PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Nursing knowledge of and attitude in cardiopulmonary arrest: cross-sectional survey analysis
items: Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure
items: A survey on zoo mortality over a 12-year period in Italy
items: Turtles of the genera Geoemyda and Pangshura (Testudines: Geoemydidae) lack differentiated sex chromosomes: the end of a 40-year error cascade for Pangshura
items: kuenm: an R package for detailed development of ecological niche models using Maxent
items: The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
items: Species turnover reveals hidden effects of decreasing nitrogen deposition in mountain hay meadows
items: Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis
items: Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient
items: Genetic alteration of histone lysine methyltransferases and their significance in renal cell carcinoma

Nursing knowledge of and attitude in cardiopulmonary arrest: cross-sectional survey analysis
type: item
type: AcademicArticle
description: Background Nurses are often the first to activate the chain of survival when a cardiorespiratory arrest happens. That is why it is crucial that they keep their knowledge and skills up-to-date and their attitudes to resuscitation are very important. The main aim of this study was to analyse whether the level of theoretical and practical understanding affected the attitudes of nursing staff. Methods A questionnaire was designed using the Delphi technique (three rounds). The questionnaire was adjusted and it was piloted on a test-retest basis with a convenience sample of 30 registered nurses. The psychometric characteristics were evaluated using a sample of 347 nurses using Cronbach’s alpha. Descriptive analysis was performed to describe the sociodemographic variables and Spearman’s correlation coefficient to assess the relationship between two scale variables. Pearson’s chi-squared test has been used to study the relationship between two categorical variables. Wilcoxon Mann Whitney test and the Kruskal–Wallis test were performed to establish relationships between the demographic/work related characteristics and the level of understanding. Results The Knowledge and Attitude of Nurses in the Event of a Cardiorespiratory Arrest (CAEPCR) questionnaire comprised three sections: sociodemographic information, theoretical and practical understanding, and attitudes of ethical issues. Cronbach’s alpha for the internal consistency of the attitudes questionnaire was 0.621. The knowledge that nurses self-reported with regard to cardiopulmonary arrest directly affected their attitudes. Their responses raised a number of bioethical issues. Conclusions CAEPCR questionnaire is the first one which successfully linked knowledge of cardiopulmonary resuscitation to the attitudes towards ethical issues Health policies should ensure that CPR training is mandatory for nurses and all healthcare workers, and this training should include the ethical aspects.
format: application/pdf
format: text/html
creator: Verónica Tíscar-González
creator: Joan Blanco-Blanco
creator: Montserrat Gea-Sánchez
creator: Ascensión Rodriguez Molinuevo
creator: Teresa Moreno-Casbas
subject: Cardiology
subject: Emergency and Critical Care
subject: Nursing
subject: Ethical Issues
description: doi:10.7717/peerj.6410
publisher: PeerJ Inc.
rights: © 2019 Tíscar-González et al.
abstract: Background Nurses are often the first to activate the chain of survival when a cardiorespiratory arrest happens. That is why it is crucial that they keep their knowledge and skills up-to-date and their attitudes to resuscitation are very important. The main aim of this study was to analyse whether the level of theoretical and practical understanding affected the attitudes of nursing staff. Methods A questionnaire was designed using the Delphi technique (three rounds). The questionnaire was adjusted and it was piloted on a test-retest basis with a convenience sample of 30 registered nurses. The psychometric characteristics were evaluated using a sample of 347 nurses using Cronbach’s alpha. Descriptive analysis was performed to describe the sociodemographic variables and Spearman’s correlation coefficient to assess the relationship between two scale variables. Pearson’s chi-squared test has been used to study the relationship between two categorical variables. Wilcoxon Mann Whitney test and the Kruskal–Wallis test were performed to establish relationships between the demographic/work related characteristics and the level of understanding. Results The Knowledge and Attitude of Nurses in the Event of a Cardiorespiratory Arrest (CAEPCR) questionnaire comprised three sections: sociodemographic information, theoretical and practical understanding, and attitudes of ethical issues. Cronbach’s alpha for the internal consistency of the attitudes questionnaire was 0.621. The knowledge that nurses self-reported with regard to cardiopulmonary arrest directly affected their attitudes. Their responses raised a number of bioethical issues. Conclusions CAEPCR questionnaire is the first one which successfully linked knowledge of cardiopulmonary resuscitation to the attitudes towards ethical issues Health policies should ensure that CPR training is mandatory for nurses and all healthcare workers, and this training should include the ethical aspects.
bibliographic citation: Tíscar-González et al. (2019) Nursing knowledge of and attitude in cardiopulmonary arrest: cross-sectional survey analysis. PeerJ 7:e6410 https://doi.org/10.7717/peerj.6410
date submitted: 2018-08-22
date accepted: 2019-01-07
issued: 2019-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tíscar-González
  given name: Verónica
author list: Agent
  family name: Blanco-Blanco
  given name: Joan
author list: Agent
  family name: Gea-Sánchez
  given name: Montserrat
author list: Agent
  family name: Rodriguez Molinuevo
  given name: Ascensión
author list: Agent
  family name: Moreno-Casbas
  given name: Teresa
doi: 10.7717/peerj.6410
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-07
copyright: ©2019 Tíscar-González et al.
attribution name: Tíscar-González et al.

Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure
type: item
type: AcademicArticle
description: NAD glycohydrolase (EC 3.2.2.5) (NADase) sequences have been identified in 10 elapid and crotalid venom gland transcriptomes, eight of which are complete. These sequences show very high homology, but elapid and crotalid sequences also display consistent differences. As in Aplysia kurodai ADP-ribosyl cyclase and vertebrate CD38 genes, snake venom NADase genes comprise eight exons; however, in the Protobothrops mucrosquamatus genome, the sixth exon is sometimes not transcribed, yielding a shortened NADase mRNA that encodes all six disulfide bonds, but an active site that lacks the catalytic glutamate residue. The function of this shortened protein, if expressed, is unknown. While many vertebrate CD38s are multifunctional, liberating both ADP-ribose and small quantities of cyclic ADP-ribose (cADPR), snake venom CD38 homologs are dedicated NADases. They possess the invariant TLEDTL sequence (residues 144–149) that bounds the active site and the catalytic residue, Glu228. In addition, they possess a disulfide bond (Cys121–Cys202) that specifically prevents ADP-ribosyl cyclase activity in combination with Ile224, in lieu of phenylalanine, which is requisite for ADPR cyclases. In concert with venom phosphodiesterase and 5′-nucleotidase and their ecto-enzyme homologs in prey tissues, snake venom NADases comprise part of an envenomation strategy to liberate purine nucleosides, and particularly adenosine, in the prey, promoting prey immobilization via hypotension and paralysis.
format: application/pdf
format: text/html
creator: Ivan Koludarov
creator: Steven D. Aird
subject: Biochemistry
subject: Genomics
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.6154
publisher: PeerJ Inc.
rights: © 2019 Koludarov and Aird
abstract: NAD glycohydrolase (EC 3.2.2.5) (NADase) sequences have been identified in 10 elapid and crotalid venom gland transcriptomes, eight of which are complete. These sequences show very high homology, but elapid and crotalid sequences also display consistent differences. As in Aplysia kurodai ADP-ribosyl cyclase and vertebrate CD38 genes, snake venom NADase genes comprise eight exons; however, in the Protobothrops mucrosquamatus genome, the sixth exon is sometimes not transcribed, yielding a shortened NADase mRNA that encodes all six disulfide bonds, but an active site that lacks the catalytic glutamate residue. The function of this shortened protein, if expressed, is unknown. While many vertebrate CD38s are multifunctional, liberating both ADP-ribose and small quantities of cyclic ADP-ribose (cADPR), snake venom CD38 homologs are dedicated NADases. They possess the invariant TLEDTL sequence (residues 144–149) that bounds the active site and the catalytic residue, Glu228. In addition, they possess a disulfide bond (Cys121–Cys202) that specifically prevents ADP-ribosyl cyclase activity in combination with Ile224, in lieu of phenylalanine, which is requisite for ADPR cyclases. In concert with venom phosphodiesterase and 5′-nucleotidase and their ecto-enzyme homologs in prey tissues, snake venom NADases comprise part of an envenomation strategy to liberate purine nucleosides, and particularly adenosine, in the prey, promoting prey immobilization via hypotension and paralysis.
bibliographic citation: Koludarov et al. (2019) Snake venom NAD glycohydrolases: primary structures, genomic location, and gene structure. PeerJ 7:e6154 https://doi.org/10.7717/peerj.6154
date submitted: 2018-09-26
date accepted: 2018-11-25
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Koludarov
  given name: Ivan
author list: Agent
  family name: Aird
  given name: Steven D.
doi: 10.7717/peerj.6154
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Koludarov and Aird
attribution name: Koludarov and Aird

A survey on zoo mortality over a 12-year period in Italy
type: item
type: AcademicArticle
description: Background The zoo is a unique environment in which to study animals. Zoos have a long history of research into aspects of animal biology, even if this was not the primary purpose for which they were established. The data collected from zoo animals can have a great biological relevance and it can tell us more about what these animals are like outside the captive environment. In order to ensure the health of all captive animals, it is important to perform a post-mortem examination on all the animals that die in captivity. Methods The causes of mortality of two hundred and eighty two mammals which died between 2004 and 2015 in three different Italian zoos (a Biopark, a Safari Park and a private conservation center) have been investigated. Results Post mortem findings have been evaluated reporting the cause of death, zoo type, year and animal category. The animals frequently died from infectious diseases, in particular the causes of death in ruminants were mostly related to gastro-intestinal pathologies. pulmonary diseases were also very common in each of the zoos in the study. Moreover, death was sometimes attributable to traumas, as a result of fighting between conspecifics or during mating. Cases of genetic diseases and malformations have also been registered. Discussion This research was a confirmation of how conservation, histology and pathology are all connected through individual animals. These areas of expertise are extremely important to ensure the survival of rare and endangered species and to learn more about their morphological and physiological conditions. They are also useful to control pathologies, parasites and illnesses that can have a great impact on the species in captivity. Finally, this study underlines the importance of a close collaboration between veterinarians, zoo biologists and pathologists. Necropsy findings can help conservationists to determine how to support wild animal populations.
format: application/pdf
format: text/html
creator: Frine Eleonora Scaglione
creator: Cristina Biolatti
creator: Paola Pregel
creator: Enrica Berio
creator: Francesca Tiziana Cannizzo
creator: Bartolomeo Biolatti
creator: Enrico Bollo
subject: Conservation Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6198
publisher: PeerJ Inc.
rights: © 2019 Scaglione et al.
abstract: Background The zoo is a unique environment in which to study animals. Zoos have a long history of research into aspects of animal biology, even if this was not the primary purpose for which they were established. The data collected from zoo animals can have a great biological relevance and it can tell us more about what these animals are like outside the captive environment. In order to ensure the health of all captive animals, it is important to perform a post-mortem examination on all the animals that die in captivity. Methods The causes of mortality of two hundred and eighty two mammals which died between 2004 and 2015 in three different Italian zoos (a Biopark, a Safari Park and a private conservation center) have been investigated. Results Post mortem findings have been evaluated reporting the cause of death, zoo type, year and animal category. The animals frequently died from infectious diseases, in particular the causes of death in ruminants were mostly related to gastro-intestinal pathologies. pulmonary diseases were also very common in each of the zoos in the study. Moreover, death was sometimes attributable to traumas, as a result of fighting between conspecifics or during mating. Cases of genetic diseases and malformations have also been registered. Discussion This research was a confirmation of how conservation, histology and pathology are all connected through individual animals. These areas of expertise are extremely important to ensure the survival of rare and endangered species and to learn more about their morphological and physiological conditions. They are also useful to control pathologies, parasites and illnesses that can have a great impact on the species in captivity. Finally, this study underlines the importance of a close collaboration between veterinarians, zoo biologists and pathologists. Necropsy findings can help conservationists to determine how to support wild animal populations.
bibliographic citation: Scaglione et al. (2019) A survey on zoo mortality over a 12-year period in Italy. PeerJ 7:e6198 https://doi.org/10.7717/peerj.6198
date submitted: 2017-04-07
date accepted: 2018-12-02
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scaglione
  given name: Frine Eleonora
author list: Agent
  family name: Biolatti
  given name: Cristina
author list: Agent
  family name: Pregel
  given name: Paola
author list: Agent
  family name: Berio
  given name: Enrica
author list: Agent
  family name: Cannizzo
  given name: Francesca Tiziana
author list: Agent
  family name: Biolatti
  given name: Bartolomeo
author list: Agent
  family name: Bollo
  given name: Enrico
doi: 10.7717/peerj.6198
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Scaglione et al.
attribution name: Scaglione et al.

Turtles of the genera Geoemyda and Pangshura (Testudines: Geoemydidae) lack differentiated sex chromosomes: the end of a 40-year error cascade for Pangshura
type: item
type: AcademicArticle
description: For a long time, turtles of the family Geoemydidae have been considered exceptional because representatives of this family were thought to possess a wide variety of sex determination systems. In the present study, we cytogenetically studied Geoemyda spengleri and G. japonica and re-examined the putative presence of sex chromosomes in Pangshura smithii. Karyotypes were examined by assessing the occurrence of constitutive heterochromatin, by comparative genome hybridization and in situ hybridization with repetitive motifs, which are often accumulated on differentiated sex chromosomes in reptiles. We found similar karyotypes, similar distributions of constitutive heterochromatin and a similar topology of tested repetitive motifs for all three species. We did not detect differentiated sex chromosomes in any of the species. For P. smithii, a ZZ/ZW sex determination system, with differentiated sex chromosomes, was described more than 40 years ago, but this finding has never been re-examined and was cited in all reviews of sex determination in reptiles. Here, we show that the identification of sex chromosomes in the original report was based on the erroneous pairing of chromosomes in the karyogram, causing over decades an error cascade regarding the inferences derived from the putative existence of female heterogamety in geoemydid turtles.
format: application/pdf
format: text/html
creator: Sofia Mazzoleni
creator: Barbora Augstenová
creator: Lorenzo Clemente
creator: Markus Auer
creator: Uwe Fritz
creator: Peter Praschag
creator: Tomáš Protiva
creator: Petr Velenský
creator: Lukáš Kratochvíl
creator: Michail Rovatsos
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.6241
publisher: PeerJ Inc.
rights: © 2019 Mazzoleni et al.
abstract: For a long time, turtles of the family Geoemydidae have been considered exceptional because representatives of this family were thought to possess a wide variety of sex determination systems. In the present study, we cytogenetically studied Geoemyda spengleri and G. japonica and re-examined the putative presence of sex chromosomes in Pangshura smithii. Karyotypes were examined by assessing the occurrence of constitutive heterochromatin, by comparative genome hybridization and in situ hybridization with repetitive motifs, which are often accumulated on differentiated sex chromosomes in reptiles. We found similar karyotypes, similar distributions of constitutive heterochromatin and a similar topology of tested repetitive motifs for all three species. We did not detect differentiated sex chromosomes in any of the species. For P. smithii, a ZZ/ZW sex determination system, with differentiated sex chromosomes, was described more than 40 years ago, but this finding has never been re-examined and was cited in all reviews of sex determination in reptiles. Here, we show that the identification of sex chromosomes in the original report was based on the erroneous pairing of chromosomes in the karyogram, causing over decades an error cascade regarding the inferences derived from the putative existence of female heterogamety in geoemydid turtles.
bibliographic citation: Mazzoleni et al. (2019) Turtles of the genera Geoemyda and Pangshura (Testudines: Geoemydidae) lack differentiated sex chromosomes: the end of a 40-year error cascade for Pangshura. PeerJ 7:e6241 https://doi.org/10.7717/peerj.6241
date submitted: 2018-10-29
date accepted: 2018-12-08
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mazzoleni
  given name: Sofia
author list: Agent
  family name: Augstenová
  given name: Barbora
author list: Agent
  family name: Clemente
  given name: Lorenzo
author list: Agent
  family name: Auer
  given name: Markus
author list: Agent
  family name: Fritz
  given name: Uwe
author list: Agent
  family name: Praschag
  given name: Peter
author list: Agent
  family name: Protiva
  given name: Tomáš
author list: Agent
  family name: Velenský
  given name: Petr
author list: Agent
  family name: Kratochvíl
  given name: Lukáš
author list: Agent
  family name: Rovatsos
  given name: Michail
doi: 10.7717/peerj.6241
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Mazzoleni et al.
attribution name: Mazzoleni et al.

kuenm: an R package for detailed development of ecological niche models using Maxent
type: item
type: AcademicArticle
description: Background Ecological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way. Results This package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric. Discussion Use of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes.
format: application/pdf
format: text/html
creator: Marlon E. Cobos
creator: A. Townsend Peterson
creator: Narayani Barve
creator: Luis Osorio-Olvera
subject: Biogeography
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.6281
publisher: PeerJ Inc.
rights: © 2019 Cobos et al.
abstract: Background Ecological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way. Results This package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric. Discussion Use of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes.
bibliographic citation: Cobos et al. (2019) kuenm: an R package for detailed development of ecological niche models using Maxent. PeerJ 7:e6281 https://doi.org/10.7717/peerj.6281
date submitted: 2018-10-05
date accepted: 2018-12-13
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cobos
  given name: Marlon E.
author list: Agent
  family name: Peterson
  given name: A. Townsend
author list: Agent
  family name: Barve
  given name: Narayani
author list: Agent
  family name: Osorio-Olvera
  given name: Luis
doi: 10.7717/peerj.6281
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Cobos et al.
attribution name: Cobos et al.

The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
type: item
type: AcademicArticle
description: In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes (T1D), and 12 children with newly diagnosed T2D. These data were used for differentially expressed genes (DGEs) analysis and weighted co-expression network analysis (WGCNA). We identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to figure out the functions and related pathways of genes, which were identified in the results of DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the protein-protein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the transcription factors and references related to genes with conspicuous logFC or high-degree genes, which were present in both the modules of WGCNA and PPI network. Current research shows that EGR1 and NAMPT can be used as marker genes for childhood-onset T2D. Gestational diabetes and chronic inflammation are risk factors that lead to the development of childhood-onset T2D.
format: application/pdf
format: text/html
creator: Keren Jia
creator: Yingcheng Wu
creator: Jingyi Ju
creator: Liyang Wang
creator: Lili Shi
creator: Huiqun Wu
creator: Kui Jiang
creator: Jiancheng Dong
subject: Bioinformatics
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6343
publisher: PeerJ Inc.
rights: © 2019 Jia et al.
abstract: In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes (T1D), and 12 children with newly diagnosed T2D. These data were used for differentially expressed genes (DGEs) analysis and weighted co-expression network analysis (WGCNA). We identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to figure out the functions and related pathways of genes, which were identified in the results of DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the protein-protein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the transcription factors and references related to genes with conspicuous logFC or high-degree genes, which were present in both the modules of WGCNA and PPI network. Current research shows that EGR1 and NAMPT can be used as marker genes for childhood-onset T2D. Gestational diabetes and chronic inflammation are risk factors that lead to the development of childhood-onset T2D.
bibliographic citation: Jia et al. (2019) The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes. PeerJ 7:e6343 https://doi.org/10.7717/peerj.6343
date submitted: 2018-10-03
date accepted: 2018-12-24
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jia
  given name: Keren
author list: Agent
  family name: Wu
  given name: Yingcheng
author list: Agent
  family name: Ju
  given name: Jingyi
author list: Agent
  family name: Wang
  given name: Liyang
author list: Agent
  family name: Shi
  given name: Lili
author list: Agent
  family name: Wu
  given name: Huiqun
author list: Agent
  family name: Jiang
  given name: Kui
author list: Agent
  family name: Dong
  given name: Jiancheng
doi: 10.7717/peerj.6343
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: ©2019 Jia et al.
attribution name: Jia et al.

Species turnover reveals hidden effects of decreasing nitrogen deposition in mountain hay meadows
type: item
type: AcademicArticle
description: Nitrogen (N) deposition is a major threat to biodiversity in many habitats. The recent introduction of cleaner technologies in Switzerland has led to a reduction in the emissions of nitrogen oxides, with a consequent decrease in N deposition. We examined different drivers of plant community change, that is, N deposition, climate warming, and land-use change, in Swiss mountain hay meadows, using data from the Swiss biodiversity monitoring program. We compared indicator values of species that disappeared from or colonized a site (species turnover) with the indicator values of randomly chosen species from the same site. While oligotrophic plant species were more likely to colonize, compared to random expectation, we found only weak shifts in plant community composition. In particular, the average nutrient value of plant communities remained stable over time (2003–2017). We found the largest deviations from random expectation in the nutrient values of colonizing species, suggesting that N deposition or other factors that change the nutrient content of soils were important drivers of the species composition change over the last 15 years in Swiss mountain hay meadows. In addition, we observed an overall replacement of species with lower indicator values for temperature with species with higher values. Apparently, the community effects of the replacement of eutrophic species with oligotrophic species was outweighed by climate warming. Our results add to the increasing evidence that plant communities in changing environments may be relatively stable regarding average species richness or average indicator values, but that this apparent stability is often accompanied by a marked turnover of species.
format: application/pdf
format: text/html
creator: Tobias Roth
creator: Lukas Kohli
creator: Christoph Bühler
creator: Beat Rihm
creator: Reto Giulio Meuli
creator: Reto Meier
creator: Valentin Amrhein
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Climate Change Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.6347
publisher: PeerJ Inc.
rights: © 2019 Roth et al.
abstract: Nitrogen (N) deposition is a major threat to biodiversity in many habitats. The recent introduction of cleaner technologies in Switzerland has led to a reduction in the emissions of nitrogen oxides, with a consequent decrease in N deposition. We examined different drivers of plant community change, that is, N deposition, climate warming, and land-use change, in Swiss mountain hay meadows, using data from the Swiss biodiversity monitoring program. We compared indicator values of species that disappeared from or colonized a site (species turnover) with the indicator values of randomly chosen species from the same site. While oligotrophic plant species were more likely to colonize, compared to random expectation, we found only weak shifts in plant community composition. In particular, the average nutrient value of plant communities remained stable over time (2003–2017). We found the largest deviations from random expectation in the nutrient values of colonizing species, suggesting that N deposition or other factors that change the nutrient content of soils were important drivers of the species composition change over the last 15 years in Swiss mountain hay meadows. In addition, we observed an overall replacement of species with lower indicator values for temperature with species with higher values. Apparently, the community effects of the replacement of eutrophic species with oligotrophic species was outweighed by climate warming. Our results add to the increasing evidence that plant communities in changing environments may be relatively stable regarding average species richness or average indicator values, but that this apparent stability is often accompanied by a marked turnover of species.
bibliographic citation: Roth et al. (2019) Species turnover reveals hidden effects of decreasing nitrogen deposition in mountain hay meadows. PeerJ 7:e6347 https://doi.org/10.7717/peerj.6347
date submitted: 2018-09-14
date accepted: 2018-12-24
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roth
  given name: Tobias
author list: Agent
  family name: Kohli
  given name: Lukas
author list: Agent
  family name: Bühler
  given name: Christoph
author list: Agent
  family name: Rihm
  given name: Beat
author list: Agent
  family name: Meuli
  given name: Reto Giulio
author list: Agent
  family name: Meier
  given name: Reto
author list: Agent
  family name: Amrhein
  given name: Valentin
doi: 10.7717/peerj.6347
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Roth et al.
attribution name: Roth et al.

Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis
type: item
type: AcademicArticle
description: Background Alcohol-related hepatocellular carcinoma (HCC) was reported to be diagnosed at a later stage, but the mechanism was unknown. This study aimed to identify special key genes (SKGs) during alcohol-related HCC development and progression. Methods The mRNA data of 369 HCC patients and the clinical information were downloaded from the Cancer Genome Atlas project (TCGA). The 310 patients with certain HCC-related risk factors were included for analysis and divided into seven groups according to the risk factors. Survival analyses were applied for the HCC patients of different groups. The patients with hepatitis B virus or hepatitis C virus infection only were combined into the HCC-V group for further analysis. The differentially expressed genes (DEGs) between the HCCs with alcohol consumption only (HCC-A) and HCC-V tumors were identified through limma package in R with cutoff criteria│log2 fold change (logFC)|>1.0 and p < 0.05. The DEGs between eight alcohol-related HCCs and their paired normal livers of GSE59259 from the Gene Expression Omnibus (GEO) were identified through GEO2R (a built-in tool in GEO database) with cutoff criteria |logFC|> 2.0 and adj.p < 0.05. The intersection of the two sets of DEGs was considered SKGs which were then investigated for their specificity through comparisons between HCC-A and other four HCC groups. The SKGs were analyzed for their correlations with HCC-A stage and grade and their prognostic power for HCC-A patients. The expressional differences of the SKGs in the HCCs in whole were also investigated through Gene Expression Profiling Interactive Analysis (GEPIA). The SKGs in HCC were validated through Oncomine database analysis. Results Pathological stage is an independent prognostic factor for HCC patients. HCC-A patients were diagnosed later than HCC patients with other risk factors. Ten SKGs were identified and nine of them were confirmed for their differences in paired samples of HCC-A patients. Three (SLC22A10, CD5L, and U…
format: application/pdf
format: text/html
creator: Xiuzhi Zhang
creator: Chunyan Kang
creator: Ningning Li
creator: Xiaoli Liu
creator: Jinzhong Zhang
creator: Fenglan Gao
creator: Liping Dai
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Global Health
subject: Oncology
description: doi:10.7717/peerj.6375
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Alcohol-related hepatocellular carcinoma (HCC) was reported to be diagnosed at a later stage, but the mechanism was unknown. This study aimed to identify special key genes (SKGs) during alcohol-related HCC development and progression. Methods The mRNA data of 369 HCC patients and the clinical information were downloaded from the Cancer Genome Atlas project (TCGA). The 310 patients with certain HCC-related risk factors were included for analysis and divided into seven groups according to the risk factors. Survival analyses were applied for the HCC patients of different groups. The patients with hepatitis B virus or hepatitis C virus infection only were combined into the HCC-V group for further analysis. The differentially expressed genes (DEGs) between the HCCs with alcohol consumption only (HCC-A) and HCC-V tumors were identified through limma package in R with cutoff criteria│log2 fold change (logFC)|>1.0 and p < 0.05. The DEGs between eight alcohol-related HCCs and their paired normal livers of GSE59259 from the Gene Expression Omnibus (GEO) were identified through GEO2R (a built-in tool in GEO database) with cutoff criteria |logFC|> 2.0 and adj.p < 0.05. The intersection of the two sets of DEGs was considered SKGs which were then investigated for their specificity through comparisons between HCC-A and other four HCC groups. The SKGs were analyzed for their correlations with HCC-A stage and grade and their prognostic power for HCC-A patients. The expressional differences of the SKGs in the HCCs in whole were also investigated through Gene Expression Profiling Interactive Analysis (GEPIA). The SKGs in HCC were validated through Oncomine database analysis. Results Pathological stage is an independent prognostic factor for HCC patients. HCC-A patients were diagnosed later than HCC patients with other risk factors. Ten SKGs were identified and nine of them were confirmed for their differences in paired samples of HCC-A patients. Three (SLC22A10, CD5L, and U…
bibliographic citation: Zhang et al. (2019) Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis. PeerJ 7:e6375 https://doi.org/10.7717/peerj.6375
date submitted: 2018-09-18
date accepted: 2018-12-31
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xiuzhi
author list: Agent
  family name: Kang
  given name: Chunyan
author list: Agent
  family name: Li
  given name: Ningning
author list: Agent
  family name: Liu
  given name: Xiaoli
author list: Agent
  family name: Zhang
  given name: Jinzhong
author list: Agent
  family name: Gao
  given name: Fenglan
author list: Agent
  family name: Dai
  given name: Liping
doi: 10.7717/peerj.6375
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient
type: item
type: AcademicArticle
description: Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonst…
format: application/pdf
format: text/html
creator: Joseph D. DiBattista
creator: James D. Reimer
creator: Michael Stat
creator: Giovanni D. Masucci
creator: Piera Biondi
creator: Maarten De Brauwer
creator: Michael Bunce
subject: Biodiversity
subject: Marine Biology
description: doi:10.7717/peerj.6379
publisher: PeerJ Inc.
rights: © 2019 DiBattista et al.
abstract: Background Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion Overall, our pilot study demonst…
bibliographic citation: DiBattista et al. (2019) Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ 7:e6379 https://doi.org/10.7717/peerj.6379
date submitted: 2018-10-15
date accepted: 2018-12-24
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DiBattista
  given name: Joseph D.
author list: Agent
  family name: Reimer
  given name: James D.
author list: Agent
  family name: Stat
  given name: Michael
author list: Agent
  family name: Masucci
  given name: Giovanni D.
author list: Agent
  family name: Biondi
  given name: Piera
author list: Agent
  family name: De Brauwer
  given name: Maarten
author list: Agent
  family name: Bunce
  given name: Michael
doi: 10.7717/peerj.6379
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 DiBattista et al.
attribution name: DiBattista et al.

Genetic alteration of histone lysine methyltransferases and their significance in renal cell carcinoma
type: item
type: AcademicArticle
description: Background Histone lysine methyltransferases (HMTs), a category of enzymes, play essential roles in regulating transcription, cellular differentiation, and chromatin construction. The genomic landscape and clinical significance of HMTs in renal cell carcinoma (RCC) remain uncovered. Methods We conducted an integrative analysis of 50 HMTs in RCC and discovered the internal relations among copy number alterations (CNAs), expressive abundance, mutations, and clinical outcome. Results We confirmed 12 HMTs with the highest frequency of genetic alterations, including seven HMTs with high-level amplification, two HMTs with somatic mutation, and three HMTs with putative homozygous deletion. Patterns of copy number and expression varied among different subtypes of RCC, including clear cell renal cell carcinoma, papillary cell carcinoma, and chromophobe renal carcinoma. Kaplan–Meier survival analysis and multivariate analysis identified that CNA or mRNA expression in some HMTs were significantly associated with shorter overall patient survival. Systematic analysis identified six HMTs (ASH1L, PRDM6, NSD1, EZH2, WHSC1L1, SETD2) which were dysregulated by genetic alterations as candidate therapeutic targets. Discussion In summary, our findings strongly evidenced that genetic alteration of HMTs may play an important role in generation and development of RCC, which lays a solid foundation for the mechanism for further research in the future.
format: application/pdf
format: text/html
creator: Libin Yan
creator: Yangjun Zhang
creator: Beichen Ding
creator: Hui Zhou
creator: Weimin Yao
creator: Hua Xu
subject: Genetics
subject: Oncology
subject: Urology
description: doi:10.7717/peerj.6396
publisher: PeerJ Inc.
rights: © 2019 Yan et al.
abstract: Background Histone lysine methyltransferases (HMTs), a category of enzymes, play essential roles in regulating transcription, cellular differentiation, and chromatin construction. The genomic landscape and clinical significance of HMTs in renal cell carcinoma (RCC) remain uncovered. Methods We conducted an integrative analysis of 50 HMTs in RCC and discovered the internal relations among copy number alterations (CNAs), expressive abundance, mutations, and clinical outcome. Results We confirmed 12 HMTs with the highest frequency of genetic alterations, including seven HMTs with high-level amplification, two HMTs with somatic mutation, and three HMTs with putative homozygous deletion. Patterns of copy number and expression varied among different subtypes of RCC, including clear cell renal cell carcinoma, papillary cell carcinoma, and chromophobe renal carcinoma. Kaplan–Meier survival analysis and multivariate analysis identified that CNA or mRNA expression in some HMTs were significantly associated with shorter overall patient survival. Systematic analysis identified six HMTs (ASH1L, PRDM6, NSD1, EZH2, WHSC1L1, SETD2) which were dysregulated by genetic alterations as candidate therapeutic targets. Discussion In summary, our findings strongly evidenced that genetic alteration of HMTs may play an important role in generation and development of RCC, which lays a solid foundation for the mechanism for further research in the future.
bibliographic citation: Yan et al. (2019) Genetic alteration of histone lysine methyltransferases and their significance in renal cell carcinoma. PeerJ 7:e6396 https://doi.org/10.7717/peerj.6396
date submitted: 2018-08-01
date accepted: 2019-01-05
issued: 2019-02-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Libin
author list: Agent
  family name: Zhang
  given name: Yangjun
author list: Agent
  family name: Ding
  given name: Beichen
author list: Agent
  family name: Zhou
  given name: Hui
author list: Agent
  family name: Yao
  given name: Weimin
author list: Agent
  family name: Xu
  given name: Hua
doi: 10.7717/peerj.6396
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-06
copyright: © 2019 Yan et al.
attribution name: Yan et al.

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