PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites
items: Fine-scale substrate heterogeneity does not affect arthropod communities on green roofs
items: Large carnivore habitat suitability modelling for Romania and associated predictions for protected areas
items: Identification of gene-phenotype connectivity associated with flavanone naringenin by functional network analysis
items: Increased risk of thyroid disease in patients with Sjogren's syndrome: a systematic review and meta-analysis
items: Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets
items: Long-term high physical activity modulates event-related potential indices of inhibitory control in postmenopausal women
items: Estimating probabilistic context-free grammars for proteins using contact map constraints
items: Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean
items: Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys

Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites
type: item
type: AcademicArticle
description: Background Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush. Methods Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010–2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences. Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate. Results Our results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified. Discussion This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangere…
format: application/pdf
format: text/html
creator: Guoling Chen
creator: Chenqing Zheng
creator: Nelson Wan
creator: Daoqiang Liu
creator: Vivian Wing Kan Fu
creator: Xu Yang
creator: Yat-tung Yu
creator: Yang Liu
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.6643
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background Captive populations permit research and conservation of endangered species in which these efforts are hardly implemented in wild populations. Thus, analysing genetic diversity and structure of captive populations offers unique opportunities. One example is the critically endangered Blue-crowned Laughingthrush, Garrulax courtoisi, which has only two known wild populations in Wuyuan, Jiangxi and Simao, Yunnan, China. We carried out the first conservation genetic study, in order to provide useful implications that allow for successful ex situ conservation and management of the Blue-crowned Laughingthrush. Methods Using the novel microsatellite markers developed by whole-genome sequencing, we genotyped two captive populations, from the Ocean Park Hong Kong, which are of unknown origin, and the Nanchang Zoo, which were introduced from the Wuyuan wild population since the year 2010–2011, respectively. The genetic diversity of captive Blue-crowned Laughingthrush populations was estimated based on genetic polymorphisms revealed by a new microsatellite data set and mitochondrial sequences. Then, we characterised the population structure using STRUCTURE, principal coordinates analysis, population assignment test using the microsatellite data, and haplotype analysis of mitochondrial data. Additionally, we quantified genetic relatedness based on the microsatellite data with ML-Relate. Results Our results showed equally low levels of genetic diversity of the two captive Blue-crowned Laughingthrush populations. The population structure analysis, population assignment test using the microsatellite data, and haplotype analysis of the mitochondrial data showed weak population structuring between these two populations. The average pairwise relatedness coefficient was not significant, and their genetic relatedness was quantified. Discussion This study offers a genetic tool and consequently reveals a low level of genetic diversity within populations of a critically endangere…
bibliographic citation: Chen et al. (2019) Low genetic diversity in captive populations of the critically endangered Blue-crowned Laughingthrush (Garrulax courtoisi) revealed by a panel of novel microsatellites. PeerJ 7:e6643 https://doi.org/10.7717/peerj.6643
date submitted: 2018-07-16
date accepted: 2019-02-19
issued: 2019-03-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Guoling
author list: Agent
  family name: Zheng
  given name: Chenqing
author list: Agent
  family name: Wan
  given name: Nelson
author list: Agent
  family name: Liu
  given name: Daoqiang
author list: Agent
  family name: Fu
  given name: Vivian Wing Kan
author list: Agent
  family name: Yang
  given name: Xu
author list: Agent
  family name: Yu
  given name: Yat-tung
author list: Agent
  family name: Liu
  given name: Yang
doi: 10.7717/peerj.6643
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-20
copyright: © 2019 Chen et al.
attribution name: Chen et al.

Fine-scale substrate heterogeneity does not affect arthropod communities on green roofs
type: item
type: AcademicArticle
description: Green roofs, which are roofs with growing substrate and vegetation, can provide habitat for arthropods in cities. Maintaining a diversity of arthropods in an urban environment can enhance the functions they fill, such as pest control and soil development. Theory suggests that the creation of a heterogeneous environment on green roofs would enhance arthropod diversity. Several studies have examined how arthropod diversity can be enhanced on green roofs, and particularly whether substrate properties affect the arthropod community, but a gap remains in identifying the effect of substrate heterogeneity within a green roof on the arthropod community. In this paper, it is hypothesized that creating heterogeneity in the substrate would directly affect the diversity and abundance of some arthropod taxa, and indirectly increase arthropod diversity through increased plant diversity. These hypotheses were tested using green roof plots in four treatments of substrate heterogeneity: (1) homogeneous dispersion; (2) mineral heterogeneity—with increased tuff concentration in subplots; (3) organic heterogeneity—with decreased compost concentrations in subplots; (4) both mineral and organic heterogeneity. Each of the four treatments was replicated twice on each of three roofs (six replicates per treatment) in a Mediterranean region. There was no effect of substrate heterogeneity on arthropod diversity, abundance, or community composition, but there were differences in arthropod communities among roofs. This suggests that the location of a green roof, which can differ in local climatic conditions, can have a strong effect on the composition of the arthropod community. Thus, arthropod diversity may be promoted by building green roofs in a variety of locations throughout a city, even if the roof construction is similar on all roofs.
format: application/pdf
format: text/html
creator: Bracha Y. Schindler
creator: Amiel Vasl
creator: Leon Blaustein
creator: David Gurevich
creator: Gyongyver J. Kadas
creator: Merav Seifan
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.6445
publisher: PeerJ Inc.
rights: © 2019 Schindler et al.
abstract: Green roofs, which are roofs with growing substrate and vegetation, can provide habitat for arthropods in cities. Maintaining a diversity of arthropods in an urban environment can enhance the functions they fill, such as pest control and soil development. Theory suggests that the creation of a heterogeneous environment on green roofs would enhance arthropod diversity. Several studies have examined how arthropod diversity can be enhanced on green roofs, and particularly whether substrate properties affect the arthropod community, but a gap remains in identifying the effect of substrate heterogeneity within a green roof on the arthropod community. In this paper, it is hypothesized that creating heterogeneity in the substrate would directly affect the diversity and abundance of some arthropod taxa, and indirectly increase arthropod diversity through increased plant diversity. These hypotheses were tested using green roof plots in four treatments of substrate heterogeneity: (1) homogeneous dispersion; (2) mineral heterogeneity—with increased tuff concentration in subplots; (3) organic heterogeneity—with decreased compost concentrations in subplots; (4) both mineral and organic heterogeneity. Each of the four treatments was replicated twice on each of three roofs (six replicates per treatment) in a Mediterranean region. There was no effect of substrate heterogeneity on arthropod diversity, abundance, or community composition, but there were differences in arthropod communities among roofs. This suggests that the location of a green roof, which can differ in local climatic conditions, can have a strong effect on the composition of the arthropod community. Thus, arthropod diversity may be promoted by building green roofs in a variety of locations throughout a city, even if the roof construction is similar on all roofs.
bibliographic citation: Schindler et al. (2019) Fine-scale substrate heterogeneity does not affect arthropod communities on green roofs. PeerJ 7:e6445 https://doi.org/10.7717/peerj.6445
date submitted: 2018-08-17
date accepted: 2019-01-13
issued: 2019-03-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Schindler
  given name: Bracha Y.
author list: Agent
  family name: Vasl
  given name: Amiel
author list: Agent
  family name: Blaustein
  given name: Leon
author list: Agent
  family name: Gurevich
  given name: David
author list: Agent
  family name: Kadas
  given name: Gyongyver J.
author list: Agent
  family name: Seifan
  given name: Merav
doi: 10.7717/peerj.6445
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-19
copyright: ©2019 Schindler et al.
attribution name: Schindler et al.

Large carnivore habitat suitability modelling for Romania and associated predictions for protected areas
type: item
type: AcademicArticle
description: Habitat characteristics associated with species occurrences represent important baseline information for wildlife management and conservation, but have rarely been assessed for countries recently joining the EU. We used footprint tracking data and landscape characteristics in Romania to investigate the occurrence of brown bear (Ursus arctos), gray wolf (Canis lupus) and Eurasian lynx (Lynx lynx) and to compare model predictions between Natura 2000 and national-level protected areas (gap analysis). Wolves were more likely to occur where rugged terrain was present. Increasing proportion of forest was positively associated with occurrence of all large carnivores, but forest type (broadleaf, mixed, or conifer) generally varied with carnivore species. Areas where cultivated lands were extensive had little suitable habitat for lynx, whereas bear occurrence probability decreased with increasing proportion of built areas. Pastures were positively associated with wolf and lynx occurrence. Brown bears occurred primarily where national roads with high traffic volumes were at low density, while bears and lynx occurred at medium-high densities of communal roads that had lower traffic volumes. Based on predictions of carnivore distributions, natural areas protected in national parks were most suitable for carnivores, nature parks were less suitable, whereas EU-legislated Natura 2000 sites had the lowest probability of carnivore presence. Our spatially explicit carnivore habitat suitability predictions can be used by managers to amend borders of existing sites, delineate new protected areas, and establish corridors for ecological connectivity. To assist recovery and recolonization, management could also focus on habitat predicted to be suitable but where carnivores were not tracked.
format: application/pdf
format: text/html
creator: Bogdan Cristescu
creator: Csaba Domokos
creator: Kristine J. Teichman
creator: Scott E. Nielsen
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
description: doi:10.7717/peerj.6549
publisher: PeerJ Inc.
rights: © 2019 Cristescu et al.
abstract: Habitat characteristics associated with species occurrences represent important baseline information for wildlife management and conservation, but have rarely been assessed for countries recently joining the EU. We used footprint tracking data and landscape characteristics in Romania to investigate the occurrence of brown bear (Ursus arctos), gray wolf (Canis lupus) and Eurasian lynx (Lynx lynx) and to compare model predictions between Natura 2000 and national-level protected areas (gap analysis). Wolves were more likely to occur where rugged terrain was present. Increasing proportion of forest was positively associated with occurrence of all large carnivores, but forest type (broadleaf, mixed, or conifer) generally varied with carnivore species. Areas where cultivated lands were extensive had little suitable habitat for lynx, whereas bear occurrence probability decreased with increasing proportion of built areas. Pastures were positively associated with wolf and lynx occurrence. Brown bears occurred primarily where national roads with high traffic volumes were at low density, while bears and lynx occurred at medium-high densities of communal roads that had lower traffic volumes. Based on predictions of carnivore distributions, natural areas protected in national parks were most suitable for carnivores, nature parks were less suitable, whereas EU-legislated Natura 2000 sites had the lowest probability of carnivore presence. Our spatially explicit carnivore habitat suitability predictions can be used by managers to amend borders of existing sites, delineate new protected areas, and establish corridors for ecological connectivity. To assist recovery and recolonization, management could also focus on habitat predicted to be suitable but where carnivores were not tracked.
bibliographic citation: Cristescu et al. (2019) Large carnivore habitat suitability modelling for Romania and associated predictions for protected areas. PeerJ 7:e6549 https://doi.org/10.7717/peerj.6549
date submitted: 2017-11-01
date accepted: 2019-01-31
issued: 2019-03-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cristescu
  given name: Bogdan
author list: Agent
  family name: Domokos
  given name: Csaba
author list: Agent
  family name: Teichman
  given name: Kristine J.
author list: Agent
  family name: Nielsen
  given name: Scott E.
doi: 10.7717/peerj.6549
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-19
copyright: ©2019 Cristescu et al.
attribution name: Cristescu et al.

Identification of gene-phenotype connectivity associated with flavanone naringenin by functional network analysis
type: item
type: AcademicArticle
description: Naringenin, extracted from grapefruits and citrus fruits, is a bioactive flavonoid with antioxidative, anti-inflammatory, antifibrogenic, and anticancer properties. In the past two decades, the growth of publications of naringenin in PubMed suggests that naringenin is quickly gaining interest. However, systematically regarding its biological functions connected to its direct and indirect target proteins remains difficult but necessary. Herein, we employed a set of bioinformatic platforms to integrate and dissect available published data of naringenin. Analysis based on DrugBank and the Search Tool for the Retrieval of Interacting Genes/Proteins revealed seven direct protein targets and 102 indirect protein targets. The protein–protein interaction (PPI) network of total 109 naringenin-mediated proteins was next visualized using Cytoscape. What’s more, all naringenin-mediated proteins were subject to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis by the Database for Annotation, Visualization and Integrated Discovery, which resulted in three ESR1-related signaling pathways and prostate cancer pathway. Refined analysis of PPI network and KEGG pathway identified four genes (ESR1, PIK3CA, AKT1, and MAPK1). Further genomic analysis of four genes using cBioPortal indicated that naringenin might exert biological effects via ESR1 signaling axis. In general, this work scrutinized naringenin-relevant knowledge and provided an insight into the regulation and mediation of naringenin on prostate cancer.
format: application/pdf
format: text/html
creator: Suhong Fu
creator: Yongqun Zhang
creator: Jing Shi
creator: Doudou Hao
creator: Pengfei Zhang
subject: Bioinformatics
subject: Genomics
subject: Drugs and Devices
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6611
publisher: PeerJ Inc.
rights: © 2019 Fu et al.
abstract: Naringenin, extracted from grapefruits and citrus fruits, is a bioactive flavonoid with antioxidative, anti-inflammatory, antifibrogenic, and anticancer properties. In the past two decades, the growth of publications of naringenin in PubMed suggests that naringenin is quickly gaining interest. However, systematically regarding its biological functions connected to its direct and indirect target proteins remains difficult but necessary. Herein, we employed a set of bioinformatic platforms to integrate and dissect available published data of naringenin. Analysis based on DrugBank and the Search Tool for the Retrieval of Interacting Genes/Proteins revealed seven direct protein targets and 102 indirect protein targets. The protein–protein interaction (PPI) network of total 109 naringenin-mediated proteins was next visualized using Cytoscape. What’s more, all naringenin-mediated proteins were subject to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis by the Database for Annotation, Visualization and Integrated Discovery, which resulted in three ESR1-related signaling pathways and prostate cancer pathway. Refined analysis of PPI network and KEGG pathway identified four genes (ESR1, PIK3CA, AKT1, and MAPK1). Further genomic analysis of four genes using cBioPortal indicated that naringenin might exert biological effects via ESR1 signaling axis. In general, this work scrutinized naringenin-relevant knowledge and provided an insight into the regulation and mediation of naringenin on prostate cancer.
bibliographic citation: Fu et al. (2019) Identification of gene-phenotype connectivity associated with flavanone naringenin by functional network analysis. PeerJ 7:e6611 https://doi.org/10.7717/peerj.6611
date submitted: 2018-11-02
date accepted: 2019-02-12
issued: 2019-03-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fu
  given name: Suhong
author list: Agent
  family name: Zhang
  given name: Yongqun
author list: Agent
  family name: Shi
  given name: Jing
author list: Agent
  family name: Hao
  given name: Doudou
author list: Agent
  family name: Zhang
  given name: Pengfei
doi: 10.7717/peerj.6611
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-19
copyright: © 2019 Fu et al.
attribution name: Fu et al.

Increased risk of thyroid disease in patients with Sjogren's syndrome: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Sjogren’s syndrome (SS) is a chronic autoimmune epithelitis characterized by disruption of epithelial cells, ensuing lymphoplasmocytic infiltration of exocrine glands, and subsequent dryness of the mouth and eyes. Individuals with SS are more likely to have the thyroid disease. However, this association remains controversial. This meta-analysis aimed to evaluate the risk of thyroid disease in patients with SS. Methods We performed this systematic review by searching both English and Chinese literature databases. Random- or fixed-effects models were used to summarize the association between thyroid disease and SS. The results were subjected to meta-analysis with odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Results The eight articles in this meta-analysis included 988 SS cases and 2,884 controls. Overall, the risk of thyroid disease in patients with SS was significantly increased compared with controls (OR, 3.29; 95% CI [2.08–5.21]). The risk of autoimmune thyroid disease (AITD) and non-AITD were also higher in patients with SS than in controls (OR, 3.48; 95% CI [1.59–7.63]; and OR, 2.90; 95% CI [1.51–5.57], respectively). Conclusions To the best of our knowledge, this systematic review is the first to demonstrate that the risk of thyroid disease was increased in SS compared to controls, suggesting that SS patients should be screened for thyroid disease.
format: application/pdf
format: text/html
creator: Xin Sun
creator: Li Lu
creator: Yanbin Li
creator: Rong Yang
creator: Ling Shan
creator: Yang Wang
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Rheumatology
description: doi:10.7717/peerj.6737
publisher: PeerJ Inc.
rights: © 2019 Sun et al.
abstract: Background Sjogren’s syndrome (SS) is a chronic autoimmune epithelitis characterized by disruption of epithelial cells, ensuing lymphoplasmocytic infiltration of exocrine glands, and subsequent dryness of the mouth and eyes. Individuals with SS are more likely to have the thyroid disease. However, this association remains controversial. This meta-analysis aimed to evaluate the risk of thyroid disease in patients with SS. Methods We performed this systematic review by searching both English and Chinese literature databases. Random- or fixed-effects models were used to summarize the association between thyroid disease and SS. The results were subjected to meta-analysis with odds ratios (ORs) and corresponding 95% confidence intervals (CIs). Results The eight articles in this meta-analysis included 988 SS cases and 2,884 controls. Overall, the risk of thyroid disease in patients with SS was significantly increased compared with controls (OR, 3.29; 95% CI [2.08–5.21]). The risk of autoimmune thyroid disease (AITD) and non-AITD were also higher in patients with SS than in controls (OR, 3.48; 95% CI [1.59–7.63]; and OR, 2.90; 95% CI [1.51–5.57], respectively). Conclusions To the best of our knowledge, this systematic review is the first to demonstrate that the risk of thyroid disease was increased in SS compared to controls, suggesting that SS patients should be screened for thyroid disease.
bibliographic citation: Sun et al. (2019) Increased risk of thyroid disease in patients with Sjogren's syndrome: a systematic review and meta-analysis. PeerJ 7:e6737 https://doi.org/10.7717/peerj.6737
date submitted: 2018-10-22
date accepted: 2019-03-07
issued: 2019-03-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xin
author list: Agent
  family name: Lu
  given name: Li
author list: Agent
  family name: Li
  given name: Yanbin
author list: Agent
  family name: Yang
  given name: Rong
author list: Agent
  family name: Shan
  given name: Ling
author list: Agent
  family name: Wang
  given name: Yang
doi: 10.7717/peerj.6737
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-19
copyright: © 2019 Sun et al.
attribution name: Sun et al.

Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets
type: item
type: AcademicArticle
description: Background Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed. Methods To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment. Results We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr). Conclusion In general, the identified biomarker genes could …
format: application/pdf
format: text/html
creator: Chao Niu
creator: Min Jiang
creator: Na Li
creator: Jianguo Cao
creator: Meifang Hou
creator: Di-an Ni
creator: Zhaoqing Chu
subject: Molecular Biology
subject: Plant Science
subject: Data Mining and Machine Learning
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6495
publisher: PeerJ Inc.
rights: © 2019 Niu et al.
abstract: Background Current environmental pollution factors, particularly the distribution and diffusion of heavy metals in soil and water, are a high risk to local environments and humans. Despite striking advances in methods to detect contaminants by a variety of chemical and physical solutions, these methods have inherent limitations such as small dimensions and very low coverage. Therefore, identifying novel contaminant biomarkers are urgently needed. Methods To better track heavy metal contaminations in soil and water, integrated bioinformatics analysis to identify biomarkers of relevant heavy metal, such as As, Cd, Pb and Cu, is a suitable method for long-term and large-scale surveys of such heavy metal pollutants. Subsequently, the accuracy and stability of the results screened were experimentally validated by quantitative PCR experiment. Results We obtained 168 differentially expressed genes (DEGs) which contained 59 up-regulated genes and 109 down-regulated genes through comparative bioinformatics analyses. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichments of these DEGs were performed, respectively. GO analyses found that these DEGs were mainly related to responses to chemicals, responses to stimulus, responses to stress, responses to abiotic stimulus, and so on. KEGG pathway analyses of DEGs were mainly involved in the protein degradation process and other biologic process, such as the phenylpropanoid biosynthesis pathways and nitrogen metabolism. Moreover, we also speculated that nine candidate core biomarker genes (namely, NILR1, PGPS1, WRKY33, BCS1, AR781, CYP81D8, NR1, EAP1 and MYB15) might be tightly correlated with the response or transport of heavy metals. Finally, experimental results displayed that these genes had the same expression trend response to different stresses as mentioned above (Cd, Pb and Cu) and no mentioned above (Zn and Cr). Conclusion In general, the identified biomarker genes could …
bibliographic citation: Niu et al. (2019) Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through Arabidopsis thaliana GEO datasets. PeerJ 7:e6495 https://doi.org/10.7717/peerj.6495
date submitted: 2018-10-26
date accepted: 2019-01-19
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Chao
author list: Agent
  family name: Jiang
  given name: Min
author list: Agent
  family name: Li
  given name: Na
author list: Agent
  family name: Cao
  given name: Jianguo
author list: Agent
  family name: Hou
  given name: Meifang
author list: Agent
  family name: Ni
  given name: Di-an
author list: Agent
  family name: Chu
  given name: Zhaoqing
doi: 10.7717/peerj.6495
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: ©2019 Niu et al.
attribution name: Niu et al.

Long-term high physical activity modulates event-related potential indices of inhibitory control in postmenopausal women
type: item
type: AcademicArticle
description: Background Inhibition processing is sensitive to aging, and an age-related decline in inhibition processing has been associated with an accelerated rate of progression to Alzheimer disease. Elderly women are two to three times more likely than age-matched men to have Alzheimer disease. Therefore, this study examined whether long-term high physical activity affects inhibitory processing, specifically among postmenopausal women. Methods In total, 251 candidates were screened using the Montreal Cognitive Assessment and the Raven’s Standard Progressive Matrices to assess their cognitive abilities and the International Physical Activity Questionnaire (Chinese version) to assess their physical activity levels. The participants were then grouped into either a long-term high physical activity group (defined as more than 3 days of high intensity activity per week and gross metabolic equivalent minutes (MET-minutes) higher than 1,500 MET-minutes/week or a gross MET higher than 3,000 MET-minutes/week obtained through walking or other moderate or high intensity activity) or a control group and matched for demographic and health characteristics as well as cognitive scores. Event-related potentials (ERPs) were recorded as participants performed a Go/No-go task to assess inhibition processing. Results The long-term high physical activity group (n = 30) had faster Go reaction times than the control group (n = 30), whereas no significant difference between the two groups was found in their performance accuracy on the No-go task. For the ERP results, the latency of N2 component was significantly shorter in the long-term high physical activity group than that in the control group. Discussion The results of this study suggested that long-term high physical activity may increase the efficiency of the inhibitory control system by increasing the activity of response monitoring processes.
format: application/pdf
format: text/html
creator: Chang Xu
creator: Yingzhi Lu
creator: Biye Wang
creator: Chenglin Zhou
subject: Neuroscience
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Public Health
subject: Women's Health
description: doi:10.7717/peerj.6523
publisher: PeerJ Inc.
rights: © 2019 Xu et al.
abstract: Background Inhibition processing is sensitive to aging, and an age-related decline in inhibition processing has been associated with an accelerated rate of progression to Alzheimer disease. Elderly women are two to three times more likely than age-matched men to have Alzheimer disease. Therefore, this study examined whether long-term high physical activity affects inhibitory processing, specifically among postmenopausal women. Methods In total, 251 candidates were screened using the Montreal Cognitive Assessment and the Raven’s Standard Progressive Matrices to assess their cognitive abilities and the International Physical Activity Questionnaire (Chinese version) to assess their physical activity levels. The participants were then grouped into either a long-term high physical activity group (defined as more than 3 days of high intensity activity per week and gross metabolic equivalent minutes (MET-minutes) higher than 1,500 MET-minutes/week or a gross MET higher than 3,000 MET-minutes/week obtained through walking or other moderate or high intensity activity) or a control group and matched for demographic and health characteristics as well as cognitive scores. Event-related potentials (ERPs) were recorded as participants performed a Go/No-go task to assess inhibition processing. Results The long-term high physical activity group (n = 30) had faster Go reaction times than the control group (n = 30), whereas no significant difference between the two groups was found in their performance accuracy on the No-go task. For the ERP results, the latency of N2 component was significantly shorter in the long-term high physical activity group than that in the control group. Discussion The results of this study suggested that long-term high physical activity may increase the efficiency of the inhibitory control system by increasing the activity of response monitoring processes.
bibliographic citation: Xu et al. (2019) Long-term high physical activity modulates event-related potential indices of inhibitory control in postmenopausal women. PeerJ 7:e6523 https://doi.org/10.7717/peerj.6523
date submitted: 2017-12-26
date accepted: 2019-01-27
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Chang
author list: Agent
  family name: Lu
  given name: Yingzhi
author list: Agent
  family name: Wang
  given name: Biye
author list: Agent
  family name: Zhou
  given name: Chenglin
doi: 10.7717/peerj.6523
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: © 2019 Xu et al.
attribution name: Xu et al.

Estimating probabilistic context-free grammars for proteins using contact map constraints
type: item
type: AcademicArticle
description: Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins. These non-local interactions ought to be taken into account when modeling collections of proteins. Yet the most popular representations of sets of related protein sequences remain the profile Hidden Markov Models. By modeling independently the distributions of the conserved columns from an underlying multiple sequence alignment of the proteins, these models are unable to capture dependencies between the protein residues. Non-local interactions can be represented by using more expressive grammatical models. However, learning such grammars is difficult. In this work, we propose to use information on protein contacts to facilitate the training of probabilistic context-free grammars representing families of protein sequences. We develop the theory behind the introduction of contact constraints in maximum-likelihood and contrastive estimation schemes and implement it in a machine learning framework for protein grammars. The proposed framework is tested on samples of protein motifs in comparison with learning without contact constraints. The evaluation shows high fidelity of grammatical descriptors to protein structures and improved precision in recognizing sequences. Finally, we present an example of using our method in a practical setting and demonstrate its potential beyond the current state of the art by creating a grammatical model of a meta-family of protein motifs. We conclude that the current piece of research is a significant step towards more flexible and accurate modeling of collections of protein sequences. The software package is made available to the community.
format: application/pdf
format: text/html
creator: Witold Dyrka
creator: Mateusz Pyzik
creator: François Coste
creator: Hugo Talibart
subject: Bioinformatics
subject: Mathematical Biology
subject: Computational Science
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6559
publisher: PeerJ Inc.
rights: © 2019 Dyrka et al.
abstract: Interactions between amino acids that are close in the spatial structure, but not necessarily in the sequence, play important structural and functional roles in proteins. These non-local interactions ought to be taken into account when modeling collections of proteins. Yet the most popular representations of sets of related protein sequences remain the profile Hidden Markov Models. By modeling independently the distributions of the conserved columns from an underlying multiple sequence alignment of the proteins, these models are unable to capture dependencies between the protein residues. Non-local interactions can be represented by using more expressive grammatical models. However, learning such grammars is difficult. In this work, we propose to use information on protein contacts to facilitate the training of probabilistic context-free grammars representing families of protein sequences. We develop the theory behind the introduction of contact constraints in maximum-likelihood and contrastive estimation schemes and implement it in a machine learning framework for protein grammars. The proposed framework is tested on samples of protein motifs in comparison with learning without contact constraints. The evaluation shows high fidelity of grammatical descriptors to protein structures and improved precision in recognizing sequences. Finally, we present an example of using our method in a practical setting and demonstrate its potential beyond the current state of the art by creating a grammatical model of a meta-family of protein motifs. We conclude that the current piece of research is a significant step towards more flexible and accurate modeling of collections of protein sequences. The software package is made available to the community.
bibliographic citation: Dyrka et al. (2019) Estimating probabilistic context-free grammars for proteins using contact map constraints. PeerJ 7:e6559 https://doi.org/10.7717/peerj.6559
date submitted: 2018-07-26
date accepted: 2019-02-03
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dyrka
  given name: Witold
author list: Agent
  family name: Pyzik
  given name: Mateusz
author list: Agent
  family name: Coste
  given name: François
author list: Agent
  family name: Talibart
  given name: Hugo
doi: 10.7717/peerj.6559
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: ©2019 Dyrka et al.
attribution name: Dyrka et al.

Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean
type: item
type: AcademicArticle
description: Reef-forming cnidarians are extremely susceptible to the “bleaching” phenomenon caused by global warming. The effect of elevated seawater temperature has been extensively studied on Anthozoans; however, to date the impact of thermal stress on the expression of genes and proteins in Hydrozoan species has not been investigated. The present study aimed to determine the differential proteomic profile of Millepora alcicornis, which inhabits the Mexican Caribbean, in response to the El Niño-Southern Oscillation 2015–2016. Additionally, the cytolytic activity of the soluble proteomes obtained from normal and bleached M. alcicornis was assessed. Bleached specimens showed decreased symbiont’s density and chlorophyll a and c2 levels. After bleaching, we observed a differential expression of 17 key proteins, tentatively identified as related to exocytosis, calcium homeostasis, cytoskeletal organization, and potential toxins, including a metalloprotease, a phospholipase A2 (PLA2), and an actitoxin. Although, some of the differentially expressed proteins included potential toxins, the hemolytic, PLA2, and proteolytic activities elicited by the soluble proteomes from bleached and normal specimens were not significantly different. The present study provides heretofore-unknown evidence that thermal stress produces a differential expression of proteins involved in essential cellular processes of Hydrozoan species. Even though our results showed an over-expression of some potential toxin-related proteins, the cytolytic effect (as assessed by hemolytic, PLA2, and caseinolytic activities) was not increased in bleached M. alcicornis, which suggests that the cytolysis is mainly produced by toxins whose expression was not affected by temperature stress. These findings allow hypothesizing that this hydrocoral is able to prey heterotrophically when suffering from moderate bleaching, giving it a better chance to withstand the effects of high temperature.
format: application/pdf
format: text/html
creator: Norma Olguín-López
creator: Víctor Hugo Hérnandez-Elizárraga
creator: Rosalina Hernández-Matehuala
creator: Andrés Cruz-Hernández
creator: Ramón Guevara-González
creator: Juan Caballero-Pérez
creator: César Ibarra-Alvarado
creator: Alejandra Rojas-Molina
subject: Ecology
subject: Climate Change Biology
description: doi:10.7717/peerj.6593
publisher: PeerJ Inc.
rights: © 2019 Olguín-López et al.
abstract: Reef-forming cnidarians are extremely susceptible to the “bleaching” phenomenon caused by global warming. The effect of elevated seawater temperature has been extensively studied on Anthozoans; however, to date the impact of thermal stress on the expression of genes and proteins in Hydrozoan species has not been investigated. The present study aimed to determine the differential proteomic profile of Millepora alcicornis, which inhabits the Mexican Caribbean, in response to the El Niño-Southern Oscillation 2015–2016. Additionally, the cytolytic activity of the soluble proteomes obtained from normal and bleached M. alcicornis was assessed. Bleached specimens showed decreased symbiont’s density and chlorophyll a and c2 levels. After bleaching, we observed a differential expression of 17 key proteins, tentatively identified as related to exocytosis, calcium homeostasis, cytoskeletal organization, and potential toxins, including a metalloprotease, a phospholipase A2 (PLA2), and an actitoxin. Although, some of the differentially expressed proteins included potential toxins, the hemolytic, PLA2, and proteolytic activities elicited by the soluble proteomes from bleached and normal specimens were not significantly different. The present study provides heretofore-unknown evidence that thermal stress produces a differential expression of proteins involved in essential cellular processes of Hydrozoan species. Even though our results showed an over-expression of some potential toxin-related proteins, the cytolytic effect (as assessed by hemolytic, PLA2, and caseinolytic activities) was not increased in bleached M. alcicornis, which suggests that the cytolysis is mainly produced by toxins whose expression was not affected by temperature stress. These findings allow hypothesizing that this hydrocoral is able to prey heterotrophically when suffering from moderate bleaching, giving it a better chance to withstand the effects of high temperature.
bibliographic citation: Olguín-López et al. (2019) Impact of El Niño-Southern Oscillation 2015-2016 on the soluble proteomic profile and cytolytic activity of Millepora alcicornis (“fire coral”) from the Mexican Caribbean. PeerJ 7:e6593 https://doi.org/10.7717/peerj.6593
date submitted: 2018-11-15
date accepted: 2019-02-09
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olguín-López
  given name: Norma
author list: Agent
  family name: Hérnandez-Elizárraga
  given name: Víctor Hugo
author list: Agent
  family name: Hernández-Matehuala
  given name: Rosalina
author list: Agent
  family name: Cruz-Hernández
  given name: Andrés
author list: Agent
  family name: Guevara-González
  given name: Ramón
author list: Agent
  family name: Caballero-Pérez
  given name: Juan
author list: Agent
  family name: Ibarra-Alvarado
  given name: César
author list: Agent
  family name: Rojas-Molina
  given name: Alejandra
doi: 10.7717/peerj.6593
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: © 2019 Olguín-López et al.
attribution name: Olguín-López et al.

Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys
type: item
type: AcademicArticle
description: Background Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500–4,500 m) temperate forests in southern and central China. Methods We used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences. Results We identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host. Conclusions Our results indicate that ERV sequences are widely …
format: application/pdf
format: text/html
creator: Xiao Wang
creator: Boshi Wang
creator: Zhijin Liu
creator: Paul A. Garber
creator: Huijuan Pan
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.6602
publisher: PeerJ Inc.
rights: © 2019 Wang et al.
abstract: Background Endogenous retroviruses (ERV) are remnants of former exogenous retroviruses that had previously invaded the germ line of the host that can be vertically transmitted across generations. While the majority of ERVs lack infectious capacity due to the accumulation of deleterious mutations, some ERVs remain active and produce potentially infectious viral particles. ERV sequences have been reported in all mammals; however, the distribution and diversity of ERVs in several primate taxa remains unclear. The aim of this study was to identify and classify the ERV sequences in the genomes of the golden snub-nosed monkey (Rhinopithecus roxellana) and the black and white snub-nosed monkey (Rhinopithecus bieti), two endangered primate species that exploit high altitude (2,500–4,500 m) temperate forests in southern and central China. Methods We used a TBLASTN program to search the ERV sequences of golden snub-nosed monkey genome and the black and white snub-nosed monkey genome. We retrieved all complete accession sequences from the homology search and then used the program, RetroTector, to check and identify the ERV sequences. Results We identified 284 and 263 endogenous retrovirus sequences in R. roxellana and R. bieti respectively. The proportion of full-length sequences of all ERV was 30% in R. roxellana and 21% in R. bieti and they were described as class I and class II or gamma-retrovirus and beta-retrovirus genera. The truncation pattern distribution in the two species was virtually identical. By analyzing and comparing ERV orthologues among 6 primate species, we identified the co-evolution of ERVs with their host. We also examined ERV-like sequences and found 48 such genes in R. roxellana and 63 in R. bieti. Some of those genes are associated with diseases, suggesting that ERVs might have involved the abnormal expression of certain genes that have contributed to deleterious consequences for the host. Conclusions Our results indicate that ERV sequences are widely …
bibliographic citation: Wang et al. (2019) Genome-wide characterization of endogenous retroviruses in snub-nosed monkeys. PeerJ 7:e6602 https://doi.org/10.7717/peerj.6602
date submitted: 2018-10-25
date accepted: 2019-02-11
issued: 2019-03-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiao
author list: Agent
  family name: Wang
  given name: Boshi
author list: Agent
  family name: Liu
  given name: Zhijin
author list: Agent
  family name: Garber
  given name: Paul A.
author list: Agent
  family name: Pan
  given name: Huijuan
doi: 10.7717/peerj.6602
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-18
copyright: ©2019 Wang et al.
attribution name: Wang et al.

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