PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Association analysis between chronic obstructive pulmonary disease and polymorphisms in circadian genes
items: Quantitative proteomics suggests changes in the carbohydrate metabolism of maize in response to larvae of the belowground herbivore Holotrichia parallela
items: Growth parameter k and location affect body size responses to spatial protection by exploited rockfishes
items: Why people select the outpatient clinic of medical centers: a nationwide analysis in Taiwan
items: In situ SEM/EDS compositional characterization of osteocytes and blood vessels in fossil and extant turtles on untreated bone surfaces; different preservational pathways microns away
items: Spatial distribution of microbial communities among colonies and genotypes in nursery-reared Acropora cervicornis
items: In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis
items: Extracellular vesicles in patients in the acute phase of psychosis and after clinical improvement: an explorative study
items: Idiosyncratic liver pigment alterations of five frog species in response to contrasting land use patterns in the Brazilian Cerrado
items: HPLC profiling of selected phenolic acids and flavonoids in Salvia eigii, Salvia hierosolymitana and Salvia viridis growing wild in Jordan and their in vitro antioxidant activity

Association analysis between chronic obstructive pulmonary disease and polymorphisms in circadian genes
type: item
type: AcademicArticle
description: Background Circadian genes have been suggested to play an important role in lung pathology. However, it remains unknown whether polymorphisms of these genes are associated with chronic obstructive pulmonary disease (COPD). Here, we aimed to investigate the association of circadian genes polymorphisms with COPD in a case-control study of 477 COPD patient and 323 control Han Chinese persons. Methods Genotyping assays were carried out for nine single nucleotide polymorphisms (SNPs) from five circadian genes (PER3, CLOCK, RORB, BMAL1 and CRY2) that were previously identified in lung pathology. Age, sex, BMI and smoking status and comorbidities were recorded for all subjects. Results No significant association was found in all SNP sites in overall subjects and no significant difference was found in age, sex, smoking status stratification analysis. Discussion The findings of this investigation indicated the effect of circadian genes polymorphisms on COPD susceptibility may only be small and possibly dependent on the subject factors, such as age and sex.
format: application/pdf
format: text/html
creator: Guo Chen
creator: Jingwei Zhang
creator: Lijuan Zhang
creator: Xuan Xiong
creator: Dongke Yu
creator: Yuan Zhang
subject: Geriatrics
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.9806
publisher: PeerJ Inc.
rights: © 2020 Chen et al.
abstract: Background Circadian genes have been suggested to play an important role in lung pathology. However, it remains unknown whether polymorphisms of these genes are associated with chronic obstructive pulmonary disease (COPD). Here, we aimed to investigate the association of circadian genes polymorphisms with COPD in a case-control study of 477 COPD patient and 323 control Han Chinese persons. Methods Genotyping assays were carried out for nine single nucleotide polymorphisms (SNPs) from five circadian genes (PER3, CLOCK, RORB, BMAL1 and CRY2) that were previously identified in lung pathology. Age, sex, BMI and smoking status and comorbidities were recorded for all subjects. Results No significant association was found in all SNP sites in overall subjects and no significant difference was found in age, sex, smoking status stratification analysis. Discussion The findings of this investigation indicated the effect of circadian genes polymorphisms on COPD susceptibility may only be small and possibly dependent on the subject factors, such as age and sex.
bibliographic citation: Chen et al. (2020) Association analysis between chronic obstructive pulmonary disease and polymorphisms in circadian genes. PeerJ 8:e9806 https://doi.org/10.7717/peerj.9806
date submitted: 2020-04-22
date accepted: 2020-08-03
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Guo
author list: Agent
  family name: Zhang
  given name: Jingwei
author list: Agent
  family name: Zhang
  given name: Lijuan
author list: Agent
  family name: Xiong
  given name: Xuan
author list: Agent
  family name: Yu
  given name: Dongke
author list: Agent
  family name: Zhang
  given name: Yuan
doi: 10.7717/peerj.9806
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: © 2020 Chen et al.
attribution name: Chen et al.

Quantitative proteomics suggests changes in the carbohydrate metabolism of maize in response to larvae of the belowground herbivore Holotrichia parallela
type: item
type: AcademicArticle
description: The larvae of Holotrichia parallela, a destructive belowground herbivore, may cause yield losses of up to 20% in maize in a typical year. To understand the protein-level mechanisms governing the response of maize to this herbivore, tandem mass tag (TMT) quantitative proteomics was used for the comparative analysis of protein abundance in the maize roots after H. parallela larval attack. A total of 351 upregulated proteins and 303 downregulated proteins were identified. Pathway enrichment analysis revealed that the differentially abundant proteins (DAPs) were most strongly associated with carbohydrate and energy metabolism pathways, such as glycolysis, pentose phosphate pathway and fructose and mannose metabolism. Most glycolysis-related proteins were significantly induced. In addition, H. parallela larval attack decreased the glucose concentrations in the roots. This study demonstrates that maize can manipulate carbohydrate metabolism by modifying glycolysis and pentose phosphate pathway response to root-feeding herbivorous attackers. The results of this study may help to establish a foundation for further functional studies of key protein-mediated responses to H. parallela larvae in maize.
format: application/pdf
format: text/html
creator: Yu Pan
creator: Shiwen Zhao
creator: Zhun Wang
creator: Xiao Wang
creator: Xinxin Zhang
creator: Yunshuo Lee
creator: Jinghui Xi
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.9819
publisher: PeerJ Inc.
rights: © 2020 Pan et al.
abstract: The larvae of Holotrichia parallela, a destructive belowground herbivore, may cause yield losses of up to 20% in maize in a typical year. To understand the protein-level mechanisms governing the response of maize to this herbivore, tandem mass tag (TMT) quantitative proteomics was used for the comparative analysis of protein abundance in the maize roots after H. parallela larval attack. A total of 351 upregulated proteins and 303 downregulated proteins were identified. Pathway enrichment analysis revealed that the differentially abundant proteins (DAPs) were most strongly associated with carbohydrate and energy metabolism pathways, such as glycolysis, pentose phosphate pathway and fructose and mannose metabolism. Most glycolysis-related proteins were significantly induced. In addition, H. parallela larval attack decreased the glucose concentrations in the roots. This study demonstrates that maize can manipulate carbohydrate metabolism by modifying glycolysis and pentose phosphate pathway response to root-feeding herbivorous attackers. The results of this study may help to establish a foundation for further functional studies of key protein-mediated responses to H. parallela larvae in maize.
bibliographic citation: Pan et al. (2020) Quantitative proteomics suggests changes in the carbohydrate metabolism of maize in response to larvae of the belowground herbivore Holotrichia parallela. PeerJ 8:e9819 https://doi.org/10.7717/peerj.9819
date submitted: 2020-03-23
date accepted: 2020-08-05
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Yu
author list: Agent
  family name: Zhao
  given name: Shiwen
author list: Agent
  family name: Wang
  given name: Zhun
author list: Agent
  family name: Wang
  given name: Xiao
author list: Agent
  family name: Zhang
  given name: Xinxin
author list: Agent
  family name: Lee
  given name: Yunshuo
author list: Agent
  family name: Xi
  given name: Jinghui
doi: 10.7717/peerj.9819
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: ©2020 Pan et al.
attribution name: Pan et al.

Growth parameter k and location affect body size responses to spatial protection by exploited rockfishes
type: item
type: AcademicArticle
description: For many fish taxa, trophic position and relative fecundity increase with body size, yet fisheries remove the largest individuals, altering food webs and reducing population productivity. Marine reserves and other forms of spatial protection can help mitigate this problem, but the effectiveness of these management tools may vary interspecifically and spatially. Using visual survey data collected on the Central Coast of British Columbia, for 12 species of exploited rockfish we found that body size responses to spatial fishery closures depended on interspecific variation in growth parameter k (the rate at which the asymptotic body size is approached) and on location. For two closures, relative body sizes were larger at protected than at adjacent fished sites, and these differences were greater for species with lower k values. Reduced fishery mortality likely drove these results, as an unfished species did not respond to spatial protection. For three closures, however, body sizes did not differ between protected and adjacent fished sites, and for another closure species with higher k values were larger at fished than at protected sites while species with lower k values had similar sizes in both treatments. Variation in the age of closures is unlikely to have influenced results, as most data were collected when closures were 13 to 15-years-old. Rather, the lack of larger fish inside four of six spatial fishery closures potentially reflects a combination of smaller size of the area protected, poor fisher compliance, and lower oceanographic productivity. Interspecific differences in movement behavior did not affect body size responses to spatial protection. To improve understanding, additional research should be conducted at deeper depths encompassing the distribution of older, larger fish. Our study—which was conceptualized and executed by an alliance of Indigenous peoples seeking to restore rockfishes—illustrates how life history and behavioral theory provide a useful l…
format: application/pdf
format: text/html
creator: Madeleine McGreer
creator: Alejandro Frid
creator: Tristan Blaine
creator: Sandie Hankewich
creator: Ernest Mason
creator: Mike Reid
creator: Hannah Kobluk
subject: Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.9825
publisher: PeerJ Inc.
rights: © 2020 McGreer et al.
abstract: For many fish taxa, trophic position and relative fecundity increase with body size, yet fisheries remove the largest individuals, altering food webs and reducing population productivity. Marine reserves and other forms of spatial protection can help mitigate this problem, but the effectiveness of these management tools may vary interspecifically and spatially. Using visual survey data collected on the Central Coast of British Columbia, for 12 species of exploited rockfish we found that body size responses to spatial fishery closures depended on interspecific variation in growth parameter k (the rate at which the asymptotic body size is approached) and on location. For two closures, relative body sizes were larger at protected than at adjacent fished sites, and these differences were greater for species with lower k values. Reduced fishery mortality likely drove these results, as an unfished species did not respond to spatial protection. For three closures, however, body sizes did not differ between protected and adjacent fished sites, and for another closure species with higher k values were larger at fished than at protected sites while species with lower k values had similar sizes in both treatments. Variation in the age of closures is unlikely to have influenced results, as most data were collected when closures were 13 to 15-years-old. Rather, the lack of larger fish inside four of six spatial fishery closures potentially reflects a combination of smaller size of the area protected, poor fisher compliance, and lower oceanographic productivity. Interspecific differences in movement behavior did not affect body size responses to spatial protection. To improve understanding, additional research should be conducted at deeper depths encompassing the distribution of older, larger fish. Our study—which was conceptualized and executed by an alliance of Indigenous peoples seeking to restore rockfishes—illustrates how life history and behavioral theory provide a useful l…
bibliographic citation: McGreer et al. (2020) Growth parameter k and location affect body size responses to spatial protection by exploited rockfishes. PeerJ 8:e9825 https://doi.org/10.7717/peerj.9825
date submitted: 2020-05-13
date accepted: 2020-08-05
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: McGreer
  given name: Madeleine
author list: Agent
  family name: Frid
  given name: Alejandro
author list: Agent
  family name: Blaine
  given name: Tristan
author list: Agent
  family name: Hankewich
  given name: Sandie
author list: Agent
  family name: Mason
  given name: Ernest
author list: Agent
  family name: Reid
  given name: Mike
author list: Agent
  family name: Kobluk
  given name: Hannah
doi: 10.7717/peerj.9825
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: ©2020 McGreer et al.
attribution name: McGreer et al.

Why people select the outpatient clinic of medical centers: a nationwide analysis in Taiwan
type: item
type: AcademicArticle
description: Introduction In contrast to other countries, Taiwan’s National Health Insurance (NHI) program allows patients to freely select the specialists and tiers of medical care facility without a referral. Some medical centers in Taiwan receive over 10,000 outpatients per day. In the NHI program, the co-payment was increased for high-tier facilities for outpatient visits in 2002, 2005, and 2017. However, the policies only mildly reduced the use of high-tier medical care facilities. The main purpose of this study was to evaluate the factors contributing to the patients’ selection of the outpatient clinic of medical centers without a referral. Methods An online anonymous survey was conducted by using the Google Forms platform utilizing a self-constructed questionnaire from September to October 2018. A nationwide sample in Taiwan was recruited using convenience sampling through social media. Based on a literature review and a focus group, 20 factors that may affect the choice of the outpatient institution were constructed. The associations between items that affect the patients selection of outpatient clinics were assessed using exploratory factor analysis. Principal axis factoring was performed to identify the major factors affecting the decision. Multiple logistic regression was performed to determine which factors satisfactorily explained “visiting the outpatient clinic of the medical center for an illness without a referral.” Results During the survey period, 5,060 people browsed the online survey, and 1,003 responded and completed the online questionnaire. Therefore, the response rate was 19.8%. A total of 987 valid responses was collected. Exploratory factor analysis revealed that three main factors, namely the “physician factor”, “image and reputation factor”, and “facility and medication factor”, affected the selection of outpatient clinics. A series of logistic regressions indicated that patients who reported that hospital facilities, high-quality drugs, and diverse s…
format: application/pdf
format: text/html
creator: Ming-Hwai Lin
creator: Hsiao-Ting Chang
creator: Tzeng-Ji Chen
creator: Shinn-Jang Hwang
subject: Health Policy
subject: Public Health
description: doi:10.7717/peerj.9829
publisher: PeerJ Inc.
rights: © 2020 Lin et al.
abstract: Introduction In contrast to other countries, Taiwan’s National Health Insurance (NHI) program allows patients to freely select the specialists and tiers of medical care facility without a referral. Some medical centers in Taiwan receive over 10,000 outpatients per day. In the NHI program, the co-payment was increased for high-tier facilities for outpatient visits in 2002, 2005, and 2017. However, the policies only mildly reduced the use of high-tier medical care facilities. The main purpose of this study was to evaluate the factors contributing to the patients’ selection of the outpatient clinic of medical centers without a referral. Methods An online anonymous survey was conducted by using the Google Forms platform utilizing a self-constructed questionnaire from September to October 2018. A nationwide sample in Taiwan was recruited using convenience sampling through social media. Based on a literature review and a focus group, 20 factors that may affect the choice of the outpatient institution were constructed. The associations between items that affect the patients selection of outpatient clinics were assessed using exploratory factor analysis. Principal axis factoring was performed to identify the major factors affecting the decision. Multiple logistic regression was performed to determine which factors satisfactorily explained “visiting the outpatient clinic of the medical center for an illness without a referral.” Results During the survey period, 5,060 people browsed the online survey, and 1,003 responded and completed the online questionnaire. Therefore, the response rate was 19.8%. A total of 987 valid responses was collected. Exploratory factor analysis revealed that three main factors, namely the “physician factor”, “image and reputation factor”, and “facility and medication factor”, affected the selection of outpatient clinics. A series of logistic regressions indicated that patients who reported that hospital facilities, high-quality drugs, and diverse s…
bibliographic citation: Lin et al. (2020) Why people select the outpatient clinic of medical centers: a nationwide analysis in Taiwan. PeerJ 8:e9829 https://doi.org/10.7717/peerj.9829
date submitted: 2020-04-27
date accepted: 2020-08-06
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Ming-Hwai
author list: Agent
  family name: Chang
  given name: Hsiao-Ting
author list: Agent
  family name: Chen
  given name: Tzeng-Ji
author list: Agent
  family name: Hwang
  given name: Shinn-Jang
doi: 10.7717/peerj.9829
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: ©2020 Lin et al.
attribution name: Lin et al.

In situ SEM/EDS compositional characterization of osteocytes and blood vessels in fossil and extant turtles on untreated bone surfaces; different preservational pathways microns away
type: item
type: AcademicArticle
description: Osteocytes and blood vessels are the main cellular and tissue components of the bone tissue of vertebrates. Evidence of these soft-tissue microstructures has been widely documented in the fossil record of Mesozoic and Cenozoic turtles. However, all these studies have characterized morphologically and elementally these microstructures via isolation from the fossilized bone matrix where they were preserved or in ground sections, which could raise skepticism about the results due to potential cross-contamination or reagents effects. Fossil turtle bones from three different localities with distinct preservation environments and geological settings, including Mongolemys elegans from the Late Cretaceous of Mongolia, Allaeochelys crassesculpta from the Eocene of Germany, and a podocnemidid indet. from the Miocene of Colombia are studied here. Bone from two extant turtle species, Lepidochelys olivacea, and Podocnemis lewyana, as well as a commercial chicken Gallus gallus were used for comparisons. Scanning Electron Microscopy-Energy Dispersive Spectroscopy analyses performed directly on untreated fresh surfaces show that osteocytes-like in the fossil turtle bone are mostly composed of iron and manganese. In contrast, the in situ blood vessels-like of the fossil turtles, as well as those from the extant taxa are rich in elements typically organic in origin (carbon and nitrogen), which are absent to minimally present in the surrounding bone or rock matrix; this suggests a possible endogenous composition for these fossil structures. Also, the results presented here show that although originally both (osteocytes and blood vessels) are organic soft components of bone as evidenced in the extant turtles and chicken, they can experience completely different preservational pathways only microns away from each other in the same fossil bone.
format: application/pdf
format: text/html
creator: Edwin-Alberto Cadena
subject: Cell Biology
subject: Paleontology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.9833
publisher: PeerJ Inc.
rights: © 2020 Cadena
abstract: Osteocytes and blood vessels are the main cellular and tissue components of the bone tissue of vertebrates. Evidence of these soft-tissue microstructures has been widely documented in the fossil record of Mesozoic and Cenozoic turtles. However, all these studies have characterized morphologically and elementally these microstructures via isolation from the fossilized bone matrix where they were preserved or in ground sections, which could raise skepticism about the results due to potential cross-contamination or reagents effects. Fossil turtle bones from three different localities with distinct preservation environments and geological settings, including Mongolemys elegans from the Late Cretaceous of Mongolia, Allaeochelys crassesculpta from the Eocene of Germany, and a podocnemidid indet. from the Miocene of Colombia are studied here. Bone from two extant turtle species, Lepidochelys olivacea, and Podocnemis lewyana, as well as a commercial chicken Gallus gallus were used for comparisons. Scanning Electron Microscopy-Energy Dispersive Spectroscopy analyses performed directly on untreated fresh surfaces show that osteocytes-like in the fossil turtle bone are mostly composed of iron and manganese. In contrast, the in situ blood vessels-like of the fossil turtles, as well as those from the extant taxa are rich in elements typically organic in origin (carbon and nitrogen), which are absent to minimally present in the surrounding bone or rock matrix; this suggests a possible endogenous composition for these fossil structures. Also, the results presented here show that although originally both (osteocytes and blood vessels) are organic soft components of bone as evidenced in the extant turtles and chicken, they can experience completely different preservational pathways only microns away from each other in the same fossil bone.
bibliographic citation: Cadena (2020) In situ SEM/EDS compositional characterization of osteocytes and blood vessels in fossil and extant turtles on untreated bone surfaces; different preservational pathways microns away. PeerJ 8:e9833 https://doi.org/10.7717/peerj.9833
date submitted: 2020-07-03
date accepted: 2020-08-07
issued: 2020-08-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cadena
  given name: Edwin-Alberto
doi: 10.7717/peerj.9833
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-27
copyright: ©2020 Cadena
attribution name: Cadena

Spatial distribution of microbial communities among colonies and genotypes in nursery-reared Acropora cervicornis
type: item
type: AcademicArticle
description: Background The architecturally important coral species Acropora cervicornis and A. palmata were historically common in the Caribbean, but have declined precipitously since the early 1980s. Substantial resources are currently being dedicated to coral gardening and the subsequent outplanting of asexually reproduced colonies of Acropora, activities that provide abundant biomass for both restoration efforts and for experimental studies to better understand the ecology of these critically endangered coral species. Methods We characterized the bacterial and archaeal community composition of A. cervicornis corals in a Caribbean nursery to determine the heterogeneity of the microbiome within and among colonies. Samples were taken from three distinct locations (basal branch, intermediate branch, and branch tip) from colonies of three different coral genotypes. Results Overall, microbial community composition was similar among colonies due to high relative abundances of the Rickettsiales genus MD3-55 (Candidatus Aquarickettsia) in nearly all samples. While microbial communities were not different among locations within the same colony, they were significantly different between coral genotypes. These findings suggest that sampling from any one location on a coral host is likely to provide a representative sample of the microbial community for the entire colony. Our results also suggest that subtle differences in microbiome composition may be influenced by the coral host, where different coral genotypes host slightly different microbiomes. Finally, this study provides baseline data for future studies seeking to understand the microbiome of nursery-reared A. cervicornis and its roles in coral health, adaptability, and resilience.
format: application/pdf
format: text/html
creator: Nicole Miller
creator: Paul Maneval
creator: Carrie Manfrino
creator: Thomas K. Frazer
creator: Julie L. Meyer
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Population Biology
description: doi:10.7717/peerj.9635
publisher: PeerJ Inc.
rights: © 2020 Miller et al.
abstract: Background The architecturally important coral species Acropora cervicornis and A. palmata were historically common in the Caribbean, but have declined precipitously since the early 1980s. Substantial resources are currently being dedicated to coral gardening and the subsequent outplanting of asexually reproduced colonies of Acropora, activities that provide abundant biomass for both restoration efforts and for experimental studies to better understand the ecology of these critically endangered coral species. Methods We characterized the bacterial and archaeal community composition of A. cervicornis corals in a Caribbean nursery to determine the heterogeneity of the microbiome within and among colonies. Samples were taken from three distinct locations (basal branch, intermediate branch, and branch tip) from colonies of three different coral genotypes. Results Overall, microbial community composition was similar among colonies due to high relative abundances of the Rickettsiales genus MD3-55 (Candidatus Aquarickettsia) in nearly all samples. While microbial communities were not different among locations within the same colony, they were significantly different between coral genotypes. These findings suggest that sampling from any one location on a coral host is likely to provide a representative sample of the microbial community for the entire colony. Our results also suggest that subtle differences in microbiome composition may be influenced by the coral host, where different coral genotypes host slightly different microbiomes. Finally, this study provides baseline data for future studies seeking to understand the microbiome of nursery-reared A. cervicornis and its roles in coral health, adaptability, and resilience.
bibliographic citation: Miller et al. (2020) Spatial distribution of microbial communities among colonies and genotypes in nursery-reared Acropora cervicornis. PeerJ 8:e9635 https://doi.org/10.7717/peerj.9635
date submitted: 2020-05-05
date accepted: 2020-07-09
issued: 2020-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miller
  given name: Nicole
author list: Agent
  family name: Maneval
  given name: Paul
author list: Agent
  family name: Manfrino
  given name: Carrie
author list: Agent
  family name: Frazer
  given name: Thomas K.
author list: Agent
  family name: Meyer
  given name: Julie L.
doi: 10.7717/peerj.9635
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-26
copyright: ©2020 Miller et al.
attribution name: Miller et al.

In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis
type: item
type: AcademicArticle
description: Corynebacterium pseudotuberculosis is a pathogen of veterinary relevance diseases, being divided into two biovars: equi and ovis; causing ulcerative lymphangitis and caseous lymphadenitis, respectively. The isolation and sequencing of C. pseudotuberculosis biovar ovis strains in the Northern and Northeastern regions of Brazil exhibited the emergence of this pathogen, which causes economic losses to small ruminant producers, and condemnation of carcasses and skins of animals. Through the pan-genomic approach, it is possible to determine and analyze genes that are shared by all strains of a species—the core genome. However, many of these genes do not have any predicted function, being characterized as hypothetical proteins (HP). In this study, we considered 32 C. pseudotuberculosis biovar ovis genomes for the pan-genomic analysis, where were identified 172 HP present in a core genome composed by 1255 genes. We are able to functionally annotate 80 sequences previously characterized as HP through the identification of structural features as conserved domains and families. Furthermore, we analyzed the physicochemical properties, subcellular localization and molecular function. Additionally, through RNA-seq data, we investigated the differential gene expression of the annotated HP. Genes inserted in pathogenicity islands had their virulence potential evaluated. Also, we have analyzed the existence of functional associations for their products based on protein–protein interaction networks, and perform the structural prediction of three targets. Due to the integration of different strategies, this study can underlie deeper in vitro researches in the characterization of these HP and the search for new solutions for combat this pathogen.
format: application/pdf
format: text/html
creator: Carlos Leonardo Araújo
creator: Iago Blanco
creator: Luciana Souza
creator: Sandeep Tiwari
creator: Lino César Pereira
creator: Preetam Ghosh
creator: Vasco Azevedo
creator: Artur Silva
creator: Adriana Folador
subject: Computational Biology
subject: Genomics
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.9643
publisher: PeerJ Inc.
rights: © 2020 Araújo et al.
abstract: Corynebacterium pseudotuberculosis is a pathogen of veterinary relevance diseases, being divided into two biovars: equi and ovis; causing ulcerative lymphangitis and caseous lymphadenitis, respectively. The isolation and sequencing of C. pseudotuberculosis biovar ovis strains in the Northern and Northeastern regions of Brazil exhibited the emergence of this pathogen, which causes economic losses to small ruminant producers, and condemnation of carcasses and skins of animals. Through the pan-genomic approach, it is possible to determine and analyze genes that are shared by all strains of a species—the core genome. However, many of these genes do not have any predicted function, being characterized as hypothetical proteins (HP). In this study, we considered 32 C. pseudotuberculosis biovar ovis genomes for the pan-genomic analysis, where were identified 172 HP present in a core genome composed by 1255 genes. We are able to functionally annotate 80 sequences previously characterized as HP through the identification of structural features as conserved domains and families. Furthermore, we analyzed the physicochemical properties, subcellular localization and molecular function. Additionally, through RNA-seq data, we investigated the differential gene expression of the annotated HP. Genes inserted in pathogenicity islands had their virulence potential evaluated. Also, we have analyzed the existence of functional associations for their products based on protein–protein interaction networks, and perform the structural prediction of three targets. Due to the integration of different strategies, this study can underlie deeper in vitro researches in the characterization of these HP and the search for new solutions for combat this pathogen.
bibliographic citation: Araújo et al. (2020) In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis. PeerJ 8:e9643 https://doi.org/10.7717/peerj.9643
date submitted: 2020-01-29
date accepted: 2020-07-10
issued: 2020-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Araújo
  given name: Carlos Leonardo
author list: Agent
  family name: Blanco
  given name: Iago
author list: Agent
  family name: Souza
  given name: Luciana
author list: Agent
  family name: Tiwari
  given name: Sandeep
author list: Agent
  family name: Pereira
  given name: Lino César
author list: Agent
  family name: Ghosh
  given name: Preetam
author list: Agent
  family name: Azevedo
  given name: Vasco
author list: Agent
  family name: Silva
  given name: Artur
author list: Agent
  family name: Folador
  given name: Adriana
doi: 10.7717/peerj.9643
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-26
copyright: © 2020 Araújo et al.
attribution name: Araújo et al.

Extracellular vesicles in patients in the acute phase of psychosis and after clinical improvement: an explorative study
type: item
type: AcademicArticle
description: Extracellular vesicles (EVs) are cell-derived structures that transport proteins, lipids and nucleic acids between cells, thereby affecting the phenotype of the recipient cell. As the content of EVs reflects the status of the originating cell, EVs can have potential as biomarkers. Identifying EVs, including their cells of origin and their cargo, may provide insights in the pathophysiology of psychosis. Here, we present an in-depth analysis and proteomics of EVs from peripheral blood in patients (n = 25) during and after the acute phase of psychosis. Concentration and protein content of EVs in psychotic patients were twofold higher than in 25 age- and sex-matched healthy controls (p < 0.001 for both concentration and protein content), and the diameter of EVs was larger in patients (p = 0.02). Properties of EVs did not differ significantly in blood sampled during and after the acute psychotic episode. Proteomic analyses on isolated EVs from individual patients revealed 1,853 proteins, whereof 45 were brain-elevated proteins. Of these, five proteins involved in regulation of plasticity of glutamatergic synapses were significantly different in psychotic patients compared to controls; neurogranin (NRGN), neuron-specific calcium-binding protein hippocalcin (HPCA), kalirin (KALRN), beta-adducin (ADD2) and ankyrin-2 (ANK2). To summarize, our results show that peripheral EVs in psychotic patients are different from those in healthy controls and point at alterations on the glutamatergic system. We suggest that EVs allow investigation of blood-borne brain-originating biological material and that their role as biomarkers in patients with psychotic disorders is worthy of further exploration.
format: application/pdf
format: text/html
creator: Mette Elise Tunset
creator: Hanne Haslene-Hox
creator: Tim Van Den Bossche
creator: Arne Einar Vaaler
creator: Einar Sulheim
creator: Daniel Kondziella
subject: Bioinformatics
subject: Neuroscience
subject: Immunology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9714
publisher: PeerJ Inc.
rights: © 2020 Tunset et al.
abstract: Extracellular vesicles (EVs) are cell-derived structures that transport proteins, lipids and nucleic acids between cells, thereby affecting the phenotype of the recipient cell. As the content of EVs reflects the status of the originating cell, EVs can have potential as biomarkers. Identifying EVs, including their cells of origin and their cargo, may provide insights in the pathophysiology of psychosis. Here, we present an in-depth analysis and proteomics of EVs from peripheral blood in patients (n = 25) during and after the acute phase of psychosis. Concentration and protein content of EVs in psychotic patients were twofold higher than in 25 age- and sex-matched healthy controls (p < 0.001 for both concentration and protein content), and the diameter of EVs was larger in patients (p = 0.02). Properties of EVs did not differ significantly in blood sampled during and after the acute psychotic episode. Proteomic analyses on isolated EVs from individual patients revealed 1,853 proteins, whereof 45 were brain-elevated proteins. Of these, five proteins involved in regulation of plasticity of glutamatergic synapses were significantly different in psychotic patients compared to controls; neurogranin (NRGN), neuron-specific calcium-binding protein hippocalcin (HPCA), kalirin (KALRN), beta-adducin (ADD2) and ankyrin-2 (ANK2). To summarize, our results show that peripheral EVs in psychotic patients are different from those in healthy controls and point at alterations on the glutamatergic system. We suggest that EVs allow investigation of blood-borne brain-originating biological material and that their role as biomarkers in patients with psychotic disorders is worthy of further exploration.
bibliographic citation: Tunset et al. (2020) Extracellular vesicles in patients in the acute phase of psychosis and after clinical improvement: an explorative study. PeerJ 8:e9714 https://doi.org/10.7717/peerj.9714
date submitted: 2020-05-05
date accepted: 2020-07-23
issued: 2020-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tunset
  given name: Mette Elise
author list: Agent
  family name: Haslene-Hox
  given name: Hanne
author list: Agent
  family name: Van Den Bossche
  given name: Tim
author list: Agent
  family name: Vaaler
  given name: Arne Einar
author list: Agent
  family name: Sulheim
  given name: Einar
author list: Agent
  family name: Kondziella
  given name: Daniel
doi: 10.7717/peerj.9714
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-26
copyright: ©2020 Tunset et al.
attribution name: Tunset et al.

Idiosyncratic liver pigment alterations of five frog species in response to contrasting land use patterns in the Brazilian Cerrado
type: item
type: AcademicArticle
description: Background Changes in land use trigger environmental changes that can lead to decreased biodiversity and species loss. The liver is an essential detoxification organ that reflects systemic physiological responses to environmental changes. Here, we tested whether contrasting land use patterns influence the amount of substances from the hepatic cellular catabolism and melanomacrophages (MMs) of five anuran species in the Brazilian Cerrado. Methods We collected the same five species of pond-dwelling frogs in one protected area and in an area with intense agricultural activity. We used routine histological and histochemical techniques to quantify the area occupied by lipofuscin, melanin, and hemosiderin in the liver of two frogs Leptodactylus fuscus, Physalaemus cuvieri, and three tree-frogs Dendropsophus minutus, Scinax fuscomarginatus, and Boana albopunctata. We classified land use types in a buffer around each pond based on satellite images. We then used a double-constrained Correspondence Analysis, a recently developed ecological method to relate functional traits to environmental variables, to test the effect of each land use type on the area of each liver pigment. Results There was an increase in the amount of melanin in environments with high proportion of agriculture, as well as variation in the amount of lipofuscin and hemosiderin. Liver pigments of P. cuvieri and B. albopunctata varied more strongly in response to land use types, suggesting they could be good indicator species. Therefore, the area of MMs in the liver and the metabolic products in their cytoplasm can be used as biomarkers of environmental changes in regions with intense agricultural activities. Our results add a new perspective to the influence of land use patterns on environmental health by highlighting the effect of environmental changes on internal morphological aspects of animals.
format: application/pdf
format: text/html
creator: Lilian Franco-Belussi
creator: Diogo B. Provete
creator: Rinneu E. Borges
creator: Classius De Oliveira
creator: Lia Raquel S. Santos
subject: Cell Biology
subject: Zoology
subject: Histology
subject: Ecotoxicology
subject: Environmental Impacts
description: doi:10.7717/peerj.9751
publisher: PeerJ Inc.
rights: © 2020 Franco-Belussi et al.
abstract: Background Changes in land use trigger environmental changes that can lead to decreased biodiversity and species loss. The liver is an essential detoxification organ that reflects systemic physiological responses to environmental changes. Here, we tested whether contrasting land use patterns influence the amount of substances from the hepatic cellular catabolism and melanomacrophages (MMs) of five anuran species in the Brazilian Cerrado. Methods We collected the same five species of pond-dwelling frogs in one protected area and in an area with intense agricultural activity. We used routine histological and histochemical techniques to quantify the area occupied by lipofuscin, melanin, and hemosiderin in the liver of two frogs Leptodactylus fuscus, Physalaemus cuvieri, and three tree-frogs Dendropsophus minutus, Scinax fuscomarginatus, and Boana albopunctata. We classified land use types in a buffer around each pond based on satellite images. We then used a double-constrained Correspondence Analysis, a recently developed ecological method to relate functional traits to environmental variables, to test the effect of each land use type on the area of each liver pigment. Results There was an increase in the amount of melanin in environments with high proportion of agriculture, as well as variation in the amount of lipofuscin and hemosiderin. Liver pigments of P. cuvieri and B. albopunctata varied more strongly in response to land use types, suggesting they could be good indicator species. Therefore, the area of MMs in the liver and the metabolic products in their cytoplasm can be used as biomarkers of environmental changes in regions with intense agricultural activities. Our results add a new perspective to the influence of land use patterns on environmental health by highlighting the effect of environmental changes on internal morphological aspects of animals.
bibliographic citation: Franco-Belussi et al. (2020) Idiosyncratic liver pigment alterations of five frog species in response to contrasting land use patterns in the Brazilian Cerrado. PeerJ 8:e9751 https://doi.org/10.7717/peerj.9751
date submitted: 2020-04-13
date accepted: 2020-07-28
issued: 2020-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Franco-Belussi
  given name: Lilian
author list: Agent
  family name: Provete
  given name: Diogo B.
author list: Agent
  family name: Borges
  given name: Rinneu E.
author list: Agent
  family name: De Oliveira
  given name: Classius
author list: Agent
  family name: Santos
  given name: Lia Raquel S.
doi: 10.7717/peerj.9751
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-26
copyright: © 2020 Franco-Belussi et al.
attribution name: Franco-Belussi et al.

HPLC profiling of selected phenolic acids and flavonoids in Salvia eigii, Salvia hierosolymitana and Salvia viridis growing wild in Jordan and their in vitro antioxidant activity
type: item
type: AcademicArticle
description: Background Salvia eigii., Salvia hierosolymitana and Salvia viridis are native to the Mediterranean region, and are used in traditional medicine for the treatment of many ailments. In the current investigation, the methanolic extracts obtained from the air dried aerial parts of S. eigii, S. hierosolymitana and S. viridis from Jordan were screened for their total phenolics content (TPC), total flavonoids content (TFC) and their in vitro antioxidant activity. Additionally, the presence of four bioactive phenolic acids including gallic acid, caffeic acid, rosmarinic acid and salvianolic acid B and other seven flavonoids including luteolin-7-O-glucoside, apigenin, apigenin-7-O-glucoside, rutin, nariginin, hesperidin and quercetin was determined using Liquid chromatography-Electron Spray Ionization-Tandom Mass Spectrometry (LC-ESI-MS/MS). Methods Antioxidant activity of the obtained three extracts were examined via the DPPH•, ABTS• + radical scavenging methods in addition to Ferrous Ion Chelating (FIC) effect. TFC and TPC of the extracts were measured using the aluminum chloride colorimetric method and the Folin-Ciocalteau method, respectively. The presence and concentration of the selected 11 compounds was further determined through LC-ESI-MS/MS. Results The results indicated that three Salvia species had high total flavonoids content expressed in mg quercetin/g dry extract (S. heirosolymitana: 770.85 ± 5.26; S. eigii: 520.60 ± 6.24, S. viridis: 311.36 ± 4.41). S. heirosolymitana had the highest DPPH• activity (0.184 ± 1.22 × 10−2 mg/ml) and FIC effect (0.354 ± 0.018 mg/ml). S. heirosolymitana had slightly higher ABTS• + scavenging activity than S. eigii (0.176 ± 1.16 × 10−2 mg/ml; 0.183 ± 0.031 mg/ml, respectively). All 11 compounds were detected in the extracts of the three Salvia species. Luteolin-7-O-glucoside was detected in high concentration levels in the three species (1756.73, 21651.36, and 26125.14 mg/kg dry plant; S. eigii, S. hierosolyimitana and S. viridis,…
format: application/pdf
format: text/html
creator: Hala I. Al-Jaber
creator: Ashok K. Shakya
creator: Zaha A. Elagbar
subject: Biochemistry
subject: Biophysics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9769
publisher: PeerJ Inc.
rights: © 2020 Al-Jaber et al.
abstract: Background Salvia eigii., Salvia hierosolymitana and Salvia viridis are native to the Mediterranean region, and are used in traditional medicine for the treatment of many ailments. In the current investigation, the methanolic extracts obtained from the air dried aerial parts of S. eigii, S. hierosolymitana and S. viridis from Jordan were screened for their total phenolics content (TPC), total flavonoids content (TFC) and their in vitro antioxidant activity. Additionally, the presence of four bioactive phenolic acids including gallic acid, caffeic acid, rosmarinic acid and salvianolic acid B and other seven flavonoids including luteolin-7-O-glucoside, apigenin, apigenin-7-O-glucoside, rutin, nariginin, hesperidin and quercetin was determined using Liquid chromatography-Electron Spray Ionization-Tandom Mass Spectrometry (LC-ESI-MS/MS). Methods Antioxidant activity of the obtained three extracts were examined via the DPPH•, ABTS• + radical scavenging methods in addition to Ferrous Ion Chelating (FIC) effect. TFC and TPC of the extracts were measured using the aluminum chloride colorimetric method and the Folin-Ciocalteau method, respectively. The presence and concentration of the selected 11 compounds was further determined through LC-ESI-MS/MS. Results The results indicated that three Salvia species had high total flavonoids content expressed in mg quercetin/g dry extract (S. heirosolymitana: 770.85 ± 5.26; S. eigii: 520.60 ± 6.24, S. viridis: 311.36 ± 4.41). S. heirosolymitana had the highest DPPH• activity (0.184 ± 1.22 × 10−2 mg/ml) and FIC effect (0.354 ± 0.018 mg/ml). S. heirosolymitana had slightly higher ABTS• + scavenging activity than S. eigii (0.176 ± 1.16 × 10−2 mg/ml; 0.183 ± 0.031 mg/ml, respectively). All 11 compounds were detected in the extracts of the three Salvia species. Luteolin-7-O-glucoside was detected in high concentration levels in the three species (1756.73, 21651.36, and 26125.14 mg/kg dry plant; S. eigii, S. hierosolyimitana and S. viridis,…
bibliographic citation: Al-Jaber et al. (2020) HPLC profiling of selected phenolic acids and flavonoids in Salvia eigii, Salvia hierosolymitana and Salvia viridis growing wild in Jordan and their in vitro antioxidant activity. PeerJ 8:e9769 https://doi.org/10.7717/peerj.9769
date submitted: 2020-02-27
date accepted: 2020-07-30
issued: 2020-08-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-Jaber
  given name: Hala I.
author list: Agent
  family name: Shakya
  given name: Ashok K.
author list: Agent
  family name: Elagbar
  given name: Zaha A.
doi: 10.7717/peerj.9769
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-08-26
copyright: ©2020 Al-Jaber et al.
attribution name: Al-Jaber et al.

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