademicArticle
description: Background Paraquat (PQ) is an effective and widely used herbicide and causes numerous fatalities by accidental or voluntary ingestion. However, neither the final cytotoxic mechanism nor effective treatments for PQ poisoning have been discovered. Phenotypic drug discovery (PDD), which does not rely on the molecular mechanism of the diseases, is having a renaissance in recent years owing to its potential to address the incompletely understood complexity of diseases. Herein, the C. elegans PDD model was established to pave the way for the future phenotypic discovery of potential agents for treating PQ poisoning. Methods C. elegans were treated with PQ-containing solid medium followed by statistical analysis of worm survival, pharyngeal pumping, and movement ability. Furthermore, coenzyme Q10 (CoQ10) was used to test the C. elegans model of PQ poisoning by measuring the levels of reactive oxygen species (ROS) and malondialdehyde (MDA), mitochondrial morphology, and worm survival rate. Additionally, we used the classic mice model of PQ intoxication to evaluate the validity of the C. elegans model of PQ poisoning by measuring the effect of CoQ10 as a potential antidote for PQ poisoning. Results In the C. elegans model of PQ poisoning, 5 mg/mL PQ increased the levels of ROS, MDA content, mitochondrial fragments, which significantly shortened the lifespan, while CoQ10 alleviated these phenotypes. In the mice model of PQ poisoning, CoQ10 increased the chance of survival in PQ poisoned mice while reducing ROS, MDA content in lung tissue and inhibiting PQ-induced lung edema. Moreover, CoQ10 alleviated the lung morphopathological changes induced by PQ. Conclusion Here we established a C. elegans model of PQ poisoning, whose validity was confirmed by the classic mice model of PQ intoxication.
format: application/pdf
format: text/html
creator: Peng Ji
creator: Hongyuan Li
creator: Yushan Jin
creator: Yinghua Peng
creator: Lihui Zhao
creator: Xiaohui Wang
subject: Biochemistry
subject: Toxicology
subject: Histology
description: doi:10.7717/peerj.12866
publisher: PeerJ Inc.
rights: © 2022 Ji et al.
abstract: Background Paraquat (PQ) is an effective and widely used herbicide and causes numerous fatalities by accidental or voluntary ingestion. However, neither the final cytotoxic mechanism nor effective treatments for PQ poisoning have been discovered. Phenotypic drug discovery (PDD), which does not rely on the molecular mechanism of the diseases, is having a renaissance in recent years owing to its potential to address the incompletely understood complexity of diseases. Herein, the C. elegans PDD model was established to pave the way for the future phenotypic discovery of potential agents for treating PQ poisoning. Methods C. elegans were treated with PQ-containing solid medium followed by statistical analysis of worm survival, pharyngeal pumping, and movement ability. Furthermore, coenzyme Q10 (CoQ10) was used to test the C. elegans model of PQ poisoning by measuring the levels of reactive oxygen species (ROS) and malondialdehyde (MDA), mitochondrial morphology, and worm survival rate. Additionally, we used the classic mice model of PQ intoxication to evaluate the validity of the C. elegans model of PQ poisoning by measuring the effect of CoQ10 as a potential antidote for PQ poisoning. Results In the C. elegans model of PQ poisoning, 5 mg/mL PQ increased the levels of ROS, MDA content, mitochondrial fragments, which significantly shortened the lifespan, while CoQ10 alleviated these phenotypes. In the mice model of PQ poisoning, CoQ10 increased the chance of survival in PQ poisoned mice while reducing ROS, MDA content in lung tissue and inhibiting PQ-induced lung edema. Moreover, CoQ10 alleviated the lung morphopathological changes induced by PQ. Conclusion Here we established a C. elegans model of PQ poisoning, whose validity was confirmed by the classic mice model of PQ intoxication.
bibliographic citation: Ji et al. (2022) C. elegans as an in vivo model system for the phenotypic drug discovery for treating paraquat poisoning. PeerJ 10:e12866 https://doi.org/10.7717/peerj.12866
date submitted: 2021-04-30
date accepted: 2022-01-10
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ji
  given name: Peng
author list: Agent
  family name: Li
  given name: Hongyuan
author list: Agent
  family name: Jin
  given name: Yushan
author list: Agent
  family name: Peng
  given name: Yinghua
author list: Agent
  family name: Zhao
  given name: Lihui
author list: Agent
  family name: Wang
  given name: Xiaohui
doi: 10.7717/peerj.12866
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: ©2022 Ji et al.
attribution name: Ji et al.

BIRC5 promotes cancer progression and predicts prognosis in laryngeal squamous cell carcinoma
type: item
type: AcademicArticle
description: Background Laryngeal squamous cell carcinoma (LSCC) remains one of the most common respiratory tumors worldwide. Baculoviral inhibitor of apoptosis repeat containing 5 (BIRC5) is a member of the inhibitor-of-apoptosis protein family. BIRC5 plays an important role in various types of cell proliferation, differentiation, migration and invasion. However, the specific role of BIRC5 in LSCC remains unclear. Methods To provide a prognostic biomarker for LSCC, we screened the prognostic genes of LSCC via bioinformatics. PPI network and KEGG pathways were used to select hub genes. Clinical prognoses were performed using a Kaplan–Meier plotter and Cox proportional-hazard analysis. BIRC5 expression in LSCC tissues and cell lines were detected by RT-PCR, Western blot and Immunohistochemistry (IHC). Cell proliferation, cell cycle and cell apoptosis were detected with Cell Counting Kit-8 (CCK-8) and Flow Cytometry assay, respectively. Results Here, BIRC5 was strongly correlated with higher tumor grade and differentiation. BIRC5 was highly expressed in LSCC tissues when compared with normal tissues and increased expression of BIRC5 was associated with overall survival in LSCC patients. The suppression of BIRC5 induced cell apoptosis and cell cycle arrest, thereby inhibiting the proliferation of LSCC cells. The survival analysis confirmed that higher level of BIRC5 expression predicted poor prognosis of LSCC patients. BIRC5 may act as an oncogene of LSCC development and was suggested as a promising prognostic biomarker for LSCC.
format: application/pdf
format: text/html
creator: Nan Wang
creator: Xuanyu Huang
creator: Jinsheng Cheng
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Otorhinolaryngology
subject: Medical Genetics
description: doi:10.7717/peerj.12871
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Background Laryngeal squamous cell carcinoma (LSCC) remains one of the most common respiratory tumors worldwide. Baculoviral inhibitor of apoptosis repeat containing 5 (BIRC5) is a member of the inhibitor-of-apoptosis protein family. BIRC5 plays an important role in various types of cell proliferation, differentiation, migration and invasion. However, the specific role of BIRC5 in LSCC remains unclear. Methods To provide a prognostic biomarker for LSCC, we screened the prognostic genes of LSCC via bioinformatics. PPI network and KEGG pathways were used to select hub genes. Clinical prognoses were performed using a Kaplan–Meier plotter and Cox proportional-hazard analysis. BIRC5 expression in LSCC tissues and cell lines were detected by RT-PCR, Western blot and Immunohistochemistry (IHC). Cell proliferation, cell cycle and cell apoptosis were detected with Cell Counting Kit-8 (CCK-8) and Flow Cytometry assay, respectively. Results Here, BIRC5 was strongly correlated with higher tumor grade and differentiation. BIRC5 was highly expressed in LSCC tissues when compared with normal tissues and increased expression of BIRC5 was associated with overall survival in LSCC patients. The suppression of BIRC5 induced cell apoptosis and cell cycle arrest, thereby inhibiting the proliferation of LSCC cells. The survival analysis confirmed that higher level of BIRC5 expression predicted poor prognosis of LSCC patients. BIRC5 may act as an oncogene of LSCC development and was suggested as a promising prognostic biomarker for LSCC.
bibliographic citation: Wang et al. (2022) BIRC5 promotes cancer progression and predicts prognosis in laryngeal squamous cell carcinoma. PeerJ 10:e12871 https://doi.org/10.7717/peerj.12871
date submitted: 2021-07-09
date accepted: 2022-01-11
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Nan
author list: Agent
  family name: Huang
  given name: Xuanyu
author list: Agent
  family name: Cheng
  given name: Jinsheng
doi: 10.7717/peerj.12871
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Wang et al.
attribution name: Wang et al.

https://peerj.com/articles/12873
type: item
type: AcademicArticle
title: A revision of Plectanocotyle (Monogenea, Plectanocotylidae), with molecular barcoding of three species and the description of a new species from the streaked gurnard Chelidonichthys lastoviza off Algeria
description: Background The family Plectanocotylidae includes parasites of the gills of marine fish; although nine genera and about 20 species have been described, almost no molecular information is available. Putting aside Plectanocotyle elliptica Diesing, 1850, supposedly a parasite of the white perch Morone americana, never found again since its original description, two species were valid within Plectanocotyle Diesing, 1850 before this work: Plectanocotyle gurnardi (Van Beneden & Hesse, 1863) Llewellyn, 1941 and Plectanocotyle major Boudaya, Neifar & Euzet, 2006. Methods In this paper, we describe the third species of the genus Plectanocotyle and perform a comparative morphological and molecular analysis of the three species and of Triglicola obscura (Euzet & Suriano, 1974) Mamaev, 1976. Host fishes were also barcoded (COI) for confirmation of host identifications. Results Plectanocotyle lastovizae n. sp. is described from the gills of the streaked gurnard Chelidonichthys lastoviza collected off Algeria. The species is compared with specimens of Plectanocotyle cf. gurnardi (from C. lastoviza) from the same locality and P. major and T. obscura (both from the longfin gurnard C. obscurus). Molecules from Plectanocotyle cf. gurnardi could not be compared with P. gurnardi from the type-host and type-locality and we kept the status of the Mediterranean specimens as pending. Algeria is a new geographic record for P. major and T. obscura. Plectanocotyle lastovizae n. sp. is distinguished from the other species found in the Mediterranean by the measurements of clamps, number of testes, and COI sequences, with notable divergence (7.8–11.8%) from the other two species of the genus. Discussion We briefly present a list of currently known members of the family Plectanocotylidae, their biology and their hosts.
format: application/pdf
format: text/html
creator: Zouhour El Mouna Ayadi
creator: Fadila Tazerouti
creator: Delphine Gey
creator: Jean-Lou Justine
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Parasitology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12873
publisher: PeerJ Inc.
rights: © 2022 Ayadi et al.
abstract: Background The family Plectanocotylidae includes parasites of the gills of marine fish; although nine genera and about 20 species have been described, almost no molecular information is available. Putting aside Plectanocotyle elliptica Diesing, 1850, supposedly a parasite of the white perch Morone americana, never found again since its original description, two species were valid within Plectanocotyle Diesing, 1850 before this work: Plectanocotyle gurnardi (Van Beneden & Hesse, 1863) Llewellyn, 1941 and Plectanocotyle major Boudaya, Neifar & Euzet, 2006. Methods In this paper, we describe the third species of the genus Plectanocotyle and perform a comparative morphological and molecular analysis of the three species and of Triglicola obscura (Euzet & Suriano, 1974) Mamaev, 1976. Host fishes were also barcoded (COI) for confirmation of host identifications. Results Plectanocotyle lastovizae n. sp. is described from the gills of the streaked gurnard Chelidonichthys lastoviza collected off Algeria. The species is compared with specimens of Plectanocotyle cf. gurnardi (from C. lastoviza) from the same locality and P. major and T. obscura (both from the longfin gurnard C. obscurus). Molecules from Plectanocotyle cf. gurnardi could not be compared with P. gurnardi from the type-host and type-locality and we kept the status of the Mediterranean specimens as pending. Algeria is a new geographic record for P. major and T. obscura. Plectanocotyle lastovizae n. sp. is distinguished from the other species found in the Mediterranean by the measurements of clamps, number of testes, and COI sequences, with notable divergence (7.8–11.8%) from the other two species of the genus. Discussion We briefly present a list of currently known members of the family Plectanocotylidae, their biology and their hosts.
bibliographic citation: Ayadi et al. (2022) A revision of Plectanocotyle (Monogenea, Plectanocotylidae), with molecular barcoding of three species and the description of a new species from the streaked gurnard Chelidonichthys lastoviza off Algeria. PeerJ 10:e12873 https://doi.org/10.7717/peerj.12873
date submitted: 2018-02-09
date accepted: 2022-01-11
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ayadi
  given name: Zouhour El Mouna
author list: Agent
  family name: Tazerouti
  given name: Fadila
author list: Agent
  family name: Gey
  given name: Delphine
author list: Agent
  family name: Justine
  given name: Jean-Lou
doi: 10.7717/peerj.12873
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: © 2022 Ayadi et al.
attribution name: Ayadi et al.

Differential modulation of behavior by infraslow activities of different brain regions
type: item
type: AcademicArticle
description: The oscillation phase of electroencephalograms (EEGs) is associated with behavioral performance. Several studies have demonstrated this association for relatively fast oscillations (>1 Hz); a similar finding has also been reported for slower oscillations, showing that behavioral performance is correlated with the phase of infraslow activity (ISA, 0.01–0.1 Hz) of electroencephalography (EEG). However, the previous study only investigated ISA in a local brain region using a relatively simple task (somatosensory discrimination task), leaving it difficult to determine how the EEG ISA for various brain regions is associated with behavioral performance. In addition, it is not known whether the EEG ISA phase modulates more complex behavioral task performance. In the present study, we analyzed the ISA of whole-brain EEG of participants performing various behaviors while playing video games. We found that behavior was associated with the specific oscillation phase of EEG ISA when that behavior was independent of other behaviors. In addition, we found that the EEG ISA oscillation phases modulating the different behaviors varied across brain regions. Our results suggest that the EEG ISA for different brain regions modulates behavioral performance in different ways and such modulation of EEG ISA can be generalized to diverse behaviors. This study may deepen the understanding of how EEG ISA modulates behavior and increases the applicability of EEG ISA.
format: application/pdf
format: text/html
creator: Duho Sihn
creator: Sung-Phil Kim
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.12875
publisher: PeerJ Inc.
rights: © 2022 Sihn and Kim
abstract: The oscillation phase of electroencephalograms (EEGs) is associated with behavioral performance. Several studies have demonstrated this association for relatively fast oscillations (>1 Hz); a similar finding has also been reported for slower oscillations, showing that behavioral performance is correlated with the phase of infraslow activity (ISA, 0.01–0.1 Hz) of electroencephalography (EEG). However, the previous study only investigated ISA in a local brain region using a relatively simple task (somatosensory discrimination task), leaving it difficult to determine how the EEG ISA for various brain regions is associated with behavioral performance. In addition, it is not known whether the EEG ISA phase modulates more complex behavioral task performance. In the present study, we analyzed the ISA of whole-brain EEG of participants performing various behaviors while playing video games. We found that behavior was associated with the specific oscillation phase of EEG ISA when that behavior was independent of other behaviors. In addition, we found that the EEG ISA oscillation phases modulating the different behaviors varied across brain regions. Our results suggest that the EEG ISA for different brain regions modulates behavioral performance in different ways and such modulation of EEG ISA can be generalized to diverse behaviors. This study may deepen the understanding of how EEG ISA modulates behavior and increases the applicability of EEG ISA.
bibliographic citation: Sihn et al. (2022) Differential modulation of behavior by infraslow activities of different brain regions. PeerJ 10:e12875 https://doi.org/10.7717/peerj.12875
date submitted: 2021-11-15
date accepted: 2022-01-11
issued: 2022-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sihn
  given name: Duho
author list: Agent
  family name: Kim
  given name: Sung-Phil
doi: 10.7717/peerj.12875
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-02-01
copyright: ©2022 Sihn and Kim
attribution name: Sihn and Kim

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