PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification of a novel association for the WWOX/HIF1A axis with gestational diabetes mellitus (GDM)
items: Tumor microenvironment related novel signature predict lung adenocarcinoma survival
items: Comparative analysis and implications of the chloroplast genomes of three thistles (Carduus L., Asteraceae)
items: Taphonomic patterns mimic biologic structures: diagenetic Liesegang rings in Mesozoic coleoids and coprolites
items: Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway
items: Blood markers of endothelial dysfunction and their correlation to cerebrovascular reactivity in patients with chronic hepatitis C infection
items: https://peerj.com/articles/10727
items: Geographic potential of the world’s largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America
items: Antibiotic prescription practices and attitudes towards the use of antimicrobials among veterinarians in the City of Tshwane, South Africa
items: Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary

Identification of a novel association for the WWOX/HIF1A axis with gestational diabetes mellitus (GDM)
type: item
type: AcademicArticle
description: Background Although the WW-domain-containing oxidoreductase (WWOX)/Hypoxia-inducible factor 1 (HIF1) pathway is a well-known regulator of cellular glucose and energy metabolism in pathophysiological processes, its role in gestational diabetes mellitus (GDM), remains elusive. We undertook this study to determine the effect of WWOX/HIF1A signaling on the expression of glucose metabolism genes in GDM patients. Methods Leukocytes were obtained from 135 pregnant women with (n = 98) or without (n = 37) GDM and, in turn, 3 months (n = 8) and 1 year (n = 12) postpartum. Quantitative RT-PCR was performed to determine gene expression profiles of the WWOX/HIF1A-related genes, including those involved in glucose transport (SLC2A1, SLC2A4), glycolytic pathway (HK2, PKM2, PFK, LDHA), Wnt pathway (DVL2, CTNNB1), and inflammatory response (NFKB1). Results GDM patients displayed a significant downregulation of WWOX with simultaneous upregulation of HIF1A which resulted in approximately six times reduction in WWOX/HIF1A ratio. As a consequence, HIF1A induced genes (SLC2A1, HK2, PFK, PKM) were found to be overexpressed in GDM compared to normal pregnancy and negative correlate with WWOX/HIF1A ratio. The postpartum WWOX expression was higher than during GDM, but its level was comparable to that observed in normal pregnancy. Conclusions The obtained results suggest a significant contribution of the WWOX gene to glucose metabolism in patients with gestational diabetes. Decreased WWOX expression in GDM compared to normal pregnancy, and in particular reduction of WWOX/HIF1A ratio, indicate that WWOX modulates HIF1α activity in normal tissues as described in the tumor. The effect of HIF1α excessive activation is to increase the expression of genes encoding proteins directly involved in the glycolysis which may lead to pathological changes in glucose metabolism observed in gestational diabetes.
format: application/pdf
format: text/html
creator: Izabela Baryla
creator: Elzbieta Pluciennik
creator: Katarzyna Kośla
creator: Marzena Wojcik
creator: Andrzej Zieleniak
creator: Monika Zurawska-Klis
creator: Katarzyna Cypryk
creator: Lucyna Alicja Wozniak
creator: Andrzej K Bednarek
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Women’s Health
description: doi:10.7717/peerj.10604
publisher: PeerJ Inc.
rights: © 2021 Baryla et al.
abstract: Background Although the WW-domain-containing oxidoreductase (WWOX)/Hypoxia-inducible factor 1 (HIF1) pathway is a well-known regulator of cellular glucose and energy metabolism in pathophysiological processes, its role in gestational diabetes mellitus (GDM), remains elusive. We undertook this study to determine the effect of WWOX/HIF1A signaling on the expression of glucose metabolism genes in GDM patients. Methods Leukocytes were obtained from 135 pregnant women with (n = 98) or without (n = 37) GDM and, in turn, 3 months (n = 8) and 1 year (n = 12) postpartum. Quantitative RT-PCR was performed to determine gene expression profiles of the WWOX/HIF1A-related genes, including those involved in glucose transport (SLC2A1, SLC2A4), glycolytic pathway (HK2, PKM2, PFK, LDHA), Wnt pathway (DVL2, CTNNB1), and inflammatory response (NFKB1). Results GDM patients displayed a significant downregulation of WWOX with simultaneous upregulation of HIF1A which resulted in approximately six times reduction in WWOX/HIF1A ratio. As a consequence, HIF1A induced genes (SLC2A1, HK2, PFK, PKM) were found to be overexpressed in GDM compared to normal pregnancy and negative correlate with WWOX/HIF1A ratio. The postpartum WWOX expression was higher than during GDM, but its level was comparable to that observed in normal pregnancy. Conclusions The obtained results suggest a significant contribution of the WWOX gene to glucose metabolism in patients with gestational diabetes. Decreased WWOX expression in GDM compared to normal pregnancy, and in particular reduction of WWOX/HIF1A ratio, indicate that WWOX modulates HIF1α activity in normal tissues as described in the tumor. The effect of HIF1α excessive activation is to increase the expression of genes encoding proteins directly involved in the glycolysis which may lead to pathological changes in glucose metabolism observed in gestational diabetes.
bibliographic citation: Baryla et al. (2021) Identification of a novel association for the WWOX/HIF1A axis with gestational diabetes mellitus (GDM). PeerJ 9:e10604 https://doi.org/10.7717/peerj.10604
date submitted: 2020-07-17
date accepted: 2020-11-28
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baryla
  given name: Izabela
author list: Agent
  family name: Pluciennik
  given name: Elzbieta
author list: Agent
  family name: Kośla
  given name: Katarzyna
author list: Agent
  family name: Wojcik
  given name: Marzena
author list: Agent
  family name: Zieleniak
  given name: Andrzej
author list: Agent
  family name: Zurawska-Klis
  given name: Monika
author list: Agent
  family name: Cypryk
  given name: Katarzyna
author list: Agent
  family name: Wozniak
  given name: Lucyna Alicja
author list: Agent
  family name: Bednarek
  given name: Andrzej K
doi: 10.7717/peerj.10604
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: ©2021 Baryla et al.
attribution name: Baryla et al.

Tumor microenvironment related novel signature predict lung adenocarcinoma survival
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma (LUAD) is the most common histological type of lung cancers, which is the primary cause of cancer‐related mortality worldwide. Growing evidence has suggested that tumor microenvironment (TME) plays a pivotal role in tumorigenesis and progression. Hence, we investigate the correlation of TME related genes with LUAD prognosis. Method The information of LUAD gene expression data was obtained from The Cancer Genome Atlas (TCGA). According to their immune/stromal scores calculated by the ESTIMATE algorithm, differentially expressed genes (DEGs) were identified. Then, we performed univariate Cox regression analysis on DEGs to obtain genes that are apparently bound up with LUAD survival (SurGenes). Functional annotation and protein-protein interaction (PPI) was also conducted on SurGenes. By validating the SurGenes with data sets of lung cancer from the Gene Expression Omnibus (GEO), 106 TME related SurGenes were generated. Further, intersection analysis was executed between the 106 TME related SurGenes and hub genes from PPI network, PTPRC and CD19 were obtained. Gene Set Enrichment Analysis and CIBERSORT analysis were performed on PTPRC and CD19. Based on the TCGA LUAD dataset, we conducted factor analysis and Step-wise multivariate Cox regression analysis for 106 TME related SurGenes to construct the prognostic model for LUAD survival prediction. The LUAD dataset in GEO (GSE68465) was used as the testing dataset to confirm the prognostic model. Multivariate Cox regression analysis was used between risk score from the prognostic model and clinical parameters. Result A total of 106 TME related genes were collected in our research totally, which were markedly correlated with the overall survival (OS) of LUAD patient. Bioinformatics analysis suggest them mainly concentrated on immune response, cell adhesion, and extracellular matrix. More importantly, among 106 TME related SurGenes, PTPRC and CD19 were highly interconnected nodes among PPI net…
format: application/pdf
format: text/html
creator: Juan Chen
creator: Rui Zhou
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Statistics
description: doi:10.7717/peerj.10628
publisher: PeerJ Inc.
rights: © 2021 Chen and Zhou
abstract: Background Lung adenocarcinoma (LUAD) is the most common histological type of lung cancers, which is the primary cause of cancer‐related mortality worldwide. Growing evidence has suggested that tumor microenvironment (TME) plays a pivotal role in tumorigenesis and progression. Hence, we investigate the correlation of TME related genes with LUAD prognosis. Method The information of LUAD gene expression data was obtained from The Cancer Genome Atlas (TCGA). According to their immune/stromal scores calculated by the ESTIMATE algorithm, differentially expressed genes (DEGs) were identified. Then, we performed univariate Cox regression analysis on DEGs to obtain genes that are apparently bound up with LUAD survival (SurGenes). Functional annotation and protein-protein interaction (PPI) was also conducted on SurGenes. By validating the SurGenes with data sets of lung cancer from the Gene Expression Omnibus (GEO), 106 TME related SurGenes were generated. Further, intersection analysis was executed between the 106 TME related SurGenes and hub genes from PPI network, PTPRC and CD19 were obtained. Gene Set Enrichment Analysis and CIBERSORT analysis were performed on PTPRC and CD19. Based on the TCGA LUAD dataset, we conducted factor analysis and Step-wise multivariate Cox regression analysis for 106 TME related SurGenes to construct the prognostic model for LUAD survival prediction. The LUAD dataset in GEO (GSE68465) was used as the testing dataset to confirm the prognostic model. Multivariate Cox regression analysis was used between risk score from the prognostic model and clinical parameters. Result A total of 106 TME related genes were collected in our research totally, which were markedly correlated with the overall survival (OS) of LUAD patient. Bioinformatics analysis suggest them mainly concentrated on immune response, cell adhesion, and extracellular matrix. More importantly, among 106 TME related SurGenes, PTPRC and CD19 were highly interconnected nodes among PPI net…
bibliographic citation: Chen et al. (2021) Tumor microenvironment related novel signature predict lung adenocarcinoma survival. PeerJ 9:e10628 https://doi.org/10.7717/peerj.10628
date submitted: 2020-01-14
date accepted: 2020-12-01
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Juan
author list: Agent
  family name: Zhou
  given name: Rui
doi: 10.7717/peerj.10628
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: © 2021 Chen and Zhou
attribution name: Chen and Zhou

Comparative analysis and implications of the chloroplast genomes of three thistles (Carduus L., Asteraceae)
type: item
type: AcademicArticle
description: Background Carduus, commonly known as plumeless thistles, is a genus in the Asteraceae family that exhibits both medicinal value and invasive tendencies. However, the genomic data of Carduus (i.e., complete chloroplast genomes) have not been sequenced. Methods We sequenced and assembled the chloroplast genome (cpDNA) sequences of three Carduus species using the Illumina Miseq sequencing system and Geneious Prime. Phylogenetic relationships between Carduus and related taxa were reconstructed using Maximum Likelihood and Bayesian Inference analyses. In addition, we used a single nucleotide polymorphism (SNP) in the protein coding region of the matK gene to develop molecular markers to distinguish C. crispus from C. acanthoides and C. tenuiflorus. Results The cpDNA sequences of C. crispus, C. acanthoides, and C. tenuiflorus ranged from 152,342 bp to 152,617 bp in length. Comparative genomic analysis revealed high conservation in terms of gene content (including 80 protein-coding, 30 tRNA, and four rRNA genes) and gene order within the three focal species and members of subfamily Carduoideae. Despite their high similarity, the three species differed with respect to the number and content of repeats in the chloroplast genome. Additionally, eight hotspot regions, including psbI-trnS_GCU, trnE_UUC-rpoB, trnR_UCU-trnG_UCC, psbC-trnS_UGA, trnT_UGU-trnL_UAA, psbT-psbN, petD-rpoA, and rpl16-rps3, were identified in the study species. Phylogenetic analyses inferred from 78 protein-coding and non-coding regions indicated that Carduus is polyphyletic, suggesting the need for additional studies to reconstruct relationships between thistles and related taxa. Based on a SNP in matK, we successfully developed a molecular marker and protocol for distinguishing C. crispus from the other two focal species. Our study provides preliminary chloroplast genome data for further studies on plastid genome evolution, phylogeny, and development of species-level markers in Carduus.
format: application/pdf
format: text/html
creator: Joonhyung Jung
creator: Hoang Dang Khoa Do
creator: JongYoung Hyun
creator: Changkyun Kim
creator: Joo-Hwan Kim
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.10687
publisher: PeerJ Inc.
rights: © 2021 Jung et al.
abstract: Background Carduus, commonly known as plumeless thistles, is a genus in the Asteraceae family that exhibits both medicinal value and invasive tendencies. However, the genomic data of Carduus (i.e., complete chloroplast genomes) have not been sequenced. Methods We sequenced and assembled the chloroplast genome (cpDNA) sequences of three Carduus species using the Illumina Miseq sequencing system and Geneious Prime. Phylogenetic relationships between Carduus and related taxa were reconstructed using Maximum Likelihood and Bayesian Inference analyses. In addition, we used a single nucleotide polymorphism (SNP) in the protein coding region of the matK gene to develop molecular markers to distinguish C. crispus from C. acanthoides and C. tenuiflorus. Results The cpDNA sequences of C. crispus, C. acanthoides, and C. tenuiflorus ranged from 152,342 bp to 152,617 bp in length. Comparative genomic analysis revealed high conservation in terms of gene content (including 80 protein-coding, 30 tRNA, and four rRNA genes) and gene order within the three focal species and members of subfamily Carduoideae. Despite their high similarity, the three species differed with respect to the number and content of repeats in the chloroplast genome. Additionally, eight hotspot regions, including psbI-trnS_GCU, trnE_UUC-rpoB, trnR_UCU-trnG_UCC, psbC-trnS_UGA, trnT_UGU-trnL_UAA, psbT-psbN, petD-rpoA, and rpl16-rps3, were identified in the study species. Phylogenetic analyses inferred from 78 protein-coding and non-coding regions indicated that Carduus is polyphyletic, suggesting the need for additional studies to reconstruct relationships between thistles and related taxa. Based on a SNP in matK, we successfully developed a molecular marker and protocol for distinguishing C. crispus from the other two focal species. Our study provides preliminary chloroplast genome data for further studies on plastid genome evolution, phylogeny, and development of species-level markers in Carduus.
bibliographic citation: Jung et al. (2021) Comparative analysis and implications of the chloroplast genomes of three thistles (Carduus L., Asteraceae). PeerJ 9:e10687 https://doi.org/10.7717/peerj.10687
date submitted: 2020-02-28
date accepted: 2020-12-11
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jung
  given name: Joonhyung
author list: Agent
  family name: Do
  given name: Hoang Dang Khoa
author list: Agent
  family name: Hyun
  given name: JongYoung
author list: Agent
  family name: Kim
  given name: Changkyun
author list: Agent
  family name: Kim
  given name: Joo-Hwan
doi: 10.7717/peerj.10687
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: ©2021 Jung et al.
attribution name: Jung et al.

Taphonomic patterns mimic biologic structures: diagenetic Liesegang rings in Mesozoic coleoids and coprolites
type: item
type: AcademicArticle
description: Because of physiology of coleoids, their fossils preserve soft-tissue-remains more often than other cephalopods. Sometimes, the phosphatized soft-tissues, particularly parts of the muscular mantle, display dark circular patterns. Here, we showcase that these patterns, here documented for fossil coleoids from the Jurassic of Germany and the Cretaceous of Lebanon, superficially resemble chromatophores (which enable living coleoids to alter their coloration). We examined and chemically analyzed the circular structures in these specimens, describe them, and discuss their genesis. Based on their structure and color, we visually differentiate between three types of circles. By comparison with similar structures, we suggest that these structures are not biogenic but Liesegang rings, which formed due to reaction-diffusion processes very soon after death.
format: application/pdf
format: text/html
creator: Christian Klug
creator: Gianpaolo Di Silvestro
creator: Rene Hoffmann
creator: Guenter Schweigert
creator: Dirk Fuchs
creator: Thomas Clements
creator: Pierre Gueriau
subject: Marine Biology
subject: Paleontology
description: doi:10.7717/peerj.10703
publisher: PeerJ Inc.
rights: © 2021 Klug et al.
abstract: Because of physiology of coleoids, their fossils preserve soft-tissue-remains more often than other cephalopods. Sometimes, the phosphatized soft-tissues, particularly parts of the muscular mantle, display dark circular patterns. Here, we showcase that these patterns, here documented for fossil coleoids from the Jurassic of Germany and the Cretaceous of Lebanon, superficially resemble chromatophores (which enable living coleoids to alter their coloration). We examined and chemically analyzed the circular structures in these specimens, describe them, and discuss their genesis. Based on their structure and color, we visually differentiate between three types of circles. By comparison with similar structures, we suggest that these structures are not biogenic but Liesegang rings, which formed due to reaction-diffusion processes very soon after death.
bibliographic citation: Klug et al. (2021) Taphonomic patterns mimic biologic structures: diagenetic Liesegang rings in Mesozoic coleoids and coprolites. PeerJ 9:e10703 https://doi.org/10.7717/peerj.10703
date submitted: 2020-08-20
date accepted: 2020-12-14
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Klug
  given name: Christian
author list: Agent
  family name: Di Silvestro
  given name: Gianpaolo
author list: Agent
  family name: Hoffmann
  given name: Rene
author list: Agent
  family name: Schweigert
  given name: Guenter
author list: Agent
  family name: Fuchs
  given name: Dirk
author list: Agent
  family name: Clements
  given name: Thomas
author list: Agent
  family name: Gueriau
  given name: Pierre
doi: 10.7717/peerj.10703
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: © 2021 Klug et al.
attribution name: Klug et al.

Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway
type: item
type: AcademicArticle
description: Target of rapamycin (TOR) operates as a hub of the signal transduction that integrates nutrient and energy signaling to promote cell proliferation and growth through mediating the transcriptional and post- transcriptional regulator networks in all eukaryotic species. MicroRNAs (miRNAs) are widespread classes of small, single-stranded, non-coding endogenous RNAs and are widely found in eukaryotes, which play a vital role in regulating gene expression by degrading targeted mRNAs or translational repression at post-transcriptional level. Recent studies found that there were necessarily close connections between miRNA and TOR pathways in mammals. However, there is little information about the interplay between the miRNA and TOR in plants. Thus, the aim of this study was to identify potential TOR-miRNA-mRNA regulatory networks in TOR signaling through global mRNA and microRNA expression profiling in potato. Based on the previous high-throughput transcriptome sequencing and filtering, a total of 2,899 genes were significantly differentially expressed in potato under TOR inhibitors treatment. Pathway analysis revealed that these genes were significantly enriched in multiple metabolic processes. Similarly, in the present study, suppression of TOR resulted in 41 miRNAs up-regulated and 45 down-regulated, revealing that TOR plays a crucial role in the regulation of miRNA regulatory network. Furthermore, integrated mRNA and miRNA expression profiling uncovered that these miRNAs participated in large-scale metabolic process in the TOR signal pathway in potato, such as regulation of autophagy and ubiquitination, and biosynthesis of secondary metabolites. Overall, the results shed new insight into TOR related post-transcriptional gene regulatory networks in potato and suggesting TOR-miRNA-targeting genes relevant networks as a potential genetic resource for potato improvement.
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format: text/html
creator: Kexuan Deng
creator: Huan Yin
creator: Fangjie Xiong
creator: Li Feng
creator: Pan Dong
creator: Maozhi Ren
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10704
publisher: PeerJ Inc.
rights: © 2021 Deng et al.
abstract: Target of rapamycin (TOR) operates as a hub of the signal transduction that integrates nutrient and energy signaling to promote cell proliferation and growth through mediating the transcriptional and post- transcriptional regulator networks in all eukaryotic species. MicroRNAs (miRNAs) are widespread classes of small, single-stranded, non-coding endogenous RNAs and are widely found in eukaryotes, which play a vital role in regulating gene expression by degrading targeted mRNAs or translational repression at post-transcriptional level. Recent studies found that there were necessarily close connections between miRNA and TOR pathways in mammals. However, there is little information about the interplay between the miRNA and TOR in plants. Thus, the aim of this study was to identify potential TOR-miRNA-mRNA regulatory networks in TOR signaling through global mRNA and microRNA expression profiling in potato. Based on the previous high-throughput transcriptome sequencing and filtering, a total of 2,899 genes were significantly differentially expressed in potato under TOR inhibitors treatment. Pathway analysis revealed that these genes were significantly enriched in multiple metabolic processes. Similarly, in the present study, suppression of TOR resulted in 41 miRNAs up-regulated and 45 down-regulated, revealing that TOR plays a crucial role in the regulation of miRNA regulatory network. Furthermore, integrated mRNA and miRNA expression profiling uncovered that these miRNAs participated in large-scale metabolic process in the TOR signal pathway in potato, such as regulation of autophagy and ubiquitination, and biosynthesis of secondary metabolites. Overall, the results shed new insight into TOR related post-transcriptional gene regulatory networks in potato and suggesting TOR-miRNA-targeting genes relevant networks as a potential genetic resource for potato improvement.
bibliographic citation: Deng et al. (2021) Genome-wide miRNA expression profiling in potato (Solanum tuberosum L.) reveals TOR-dependent post-transcriptional gene regulatory networks in diverse metabolic pathway. PeerJ 9:e10704 https://doi.org/10.7717/peerj.10704
date submitted: 2020-08-10
date accepted: 2020-12-14
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Kexuan
author list: Agent
  family name: Yin
  given name: Huan
author list: Agent
  family name: Xiong
  given name: Fangjie
author list: Agent
  family name: Feng
  given name: Li
author list: Agent
  family name: Dong
  given name: Pan
author list: Agent
  family name: Ren
  given name: Maozhi
doi: 10.7717/peerj.10704
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: ©2021 Deng et al.
attribution name: Deng et al.

Blood markers of endothelial dysfunction and their correlation to cerebrovascular reactivity in patients with chronic hepatitis C infection
type: item
type: AcademicArticle
description: Although liver cirrhosis and hepatocellular carcinoma are major consequences of hepatitis C (HCV), there has been an increasing number of studies examining extrahepatic manifestations, especially those caused by systemic chronic inflammation and metabolic complications that might predispose HCV patients to atherosclerosis and ischemic cerebrovascular disease (CVD). The aim of our study was to assess E-selectin, VCAM-1, ICAM-1 and VEGF-A serum levels in patients with chronic HCV infection and to correlate them with cerebrovascular reactivity. A blood sample was taken from eighteen patients with chronic hepatitis C infection and from the same number of healthy blood donors in the control group. The aim was to analyse markers of endothelial dysfunction and to correlate them with cerebrovascular reactivity expressed as breath-holding index (BHI) determined using transcranial color Doppler. The obtained results revealed significant differences between the groups in all endothelial markers except for the E selectin. While the ICAM-1 and sVCAM-1 were significantly increased in the hepatitis group, VEGF-A was significantly decreased. A significant reduction of 0.5 (95% CI 0.2, 0.8) in the mean BHI was found in the hepatitis group (mean BHI 0.64) compared to controls (mean BHI 1.10). No significant association between the BHI and any of the endothelial markers was found in the control group, while in the hepatitis group, the scatter plot of ICAM-1 vs BHI suggested that the association might be present. In conclusion, the results of this study confirm an association between a chronic HCV infection and altered cerebrovascular reactivity as well as higher levels of markers of endothelial activation (ICAM-1, VCAM-1) as possible indicators of an increased CVD risk.
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creator: Mirela Pavicic Ivelja
creator: Kresimir Dolic
creator: Leida Tandara
creator: Nikola Perkovic
creator: Antonio Mestrovic
creator: Ivo Ivic
subject: Virology
subject: Infectious Diseases
subject: Neurology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.10723
publisher: PeerJ Inc.
rights: © 2021 Pavicic Ivelja et al.
abstract: Although liver cirrhosis and hepatocellular carcinoma are major consequences of hepatitis C (HCV), there has been an increasing number of studies examining extrahepatic manifestations, especially those caused by systemic chronic inflammation and metabolic complications that might predispose HCV patients to atherosclerosis and ischemic cerebrovascular disease (CVD). The aim of our study was to assess E-selectin, VCAM-1, ICAM-1 and VEGF-A serum levels in patients with chronic HCV infection and to correlate them with cerebrovascular reactivity. A blood sample was taken from eighteen patients with chronic hepatitis C infection and from the same number of healthy blood donors in the control group. The aim was to analyse markers of endothelial dysfunction and to correlate them with cerebrovascular reactivity expressed as breath-holding index (BHI) determined using transcranial color Doppler. The obtained results revealed significant differences between the groups in all endothelial markers except for the E selectin. While the ICAM-1 and sVCAM-1 were significantly increased in the hepatitis group, VEGF-A was significantly decreased. A significant reduction of 0.5 (95% CI 0.2, 0.8) in the mean BHI was found in the hepatitis group (mean BHI 0.64) compared to controls (mean BHI 1.10). No significant association between the BHI and any of the endothelial markers was found in the control group, while in the hepatitis group, the scatter plot of ICAM-1 vs BHI suggested that the association might be present. In conclusion, the results of this study confirm an association between a chronic HCV infection and altered cerebrovascular reactivity as well as higher levels of markers of endothelial activation (ICAM-1, VCAM-1) as possible indicators of an increased CVD risk.
bibliographic citation: Pavicic Ivelja et al. (2021) Blood markers of endothelial dysfunction and their correlation to cerebrovascular reactivity in patients with chronic hepatitis C infection. PeerJ 9:e10723 https://doi.org/10.7717/peerj.10723
date submitted: 2020-09-23
date accepted: 2020-12-16
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pavicic Ivelja
  given name: Mirela
author list: Agent
  family name: Dolic
  given name: Kresimir
author list: Agent
  family name: Tandara
  given name: Leida
author list: Agent
  family name: Perkovic
  given name: Nikola
author list: Agent
  family name: Mestrovic
  given name: Antonio
author list: Agent
  family name: Ivic
  given name: Ivo
doi: 10.7717/peerj.10723
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: ©2021 Pavicic Ivelja et al.
attribution name: Pavicic Ivelja et al.

https://peerj.com/articles/10727
type: item
type: AcademicArticle
title: Monitoring oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast, Japan before and after the 2011 tsunami by remote sensing: their recoveries implying the sustainable development of coastal waters
description: Background Coastal ecosystems are blue infrastructures that support coastal resources and also aquaculture. Seagrass meadows, one of coastal ecosystems, provide substrates for epiphytic diatoms, which are food resources for cultured filter feeder organisms. Highly intensive coastal aquaculture degrades coastal environments to decrease seagrass meadows. Therefore, efficient aquaculture management and conservation of seagrass meadows are necessary for the sustainable development of coastal waters. In ria-type bays, non-feeding aquaculture of filter feeders such as oysters, scallops, and ascidians are actively practiced along the Sanriku Coast, Japan. Before the 2011 Great East Japan Earthquake, the over-deployment of oyster culture facilities polluted the bottom environment and formed an hypoxic bottom water layer due to the organic excrements from cultured oysters. The tsunami in 2011 devastated the aquaculture facilities and seagrass meadows along the Sanriku Coast. We mapped the oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast before and after the tsunami and monitored those and environments after the tsunami by field surveys. Methods We conducted field surveys and monitored the environmental parameters in Nagatsura-ura Lagoon every month since 2014. We used high-resolution satellite remote sensing images to map oyster culture rafts and seagrass meadows at irregular time intervals from 2006 to 2019 in order to assess their distribution. In 2019, we also used an unmanned aerial vehicle to analyze the spatial variability of the position and the number of ropes suspending oyster clumps beneath the rafts. Results In 2013, the number and distribution of the oyster culture rafts had been completely restored to the pre-tsunami conditions. The mean area of culture raft increased after the tsunami, and ropes suspending oyster clumps attached to a raft in wider space. Experienced local fishermen also developed a method to attach less ropes to …
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creator: Hiroki Murata
creator: Motoyuki Hara
creator: Chinatsu Yonezawa
creator: Teruhisa Komatsu
subject: Aquaculture, Fisheries and Fish Science
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10727
publisher: PeerJ Inc.
rights: © 2021 Murata et al.
abstract: Background Coastal ecosystems are blue infrastructures that support coastal resources and also aquaculture. Seagrass meadows, one of coastal ecosystems, provide substrates for epiphytic diatoms, which are food resources for cultured filter feeder organisms. Highly intensive coastal aquaculture degrades coastal environments to decrease seagrass meadows. Therefore, efficient aquaculture management and conservation of seagrass meadows are necessary for the sustainable development of coastal waters. In ria-type bays, non-feeding aquaculture of filter feeders such as oysters, scallops, and ascidians are actively practiced along the Sanriku Coast, Japan. Before the 2011 Great East Japan Earthquake, the over-deployment of oyster culture facilities polluted the bottom environment and formed an hypoxic bottom water layer due to the organic excrements from cultured oysters. The tsunami in 2011 devastated the aquaculture facilities and seagrass meadows along the Sanriku Coast. We mapped the oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast before and after the tsunami and monitored those and environments after the tsunami by field surveys. Methods We conducted field surveys and monitored the environmental parameters in Nagatsura-ura Lagoon every month since 2014. We used high-resolution satellite remote sensing images to map oyster culture rafts and seagrass meadows at irregular time intervals from 2006 to 2019 in order to assess their distribution. In 2019, we also used an unmanned aerial vehicle to analyze the spatial variability of the position and the number of ropes suspending oyster clumps beneath the rafts. Results In 2013, the number and distribution of the oyster culture rafts had been completely restored to the pre-tsunami conditions. The mean area of culture raft increased after the tsunami, and ropes suspending oyster clumps attached to a raft in wider space. Experienced local fishermen also developed a method to attach less ropes to …
bibliographic citation: Murata et al. (2021) Monitoring oyster culture rafts and seagrass meadows in Nagatsura-ura Lagoon, Sanriku Coast, Japan before and after the 2011 tsunami by remote sensing: their recoveries implying the sustainable development of coastal waters. PeerJ 9:e10727 https://doi.org/10.7717/peerj.10727
date submitted: 2020-07-16
date accepted: 2020-12-17
issued: 2021-01-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Murata
  given name: Hiroki
author list: Agent
  family name: Hara
  given name: Motoyuki
author list: Agent
  family name: Yonezawa
  given name: Chinatsu
author list: Agent
  family name: Komatsu
  given name: Teruhisa
doi: 10.7717/peerj.10727
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-14
copyright: ©2021 Murata et al.
attribution name: Murata et al.

Geographic potential of the world’s largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America
type: item
type: AcademicArticle
description: The Asian giant hornet (AGH, Vespa mandarinia) is the world’s largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian giant hornets was detected outside of Vancouver, British Columbia; multiple individuals were detected in British Columbia and Washington state in 2020; and another nest was found and eradicated in Washington state in November 2020, indicating that the AGH may have successfully wintered in North America. Because hornets tend to spread rapidly and become pests, reliable estimates of the potential invasive range of V. mandarinia in North America are needed to assess likely human and economic impacts, and to guide future eradication attempts. Here, we assess climatic suitability for AGH in North America, and suggest that, without control, this species could establish populations across the Pacific Northwest and much of eastern North America. Predicted suitable areas for AGH in North America overlap broadly with areas where honey production is highest, as well as with species-rich areas for native bumble bees and stingless bees of the genus Melipona in Mexico, highlighting the economic and environmental necessity of controlling this nascent invasion.
format: application/pdf
format: text/html
creator: Claudia Nuñez-Penichet
creator: Luis Osorio-Olvera
creator: Victor H. Gonzalez
creator: Marlon E. Cobos
creator: Laura Jiménez
creator: Devon A. DeRaad
creator: Abdelghafar Alkishe
creator: Rusby G. Contreras-Díaz
creator: Angela Nava-Bolaños
creator: Kaera Utsumi
creator: Uzma Ashraf
creator: Adeola Adeboje
creator: A. Townsend Peterson
creator: Jorge Soberon
subject: Biogeography
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.10690
publisher: PeerJ Inc.
rights: © 2021 Nuñez-Penichet et al.
abstract: The Asian giant hornet (AGH, Vespa mandarinia) is the world’s largest hornet, occurring naturally in the Indomalayan region, where it is a voracious predator of pollinating insects including honey bees. In September 2019, a nest of Asian giant hornets was detected outside of Vancouver, British Columbia; multiple individuals were detected in British Columbia and Washington state in 2020; and another nest was found and eradicated in Washington state in November 2020, indicating that the AGH may have successfully wintered in North America. Because hornets tend to spread rapidly and become pests, reliable estimates of the potential invasive range of V. mandarinia in North America are needed to assess likely human and economic impacts, and to guide future eradication attempts. Here, we assess climatic suitability for AGH in North America, and suggest that, without control, this species could establish populations across the Pacific Northwest and much of eastern North America. Predicted suitable areas for AGH in North America overlap broadly with areas where honey production is highest, as well as with species-rich areas for native bumble bees and stingless bees of the genus Melipona in Mexico, highlighting the economic and environmental necessity of controlling this nascent invasion.
bibliographic citation: Nuñez-Penichet et al. (2021) Geographic potential of the world’s largest hornet, Vespa mandarinia Smith (Hymenoptera: Vespidae), worldwide and particularly in North America. PeerJ 9:e10690 https://doi.org/10.7717/peerj.10690
date submitted: 2020-08-12
date accepted: 2020-12-11
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nuñez-Penichet
  given name: Claudia
author list: Agent
  family name: Osorio-Olvera
  given name: Luis
author list: Agent
  family name: Gonzalez
  given name: Victor H.
author list: Agent
  family name: Cobos
  given name: Marlon E.
author list: Agent
  family name: Jiménez
  given name: Laura
author list: Agent
  family name: DeRaad
  given name: Devon A.
author list: Agent
  family name: Alkishe
  given name: Abdelghafar
author list: Agent
  family name: Contreras-Díaz
  given name: Rusby G.
author list: Agent
  family name: Nava-Bolaños
  given name: Angela
author list: Agent
  family name: Utsumi
  given name: Kaera
author list: Agent
  family name: Ashraf
  given name: Uzma
author list: Agent
  family name: Adeboje
  given name: Adeola
author list: Agent
  family name: Peterson
  given name: A. Townsend
author list: Agent
  family name: Soberon
  given name: Jorge
doi: 10.7717/peerj.10690
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Nuñez-Penichet et al.
attribution name: Nuñez-Penichet et al.

Antibiotic prescription practices and attitudes towards the use of antimicrobials among veterinarians in the City of Tshwane, South Africa
type: item
type: AcademicArticle
description: Background Understanding the prescription practices and attitudes of veterinarians towards antimicrobial resistance (AMR) is crucial in guiding efforts to curb AMR. This study investigated prescription practices and attitudes towards AMR among veterinarians in the City of Tshwane, South Africa. Methods Out of the 83 veterinarians invited to participate in the study, 54 signed the consent form and completed the questionnaire. Percentages and 95% confidence intervals of all categorical variables were computed. A multinomial logistic model was used to identify predictors of the veterinarians’ view towards antimicrobial use. Results The majority (88%) of respondents indicated that improper use of antimicrobials contributed to selection for AMR. Veterinarians relied on clinical signs and symptoms (88%, 48/54) to decide whether to prescribe antimicrobials or not. However, the choice of antimicrobials depended on the cost of antibiotics (77.2%), route of administration (81.5%), and risk of potential adverse reactions (79.6%; 43/54). Many (61.5%) veterinarians were of the view that often antimicrobials are appropriately prescribed and 88.7% agreed that improper use of antimicrobials contributed to selection for antimicrobial resistant organisms. Compared to females, males were significantly more likely (Relative Risk Ratio (RRR) = 9.0; P = 0.0069) to agree rather than to “neither agree nor disagree” that their colleagues over-prescribed antimicrobials. Conclusions The decisions to prescribe antimicrobials by the veterinarians depended on clinical presentation of the patient, while the choice of antimicrobial depended on cost, route of administration, and risk of potential adverse reactions. Most veterinarians were of the view that antimicrobials were prescribed judiciously.
format: application/pdf
format: text/html
creator: Ronita Samuels
creator: Daniel Nenene Qekwana
creator: James W. Oguttu
creator: Agricola Odoi
subject: Microbiology
subject: Veterinary Medicine
subject: Epidemiology
description: doi:10.7717/peerj.10144
publisher: PeerJ Inc.
rights: © 2021 Samuels et al.
abstract: Background Understanding the prescription practices and attitudes of veterinarians towards antimicrobial resistance (AMR) is crucial in guiding efforts to curb AMR. This study investigated prescription practices and attitudes towards AMR among veterinarians in the City of Tshwane, South Africa. Methods Out of the 83 veterinarians invited to participate in the study, 54 signed the consent form and completed the questionnaire. Percentages and 95% confidence intervals of all categorical variables were computed. A multinomial logistic model was used to identify predictors of the veterinarians’ view towards antimicrobial use. Results The majority (88%) of respondents indicated that improper use of antimicrobials contributed to selection for AMR. Veterinarians relied on clinical signs and symptoms (88%, 48/54) to decide whether to prescribe antimicrobials or not. However, the choice of antimicrobials depended on the cost of antibiotics (77.2%), route of administration (81.5%), and risk of potential adverse reactions (79.6%; 43/54). Many (61.5%) veterinarians were of the view that often antimicrobials are appropriately prescribed and 88.7% agreed that improper use of antimicrobials contributed to selection for antimicrobial resistant organisms. Compared to females, males were significantly more likely (Relative Risk Ratio (RRR) = 9.0; P = 0.0069) to agree rather than to “neither agree nor disagree” that their colleagues over-prescribed antimicrobials. Conclusions The decisions to prescribe antimicrobials by the veterinarians depended on clinical presentation of the patient, while the choice of antimicrobial depended on cost, route of administration, and risk of potential adverse reactions. Most veterinarians were of the view that antimicrobials were prescribed judiciously.
bibliographic citation: Samuels et al. (2021) Antibiotic prescription practices and attitudes towards the use of antimicrobials among veterinarians in the City of Tshwane, South Africa. PeerJ 9:e10144 https://doi.org/10.7717/peerj.10144
date submitted: 2020-05-13
date accepted: 2020-09-20
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Samuels
  given name: Ronita
author list: Agent
  family name: Qekwana
  given name: Daniel Nenene
author list: Agent
  family name: Oguttu
  given name: James W.
author list: Agent
  family name: Odoi
  given name: Agricola
doi: 10.7717/peerj.10144
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: © 2021 Samuels et al.
attribution name: Samuels et al.

Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary
type: item
type: AcademicArticle
description: Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered…
format: application/pdf
format: text/html
creator: Romen Singh Naorem
creator: Jochen Blom
creator: Csaba Fekete
subject: Genetics
subject: Genomics
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.10185
publisher: PeerJ Inc.
rights: © 2021 Naorem et al.
abstract: Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered…
bibliographic citation: Naorem et al. (2021) Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary. PeerJ 9:e10185 https://doi.org/10.7717/peerj.10185
date submitted: 2020-05-21
date accepted: 2020-09-24
issued: 2021-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Naorem
  given name: Romen Singh
author list: Agent
  family name: Blom
  given name: Jochen
author list: Agent
  family name: Fekete
  given name: Csaba
doi: 10.7717/peerj.10185
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-13
copyright: ©2021 Naorem et al.
attribution name: Naorem et al.

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