PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Ontogenetic variation in the diet of the anuran community from a semi-arid environment in the southeastern Chihuahuan Desert
items: Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits
items: Combining simulation modeling and stable isotope analyses to reconstruct the last known movements of one of Nature’s giants
items: The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses
items: Rosiglitazone accelerates wound healing by improving endothelial precursor cell function and angiogenesis in db/db mice
items: Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
items: Relationships between key functional traits of the waterlily Nuphar lutea and wetland nutrient content
items: Differences between medically treated and untreated non-fatal self-harm reported by hotline callers in China
items: A novel form of wasp mimicry in a new species of praying mantis from the Amazon rainforest, Vespamantoida wherleyi gen. nov. sp. nov. (Mantodea, Mantoididae)
items: Identification of key genes and multiple molecular pathways of metastatic process in prostate cancer

Ontogenetic variation in the diet of the anuran community from a semi-arid environment in the southeastern Chihuahuan Desert
type: item
type: AcademicArticle
description: Although ontogeny influences dietary composition and trophic niche breadth in many anurans, its effects on diet have been little analyzed in sympatric species. In this study, we analyzed interspecific and ontogenetic variation in dietary composition and trophic niche width in an anuran community from a semi-arid environment. We found a more profound effect of species identity than body size on dietary composition, with the diet of four species dominated by formicids, that of two others by coleopterans and formicids, and that of the remaining species not dominated by specific prey types. We found ontogenetic changes in dietary composition in three of four species analyzed, in which consumption of some small insects decreased as predator size increased, regardless of species. Additionally, we did not find ontogenetic change in prey number consumed in any of the four species, but prey size increased with increasing predator size in all of them. Most species exhibited a narrow trophic niche, which was even narrower in adults in three of the four species analyzed. Costello’s modified plots revealed a high variation among individuals in termite consumption in Anaxyrus punctatus, and in more prey types in Spea multiplicata. Our results suggest that this community is not size-structured, and that ontogenetic diet shifts are mainly caused by passive sampling toward prey of different sizes. Finally, comparisons with previous data revealed an interpopulation pattern, in which trophic niche width contracts as aridity increases, possibly because of an increase in interspecific competition for trophic resources.
format: application/pdf
format: text/html
creator: Ricardo Luría-Manzano
creator: Aurelio Ramírez-Bautista
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.7908
publisher: PeerJ Inc.
rights: © 2019 Luría-Manzano and Ramírez-Bautista
abstract: Although ontogeny influences dietary composition and trophic niche breadth in many anurans, its effects on diet have been little analyzed in sympatric species. In this study, we analyzed interspecific and ontogenetic variation in dietary composition and trophic niche width in an anuran community from a semi-arid environment. We found a more profound effect of species identity than body size on dietary composition, with the diet of four species dominated by formicids, that of two others by coleopterans and formicids, and that of the remaining species not dominated by specific prey types. We found ontogenetic changes in dietary composition in three of four species analyzed, in which consumption of some small insects decreased as predator size increased, regardless of species. Additionally, we did not find ontogenetic change in prey number consumed in any of the four species, but prey size increased with increasing predator size in all of them. Most species exhibited a narrow trophic niche, which was even narrower in adults in three of the four species analyzed. Costello’s modified plots revealed a high variation among individuals in termite consumption in Anaxyrus punctatus, and in more prey types in Spea multiplicata. Our results suggest that this community is not size-structured, and that ontogenetic diet shifts are mainly caused by passive sampling toward prey of different sizes. Finally, comparisons with previous data revealed an interpopulation pattern, in which trophic niche width contracts as aridity increases, possibly because of an increase in interspecific competition for trophic resources.
bibliographic citation: Luría-Manzano et al. (2019) Ontogenetic variation in the diet of the anuran community from a semi-arid environment in the southeastern Chihuahuan Desert. PeerJ 7:e7908 https://doi.org/10.7717/peerj.7908
date submitted: 2019-04-25
date accepted: 2019-09-17
issued: 2019-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luría-Manzano
  given name: Ricardo
author list: Agent
  family name: Ramírez-Bautista
  given name: Aurelio
doi: 10.7717/peerj.7908
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-18
copyright: © 2019 Luría-Manzano and Ramírez-Bautista
attribution name: Luría-Manzano and Ramírez-Bautista

Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits
type: item
type: AcademicArticle
description: This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P < 0.001) and Lactobacillus (P = 0.043) were increased and Ruminococcaceae UCG-005 (P = 0.012) was increased first and then decreased when the alfalfa particle size decreased, while Lachnospiraceae NK4A136 group (P = 0.016), Ruminococcaceae NK4A214 (P = 0.044), Christensenellaceae R-7 group (P = 0.019), Lachnospiraceae other (Family) (P = 0.011) and Ruminococcaceae UCG-013 (P = 0.021) were decreased. The relative abundance of Methanobrevibacter was increased from 62.48% to 90.40% (P < 0.001), whereas the relative abundance …
format: application/pdf
format: text/html
creator: Mei Yuan
creator: Siqiang Liu
creator: Zhisheng Wang
creator: Lizhi Wang
creator: Bai Xue
creator: Huawei Zou
creator: Gang Tian
creator: Jingyi Cai
creator: Quanhui Peng
subject: Agricultural Science
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.7910
publisher: PeerJ Inc.
rights: © 2019 Yuan et al.
abstract: This work was aimed to investigate the effects of the different particle size of ground alfalfa hay on caecal microbial and archeal communities of rabbits. One hundred-twenty New Zealand rabbits (950.3 ± 8.82 g) were allocated into four treatments, with five replicates in each treatment and six rabbits in each replicate. The particle sizes of the alfalfa meal in the four treatment diets were 2,500, 1,000, 100 and 10 µm respectively, while the other ingredients were ground through a 2.5 mm sieve. High-throughput sequencing technology was applied to examine the differences in bacteria and methanogenic archaea diversity in the caecum of the four treatment groups of rabbits. A total of 745,946 bacterial sequences (a mean of 31,081 ± 13,901 sequences per sample) and 539,227 archaeal sequences (a mean of 22,468 ± 2,443 sequences per sample) were recovered from twenty-four caecal samples, and were clustered into 9,953 and 2,246 OTUs respectively. A total of 26 bacterial phyla with 465 genera and three archaeal phyla with 10 genera were identified after taxonomic summarization. Bioinformatic analyses illustrated that Firmicutes (58.69% ∼ 68.50%) and Bacteroidetes (23.96% ∼ 36.05%) were the two most predominant bacterial phyla and Euryarchaeota (over 99.9%) was the most predominant archaeal phyla in the caecum of all rabbits. At genus level, as the particle size of alfalfa decreased from 2,500 to 10 µm, the relative abundances of Ruminococcaceae UCG-014 (P < 0.001) and Lactobacillus (P = 0.043) were increased and Ruminococcaceae UCG-005 (P = 0.012) was increased first and then decreased when the alfalfa particle size decreased, while Lachnospiraceae NK4A136 group (P = 0.016), Ruminococcaceae NK4A214 (P = 0.044), Christensenellaceae R-7 group (P = 0.019), Lachnospiraceae other (Family) (P = 0.011) and Ruminococcaceae UCG-013 (P = 0.021) were decreased. The relative abundance of Methanobrevibacter was increased from 62.48% to 90.40% (P < 0.001), whereas the relative abundance …
bibliographic citation: Yuan et al. (2019) Effects of particle size of ground alfalfa hay on caecal bacteria and archaea populations of rabbits. PeerJ 7:e7910 https://doi.org/10.7717/peerj.7910
date submitted: 2019-03-04
date accepted: 2019-09-17
issued: 2019-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Mei
author list: Agent
  family name: Liu
  given name: Siqiang
author list: Agent
  family name: Wang
  given name: Zhisheng
author list: Agent
  family name: Wang
  given name: Lizhi
author list: Agent
  family name: Xue
  given name: Bai
author list: Agent
  family name: Zou
  given name: Huawei
author list: Agent
  family name: Tian
  given name: Gang
author list: Agent
  family name: Cai
  given name: Jingyi
author list: Agent
  family name: Peng
  given name: Quanhui
doi: 10.7717/peerj.7910
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-18
copyright: ©2019 Yuan et al.
attribution name: Yuan et al.

Combining simulation modeling and stable isotope analyses to reconstruct the last known movements of one of Nature’s giants
type: item
type: AcademicArticle
description: The spatial ecology of rare, migratory oceanic animals is difficult to study directly. Where incremental tissues are available, their chemical composition can provide valuable indirect observations of movement and diet. Interpreting the chemical record in incremental tissues can be highly uncertain, however, as multiple mechanisms interact to produce the observed data. Simulation modeling is one approach for considering alternative hypotheses in ecology and can be used to consider the relative likelihood of obtaining an observed record under different combinations of ecological and environmental processes. Here we show how a simulation modeling approach can help to infer movement behaviour based on stable carbon isotope profiles measured in incremental baleen tissues of a blue whale (Balaenoptera musculus). The life history of this particular specimen, which stranded in 1891 in the UK, was selected as a case study due to its cultural significance as part of a permanent display at the Natural History Museum, London. We specifically tested whether measured variations in stable isotope compositions across the analysed baleen plate were more consistent with residency or latitudinal migrations. The measured isotopic record was most closely reproduced with a period of residency in sub-tropical waters for at least a full year followed by three repeated annual migrations between sub-tropical and high latitude regions. The latitudinal migration cycle was interrupted in the year prior to stranding, potentially implying pregnancy and weaning, but isotopic data alone cannot test this hypothesis. Simulation methods can help reveal movement information coded in the biochemical compositions of incremental tissues such as those archived in historic collections, and provides context and inferences that are useful for retrospective studies of animal movement, especially where other sources of individual movement data are sparse or challenging to validate.
format: application/pdf
format: text/html
creator: Clive N. Trueman
creator: Andrew L. Jackson
creator: Katharyn S. Chadwick
creator: Ellen J. Coombs
creator: Laura J. Feyrer
creator: Sarah Magozzi
creator: Richard C. Sabin
creator: Natalie Cooper
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.7912
publisher: PeerJ Inc.
rights: © 2019 Trueman et al.
abstract: The spatial ecology of rare, migratory oceanic animals is difficult to study directly. Where incremental tissues are available, their chemical composition can provide valuable indirect observations of movement and diet. Interpreting the chemical record in incremental tissues can be highly uncertain, however, as multiple mechanisms interact to produce the observed data. Simulation modeling is one approach for considering alternative hypotheses in ecology and can be used to consider the relative likelihood of obtaining an observed record under different combinations of ecological and environmental processes. Here we show how a simulation modeling approach can help to infer movement behaviour based on stable carbon isotope profiles measured in incremental baleen tissues of a blue whale (Balaenoptera musculus). The life history of this particular specimen, which stranded in 1891 in the UK, was selected as a case study due to its cultural significance as part of a permanent display at the Natural History Museum, London. We specifically tested whether measured variations in stable isotope compositions across the analysed baleen plate were more consistent with residency or latitudinal migrations. The measured isotopic record was most closely reproduced with a period of residency in sub-tropical waters for at least a full year followed by three repeated annual migrations between sub-tropical and high latitude regions. The latitudinal migration cycle was interrupted in the year prior to stranding, potentially implying pregnancy and weaning, but isotopic data alone cannot test this hypothesis. Simulation methods can help reveal movement information coded in the biochemical compositions of incremental tissues such as those archived in historic collections, and provides context and inferences that are useful for retrospective studies of animal movement, especially where other sources of individual movement data are sparse or challenging to validate.
bibliographic citation: Trueman et al. (2019) Combining simulation modeling and stable isotope analyses to reconstruct the last known movements of one of Nature’s giants. PeerJ 7:e7912 https://doi.org/10.7717/peerj.7912
date submitted: 2019-02-18
date accepted: 2019-09-17
issued: 2019-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trueman
  given name: Clive N.
author list: Agent
  family name: Jackson
  given name: Andrew L.
author list: Agent
  family name: Chadwick
  given name: Katharyn S.
author list: Agent
  family name: Coombs
  given name: Ellen J.
author list: Agent
  family name: Feyrer
  given name: Laura J.
author list: Agent
  family name: Magozzi
  given name: Sarah
author list: Agent
  family name: Sabin
  given name: Richard C.
author list: Agent
  family name: Cooper
  given name: Natalie
doi: 10.7717/peerj.7912
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-18
copyright: ©2019 Trueman et al.
attribution name: Trueman et al.

The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses
type: item
type: AcademicArticle
description: Background Desmostylia is a clade of extinct aquatic mammals with no living members. Today, this clade is considered belonging to either Afrotheria or Perissodactyla. In the currently-accepted taxonomic scheme, Desmostylia includes two families, 10 to 12 genera, and 13–14 species. There have been relatively few phylogenetic analyses published on desmostylian interrelationship compared to other vertebrate taxa, and two main, alternative phylogenetic hypotheses have been proposed in previous studies. One major problem with those previous studies is that the numbers of characters and OTUs were small. Methods In this study, we analyzed the phylogenetic interrelationship of Desmostylia based on a new data matrix that includes larger numbers of characters and taxa than in any previous studies. The new data matrix was compiled mainly based on data matrices of previous studies and included three outgroups and 13 desmostylian ingroup taxa. Analyses were carried out using five kinds of parsimonious methods. Results Strict consensus trees of the most parsimonious topologies obtained in all analyses supported the monophyly of Desmostylidae and paraphyly of traditional Paleoparadoxiidae. Based on these results, we propose phylogenetic definitions of the clades Desmostylidae and Paleoparadoxiidae based on common ancestry.
format: application/pdf
format: text/html
creator: Kumiko Matsui
creator: Takanobu Tsuihiji
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.7430
publisher: PeerJ Inc.
rights: © 2019 Matsui and Tsuihiji
abstract: Background Desmostylia is a clade of extinct aquatic mammals with no living members. Today, this clade is considered belonging to either Afrotheria or Perissodactyla. In the currently-accepted taxonomic scheme, Desmostylia includes two families, 10 to 12 genera, and 13–14 species. There have been relatively few phylogenetic analyses published on desmostylian interrelationship compared to other vertebrate taxa, and two main, alternative phylogenetic hypotheses have been proposed in previous studies. One major problem with those previous studies is that the numbers of characters and OTUs were small. Methods In this study, we analyzed the phylogenetic interrelationship of Desmostylia based on a new data matrix that includes larger numbers of characters and taxa than in any previous studies. The new data matrix was compiled mainly based on data matrices of previous studies and included three outgroups and 13 desmostylian ingroup taxa. Analyses were carried out using five kinds of parsimonious methods. Results Strict consensus trees of the most parsimonious topologies obtained in all analyses supported the monophyly of Desmostylidae and paraphyly of traditional Paleoparadoxiidae. Based on these results, we propose phylogenetic definitions of the clades Desmostylidae and Paleoparadoxiidae based on common ancestry.
bibliographic citation: Matsui et al. (2019) The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses. PeerJ 7:e7430 https://doi.org/10.7717/peerj.7430
date submitted: 2019-01-14
date accepted: 2019-07-07
issued: 2019-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matsui
  given name: Kumiko
author list: Agent
  family name: Tsuihiji
  given name: Takanobu
doi: 10.7717/peerj.7430
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-17
copyright: ©2019 Matsui and Tsuihiji
attribution name: Matsui and Tsuihiji

Rosiglitazone accelerates wound healing by improving endothelial precursor cell function and angiogenesis in db/db mice
type: item
type: AcademicArticle
description: Background & Aims Endothelial precursor cell (EPC) dysfunction is one of the risk factors for diabetes mellitus (DM) which results in delayed wound healing. Rosiglitazone (RSG) is a frequently prescribed oral glucose-lowering drug. Previous studies have shown the positive effects of RSG on ameliorating EPC dysfunction in diabetic patients. Interestingly, knowledge about RSG with regard to the wound healing process caused by DM is scarce. Therefore, in this study, we investigated the possible actions of RSG on wound healing and the related mechanisms involved in db/db diabetic mice. Methods Db/db mice with spontaneous glucose metabolic disorder were used as a type 2 DM model. RSG (20 mg/kg/d, i.g.,) was administered for 4 weeks before wound creation and bone marrow derived EPC (BM-EPC) isolation. Wound closure was assessed by wound area and CD31 staining. Tubule formation and migration assays were used to judge the function of the BM-EPCs. The level of vascular endothelial growth factor (VEGF), stromal cell derived factor-1α (SDF-1α) and insulin signaling was determined by ELISA. Cell viability of the BM-EPCs was measured by CCK-8 assay. Results RSG significantly accelerated wound healing and improved angiogenesis in db/db mice. Bioactivities of tube formation and migration were decreased in db/db mice but were elevated by RSG. Level of both VEGF and SDF-1α was increased by RSG in the BM-EPCs of db/db mice. Insulin signaling was elevated by RSG reflected in the phosphorylated-to-total AKT in the BM-EPCs. In vitro, RSG improved impaired cell viability and tube formation of BM-EPCs induced by high glucose, but this was prevented by the VEGF inhibitor avastin. Conclusion Our data demonstrates that RSG has benefits for wound healing and angiogenesis in diabetic mice, and was partially associated with improvement of EPC function through activation of VEGF and stimulation of SDF-1α in db/db mice.
format: application/pdf
format: text/html
creator: Guoliang Zhou
creator: Xue Han
creator: Zhiheng Wu
creator: Qiaojuan Shi
creator: Xiaogang Bao
subject: Cell Biology
subject: Diabetes and Endocrinology
subject: Pharmacology
description: doi:10.7717/peerj.7815
publisher: PeerJ Inc.
rights: © 2019 Zhou et al.
abstract: Background & Aims Endothelial precursor cell (EPC) dysfunction is one of the risk factors for diabetes mellitus (DM) which results in delayed wound healing. Rosiglitazone (RSG) is a frequently prescribed oral glucose-lowering drug. Previous studies have shown the positive effects of RSG on ameliorating EPC dysfunction in diabetic patients. Interestingly, knowledge about RSG with regard to the wound healing process caused by DM is scarce. Therefore, in this study, we investigated the possible actions of RSG on wound healing and the related mechanisms involved in db/db diabetic mice. Methods Db/db mice with spontaneous glucose metabolic disorder were used as a type 2 DM model. RSG (20 mg/kg/d, i.g.,) was administered for 4 weeks before wound creation and bone marrow derived EPC (BM-EPC) isolation. Wound closure was assessed by wound area and CD31 staining. Tubule formation and migration assays were used to judge the function of the BM-EPCs. The level of vascular endothelial growth factor (VEGF), stromal cell derived factor-1α (SDF-1α) and insulin signaling was determined by ELISA. Cell viability of the BM-EPCs was measured by CCK-8 assay. Results RSG significantly accelerated wound healing and improved angiogenesis in db/db mice. Bioactivities of tube formation and migration were decreased in db/db mice but were elevated by RSG. Level of both VEGF and SDF-1α was increased by RSG in the BM-EPCs of db/db mice. Insulin signaling was elevated by RSG reflected in the phosphorylated-to-total AKT in the BM-EPCs. In vitro, RSG improved impaired cell viability and tube formation of BM-EPCs induced by high glucose, but this was prevented by the VEGF inhibitor avastin. Conclusion Our data demonstrates that RSG has benefits for wound healing and angiogenesis in diabetic mice, and was partially associated with improvement of EPC function through activation of VEGF and stimulation of SDF-1α in db/db mice.
bibliographic citation: Zhou et al. (2019) Rosiglitazone accelerates wound healing by improving endothelial precursor cell function and angiogenesis in db/db mice. PeerJ 7:e7815 https://doi.org/10.7717/peerj.7815
date submitted: 2019-05-31
date accepted: 2019-09-02
issued: 2019-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Guoliang
author list: Agent
  family name: Han
  given name: Xue
author list: Agent
  family name: Wu
  given name: Zhiheng
author list: Agent
  family name: Shi
  given name: Qiaojuan
author list: Agent
  family name: Bao
  given name: Xiaogang
doi: 10.7717/peerj.7815
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-17
copyright: ©2019 Zhou et al.
attribution name: Zhou et al.

Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue
type: item
type: AcademicArticle
description: The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals, and its conservation has significant ecosystem and cultural service value. Cytosine DNA methylation (5mC) is a stable epigenetic modification to the genome and has multiple functions such as gene regulation. However, DNA methylome of giant panda and its function have not been reported as of yet. Bisulfite sequencing was performed on a 4-day-old male giant panda’s brain, liver and pancreatic tissues. We found that the whole genome methylation level was about 0.05% based on reads normalization and mitochondrial DNA was not methylated. Three tissues showed similar methylation tendency in the protein-coding genes of their genomes, but the brain genome had a higher count of methylated genes. We obtained 467 and 1,013 different methylation regions (DMR) genes in brain vs. pancreas and liver, while only 260 DMR genes were obtained in liver vs pancreas. Some lncRNA were also DMR genes, indicating that methylation may affect biological processes by regulating other epigenetic factors. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that low methylated promoter, high methylated promoter and DMR genes were enriched at some important and tissue-specific items and pathways, like neurogenesis, metabolism and immunity. DNA methylation may drive or maintain tissue specificity and organic functions and it could be a crucial regulating factor for the development of newborn cubs. Our study offers the first insight into giant panda’s DNA methylome, laying a foundation for further exploration of the giant panda’s epigenetics.
format: application/pdf
format: text/html
creator: Jianying Ren
creator: Fujun Shen
creator: Liang Zhang
creator: Jie Sun
creator: Miao Yang
creator: Mingyu Yang
creator: Rong Hou
creator: Bisong Yue
creator: Xiuyue Zhang
subject: Bioinformatics
subject: Conservation Biology
subject: Genetics
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.7847
publisher: PeerJ Inc.
rights: © 2019 Ren et al.
abstract: The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals, and its conservation has significant ecosystem and cultural service value. Cytosine DNA methylation (5mC) is a stable epigenetic modification to the genome and has multiple functions such as gene regulation. However, DNA methylome of giant panda and its function have not been reported as of yet. Bisulfite sequencing was performed on a 4-day-old male giant panda’s brain, liver and pancreatic tissues. We found that the whole genome methylation level was about 0.05% based on reads normalization and mitochondrial DNA was not methylated. Three tissues showed similar methylation tendency in the protein-coding genes of their genomes, but the brain genome had a higher count of methylated genes. We obtained 467 and 1,013 different methylation regions (DMR) genes in brain vs. pancreas and liver, while only 260 DMR genes were obtained in liver vs pancreas. Some lncRNA were also DMR genes, indicating that methylation may affect biological processes by regulating other epigenetic factors. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that low methylated promoter, high methylated promoter and DMR genes were enriched at some important and tissue-specific items and pathways, like neurogenesis, metabolism and immunity. DNA methylation may drive or maintain tissue specificity and organic functions and it could be a crucial regulating factor for the development of newborn cubs. Our study offers the first insight into giant panda’s DNA methylome, laying a foundation for further exploration of the giant panda’s epigenetics.
bibliographic citation: Ren et al. (2019) Single-base-resolution methylome of giant panda’s brain, liver and pancreatic tissue. PeerJ 7:e7847 https://doi.org/10.7717/peerj.7847
date submitted: 2019-05-09
date accepted: 2019-09-08
issued: 2019-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ren
  given name: Jianying
author list: Agent
  family name: Shen
  given name: Fujun
author list: Agent
  family name: Zhang
  given name: Liang
author list: Agent
  family name: Sun
  given name: Jie
author list: Agent
  family name: Yang
  given name: Miao
author list: Agent
  family name: Yang
  given name: Mingyu
author list: Agent
  family name: Hou
  given name: Rong
author list: Agent
  family name: Yue
  given name: Bisong
author list: Agent
  family name: Zhang
  given name: Xiuyue
doi: 10.7717/peerj.7847
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-17
copyright: © 2019 Ren et al.
attribution name: Ren et al.

Relationships between key functional traits of the waterlily Nuphar lutea and wetland nutrient content
type: item
type: AcademicArticle
description: Little attention has been paid to how aquatic habitat characteristics affect the traits of plant species. Nuphar lutea (L.) Sm. is a keystone species distributed across temperate regions of Europe, northwest Africa and western Asia. Its apparently low phenotypic variability compared to other aquatic plants led us to test whether the species exhibited significant phenotypic variability and whether trait values correlated to environmental parameters. The hypotheses were that (1) the environmental variation within our set of wetlands (both water and sediment characteristics) led to significant variation among four sets of traits related respectively to growth, reproduction, defence and storage and (2) that nutrient limitation (nitrogen and especially phosphorus) should affect plant traits towards a higher investment in storage and defence and a lower investment in growth and reproduction, thereby negatively affecting the success of N. lutea. To test these hypotheses, 11 populations of N. lutea were sampled in wetlands differing in physicochemical characteristics and spread along three rivers. A total of 15 traits, grouped into four sets (growth, reproduction, storage and defence), were measured during the growing season. Most N. lutea traits were related to the environmental characteristics of wetlands. The growth and reproduction traits were mostly positively related to habitat resource conditions, whereas the defence traits were positively correlated with both ammonium concentration and temperature, outlining possible anoxic stress (habitat adversity). Nitrogen or phosphorus limitation led to the variation of only a few traits: the rhizome starch content was higher in phosphorus-limited wetlands, while the rhizome length and volume, and the number of flowers were higher in nitrogen-limited wetlands.
format: application/pdf
format: text/html
creator: Charles P. Henriot
creator: Quentin Cuenot
creator: Lise-Hélène Levrey
creator: Christophe Loup
creator: Landry Chiarello
creator: Hélène Masclaux
creator: Gudrun Bornette
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Freshwater Biology
subject: Population Biology
description: doi:10.7717/peerj.7861
publisher: PeerJ Inc.
rights: © 2019 Henriot et al.
abstract: Little attention has been paid to how aquatic habitat characteristics affect the traits of plant species. Nuphar lutea (L.) Sm. is a keystone species distributed across temperate regions of Europe, northwest Africa and western Asia. Its apparently low phenotypic variability compared to other aquatic plants led us to test whether the species exhibited significant phenotypic variability and whether trait values correlated to environmental parameters. The hypotheses were that (1) the environmental variation within our set of wetlands (both water and sediment characteristics) led to significant variation among four sets of traits related respectively to growth, reproduction, defence and storage and (2) that nutrient limitation (nitrogen and especially phosphorus) should affect plant traits towards a higher investment in storage and defence and a lower investment in growth and reproduction, thereby negatively affecting the success of N. lutea. To test these hypotheses, 11 populations of N. lutea were sampled in wetlands differing in physicochemical characteristics and spread along three rivers. A total of 15 traits, grouped into four sets (growth, reproduction, storage and defence), were measured during the growing season. Most N. lutea traits were related to the environmental characteristics of wetlands. The growth and reproduction traits were mostly positively related to habitat resource conditions, whereas the defence traits were positively correlated with both ammonium concentration and temperature, outlining possible anoxic stress (habitat adversity). Nitrogen or phosphorus limitation led to the variation of only a few traits: the rhizome starch content was higher in phosphorus-limited wetlands, while the rhizome length and volume, and the number of flowers were higher in nitrogen-limited wetlands.
bibliographic citation: Henriot et al. (2019) Relationships between key functional traits of the waterlily Nuphar lutea and wetland nutrient content. PeerJ 7:e7861 https://doi.org/10.7717/peerj.7861
date submitted: 2019-02-18
date accepted: 2019-09-10
issued: 2019-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Henriot
  given name: Charles P.
author list: Agent
  family name: Cuenot
  given name: Quentin
author list: Agent
  family name: Levrey
  given name: Lise-Hélène
author list: Agent
  family name: Loup
  given name: Christophe
author list: Agent
  family name: Chiarello
  given name: Landry
author list: Agent
  family name: Masclaux
  given name: Hélène
author list: Agent
  family name: Bornette
  given name: Gudrun
doi: 10.7717/peerj.7861
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-17
copyright: © 2019 Henriot et al.
attribution name: Henriot et al.

Differences between medically treated and untreated non-fatal self-harm reported by hotline callers in China
type: item
type: AcademicArticle
description: Background Many self-harmers do not present in hospitals due to the self-harm. It is still unclear on the differences between medically treated and untreated self-harm in China. This study described the differences of the two groups of self-harmers using the largest psychological aid hotline data. Methods The present observational study recruited 3,403 hotline callers who reported episodes of self-harm before the call. In routine assessment, information about the most recent episode of self-harm was collected, including the method of self-harm, the wish to die, goals of the self-harm, and any medical treatment (irrespective of psychological services) in the hospital. The callers were divided into two groups: those who received hospital-based medical treatment due to the most recent self-harm (treated self-harm callers) and those who did not (untreated self-harm callers). Results In the most recent episode of self-harm, 65% (n = 2,217) of callers were untreated and 55% (1,226/2,217) of the untreated self-harm callers reported a wish to die. A total of 67% of the callers reported that their main goal of self-harm was to relieve suffering. The most common self-harm methods were using instruments (knife or rope) and overdosing on medicines. Compared with treated self-harm callers, the untreated self-harm callers were less likely to have a wish to die (OR = 0.57), engage in self-harm outside the home (OR = 0.71 and 0.78), and attribute their self-harm to romantic relationship problems (OR = 0.76); however, they were more likely to use instruments, to jump, or to choose other methods (OR = 3.73, 3.83, and 7.71, respectively). Conclusions Among hotline callers, many episodes of self-harm did not receive medical treatment, despite over half reporting a wish to die. Characteristics of self-harm behaviors were different between treated and untreated self-harm callers. Our findings suggest that more strategies should improve access to hospital-based medical treatment and cover…
format: application/pdf
format: text/html
creator: Yongsheng Tong
creator: Yi Yin
creator: Nancy H. Liu
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.7868
publisher: PeerJ Inc.
rights: © 2019 Tong et al.
abstract: Background Many self-harmers do not present in hospitals due to the self-harm. It is still unclear on the differences between medically treated and untreated self-harm in China. This study described the differences of the two groups of self-harmers using the largest psychological aid hotline data. Methods The present observational study recruited 3,403 hotline callers who reported episodes of self-harm before the call. In routine assessment, information about the most recent episode of self-harm was collected, including the method of self-harm, the wish to die, goals of the self-harm, and any medical treatment (irrespective of psychological services) in the hospital. The callers were divided into two groups: those who received hospital-based medical treatment due to the most recent self-harm (treated self-harm callers) and those who did not (untreated self-harm callers). Results In the most recent episode of self-harm, 65% (n = 2,217) of callers were untreated and 55% (1,226/2,217) of the untreated self-harm callers reported a wish to die. A total of 67% of the callers reported that their main goal of self-harm was to relieve suffering. The most common self-harm methods were using instruments (knife or rope) and overdosing on medicines. Compared with treated self-harm callers, the untreated self-harm callers were less likely to have a wish to die (OR = 0.57), engage in self-harm outside the home (OR = 0.71 and 0.78), and attribute their self-harm to romantic relationship problems (OR = 0.76); however, they were more likely to use instruments, to jump, or to choose other methods (OR = 3.73, 3.83, and 7.71, respectively). Conclusions Among hotline callers, many episodes of self-harm did not receive medical treatment, despite over half reporting a wish to die. Characteristics of self-harm behaviors were different between treated and untreated self-harm callers. Our findings suggest that more strategies should improve access to hospital-based medical treatment and cover…
bibliographic citation: Tong et al. (2019) Differences between medically treated and untreated non-fatal self-harm reported by hotline callers in China. PeerJ 7:e7868 https://doi.org/10.7717/peerj.7868
date submitted: 2019-07-13
date accepted: 2019-09-11
issued: 2019-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tong
  given name: Yongsheng
author list: Agent
  family name: Yin
  given name: Yi
author list: Agent
  family name: Liu
  given name: Nancy H.
doi: 10.7717/peerj.7868
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-17
copyright: © 2019 Tong et al.
attribution name: Tong et al.

A novel form of wasp mimicry in a new species of praying mantis from the Amazon rainforest, Vespamantoida wherleyi gen. nov. sp. nov. (Mantodea, Mantoididae)
type: item
type: AcademicArticle
description: A wasp mimicking praying mantis (Mantodea) of the early evolving Mantoididae family was discovered in 2013 at a research station near the Amazon River in Northern Peru. This adult specimen exhibited a striking bright red/orange and black coloration pattern that was undocumented in all known praying mantis species. We tested the status of this new specimen using external morphology, male genital dissections, and geographic distribution. Our findings demonstrate the specimen to represent a new species, Vespamantoida wherleyi gen. nov. sp. nov., that is closely allied with a recently described species, Mantoida toulgoeti Roy, 2010, both of which are included within the newly erected genus. To support our actions, we present high resolution images of museum preserved and living specimens, morphological illustrations, a generic-level distribution map, and recorded video of the behavior of the holotype taken in the field at the time of collection. The bright red/orange coloration contrasted with black markings, the general appearance of a hymenopteran that includes a narrowed wasp waist, and the locomotory patterns and antennal movements mark this newly discovered species as unique among all hymenopteran mimicking Mantoididae as well as all other praying mantises.
format: application/pdf
format: text/html
creator: Gavin J. Svenson
creator: Henrique M. Rodrigues
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.7886
publisher: PeerJ Inc.
rights: © 2019 Svenson and Rodrigues
abstract: A wasp mimicking praying mantis (Mantodea) of the early evolving Mantoididae family was discovered in 2013 at a research station near the Amazon River in Northern Peru. This adult specimen exhibited a striking bright red/orange and black coloration pattern that was undocumented in all known praying mantis species. We tested the status of this new specimen using external morphology, male genital dissections, and geographic distribution. Our findings demonstrate the specimen to represent a new species, Vespamantoida wherleyi gen. nov. sp. nov., that is closely allied with a recently described species, Mantoida toulgoeti Roy, 2010, both of which are included within the newly erected genus. To support our actions, we present high resolution images of museum preserved and living specimens, morphological illustrations, a generic-level distribution map, and recorded video of the behavior of the holotype taken in the field at the time of collection. The bright red/orange coloration contrasted with black markings, the general appearance of a hymenopteran that includes a narrowed wasp waist, and the locomotory patterns and antennal movements mark this newly discovered species as unique among all hymenopteran mimicking Mantoididae as well as all other praying mantises.
bibliographic citation: Svenson et al. (2019) A novel form of wasp mimicry in a new species of praying mantis from the Amazon rainforest, Vespamantoida wherleyi gen. nov. sp. nov. (Mantodea, Mantoididae). PeerJ 7:e7886 https://doi.org/10.7717/peerj.7886
date submitted: 2019-05-30
date accepted: 2019-09-12
issued: 2019-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Svenson
  given name: Gavin J.
author list: Agent
  family name: Rodrigues
  given name: Henrique M.
doi: 10.7717/peerj.7886
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-17
copyright: © 2019 Svenson and Rodrigues
attribution name: Svenson and Rodrigues

Identification of key genes and multiple molecular pathways of metastatic process in prostate cancer
type: item
type: AcademicArticle
description: Background Cancer metastasis is well known as the most adverse outcome and the major cause of mortality in cancer patients, including prostate cancer (PCa). There are no credible predictors, to this day, that can reflect the metastatic ability of localized PCa. In the present study, we firstly identified the differentially expressed genes (DEGs) and molecular pathways involved in the metastaic process of PCa by comparing gene expressions of metastaic PCa with localized PCa directly, with the purpose of identifying potential markers or therapeutic targets. Methods The gene expression profiles (GSE6919 and GSE32269) were downloaded from the Gene Expression Omnibus database, which contained 141 tissue samples, including 87 primary localized PCa samples and 54 metastaic PCa samples. After data processing, DEGs were identified by R language using the Student’s t-test adjusted via the Beniamini–Hochberg method. Subsequently, the gene ontology functional and pathway enrichment analyses of DEGs were performed and the protein–protein interaction network was constructed. Hub genes were identified using the plug-in cytoHubba in Cytoscape software by MCC and degree. Furthermore, validation and prognostic significance analysis of the hub genes were performed by UALCAN and gene expression profiling interactive analysis (GEPIA). Results A total of 90 DEGs were identified between localized and metastaic PCa, which consisted of 47 upregulated and 43 downregulated genes. The enriched functions and pathways of the DEGs include catabolic process, cell cycle, response to steroid hormone, extracellular matrix (ECM)-receptor interaction and vascular smooth muscle contraction. A total of 10 genes were identified as hub genes and biological process analysis of hub genes showed that cell cycle phase, cell division, and mitotic cell cycle process were mainly enriched. The expression of hub genes were confirmed in metastaic PCa when compared with localized PCa tissues by The Cancer Genome Atla…
format: application/pdf
format: text/html
creator: Lihuang Guo
creator: Mingyue Lin
creator: Zhenbo Cheng
creator: Yi Chen
creator: Yue Huang
creator: Keqian Xu
subject: Bioinformatics
subject: Oncology
subject: Urology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.7899
publisher: PeerJ Inc.
rights: © 2019 Guo et al.
abstract: Background Cancer metastasis is well known as the most adverse outcome and the major cause of mortality in cancer patients, including prostate cancer (PCa). There are no credible predictors, to this day, that can reflect the metastatic ability of localized PCa. In the present study, we firstly identified the differentially expressed genes (DEGs) and molecular pathways involved in the metastaic process of PCa by comparing gene expressions of metastaic PCa with localized PCa directly, with the purpose of identifying potential markers or therapeutic targets. Methods The gene expression profiles (GSE6919 and GSE32269) were downloaded from the Gene Expression Omnibus database, which contained 141 tissue samples, including 87 primary localized PCa samples and 54 metastaic PCa samples. After data processing, DEGs were identified by R language using the Student’s t-test adjusted via the Beniamini–Hochberg method. Subsequently, the gene ontology functional and pathway enrichment analyses of DEGs were performed and the protein–protein interaction network was constructed. Hub genes were identified using the plug-in cytoHubba in Cytoscape software by MCC and degree. Furthermore, validation and prognostic significance analysis of the hub genes were performed by UALCAN and gene expression profiling interactive analysis (GEPIA). Results A total of 90 DEGs were identified between localized and metastaic PCa, which consisted of 47 upregulated and 43 downregulated genes. The enriched functions and pathways of the DEGs include catabolic process, cell cycle, response to steroid hormone, extracellular matrix (ECM)-receptor interaction and vascular smooth muscle contraction. A total of 10 genes were identified as hub genes and biological process analysis of hub genes showed that cell cycle phase, cell division, and mitotic cell cycle process were mainly enriched. The expression of hub genes were confirmed in metastaic PCa when compared with localized PCa tissues by The Cancer Genome Atla…
bibliographic citation: Guo et al. (2019) Identification of key genes and multiple molecular pathways of metastatic process in prostate cancer. PeerJ 7:e7899 https://doi.org/10.7717/peerj.7899
date submitted: 2019-08-05
date accepted: 2019-09-16
issued: 2019-10-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Lihuang
author list: Agent
  family name: Lin
  given name: Mingyue
author list: Agent
  family name: Cheng
  given name: Zhenbo
author list: Agent
  family name: Chen
  given name: Yi
author list: Agent
  family name: Huang
  given name: Yue
author list: Agent
  family name: Xu
  given name: Keqian
doi: 10.7717/peerj.7899
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-10-17
copyright: © 2019 Guo et al.
attribution name: Guo et al.

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