PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages
items: A review of starch biosynthesis in cereal crops and its potential breeding applications in rice (Oryza Sativa L.)
items: An estimate of the area of occupancy and population size of Brachycephalus tridactylus (Anura: Brachycephalidae) to reassess its conservation status, with a proposal for conservation measures
items: Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum
items: Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma
items: Early detection of cyanide, organophosphate and rodenticide pollution based on locomotor activity of zebrafish larvae
items: Differential expression profiles of microRNAs in musk gland of unmated and mated forest musk deer (Moschus berezovskii)
items: Electroencephalogram-derived pain index for evaluating pain during labor
items: Phenotypic differentiation of the slow worm lizards (Squamata: Anguis) across their contact zone in Central Europe
items: Interoceptive awareness and beliefs about health and the body as predictors of the intensity of emotions experienced at the beginning of the pandemic

Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages
type: item
type: AcademicArticle
description: Background MicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple (Malus x domestica Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes. Methods To answer this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and nongenetically modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. In addition, two cultivars, ‘Hanfu’ and ‘M9’, which have naturally fruit size variation, were included to identify miR172-dependent DEGs. qRT–PCRwas used to verify the reliability of our RNA-seq data. Results Overexpression of miR172 altered the expression levels of many cell proliferation- and cell expansion-related genes. Twenty-four libraries were generated, and 10,338 differentially expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. ‘Hanfu’ and ‘M9’ are two common cultivars that bear fruit of different sizes (250 g and 75 g, respectively). Six libraries were generated, and 3,627 DEGs were detected between ‘Hanfu’ and ‘M9’. After merging the two datasets, 6,888 candidate miR172-specific DEGs were identified. The potential networks associated with fruit size triggered traits were defined among genes belonging to the families of hormone synthesis, signaling pathways, and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit and a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.
format: application/pdf
format: text/html
creator: Zhe Zhou
creator: Yanmin Zhu
creator: Hengtao Zhang
creator: Ruiping Zhang
creator: Qiming Gao
creator: Tiyu Ding
creator: Huan Wang
creator: Zhenli Yan
creator: Jia-Long Yao
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12675
publisher: PeerJ Inc.
rights: © 2021 Zhou et al.
abstract: Background MicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple (Malus x domestica Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes. Methods To answer this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and nongenetically modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. In addition, two cultivars, ‘Hanfu’ and ‘M9’, which have naturally fruit size variation, were included to identify miR172-dependent DEGs. qRT–PCRwas used to verify the reliability of our RNA-seq data. Results Overexpression of miR172 altered the expression levels of many cell proliferation- and cell expansion-related genes. Twenty-four libraries were generated, and 10,338 differentially expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. ‘Hanfu’ and ‘M9’ are two common cultivars that bear fruit of different sizes (250 g and 75 g, respectively). Six libraries were generated, and 3,627 DEGs were detected between ‘Hanfu’ and ‘M9’. After merging the two datasets, 6,888 candidate miR172-specific DEGs were identified. The potential networks associated with fruit size triggered traits were defined among genes belonging to the families of hormone synthesis, signaling pathways, and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit and a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple.
bibliographic citation: Zhou et al. (2021) Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages. PeerJ 9:e12675 https://doi.org/10.7717/peerj.12675
date submitted: 2021-07-22
date accepted: 2021-12-02
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zhe
author list: Agent
  family name: Zhu
  given name: Yanmin
author list: Agent
  family name: Zhang
  given name: Hengtao
author list: Agent
  family name: Zhang
  given name: Ruiping
author list: Agent
  family name: Gao
  given name: Qiming
author list: Agent
  family name: Ding
  given name: Tiyu
author list: Agent
  family name: Wang
  given name: Huan
author list: Agent
  family name: Yan
  given name: Zhenli
author list: Agent
  family name: Yao
  given name: Jia-Long
doi: 10.7717/peerj.12675
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Zhou et al.
attribution name: Zhou et al.

A review of starch biosynthesis in cereal crops and its potential breeding applications in rice (Oryza Sativa L.)
type: item
type: AcademicArticle
description: Starch provides primary storage of carbohydrates, accounting for approximately 85% of the dry weight of cereal endosperm. Cereal seeds contribute to maximum annual starch production and provide the primary food for humans and livestock worldwide. However, the growing demand for starch in food and industry and the increasing loss of arable land with urbanization emphasizes the urgency to understand starch biosynthesis and its regulation. Here, we first summarized the regulatory signaling pathways about leaf starch biosynthesis. Subsequently, we paid more attention to how transcriptional factors (TFs) systematically respond to various stimulants via the regulation of the enzymes during starch biosynthesis. Finally, some strategies to improve cereal yield and quality were put forward based on the previous reports. This review would collectively help to design future studies on starch biosynthesis in cereal crops.
format: application/pdf
format: text/html
creator: Ruiqing Li
creator: Wenyin Zheng
creator: Meng Jiang
creator: Huali Zhang
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.12678
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Starch provides primary storage of carbohydrates, accounting for approximately 85% of the dry weight of cereal endosperm. Cereal seeds contribute to maximum annual starch production and provide the primary food for humans and livestock worldwide. However, the growing demand for starch in food and industry and the increasing loss of arable land with urbanization emphasizes the urgency to understand starch biosynthesis and its regulation. Here, we first summarized the regulatory signaling pathways about leaf starch biosynthesis. Subsequently, we paid more attention to how transcriptional factors (TFs) systematically respond to various stimulants via the regulation of the enzymes during starch biosynthesis. Finally, some strategies to improve cereal yield and quality were put forward based on the previous reports. This review would collectively help to design future studies on starch biosynthesis in cereal crops.
bibliographic citation: Li et al. (2021) A review of starch biosynthesis in cereal crops and its potential breeding applications in rice (Oryza Sativa L.). PeerJ 9:e12678 https://doi.org/10.7717/peerj.12678
date submitted: 2021-09-22
date accepted: 2021-12-02
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ruiqing
author list: Agent
  family name: Zheng
  given name: Wenyin
author list: Agent
  family name: Jiang
  given name: Meng
author list: Agent
  family name: Zhang
  given name: Huali
doi: 10.7717/peerj.12678
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: © 2021 Li et al.
attribution name: Li et al.

An estimate of the area of occupancy and population size of Brachycephalus tridactylus (Anura: Brachycephalidae) to reassess its conservation status, with a proposal for conservation measures
type: item
type: AcademicArticle
description: Background We are experiencing a global crisis in conservation, which has led to the prioritization of targets, such as nations, regions, and animal groups, which are necessary while resources are disputed. Brazil is a priority not only because of its megadiversity, high rates of endemism, and frequent descriptions of new species but also because of its high levels of deforestation. Among the species groups prioritized for conservation is the anurans (Amphibia: Anura), the population of which is severely declining. One group of anurans is the genus Brachycephalus, which includes 37 endemic species in the Brazilian Atlantic Rainforest. Some of these species have highly restricted distributions (<100 ha). Thirty new species have been described since 2000, and 55.3% of all species are threatened with extinction. Brachycephalus tridactylus was only recently described and remains restricted to its type locality. Because of its reduced geographical distribution (0.41 km2), it has been proposed to be considered as Vulnerable. The objective of this study is to reevaluate the conservation status of Brachycephalus tridactylus and propose conservation measures. Methods We searched for new populations during 2016–2020, evaluated in loco impacts and potential impacts on the species’ population, and performed an analysis of the density of this population and estimated its size. International Union for Conservation of Nature (IUCN) criteria were used to assess the conservation status of the species. Results We recorded the species in seven new localities (from 715–1,140 m above sea level) in the state of São Paulo up to 33 km from the type locality of the species (in state of Paraná). We estimated the area of occupancy as 148.44 km2, densities as one calling male per 4.05 m2 and 130.00 m2, and a total population size of 4,429,722 adult individuals. Based on our finding, we proposed three lines of management: (1) formation of fire brigades, (2) management of residents’ mules in the…
format: application/pdf
format: text/html
creator: Marcos R. Bornschein
creator: Júnior Nadaline
creator: Luiz Fernando Ribeiro
creator: Giovanna Sandretti-Silva
creator: Maria Fernanda Ferreira Rivas
creator: Bruno de Morais Guerra
creator: Larissa Teixeira
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12687
publisher: PeerJ Inc.
rights: © 2021 Bornschein et al.
abstract: Background We are experiencing a global crisis in conservation, which has led to the prioritization of targets, such as nations, regions, and animal groups, which are necessary while resources are disputed. Brazil is a priority not only because of its megadiversity, high rates of endemism, and frequent descriptions of new species but also because of its high levels of deforestation. Among the species groups prioritized for conservation is the anurans (Amphibia: Anura), the population of which is severely declining. One group of anurans is the genus Brachycephalus, which includes 37 endemic species in the Brazilian Atlantic Rainforest. Some of these species have highly restricted distributions (<100 ha). Thirty new species have been described since 2000, and 55.3% of all species are threatened with extinction. Brachycephalus tridactylus was only recently described and remains restricted to its type locality. Because of its reduced geographical distribution (0.41 km2), it has been proposed to be considered as Vulnerable. The objective of this study is to reevaluate the conservation status of Brachycephalus tridactylus and propose conservation measures. Methods We searched for new populations during 2016–2020, evaluated in loco impacts and potential impacts on the species’ population, and performed an analysis of the density of this population and estimated its size. International Union for Conservation of Nature (IUCN) criteria were used to assess the conservation status of the species. Results We recorded the species in seven new localities (from 715–1,140 m above sea level) in the state of São Paulo up to 33 km from the type locality of the species (in state of Paraná). We estimated the area of occupancy as 148.44 km2, densities as one calling male per 4.05 m2 and 130.00 m2, and a total population size of 4,429,722 adult individuals. Based on our finding, we proposed three lines of management: (1) formation of fire brigades, (2) management of residents’ mules in the…
bibliographic citation: Bornschein et al. (2021) An estimate of the area of occupancy and population size of Brachycephalus tridactylus (Anura: Brachycephalidae) to reassess its conservation status, with a proposal for conservation measures. PeerJ 9:e12687 https://doi.org/10.7717/peerj.12687
date submitted: 2021-07-12
date accepted: 2021-12-03
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bornschein
  given name: Marcos R.
author list: Agent
  family name: Nadaline
  given name: Júnior
author list: Agent
  family name: Ribeiro
  given name: Luiz Fernando
author list: Agent
  family name: Sandretti-Silva
  given name: Giovanna
author list: Agent
  family name: Rivas
  given name: Maria Fernanda Ferreira
author list: Agent
  family name: Guerra
  given name: Bruno de Morais
author list: Agent
  family name: Teixeira
  given name: Larissa
doi: 10.7717/peerj.12687
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Bornschein et al.
attribution name: Bornschein et al.

Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum
type: item
type: AcademicArticle
description: The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.
format: application/pdf
format: text/html
creator: Chunwei Li
creator: Qiuye You
creator: Panfeng Zhao
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.12689
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition.
bibliographic citation: Li et al. (2021) Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum. PeerJ 9:e12689 https://doi.org/10.7717/peerj.12689
date submitted: 2021-09-16
date accepted: 2021-12-03
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Chunwei
author list: Agent
  family name: You
  given name: Qiuye
author list: Agent
  family name: Zhao
  given name: Panfeng
doi: 10.7717/peerj.12689
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: © 2021 Li et al.
attribution name: Li et al.

Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma
type: item
type: AcademicArticle
description: Background Hepatocellular carcinoma (HCC) is one of the most common malignancies around the world. Among the risk factors involved in liver carcinogenesis, hepatitis B virus (HBV) X protein (HBx) is considered to be a key regulator in hepatocarcinogenesis. Whether HBx promotes or protects against HCC remains controversial, therefore exploring new HBx-associated genes is still important. Methods HBx was overexpressed in HepG2, HepG2.2.15 and SMMC-7721 cell lines, primary mouse hepatocytes and livers of C57BL/6N mice. High-throughput RNA sequencing profiling of HepG2 cells with HBx overexpression and related differentially-expressed genes (DEGs), pathway enrichment analysis, protein-protein interaction networks (PPIs), overlapping analysis were conducted. In addition, Gene Expression Omnibus (GEO) and proteomic datasets of HBV-positive HCC datasets were used to verify the expression and prognosis of selected DEGs. Finally, we also evaluated the known oncogenic role of HBx by oncogenic array analysis. Results A total of 523 DEGs were obtained from HBx-overexpressing HepG2 cells. Twelve DEGs were identified and validated in cells transiently transfected with HBx and three datasets of HBV-positive HCC transcription profiles. In addition, using the Kaplan-Meier plotter database, the expression levels of the twelve different genes were further analyzed to predict patient outcomes. Conclusion Among the 12 identified HBx-associated hub genes, HBV-positive HCC patients expressing ARG1 and TAT showed a good overall survival (OS) and relapse-free survival (RFS). Thus, ARG1 and TAT expression could be potential prognostic markers.
format: application/pdf
format: text/html
creator: Zhengzhong Ni
creator: Jun Lu
creator: Weiyi Huang
creator: Hanif Khan
creator: Xuejun Wu
creator: Danmei Huang
creator: Ganggang Shi
creator: Yongdong Niu
creator: Haihua Huang
subject: Oncology
description: doi:10.7717/peerj.12697
publisher: PeerJ Inc.
rights: © 2021 Ni et al.
abstract: Background Hepatocellular carcinoma (HCC) is one of the most common malignancies around the world. Among the risk factors involved in liver carcinogenesis, hepatitis B virus (HBV) X protein (HBx) is considered to be a key regulator in hepatocarcinogenesis. Whether HBx promotes or protects against HCC remains controversial, therefore exploring new HBx-associated genes is still important. Methods HBx was overexpressed in HepG2, HepG2.2.15 and SMMC-7721 cell lines, primary mouse hepatocytes and livers of C57BL/6N mice. High-throughput RNA sequencing profiling of HepG2 cells with HBx overexpression and related differentially-expressed genes (DEGs), pathway enrichment analysis, protein-protein interaction networks (PPIs), overlapping analysis were conducted. In addition, Gene Expression Omnibus (GEO) and proteomic datasets of HBV-positive HCC datasets were used to verify the expression and prognosis of selected DEGs. Finally, we also evaluated the known oncogenic role of HBx by oncogenic array analysis. Results A total of 523 DEGs were obtained from HBx-overexpressing HepG2 cells. Twelve DEGs were identified and validated in cells transiently transfected with HBx and three datasets of HBV-positive HCC transcription profiles. In addition, using the Kaplan-Meier plotter database, the expression levels of the twelve different genes were further analyzed to predict patient outcomes. Conclusion Among the 12 identified HBx-associated hub genes, HBV-positive HCC patients expressing ARG1 and TAT showed a good overall survival (OS) and relapse-free survival (RFS). Thus, ARG1 and TAT expression could be potential prognostic markers.
bibliographic citation: Ni et al. (2021) Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma. PeerJ 9:e12697 https://doi.org/10.7717/peerj.12697
date submitted: 2021-06-22
date accepted: 2021-12-06
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ni
  given name: Zhengzhong
author list: Agent
  family name: Lu
  given name: Jun
author list: Agent
  family name: Huang
  given name: Weiyi
author list: Agent
  family name: Khan
  given name: Hanif
author list: Agent
  family name: Wu
  given name: Xuejun
author list: Agent
  family name: Huang
  given name: Danmei
author list: Agent
  family name: Shi
  given name: Ganggang
author list: Agent
  family name: Niu
  given name: Yongdong
author list: Agent
  family name: Huang
  given name: Haihua
doi: 10.7717/peerj.12697
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Ni et al.
attribution name: Ni et al.

Early detection of cyanide, organophosphate and rodenticide pollution based on locomotor activity of zebrafish larvae
type: item
type: AcademicArticle
description: Cyanide, organophosphate and rodenticides are highly toxic substances widely used in agriculture and industry. These toxicants are neuro- and organotoxic to mammals at low concentrations, thus early detection of these chemicals in the aqueous environment is of utmost importance. Here, we employed the behavioral toxicity test with wildtype zebrafish larvae to determine sublethal concentrations of the above mentioned common environmental pollutants. After optimizing the test with cyanide, nine rodenticides and an organophosphate were successfully tested. The compounds dose-dependently initially (0–60-min exposure) stimulated locomotor activity of larvae but induced toxicity and reduced swimming during 60–120-min exposure. IC50 values calculated based on swimming distance after 2-h exposure, were between 0.1 and 10 mg/L for both first-generation and second-generation anticoagulant rodenticides. Three behavioral characteristics, including total distance travelled, sinuosity and burst count, were quantitatively analyzed and compared by hierarchical clustering of the effects measured by each three parameters. The toxicity results for all three behavioral endpoints were consistent, suggesting that the directly measured parameter of cumulative swimming distance could be used as a promising biomarker for the aquatic contamination. The optimized method herein showed the potential for utilization as part of a monitoring system and an ideal tool for the risk assessment of drinking water in the military and public safety.
format: application/pdf
format: text/html
creator: Binjie Wang
creator: Junhao Zhu
creator: Anli Wang
creator: Jiye Wang
creator: Yuanzhao Wu
creator: Weixuan Yao
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.12703
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Cyanide, organophosphate and rodenticides are highly toxic substances widely used in agriculture and industry. These toxicants are neuro- and organotoxic to mammals at low concentrations, thus early detection of these chemicals in the aqueous environment is of utmost importance. Here, we employed the behavioral toxicity test with wildtype zebrafish larvae to determine sublethal concentrations of the above mentioned common environmental pollutants. After optimizing the test with cyanide, nine rodenticides and an organophosphate were successfully tested. The compounds dose-dependently initially (0–60-min exposure) stimulated locomotor activity of larvae but induced toxicity and reduced swimming during 60–120-min exposure. IC50 values calculated based on swimming distance after 2-h exposure, were between 0.1 and 10 mg/L for both first-generation and second-generation anticoagulant rodenticides. Three behavioral characteristics, including total distance travelled, sinuosity and burst count, were quantitatively analyzed and compared by hierarchical clustering of the effects measured by each three parameters. The toxicity results for all three behavioral endpoints were consistent, suggesting that the directly measured parameter of cumulative swimming distance could be used as a promising biomarker for the aquatic contamination. The optimized method herein showed the potential for utilization as part of a monitoring system and an ideal tool for the risk assessment of drinking water in the military and public safety.
bibliographic citation: Wang et al. (2021) Early detection of cyanide, organophosphate and rodenticide pollution based on locomotor activity of zebrafish larvae. PeerJ 9:e12703 https://doi.org/10.7717/peerj.12703
date submitted: 2021-09-28
date accepted: 2021-12-07
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Binjie
author list: Agent
  family name: Zhu
  given name: Junhao
author list: Agent
  family name: Wang
  given name: Anli
author list: Agent
  family name: Wang
  given name: Jiye
author list: Agent
  family name: Wu
  given name: Yuanzhao
author list: Agent
  family name: Yao
  given name: Weixuan
doi: 10.7717/peerj.12703
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Differential expression profiles of microRNAs in musk gland of unmated and mated forest musk deer (Moschus berezovskii)
type: item
type: AcademicArticle
description: Background The formation of musk is a complex biophysical and biochemical process that change with the rut of male forest musk deer. We have reported that the mating status of male forest musk deer might result to the variations of chemical composition and microbiota of musk and its yields. Critical roles for microRNAs (miRNAs) of multi-tissues were profiled in our previous study; however, the role for miRNAs of the musk gland remains unclear in this species. Methods In this study, we used Illumina deep sequencing technology to sequence the small RNA transcriptome of unmated male (UM) and mated male (UM) of Chinese forest musk deer. Results We identified 1,652 known miRNAs and 45 novel miRNAs, of which there were 174 differentially expressed miRNAs between UM and MM. chi-miR-21-5p, ipu-miR-99b and bta-miR-26a were up-regulated in UM among the 10 most differentially expressed miRNAs. Functional enrichment of the target genes showed that monosaccharide biosynthetic process, protein targeting, cellular protein catabolic process enriched higher in MM. Meanwhile, structural molecule activity, secretion by cell, regulated exocytosis and circulatory system process enriched more in UM, hinting that the formation of musk in UM was mediated by target genes related to exocytosis. The miRNA-mRNA pairs such as miR-21: CHD7, miR143: HSD17B7, miR-141/200a: Noc2 might involve in musk gland development and musk secretion, which need to be verified in future study.
format: application/pdf
format: text/html
creator: Hang Jie
creator: Zhongxian Xu
creator: Jian Gao
creator: Feng Li
creator: Yinglian Chen
creator: Dejun Zeng
creator: Guijun Zhao
creator: Diyan Li
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.12710
publisher: PeerJ Inc.
rights: © 2021 Jie et al.
abstract: Background The formation of musk is a complex biophysical and biochemical process that change with the rut of male forest musk deer. We have reported that the mating status of male forest musk deer might result to the variations of chemical composition and microbiota of musk and its yields. Critical roles for microRNAs (miRNAs) of multi-tissues were profiled in our previous study; however, the role for miRNAs of the musk gland remains unclear in this species. Methods In this study, we used Illumina deep sequencing technology to sequence the small RNA transcriptome of unmated male (UM) and mated male (UM) of Chinese forest musk deer. Results We identified 1,652 known miRNAs and 45 novel miRNAs, of which there were 174 differentially expressed miRNAs between UM and MM. chi-miR-21-5p, ipu-miR-99b and bta-miR-26a were up-regulated in UM among the 10 most differentially expressed miRNAs. Functional enrichment of the target genes showed that monosaccharide biosynthetic process, protein targeting, cellular protein catabolic process enriched higher in MM. Meanwhile, structural molecule activity, secretion by cell, regulated exocytosis and circulatory system process enriched more in UM, hinting that the formation of musk in UM was mediated by target genes related to exocytosis. The miRNA-mRNA pairs such as miR-21: CHD7, miR143: HSD17B7, miR-141/200a: Noc2 might involve in musk gland development and musk secretion, which need to be verified in future study.
bibliographic citation: Jie et al. (2021) Differential expression profiles of microRNAs in musk gland of unmated and mated forest musk deer (Moschus berezovskii). PeerJ 9:e12710 https://doi.org/10.7717/peerj.12710
date submitted: 2021-07-27
date accepted: 2021-12-08
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jie
  given name: Hang
author list: Agent
  family name: Xu
  given name: Zhongxian
author list: Agent
  family name: Gao
  given name: Jian
author list: Agent
  family name: Li
  given name: Feng
author list: Agent
  family name: Chen
  given name: Yinglian
author list: Agent
  family name: Zeng
  given name: Dejun
author list: Agent
  family name: Zhao
  given name: Guijun
author list: Agent
  family name: Li
  given name: Diyan
doi: 10.7717/peerj.12710
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Jie et al.
attribution name: Jie et al.

Electroencephalogram-derived pain index for evaluating pain during labor
type: item
type: AcademicArticle
description: Background The discriminative ability of a point-of-care electroencephalogram (EEG)-derived pain index (Pi) for objectively assessing pain has been validated in chronic pain patients. The current study aimed to determine its feasibility in assessing labor pain in an obstetric setting. Methods Parturients were enrolled from the delivery room at the department of obstetrics in a tertiary hospital between February and June of 2018. Pi values and relevant numerical rating scale (NRS) scores were collected at different stages of labor in the presence or absence of epidural analgesia. The correlation between Pi values and NRS scores was analyzed using the Pearson correlation analysis. The receiver operating characteristic (ROC) curve was plotted to estimate the discriminative capability of Pi to detect labor pain in parturients. Results Eighty paturients were eligible for inclusion. The Pearson correlation analysis exhibited a positive correlation between Pi values and NRS scores in parturients (r = 0.768, P < 0.001). The ROC analysis revealed a cut-off Pi value of 18.37 to discriminate between mild and moderate-to-severe labor pain in parturients. Further analysis indicated that Pi values had the best diagnostic accuracy reflected by the highest area under the curve (AUC) of 0.857, with a sensitivity and specificity of 0.767 and 0.833, respectively, and a Youden index of 0.6. Subgroup analyses further substantiated the correlations between Pi values and NRS scores, especially in parturients with higher pain intensity. Conclusion This study indicates that Pi values derived from EEGs significantly correlate with the NRS scores, and can serve as a way to quantitatively and objectively evaluate labor pain in parturients.
format: application/pdf
format: text/html
creator: Liang Sun
creator: Hong Zhang
creator: Qiaoyu Han
creator: Yi Feng
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.12714
publisher: PeerJ Inc.
rights: © 2021 Sun et al.
abstract: Background The discriminative ability of a point-of-care electroencephalogram (EEG)-derived pain index (Pi) for objectively assessing pain has been validated in chronic pain patients. The current study aimed to determine its feasibility in assessing labor pain in an obstetric setting. Methods Parturients were enrolled from the delivery room at the department of obstetrics in a tertiary hospital between February and June of 2018. Pi values and relevant numerical rating scale (NRS) scores were collected at different stages of labor in the presence or absence of epidural analgesia. The correlation between Pi values and NRS scores was analyzed using the Pearson correlation analysis. The receiver operating characteristic (ROC) curve was plotted to estimate the discriminative capability of Pi to detect labor pain in parturients. Results Eighty paturients were eligible for inclusion. The Pearson correlation analysis exhibited a positive correlation between Pi values and NRS scores in parturients (r = 0.768, P < 0.001). The ROC analysis revealed a cut-off Pi value of 18.37 to discriminate between mild and moderate-to-severe labor pain in parturients. Further analysis indicated that Pi values had the best diagnostic accuracy reflected by the highest area under the curve (AUC) of 0.857, with a sensitivity and specificity of 0.767 and 0.833, respectively, and a Youden index of 0.6. Subgroup analyses further substantiated the correlations between Pi values and NRS scores, especially in parturients with higher pain intensity. Conclusion This study indicates that Pi values derived from EEGs significantly correlate with the NRS scores, and can serve as a way to quantitatively and objectively evaluate labor pain in parturients.
bibliographic citation: Sun et al. (2021) Electroencephalogram-derived pain index for evaluating pain during labor. PeerJ 9:e12714 https://doi.org/10.7717/peerj.12714
date submitted: 2021-08-24
date accepted: 2021-12-09
issued: 2021-12-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Liang
author list: Agent
  family name: Zhang
  given name: Hong
author list: Agent
  family name: Han
  given name: Qiaoyu
author list: Agent
  family name: Feng
  given name: Yi
doi: 10.7717/peerj.12714
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-22
copyright: ©2021 Sun et al.
attribution name: Sun et al.

Phenotypic differentiation of the slow worm lizards (Squamata: Anguis) across their contact zone in Central Europe
type: item
type: AcademicArticle
description: Background The application of molecular-phylogenetic approaches to taxonomy has had a dramatic effect on our understanding of the diversity of reptiles. These approaches have allowed researchers to reveal previously hidden lineages as well as taxonomic overestimation in morphologically plastic taxa. Slow worms, legless lizards of the genus Anguis (Squamata: Anguidae), were previously considered to comprise either one or two species, and morphology-based intraspecific taxonomy of Anguis fragilis remained controversial throughout the 20th century. After the discovery of deep genetic divergences within the genus, its taxonomy was reconsidered, and as a result, five extant species have been recognized. In order to better understand the patterns of their interspecific differentiation, here we studied phenotypic differences between the two most widespread of them—A. fragilis and A. colchica, and their putative hybrids across the contact zone of both species in Central Europe. Methods We used multivariate and univariate statistics and analyzed ten metric, eleven meristic, and six categorical phenotypic variables in material comprising a total of 326 individuals. We also genotyped individuals from the contact zone for one mitochondrial and two nuclear DNA fragments in order to delineate the distribution of individuals of hybrid and non-hybrid origin. The clines in morphological traits were studied using HZAR. Results We show that the two species are morphologically differentiated. Anguis fragilis has a less robust head, fewer scales covering the body, lower frequency of the external ear opening presence, lower frequency of separated prefrontal scales, higher frequency of prefrontal scales in contact with each other, and body coloration more similar to the juvenile coloration than A. colchica. Slow worms from the contact/hybrid zone are characterized by an intermediate morphology, with more similarities to A. fragilis than to A. colchica. Discussion None of the analyzed char…
format: application/pdf
format: text/html
creator: Norbert Benkovský
creator: Jiří Moravec
creator: Veronika Gvoždíková Javůrková
creator: Helena Šifrová
creator: Václav Gvoždík
creator: David Jandzik
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12482
publisher: PeerJ Inc.
rights: © 2021 Benkovský et al.
abstract: Background The application of molecular-phylogenetic approaches to taxonomy has had a dramatic effect on our understanding of the diversity of reptiles. These approaches have allowed researchers to reveal previously hidden lineages as well as taxonomic overestimation in morphologically plastic taxa. Slow worms, legless lizards of the genus Anguis (Squamata: Anguidae), were previously considered to comprise either one or two species, and morphology-based intraspecific taxonomy of Anguis fragilis remained controversial throughout the 20th century. After the discovery of deep genetic divergences within the genus, its taxonomy was reconsidered, and as a result, five extant species have been recognized. In order to better understand the patterns of their interspecific differentiation, here we studied phenotypic differences between the two most widespread of them—A. fragilis and A. colchica, and their putative hybrids across the contact zone of both species in Central Europe. Methods We used multivariate and univariate statistics and analyzed ten metric, eleven meristic, and six categorical phenotypic variables in material comprising a total of 326 individuals. We also genotyped individuals from the contact zone for one mitochondrial and two nuclear DNA fragments in order to delineate the distribution of individuals of hybrid and non-hybrid origin. The clines in morphological traits were studied using HZAR. Results We show that the two species are morphologically differentiated. Anguis fragilis has a less robust head, fewer scales covering the body, lower frequency of the external ear opening presence, lower frequency of separated prefrontal scales, higher frequency of prefrontal scales in contact with each other, and body coloration more similar to the juvenile coloration than A. colchica. Slow worms from the contact/hybrid zone are characterized by an intermediate morphology, with more similarities to A. fragilis than to A. colchica. Discussion None of the analyzed char…
bibliographic citation: Benkovský et al. (2021) Phenotypic differentiation of the slow worm lizards (Squamata: Anguis) across their contact zone in Central Europe. PeerJ 9:e12482 https://doi.org/10.7717/peerj.12482
date submitted: 2021-03-01
date accepted: 2021-10-21
issued: 2021-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Benkovský
  given name: Norbert
author list: Agent
  family name: Moravec
  given name: Jiří
author list: Agent
  family name: Gvoždíková Javůrková
  given name: Veronika
author list: Agent
  family name: Šifrová
  given name: Helena
author list: Agent
  family name: Gvoždík
  given name: Václav
author list: Agent
  family name: Jandzik
  given name: David
doi: 10.7717/peerj.12482
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-21
copyright: ©2021 Benkovský et al.
attribution name: Benkovský et al.

Interoceptive awareness and beliefs about health and the body as predictors of the intensity of emotions experienced at the beginning of the pandemic
type: item
type: AcademicArticle
description: Background The COVID-19 pandemic is a type of stressful event which might have an impact on psychological state. A prolonged threat of getting a serious, contagious illness is expected to be associated with an increase of negative emotions and, conversely, with a decrease of positive emotions. As the stressor is strongly linked to health and the body, we decided to investigate what types of factors related to body perception and appraisal are associated with different types of reported emotions. The purpose of the study was to verify the associations between three types of variables: interoceptive awareness as described by Mehling and colleagues (2012a, 2018), negative beliefs about health and body, and different types of emotions. Methodology A Multidimensional Assessment of Interoceptive Awareness questionnaire was applied to evaluate interoceptive awareness. The declared emotional state was diagnosed with a list of 20 emotions–divided by valence and origin. Additionally, a list of 10 negative beliefs about health and body was used. The study was held in a correlational schema with 299 subjects recruited via the social media platform Facebook who took part in an online survey. Results The study revealed that the scales of Self-Regulation and Trusting are primarily associated with negative automatic and reflective emotions and positive automatic emotions. Furthermore, the Self-Regulation, Trusting dimensions of interoceptive awareness predict an intensity of emotions categorised on the basis of valence and origin. In addition, negative beliefs about health and the body provided an adequate explanation of the variance of most of the types of emotions experienced during the pandemic. Conclusions Factors related to body perception, such as interoceptive awareness and negative beliefs about health and body provide a significant contribution to explaining emotional state at the beginning of the pandemic.
format: application/pdf
format: text/html
creator: Aleksandra Modzelewska
creator: Kamil K. Imbir
subject: Psychiatry and Psychology
subject: Public Health
subject: Science and Medical Education
subject: Mental Health
description: doi:10.7717/peerj.12542
publisher: PeerJ Inc.
rights: © 2021 Modzelewska and Imbir
abstract: Background The COVID-19 pandemic is a type of stressful event which might have an impact on psychological state. A prolonged threat of getting a serious, contagious illness is expected to be associated with an increase of negative emotions and, conversely, with a decrease of positive emotions. As the stressor is strongly linked to health and the body, we decided to investigate what types of factors related to body perception and appraisal are associated with different types of reported emotions. The purpose of the study was to verify the associations between three types of variables: interoceptive awareness as described by Mehling and colleagues (2012a, 2018), negative beliefs about health and body, and different types of emotions. Methodology A Multidimensional Assessment of Interoceptive Awareness questionnaire was applied to evaluate interoceptive awareness. The declared emotional state was diagnosed with a list of 20 emotions–divided by valence and origin. Additionally, a list of 10 negative beliefs about health and body was used. The study was held in a correlational schema with 299 subjects recruited via the social media platform Facebook who took part in an online survey. Results The study revealed that the scales of Self-Regulation and Trusting are primarily associated with negative automatic and reflective emotions and positive automatic emotions. Furthermore, the Self-Regulation, Trusting dimensions of interoceptive awareness predict an intensity of emotions categorised on the basis of valence and origin. In addition, negative beliefs about health and the body provided an adequate explanation of the variance of most of the types of emotions experienced during the pandemic. Conclusions Factors related to body perception, such as interoceptive awareness and negative beliefs about health and body provide a significant contribution to explaining emotional state at the beginning of the pandemic.
bibliographic citation: Modzelewska et al. (2021) Interoceptive awareness and beliefs about health and the body as predictors of the intensity of emotions experienced at the beginning of the pandemic. PeerJ 9:e12542 https://doi.org/10.7717/peerj.12542
date submitted: 2020-12-30
date accepted: 2021-11-04
issued: 2021-12-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Modzelewska
  given name: Aleksandra
author list: Agent
  family name: Imbir
  given name: Kamil K.
doi: 10.7717/peerj.12542
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-21
copyright: © 2021 Modzelewska and Imbir
attribution name: Modzelewska and Imbir

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