PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Dynamic visual attention characteristics and their relationship to match performance in skilled basketball players
items: Exploring the classification of cancer cell lines from multiple omic views
items: Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia
items: New records of a lost species and a geographic range expansion for sengis in the Horn of Africa
items: Transcriptomic analysis reveals ethylene signal transduction genes involved in pistil development of pumpkin
items: Behavioural variability among captive African elephants in the use of the trunk while feeding
items: The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing
items: Fan worms (Annelida: Sabellidae) from Indonesia collected by the Snellius II Expedition (1984) with descriptions of three new species and tube microstructure
items: Transcriptome analysis provides a blueprint of coral egg and sperm functions
items: Gender-specific associations between apolipoprotein A1 and arterial stiffness in patients with nonalcoholic fatty liver disease

Dynamic visual attention characteristics and their relationship to match performance in skilled basketball players
type: item
type: AcademicArticle
description: Background Dynamic visual attention is important in basketball because it may affect the performance of players and thus the match outcome. The goals of this study were to investigate the difference in dynamic visual attention characteristics between highly skilled basketball players and nonathletic college students and to explore the relationship between visual attention and game-related performance among the basketball players. Methods In total, 24 highly skilled basketball players and 24 nonathletic college students participated in a multiple object tracking task. The task was conducted so that either the number of targets that were visually tracked or the speed at which a given number of tracked targets moved was altered to examine the difference in dynamic visual attention characteristics between the basketball players and nonathletic college students. The relationship between visual tracking speed (VTS) and game-related statistics, including assists, steals, mistakes, fouls and points scored recorded for every match during the season, was assessed among the basketball players by using Pearson correlations. Results A significant main effect of target tracking load was observed (P < 0.001), with visual tracking performance significantly decreased as target number increased. In addition, the speed at which the targets moved had a significant effect on visual tracking performance (P < 0.001), with tracking performance significantly decreased as target speed increased. However, no significant difference was observed in the abilities of basketball players and nonathletic college students to simultaneously track up to six targets. By contrast, a significant interaction between group and target speed was found (P < 0.001), with the visual tracking accuracy of basketball players significantly greater than that of college students at the higher target speeds examined (P < 0.001). Among basketball players, there were positive, large, and statistically significant correla…
format: application/pdf
format: text/html
creator: Peng Jin
creator: Xiawen Li
creator: Bin Ma
creator: Hongbo Guo
creator: Zhongxi Zhang
creator: Lijuan Mao
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9803
publisher: PeerJ Inc.
rights: © 2020 Jin et al.
abstract: Background Dynamic visual attention is important in basketball because it may affect the performance of players and thus the match outcome. The goals of this study were to investigate the difference in dynamic visual attention characteristics between highly skilled basketball players and nonathletic college students and to explore the relationship between visual attention and game-related performance among the basketball players. Methods In total, 24 highly skilled basketball players and 24 nonathletic college students participated in a multiple object tracking task. The task was conducted so that either the number of targets that were visually tracked or the speed at which a given number of tracked targets moved was altered to examine the difference in dynamic visual attention characteristics between the basketball players and nonathletic college students. The relationship between visual tracking speed (VTS) and game-related statistics, including assists, steals, mistakes, fouls and points scored recorded for every match during the season, was assessed among the basketball players by using Pearson correlations. Results A significant main effect of target tracking load was observed (P < 0.001), with visual tracking performance significantly decreased as target number increased. In addition, the speed at which the targets moved had a significant effect on visual tracking performance (P < 0.001), with tracking performance significantly decreased as target speed increased. However, no significant difference was observed in the abilities of basketball players and nonathletic college students to simultaneously track up to six targets. By contrast, a significant interaction between group and target speed was found (P < 0.001), with the visual tracking accuracy of basketball players significantly greater than that of college students at the higher target speeds examined (P < 0.001). Among basketball players, there were positive, large, and statistically significant correla…
bibliographic citation: Jin et al. (2020) Dynamic visual attention characteristics and their relationship to match performance in skilled basketball players. PeerJ 8:e9803 https://doi.org/10.7717/peerj.9803
date submitted: 2020-01-20
date accepted: 2020-08-03
issued: 2020-08-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Peng
author list: Agent
  family name: Li
  given name: Xiawen
author list: Agent
  family name: Ma
  given name: Bin
author list: Agent
  family name: Guo
  given name: Hongbo
author list: Agent
  family name: Zhang
  given name: Zhongxi
author list: Agent
  family name: Mao
  given name: Lijuan
doi: 10.7717/peerj.9803
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-19
copyright: © 2020 Jin et al.
attribution name: Jin et al.

Exploring the classification of cancer cell lines from multiple omic views
type: item
type: AcademicArticle
description: Background Cancer classification is of great importance to understanding its pathogenesis, making diagnosis and developing treatment. The accumulation of extensive omics data of abundant cancer cell line provide basis for large scale classification of cancer with low cost. However, the reliability of cell lines as in vitro models of cancer has been controversial. Methods In this study, we explore the classification on pan-cancer cell line with single and integrated multiple omics data from the Cancer Cell Line Encyclopedia (CCLE) database. The representative omics data of cancer, mRNA data, miRNA data, copy number variation data, DNA methylation data and reverse-phase protein array data were taken into the analysis. TumorMap web tool was used to illustrate the landscape of molecular classification.The molecular classification of patient samples was compared with cancer cell lines. Results Eighteen molecular clusters were identified using integrated multiple omics clustering. Three pan-cancer clusters were found in integrated multiple omics clustering. By comparing with single omics clustering, we found that integrated clustering could capture both shared and complementary information from each omics data. Omics contribution analysis for clustering indicated that, although all the five omics data were of value, mRNA and proteomics data were particular important. While the classifications were generally consistent, samples from cancer patients were more diverse than cancer cell lines. Conclusions The clustering analysis based on integrated omics data provides a novel multi-dimensional map of cancer cell lines that can reflect the extent to pan-cancer cell lines represent primary tumors, and an approach to evaluate the importance of omic features in cancer classification.
format: application/pdf
format: text/html
creator: Xiaoxi Yang
creator: Yuqi Wen
creator: Xinyu Song
creator: Song He
creator: Xiaochen Bo
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.9440
publisher: PeerJ Inc.
rights: © 2020 Yang et al.
abstract: Background Cancer classification is of great importance to understanding its pathogenesis, making diagnosis and developing treatment. The accumulation of extensive omics data of abundant cancer cell line provide basis for large scale classification of cancer with low cost. However, the reliability of cell lines as in vitro models of cancer has been controversial. Methods In this study, we explore the classification on pan-cancer cell line with single and integrated multiple omics data from the Cancer Cell Line Encyclopedia (CCLE) database. The representative omics data of cancer, mRNA data, miRNA data, copy number variation data, DNA methylation data and reverse-phase protein array data were taken into the analysis. TumorMap web tool was used to illustrate the landscape of molecular classification.The molecular classification of patient samples was compared with cancer cell lines. Results Eighteen molecular clusters were identified using integrated multiple omics clustering. Three pan-cancer clusters were found in integrated multiple omics clustering. By comparing with single omics clustering, we found that integrated clustering could capture both shared and complementary information from each omics data. Omics contribution analysis for clustering indicated that, although all the five omics data were of value, mRNA and proteomics data were particular important. While the classifications were generally consistent, samples from cancer patients were more diverse than cancer cell lines. Conclusions The clustering analysis based on integrated omics data provides a novel multi-dimensional map of cancer cell lines that can reflect the extent to pan-cancer cell lines represent primary tumors, and an approach to evaluate the importance of omic features in cancer classification.
bibliographic citation: Yang et al. (2020) Exploring the classification of cancer cell lines from multiple omic views. PeerJ 8:e9440 https://doi.org/10.7717/peerj.9440
date submitted: 2019-12-02
date accepted: 2020-06-08
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Xiaoxi
author list: Agent
  family name: Wen
  given name: Yuqi
author list: Agent
  family name: Song
  given name: Xinyu
author list: Agent
  family name: He
  given name: Song
author list: Agent
  family name: Bo
  given name: Xiaochen
doi: 10.7717/peerj.9440
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: ©2020 Yang et al.
attribution name: Yang et al.

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia
type: item
type: AcademicArticle
description: Background European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors. Methods We analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms. Results We identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.
format: application/pdf
format: text/html
creator: Somasundhari Shanmuganandam
creator: Yiheng Hu
creator: Tanja Strive
creator: Benjamin Schwessinger
creator: Robyn N. Hall
subject: Ecology
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.9564
publisher: PeerJ Inc.
rights: © 2020 Shanmuganandam et al.
abstract: Background European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors. Methods We analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms. Results We identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.
bibliographic citation: Shanmuganandam et al. (2020) Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia. PeerJ 8:e9564 https://doi.org/10.7717/peerj.9564
date submitted: 2020-04-16
date accepted: 2020-06-26
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shanmuganandam
  given name: Somasundhari
author list: Agent
  family name: Hu
  given name: Yiheng
author list: Agent
  family name: Strive
  given name: Tanja
author list: Agent
  family name: Schwessinger
  given name: Benjamin
author list: Agent
  family name: Hall
  given name: Robyn N.
doi: 10.7717/peerj.9564
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: © 2020 Shanmuganandam et al.
attribution name: Shanmuganandam et al.

New records of a lost species and a geographic range expansion for sengis in the Horn of Africa
type: item
type: AcademicArticle
description: The Somali Sengi or Somali Elephant-shrew (‘Elephantulus’ revoilii, Macroscelidea, Mammalia) has been considered a “lost species” and is primarily known from about 39 museum specimens, with no new vouchered occurrence records since the early 1970s. The scientific literature contains no data concerning living Somali Sengi individuals and the species’ current Data Deficient conservation status is attributable to an absence of modern information. Almost everything that has been published about the species is derived from anatomical examinations of historic specimens, gleaned from museum collection notes, or inferred from the known habits and ecology of other sengi taxa. Here we report new evidence that the Somali Sengi is currently extant. These data include voucher specimens, georeferenced occurrence localities, body measurements, habitat parameters, and DNA sequences. While the species is historically documented as endemic to Somalia, these new records are from the neighboring Republic of Djibouti and thus expand the Somali Sengi’s known range in the Horn of Africa. Furthermore, Djiboutian locality data near international borders suggests that the Somali Sengi is also a current inhabitant of both Somalia and Ethiopia. Criteria that inform conservation status assessments (e.g., suitable habitat contiguity and occurrence in wildlife protected areas) can be positively characterized in Djibouti and therefore bode well for the survival of the Somali Sengi species. New data also inform previously undocumented substrate and sheltering affiliations. DNA analyses indicate that the Somali Sengi is a descendant of the Macroscelidini lineage and therefore reveal that the species’ referral to the genus Elephantulus is incompatible with sengi phylogeny. This taxonomic issue is resolved by recognizing a new genus replacement and recombinant binomial that redesignates the Somali Sengi as Galegeeska revoilii (gen. nov., nov. comb). An analysis of ancestral biogeography suggests that …
format: application/pdf
format: text/html
creator: Steven Heritage
creator: Houssein Rayaleh
creator: Djama G. Awaleh
creator: Galen B. Rathbun
subject: Biogeography
subject: Conservation Biology
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9652
publisher: PeerJ Inc.
rights: © 2020 Heritage et al.
abstract: The Somali Sengi or Somali Elephant-shrew (‘Elephantulus’ revoilii, Macroscelidea, Mammalia) has been considered a “lost species” and is primarily known from about 39 museum specimens, with no new vouchered occurrence records since the early 1970s. The scientific literature contains no data concerning living Somali Sengi individuals and the species’ current Data Deficient conservation status is attributable to an absence of modern information. Almost everything that has been published about the species is derived from anatomical examinations of historic specimens, gleaned from museum collection notes, or inferred from the known habits and ecology of other sengi taxa. Here we report new evidence that the Somali Sengi is currently extant. These data include voucher specimens, georeferenced occurrence localities, body measurements, habitat parameters, and DNA sequences. While the species is historically documented as endemic to Somalia, these new records are from the neighboring Republic of Djibouti and thus expand the Somali Sengi’s known range in the Horn of Africa. Furthermore, Djiboutian locality data near international borders suggests that the Somali Sengi is also a current inhabitant of both Somalia and Ethiopia. Criteria that inform conservation status assessments (e.g., suitable habitat contiguity and occurrence in wildlife protected areas) can be positively characterized in Djibouti and therefore bode well for the survival of the Somali Sengi species. New data also inform previously undocumented substrate and sheltering affiliations. DNA analyses indicate that the Somali Sengi is a descendant of the Macroscelidini lineage and therefore reveal that the species’ referral to the genus Elephantulus is incompatible with sengi phylogeny. This taxonomic issue is resolved by recognizing a new genus replacement and recombinant binomial that redesignates the Somali Sengi as Galegeeska revoilii (gen. nov., nov. comb). An analysis of ancestral biogeography suggests that …
bibliographic citation: Heritage et al. (2020) New records of a lost species and a geographic range expansion for sengis in the Horn of Africa. PeerJ 8:e9652 https://doi.org/10.7717/peerj.9652
date submitted: 2020-04-29
date accepted: 2020-07-13
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heritage
  given name: Steven
author list: Agent
  family name: Rayaleh
  given name: Houssein
author list: Agent
  family name: Awaleh
  given name: Djama G.
author list: Agent
  family name: Rathbun
  given name: Galen B.
doi: 10.7717/peerj.9652
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: © 2020 Heritage et al.
attribution name: Heritage et al.

Transcriptomic analysis reveals ethylene signal transduction genes involved in pistil development of pumpkin
type: item
type: AcademicArticle
description: Development of female flowers is an important process that directly affects the yield of Cucubits. Little information is available on the sex determination and development of female flowers in pumpkin, a typical monoecious plant. In the present study, we used aborted and normal pistils of pumpkin for RNA-Seq analysis and determined the differentially expressed genes (DEGs) to gain insights into the molecular mechanism underlying pistil development in pumpkin. A total of 3,817 DEGs were identified, among which 1,341 were upregulated and 2,476 were downregulated. The results of transcriptome analysis were confirmed by real-time quantitative RT-PCR. KEGG enrichment analysis showed that the DEGs were significantly enriched in plant hormone signal transduction and phenylpropanoid biosynthesis pathway. Eighty-four DEGs were enriched in the plant hormone signal transduction pathway, which accounted for 12.54% of the significant DEGs, and most of them were annotated as predicted ethylene responsive or insensitive transcription factor genes. Furthermore, the expression levels of four ethylene signal transduction genes in different flower structures (female calyx, pistil, male calyx, stamen, leaf, and ovary) were investigated. The ethyleneresponsive DNA binding factor, ERDBF3, and ethylene responsive transcription factor, ERTF10, showed the highest expression in pistils and the lowest expression in stamens, and their expression levels were 78- and 162-times more than that in stamens, respectively. These results suggest that plant hormone signal transduction genes, especially ethylene signal transduction genes, play an important role in the development of pistils in pumpkin. Our study provides a theoretical basis for further understanding of the mechanism of regulation of ethylene signal transduction genes in pistil development and sex determination in pumpkin.
format: application/pdf
format: text/html
creator: Qingfei Li
creator: Li Zhang
creator: Feifei Pan
creator: Weili Guo
creator: Bihua Chen
creator: Helian Yang
creator: Guangyin Wang
creator: Xinzheng Li
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.9677
publisher: PeerJ Inc.
rights: © 2020 Li et al.
abstract: Development of female flowers is an important process that directly affects the yield of Cucubits. Little information is available on the sex determination and development of female flowers in pumpkin, a typical monoecious plant. In the present study, we used aborted and normal pistils of pumpkin for RNA-Seq analysis and determined the differentially expressed genes (DEGs) to gain insights into the molecular mechanism underlying pistil development in pumpkin. A total of 3,817 DEGs were identified, among which 1,341 were upregulated and 2,476 were downregulated. The results of transcriptome analysis were confirmed by real-time quantitative RT-PCR. KEGG enrichment analysis showed that the DEGs were significantly enriched in plant hormone signal transduction and phenylpropanoid biosynthesis pathway. Eighty-four DEGs were enriched in the plant hormone signal transduction pathway, which accounted for 12.54% of the significant DEGs, and most of them were annotated as predicted ethylene responsive or insensitive transcription factor genes. Furthermore, the expression levels of four ethylene signal transduction genes in different flower structures (female calyx, pistil, male calyx, stamen, leaf, and ovary) were investigated. The ethyleneresponsive DNA binding factor, ERDBF3, and ethylene responsive transcription factor, ERTF10, showed the highest expression in pistils and the lowest expression in stamens, and their expression levels were 78- and 162-times more than that in stamens, respectively. These results suggest that plant hormone signal transduction genes, especially ethylene signal transduction genes, play an important role in the development of pistils in pumpkin. Our study provides a theoretical basis for further understanding of the mechanism of regulation of ethylene signal transduction genes in pistil development and sex determination in pumpkin.
bibliographic citation: Li et al. (2020) Transcriptomic analysis reveals ethylene signal transduction genes involved in pistil development of pumpkin. PeerJ 8:e9677 https://doi.org/10.7717/peerj.9677
date submitted: 2020-01-08
date accepted: 2020-07-16
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qingfei
author list: Agent
  family name: Zhang
  given name: Li
author list: Agent
  family name: Pan
  given name: Feifei
author list: Agent
  family name: Guo
  given name: Weili
author list: Agent
  family name: Chen
  given name: Bihua
author list: Agent
  family name: Yang
  given name: Helian
author list: Agent
  family name: Wang
  given name: Guangyin
author list: Agent
  family name: Li
  given name: Xinzheng
doi: 10.7717/peerj.9677
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: ©2020 Li et al.
attribution name: Li et al.

Behavioural variability among captive African elephants in the use of the trunk while feeding
type: item
type: AcademicArticle
description: The Proboscideans, an order of mammals including elephants, are the largest of the Earth lands animals. One probable consequence of the rapid increase of their body size is the development of the trunk, a multitask highly sensitive organ used in a large repertoire of behaviours. The absence of bones in the trunk allows a substantial degree of freedom for movement in all directions, and this ability could underlie individual-level strategies. We hypothesised a stronger behavioural variability in simple tasks, and a correlation between the employed behaviours and the shape and size of the food. The observations of a captive group of African elephants allowed us to create a complete catalogue of trunk movements in feeding activities. We noted manipulative strategies and impact of food item properties on the performed behaviours. The results show that a given item is manipulated with a small panel of behaviours, and some behaviours are specific to a single shape of items. The study of the five main feeding behaviours emphasises a significant variability between the elephants. Each individual differed from every other individual in the proportion of at least one behaviour, and every behaviour was performed in different proportions by the elephants. Our findings suggest that during their lives elephants develop individual strategies adapted to the manipulated items, which increases their feeding efficiency.
format: application/pdf
format: text/html
creator: Maëlle Lefeuvre
creator: Patrick Gouat
creator: Baptiste Mulot
creator: Raphaël Cornette
creator: Emmanuelle Pouydebat
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.9678
publisher: PeerJ Inc.
rights: © 2020 Lefeuvre et al.
abstract: The Proboscideans, an order of mammals including elephants, are the largest of the Earth lands animals. One probable consequence of the rapid increase of their body size is the development of the trunk, a multitask highly sensitive organ used in a large repertoire of behaviours. The absence of bones in the trunk allows a substantial degree of freedom for movement in all directions, and this ability could underlie individual-level strategies. We hypothesised a stronger behavioural variability in simple tasks, and a correlation between the employed behaviours and the shape and size of the food. The observations of a captive group of African elephants allowed us to create a complete catalogue of trunk movements in feeding activities. We noted manipulative strategies and impact of food item properties on the performed behaviours. The results show that a given item is manipulated with a small panel of behaviours, and some behaviours are specific to a single shape of items. The study of the five main feeding behaviours emphasises a significant variability between the elephants. Each individual differed from every other individual in the proportion of at least one behaviour, and every behaviour was performed in different proportions by the elephants. Our findings suggest that during their lives elephants develop individual strategies adapted to the manipulated items, which increases their feeding efficiency.
bibliographic citation: Lefeuvre et al. (2020) Behavioural variability among captive African elephants in the use of the trunk while feeding. PeerJ 8:e9678 https://doi.org/10.7717/peerj.9678
date submitted: 2020-04-27
date accepted: 2020-07-16
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lefeuvre
  given name: Maëlle
author list: Agent
  family name: Gouat
  given name: Patrick
author list: Agent
  family name: Mulot
  given name: Baptiste
author list: Agent
  family name: Cornette
  given name: Raphaël
author list: Agent
  family name: Pouydebat
  given name: Emmanuelle
doi: 10.7717/peerj.9678
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: © 2020 Lefeuvre et al.
attribution name: Lefeuvre et al.

The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing
type: item
type: AcademicArticle
description: Accurate characterization of the vaginal microbiome remains a fundamental goal of the Human Microbiome project (HMP). For over a decade, this goal has been made possible deploying high-throughput next generation sequencing technologies (NGS), which indeed has revolutionized medical research and enabled large-scale genomic studies. The 16S rRNA marker-gene survey is the most commonly explored approach for vaginal microbial community studies. With this approach, prior studies have elucidated substantial variations in the vaginal microbiome of women from different ethnicities. This review provides a comprehensive account of studies that have deployed this approach to describe the vaginal microbiota of African women in health and disease. On the basis of published data, the few studies reported from the African population are mainly in non-pregnant post pubertal women and calls for more detailed studies in pregnant and postnatal cohorts. We provide insight on the use of more sophisticated cutting-edge technologies in characterizing the vaginal microbiome. These technologies offer high-resolution detection of vaginal microbiome variations and community functional capabilities, which can shed light into several discrepancies observed in the vaginal microbiota of African women in an African population versus women of African descent in the diaspora.
format: application/pdf
format: text/html
creator: Nkechi Martina Odogwu
creator: Oladapo O. Olayemi
creator: Akinyinka O. Omigbodun
subject: Microbiology
subject: Molecular Biology
subject: Gynecology and Obstetrics
subject: Women’s Health
description: doi:10.7717/peerj.9684
publisher: PeerJ Inc.
rights: © 2020 Odogwu et al.
abstract: Accurate characterization of the vaginal microbiome remains a fundamental goal of the Human Microbiome project (HMP). For over a decade, this goal has been made possible deploying high-throughput next generation sequencing technologies (NGS), which indeed has revolutionized medical research and enabled large-scale genomic studies. The 16S rRNA marker-gene survey is the most commonly explored approach for vaginal microbial community studies. With this approach, prior studies have elucidated substantial variations in the vaginal microbiome of women from different ethnicities. This review provides a comprehensive account of studies that have deployed this approach to describe the vaginal microbiota of African women in health and disease. On the basis of published data, the few studies reported from the African population are mainly in non-pregnant post pubertal women and calls for more detailed studies in pregnant and postnatal cohorts. We provide insight on the use of more sophisticated cutting-edge technologies in characterizing the vaginal microbiome. These technologies offer high-resolution detection of vaginal microbiome variations and community functional capabilities, which can shed light into several discrepancies observed in the vaginal microbiota of African women in an African population versus women of African descent in the diaspora.
bibliographic citation: Odogwu et al. (2020) The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing. PeerJ 8:e9684 https://doi.org/10.7717/peerj.9684
date submitted: 2020-03-05
date accepted: 2020-07-18
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Odogwu
  given name: Nkechi Martina
author list: Agent
  family name: Olayemi
  given name: Oladapo O.
author list: Agent
  family name: Omigbodun
  given name: Akinyinka O.
doi: 10.7717/peerj.9684
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: ©2020 Odogwu et al.
attribution name: Odogwu et al.

Fan worms (Annelida: Sabellidae) from Indonesia collected by the Snellius II Expedition (1984) with descriptions of three new species and tube microstructure
type: item
type: AcademicArticle
description: The Indonesian archipelago is one of the most diverse regions in the marine World. Many contributions on polychaete worms have been published since the Dutch Siboga Expedition to the Indonesian archipelago at the end of the 19th century. In this study, we examined specimens of Sabellidae Latreille, 1825 collected during the Snellius II Expedition (1984) to Indonesia, carried out by the Dutch Research Vessel (RV) “Tyro” and the Indonesian RV “Samudera”. The results include reports of Acromegalomma acrophthalmos, A. interruptum, A. sp., Bispira manicata, B. porifera, B. secusoluta, Branchiomma boholense, Notaulax pyrrohogaster, N. tenuitorques, N. sp. 3, Parasabella crassichaetae, Perkinsiana anodina, and Sabellastarte spectabilis. In addition, three new species are described: Acromegalomma sumbense sp. nov., Claviramus olivager sp. nov., and Notaulax montiporicola sp. nov., the latter in living coral (Montipora nodosa). Further, Sabella (Potamilla) polyophthalmos Grube is transferred to Pseudopotamilla. Additional histological accounts of B. porifera and tube microstructure of A. acrophthalmos, B. porifera, P. anodina, Pseudopotamilla polyophthalmos and Sabellastarte spectabilis are also included.
format: application/pdf
format: text/html
creator: María Ana Tovar-Hernández
creator: Harry A. ten Hove
creator: Olev Vinn
creator: Michał Zatoń
creator: Jesús Angel de León-González
creator: María Elena García-Garza
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9692
publisher: PeerJ Inc.
rights: © 2020 Tovar-Hernández et al.
abstract: The Indonesian archipelago is one of the most diverse regions in the marine World. Many contributions on polychaete worms have been published since the Dutch Siboga Expedition to the Indonesian archipelago at the end of the 19th century. In this study, we examined specimens of Sabellidae Latreille, 1825 collected during the Snellius II Expedition (1984) to Indonesia, carried out by the Dutch Research Vessel (RV) “Tyro” and the Indonesian RV “Samudera”. The results include reports of Acromegalomma acrophthalmos, A. interruptum, A. sp., Bispira manicata, B. porifera, B. secusoluta, Branchiomma boholense, Notaulax pyrrohogaster, N. tenuitorques, N. sp. 3, Parasabella crassichaetae, Perkinsiana anodina, and Sabellastarte spectabilis. In addition, three new species are described: Acromegalomma sumbense sp. nov., Claviramus olivager sp. nov., and Notaulax montiporicola sp. nov., the latter in living coral (Montipora nodosa). Further, Sabella (Potamilla) polyophthalmos Grube is transferred to Pseudopotamilla. Additional histological accounts of B. porifera and tube microstructure of A. acrophthalmos, B. porifera, P. anodina, Pseudopotamilla polyophthalmos and Sabellastarte spectabilis are also included.
bibliographic citation: Tovar-Hernández et al. (2020) Fan worms (Annelida: Sabellidae) from Indonesia collected by the Snellius II Expedition (1984) with descriptions of three new species and tube microstructure. PeerJ 8:e9692 https://doi.org/10.7717/peerj.9692
date submitted: 2020-04-28
date accepted: 2020-07-20
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tovar-Hernández
  given name: María Ana
author list: Agent
  family name: ten Hove
  given name: Harry A.
author list: Agent
  family name: Vinn
  given name: Olev
author list: Agent
  family name: Zatoń
  given name: Michał
author list: Agent
  family name: de León-González
  given name: Jesús Angel
author list: Agent
  family name: García-Garza
  given name: María Elena
doi: 10.7717/peerj.9692
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: © 2020 Tovar-Hernández et al.
attribution name: Tovar-Hernández et al.

Transcriptome analysis provides a blueprint of coral egg and sperm functions
type: item
type: AcademicArticle
description: Background Reproductive biology and the evolutionary constraints acting on dispersal stages are poorly understood in many stony coral species. A key piece of missing information is egg and sperm gene expression. This is critical for broadcast spawning corals, such as our model, the Hawaiian species Montipora capitata, because eggs and sperm are exposed to environmental stressors during dispersal. Furthermore, parental effects such as transcriptome investment may provide a means for cross- or trans-generational plasticity and be apparent in egg and sperm transcriptome data. Methods Here, we analyzed M. capitata egg and sperm transcriptomic data to address three questions: (1) Which pathways and functions are actively transcribed in these gametes? (2) How does sperm and egg gene expression differ from adult tissues? (3) Does gene expression differ between these gametes? Results We show that egg and sperm display surprisingly similar levels of gene expression and overlapping functional enrichment patterns. These results may reflect similar environmental constraints faced by these motile gametes. We find significant differences in differential expression of egg vs. adult and sperm vs. adult RNA-seq data, in contrast to very few examples of differential expression when comparing egg vs. sperm transcriptomes. Lastly, using gene ontology and KEGG orthology data we show that both egg and sperm have markedly repressed transcription and translation machinery compared to the adult, suggesting a dependence on parental transcripts. We speculate that cell motility and calcium ion binding genes may be involved in gamete to gamete recognition in the water column and thus, fertilization.
format: application/pdf
format: text/html
creator: Julia Van Etten
creator: Alexander Shumaker
creator: Tali Mass
creator: Hollie M. Putnam
creator: Debashish Bhattacharya
subject: Evolutionary Studies
subject: Genomics
subject: Marine Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.9739
publisher: PeerJ Inc.
rights: © 2020 Van Etten et al.
abstract: Background Reproductive biology and the evolutionary constraints acting on dispersal stages are poorly understood in many stony coral species. A key piece of missing information is egg and sperm gene expression. This is critical for broadcast spawning corals, such as our model, the Hawaiian species Montipora capitata, because eggs and sperm are exposed to environmental stressors during dispersal. Furthermore, parental effects such as transcriptome investment may provide a means for cross- or trans-generational plasticity and be apparent in egg and sperm transcriptome data. Methods Here, we analyzed M. capitata egg and sperm transcriptomic data to address three questions: (1) Which pathways and functions are actively transcribed in these gametes? (2) How does sperm and egg gene expression differ from adult tissues? (3) Does gene expression differ between these gametes? Results We show that egg and sperm display surprisingly similar levels of gene expression and overlapping functional enrichment patterns. These results may reflect similar environmental constraints faced by these motile gametes. We find significant differences in differential expression of egg vs. adult and sperm vs. adult RNA-seq data, in contrast to very few examples of differential expression when comparing egg vs. sperm transcriptomes. Lastly, using gene ontology and KEGG orthology data we show that both egg and sperm have markedly repressed transcription and translation machinery compared to the adult, suggesting a dependence on parental transcripts. We speculate that cell motility and calcium ion binding genes may be involved in gamete to gamete recognition in the water column and thus, fertilization.
bibliographic citation: Van Etten et al. (2020) Transcriptome analysis provides a blueprint of coral egg and sperm functions. PeerJ 8:e9739 https://doi.org/10.7717/peerj.9739
date submitted: 2020-04-03
date accepted: 2020-07-26
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Van Etten
  given name: Julia
author list: Agent
  family name: Shumaker
  given name: Alexander
author list: Agent
  family name: Mass
  given name: Tali
author list: Agent
  family name: Putnam
  given name: Hollie M.
author list: Agent
  family name: Bhattacharya
  given name: Debashish
doi: 10.7717/peerj.9739
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: ©2020 Van Etten et al.
attribution name: Van Etten et al.

Gender-specific associations between apolipoprotein A1 and arterial stiffness in patients with nonalcoholic fatty liver disease
type: item
type: AcademicArticle
description: Background Lipid metabolism factors may play an important role in the progression of nonalcoholic fatty liver disease (NAFLD) and its related cardiovascular dysfunctions. The study aims to assess whether Apolipoprotein A-1 (ApoA1) was associated with vascular stiffness in NAFLD patients. Methods From 2012 to 2013, we included 2,295 non-alcohol users with fatty liver disease (1,306 male patients) and completely excluded subjects who drank any alcohol ever to eliminate the effect of alcohol intake. The serum ApoA1 levels and the brachial-ankle pulse wave velocity (baPWV) were measured. Results The baPWV in men was much higher than in female patients (1,412.79 cm/s vs. 1,358.69 cm/s, P < 0.001). ApoA1 level was positively associated with baPWV odd ratio (OR), 4.18; 95% confidence interval (CI) [1.16–15.1], P < 0.05) in patients with AST/ALT < 1 and (OR, 4.70; 95% CI [1.36–16.23], P < 0.05) in patients with AST/ALT ≥ 1 respectively. Only arterial stiffness in men was associated with ApoA1 (OR, 3.96; 95% CI [1.29–12.30], P < 0.05) in logistics regression models adjusted for age, gender, body mass index, education attainment, physical activity, smoking, history of hypertension and high-density lipoprotein. The relationship between ApoA1 and baPWV in male NAFLD patients remained significant (confidence, 156.42; 95% CI [49.34–263.50], P < 0.05) in the fully adjusted linear regression model. Conclusion The serum ApoA1 was associated with arterial stiffness in male NAFLD patients. Increased ApoA1 level should be considered as an independent risk factor for arterial stiffness in male NAFLD patients, suggesting that NAFLD may alter arterial stiffness by “ApoA1-related” mechanism in men.
format: application/pdf
format: text/html
creator: Xulong Sun
creator: Ruifang Chen
creator: Guangyu Yan
creator: Zhiheng Chen
creator: Hong Yuan
creator: Wei Huang
creator: Yao Lu
subject: Cardiology
subject: Gastroenterology and Hepatology
subject: Metabolic Sciences
description: doi:10.7717/peerj.9757
publisher: PeerJ Inc.
rights: © 2020 Sun et al.
abstract: Background Lipid metabolism factors may play an important role in the progression of nonalcoholic fatty liver disease (NAFLD) and its related cardiovascular dysfunctions. The study aims to assess whether Apolipoprotein A-1 (ApoA1) was associated with vascular stiffness in NAFLD patients. Methods From 2012 to 2013, we included 2,295 non-alcohol users with fatty liver disease (1,306 male patients) and completely excluded subjects who drank any alcohol ever to eliminate the effect of alcohol intake. The serum ApoA1 levels and the brachial-ankle pulse wave velocity (baPWV) were measured. Results The baPWV in men was much higher than in female patients (1,412.79 cm/s vs. 1,358.69 cm/s, P < 0.001). ApoA1 level was positively associated with baPWV odd ratio (OR), 4.18; 95% confidence interval (CI) [1.16–15.1], P < 0.05) in patients with AST/ALT < 1 and (OR, 4.70; 95% CI [1.36–16.23], P < 0.05) in patients with AST/ALT ≥ 1 respectively. Only arterial stiffness in men was associated with ApoA1 (OR, 3.96; 95% CI [1.29–12.30], P < 0.05) in logistics regression models adjusted for age, gender, body mass index, education attainment, physical activity, smoking, history of hypertension and high-density lipoprotein. The relationship between ApoA1 and baPWV in male NAFLD patients remained significant (confidence, 156.42; 95% CI [49.34–263.50], P < 0.05) in the fully adjusted linear regression model. Conclusion The serum ApoA1 was associated with arterial stiffness in male NAFLD patients. Increased ApoA1 level should be considered as an independent risk factor for arterial stiffness in male NAFLD patients, suggesting that NAFLD may alter arterial stiffness by “ApoA1-related” mechanism in men.
bibliographic citation: Sun et al. (2020) Gender-specific associations between apolipoprotein A1 and arterial stiffness in patients with nonalcoholic fatty liver disease. PeerJ 8:e9757 https://doi.org/10.7717/peerj.9757
date submitted: 2020-04-24
date accepted: 2020-07-28
issued: 2020-08-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xulong
author list: Agent
  family name: Chen
  given name: Ruifang
author list: Agent
  family name: Yan
  given name: Guangyu
author list: Agent
  family name: Chen
  given name: Zhiheng
author list: Agent
  family name: Yuan
  given name: Hong
author list: Agent
  family name: Huang
  given name: Wei
author list: Agent
  family name: Lu
  given name: Yao
doi: 10.7717/peerj.9757
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-18
copyright: © 2020 Sun et al.
attribution name: Sun et al.

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