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 six-gene metabolic signature predicting overall survival for patients with lung adenocarcinoma
items: Risk factors for new-onset atrial fibrillation in patients with chronic obstructive pulmonary disease: a systematic review and meta-analysis
items: Identification of significant genes signatures and prognostic biomarkers in cervical squamous carcinoma via bioinformatic data
items: Ixodes scapularis microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing
items: Phospho-islands and the evolution of phosphorylated amino acids in mammals
items: Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand
items: Genome-wide identification and evolution of HECT genes in wheat
items: Comparative genomic analysis of the principal Cryptosporidium species that infect humans
items: The gut microbiota in the common kestrel (Falco tinnunculus): a report from the Beijing Raptor Rescue Center
items: Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration

Identification of a six-gene metabolic signature predicting overall survival for patients with lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Lung cancer is the leading cause of cancer-related deaths worldwide. Lung adenocarcinoma (LUAD) is one of the main subtypes of lung cancer. Hundreds of metabolic genes are altered consistently in LUAD; however, their prognostic role remains to be explored. This study aimed to establish a molecular signature that can predict the prognosis in patients with LUAD based on metabolic gene expression. Methods The transcriptome expression profiles and corresponding clinical information of LUAD were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The differentially expressed genes (DEGs) between LUAD and paired non-tumor samples were identified by the Wilcoxon rank sum test. Univariate Cox regression analysis and the lasso Cox regression model were used to construct the best-prognosis molecular signature. A nomogram was established comprising the prognostic model for predicting overall survival. To validate the prognostic ability of the molecular signature and the nomogram, the Kaplan–Meier survival analysis, Cox proportional hazards model, and receiver operating characteristic analysis were used. Results The six-gene molecular signature (PFKP, PKM, TPI1, LDHA, PTGES, and TYMS) from the DEGs was constructed to predict the prognosis. The molecular signature demonstrated a robust independent prognostic ability in the training and validation sets. The nomogram including the prognostic model had a greater predictive accuracy than previous systems. Furthermore, a gene set enrichment analysis revealed several significantly enriched metabolic pathways, which suggests a correlation of the molecular signature with metabolic systems and may help explain the underlying mechanisms. Conclusions Our study identified a novel six-gene metabolic signature for LUAD prognosis prediction. The molecular signature could reflect the dysregulated metabolic microenvironment, provide potential biomarkers for predicting prognosis, and indicate potential novel me…
format: application/pdf
format: text/html
creator: Yubo Cao
creator: Xiaomei Lu
creator: Yue Li
creator: Jia Fu
creator: Hongyuan Li
creator: Xiulin Li
creator: Ziyou Chang
creator: Sa Liu
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
subject: Metabolic Sciences
description: doi:10.7717/peerj.10320
publisher: PeerJ Inc.
rights: © 2020 Cao et al.
abstract: Background Lung cancer is the leading cause of cancer-related deaths worldwide. Lung adenocarcinoma (LUAD) is one of the main subtypes of lung cancer. Hundreds of metabolic genes are altered consistently in LUAD; however, their prognostic role remains to be explored. This study aimed to establish a molecular signature that can predict the prognosis in patients with LUAD based on metabolic gene expression. Methods The transcriptome expression profiles and corresponding clinical information of LUAD were obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases. The differentially expressed genes (DEGs) between LUAD and paired non-tumor samples were identified by the Wilcoxon rank sum test. Univariate Cox regression analysis and the lasso Cox regression model were used to construct the best-prognosis molecular signature. A nomogram was established comprising the prognostic model for predicting overall survival. To validate the prognostic ability of the molecular signature and the nomogram, the Kaplan–Meier survival analysis, Cox proportional hazards model, and receiver operating characteristic analysis were used. Results The six-gene molecular signature (PFKP, PKM, TPI1, LDHA, PTGES, and TYMS) from the DEGs was constructed to predict the prognosis. The molecular signature demonstrated a robust independent prognostic ability in the training and validation sets. The nomogram including the prognostic model had a greater predictive accuracy than previous systems. Furthermore, a gene set enrichment analysis revealed several significantly enriched metabolic pathways, which suggests a correlation of the molecular signature with metabolic systems and may help explain the underlying mechanisms. Conclusions Our study identified a novel six-gene metabolic signature for LUAD prognosis prediction. The molecular signature could reflect the dysregulated metabolic microenvironment, provide potential biomarkers for predicting prognosis, and indicate potential novel me…
bibliographic citation: Cao et al. (2020) Identification of a six-gene metabolic signature predicting overall survival for patients with lung adenocarcinoma. PeerJ 8:e10320 https://doi.org/10.7717/peerj.10320
date submitted: 2020-08-06
date accepted: 2020-10-17
issued: 2020-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Yubo
author list: Agent
  family name: Lu
  given name: Xiaomei
author list: Agent
  family name: Li
  given name: Yue
author list: Agent
  family name: Fu
  given name: Jia
author list: Agent
  family name: Li
  given name: Hongyuan
author list: Agent
  family name: Li
  given name: Xiulin
author list: Agent
  family name: Chang
  given name: Ziyou
author list: Agent
  family name: Liu
  given name: Sa
doi: 10.7717/peerj.10320
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-02
copyright: ©2020 Cao et al.
attribution name: Cao et al.

Risk factors for new-onset atrial fibrillation in patients with chronic obstructive pulmonary disease: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background New-onset atrial fibrillation (AF) in patients with chronic obstructive pulmonary disease (COPD) is associated with an accelerated decline in lung function, and a significant increase in mortality rate. A deeper understanding of the risk factors for new-onset AF during COPD will provide insights into the relationship between COPD and AF and guide clinical practice. This systematic review and meta-analysis is designed to identify risk factors for new-onset AF in patients with COPD, and to formulate recommendations for preventing AF in COPD patients that will assist clinical decision making. Methods PubMed, Embase, Web of Science and Cochrane Library databases were searched for studies, which reported the results of potential risk factors for new-onset AF in COPD patients. Results Twenty studies involving 8,072,043 participants were included. Fifty factors were examined as potential risk factors for new-onset AF during COPD. Risk factors were grouped according to demographics, comorbid conditions, and COPD- and cardiovascular-related factors. In quantitative analysis, cardiovascular- and demographic-related factors with a greater than 50% increase in the odds of new-onset AF included age (over 65 years and over 75 years), acute care encounter, coronary artery disease, heart failure and congestive heart failure. Only one factor is related to the reduction of odds by more than 33.3%, which is black race (vs white). In qualitative analysis, the comparison of the risk factors was conducted between COPD-associated AF and non-COPD-associated AF. Cardiovascular-related factors for non-COPD-associated AF were also considered as risk factors for new-onset AF during COPD; however, the influence tended to be stronger during COPD. In addition, comorbid factors identified in non-COPD-associated AF were not associated with an increased risk of AF during COPD. Conclusions New-onset AF in COPD has significant demographic characteristics. Older age (over 65 years), males an…
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creator: Qiangru Huang
creator: Huaiyu Xiong
creator: Tiankui Shuai
creator: Meng Zhang
creator: Chuchu Zhang
creator: Yalei Wang
creator: Lei Zhu
creator: Jiaju Lu
creator: Jian Liu
subject: Cardiology
subject: Evidence Based Medicine
subject: Respiratory Medicine
description: doi:10.7717/peerj.10376
publisher: PeerJ Inc.
rights: © 2020 Huang et al.
abstract: Background New-onset atrial fibrillation (AF) in patients with chronic obstructive pulmonary disease (COPD) is associated with an accelerated decline in lung function, and a significant increase in mortality rate. A deeper understanding of the risk factors for new-onset AF during COPD will provide insights into the relationship between COPD and AF and guide clinical practice. This systematic review and meta-analysis is designed to identify risk factors for new-onset AF in patients with COPD, and to formulate recommendations for preventing AF in COPD patients that will assist clinical decision making. Methods PubMed, Embase, Web of Science and Cochrane Library databases were searched for studies, which reported the results of potential risk factors for new-onset AF in COPD patients. Results Twenty studies involving 8,072,043 participants were included. Fifty factors were examined as potential risk factors for new-onset AF during COPD. Risk factors were grouped according to demographics, comorbid conditions, and COPD- and cardiovascular-related factors. In quantitative analysis, cardiovascular- and demographic-related factors with a greater than 50% increase in the odds of new-onset AF included age (over 65 years and over 75 years), acute care encounter, coronary artery disease, heart failure and congestive heart failure. Only one factor is related to the reduction of odds by more than 33.3%, which is black race (vs white). In qualitative analysis, the comparison of the risk factors was conducted between COPD-associated AF and non-COPD-associated AF. Cardiovascular-related factors for non-COPD-associated AF were also considered as risk factors for new-onset AF during COPD; however, the influence tended to be stronger during COPD. In addition, comorbid factors identified in non-COPD-associated AF were not associated with an increased risk of AF during COPD. Conclusions New-onset AF in COPD has significant demographic characteristics. Older age (over 65 years), males an…
bibliographic citation: Huang et al. (2020) Risk factors for new-onset atrial fibrillation in patients with chronic obstructive pulmonary disease: a systematic review and meta-analysis. PeerJ 8:e10376 https://doi.org/10.7717/peerj.10376
date submitted: 2020-02-28
date accepted: 2020-10-26
issued: 2020-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Qiangru
author list: Agent
  family name: Xiong
  given name: Huaiyu
author list: Agent
  family name: Shuai
  given name: Tiankui
author list: Agent
  family name: Zhang
  given name: Meng
author list: Agent
  family name: Zhang
  given name: Chuchu
author list: Agent
  family name: Wang
  given name: Yalei
author list: Agent
  family name: Zhu
  given name: Lei
author list: Agent
  family name: Lu
  given name: Jiaju
author list: Agent
  family name: Liu
  given name: Jian
doi: 10.7717/peerj.10376
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-02
copyright: ©2020 Huang et al.
attribution name: Huang et al.

Identification of significant genes signatures and prognostic biomarkers in cervical squamous carcinoma via bioinformatic data
type: item
type: AcademicArticle
description: Background Cervical squamous cancer (CESC) is an intractable gynecological malignancy because of its high mortality rate and difficulty in early diagnosis. Several biomarkers have been found to predict the prognose of CESC using bioinformatics methods, but they still lack clinical effectiveness. Most of the existing bioinformatic studies only focus on the changes of oncogenes but neglect the differences on the protein level and molecular biology validation are rarely conducted. Methods Gene set data from the NCBI-GEO database were used in this study to compare the differences of gene and protein levels between normal and cancer tissues through significant pathway selection and core gene signature analysis to screen potential clinical biomarkers of CESC. Subsequently, the molecular and protein levels of clinical samples were verified by quantitative transcription PCR, western blot and immunohistochemistry. Results Three differentially expressed genes (RFC4, MCM2, TOP2A) were found to have a significant survival (P < 0.05) and highly expressed in CESC tissues. Molecular biological verification using quantitative reverse transcribed PCR, western blotting and immunohistochemistry assays exhibited significant differences in the expression of RFC4 between CESC and para-cancerous tissues (P < 0.05). Conclusion This study identified three potential biomarkers (RFC4, MCM2, TOP2A) of CESC which may be useful to clarify the underlying mechanisms of CESC and predict the prognosis of CESC patients.
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creator: Yunan He
creator: Shunjie Hu
creator: Jiaojiao Zhong
creator: Anran Cheng
creator: Nianchun Shan
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Oncology
subject: Women’s Health
subject: Medical Genetics
description: doi:10.7717/peerj.10386
publisher: PeerJ Inc.
rights: © 2020 He et al.
abstract: Background Cervical squamous cancer (CESC) is an intractable gynecological malignancy because of its high mortality rate and difficulty in early diagnosis. Several biomarkers have been found to predict the prognose of CESC using bioinformatics methods, but they still lack clinical effectiveness. Most of the existing bioinformatic studies only focus on the changes of oncogenes but neglect the differences on the protein level and molecular biology validation are rarely conducted. Methods Gene set data from the NCBI-GEO database were used in this study to compare the differences of gene and protein levels between normal and cancer tissues through significant pathway selection and core gene signature analysis to screen potential clinical biomarkers of CESC. Subsequently, the molecular and protein levels of clinical samples were verified by quantitative transcription PCR, western blot and immunohistochemistry. Results Three differentially expressed genes (RFC4, MCM2, TOP2A) were found to have a significant survival (P < 0.05) and highly expressed in CESC tissues. Molecular biological verification using quantitative reverse transcribed PCR, western blotting and immunohistochemistry assays exhibited significant differences in the expression of RFC4 between CESC and para-cancerous tissues (P < 0.05). Conclusion This study identified three potential biomarkers (RFC4, MCM2, TOP2A) of CESC which may be useful to clarify the underlying mechanisms of CESC and predict the prognosis of CESC patients.
bibliographic citation: He et al. (2020) Identification of significant genes signatures and prognostic biomarkers in cervical squamous carcinoma via bioinformatic data. PeerJ 8:e10386 https://doi.org/10.7717/peerj.10386
date submitted: 2020-07-28
date accepted: 2020-10-27
issued: 2020-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: He
  given name: Yunan
author list: Agent
  family name: Hu
  given name: Shunjie
author list: Agent
  family name: Zhong
  given name: Jiaojiao
author list: Agent
  family name: Cheng
  given name: Anran
author list: Agent
  family name: Shan
  given name: Nianchun
doi: 10.7717/peerj.10386
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-02
copyright: ©2020 He et al.
attribution name: He et al.

Ixodes scapularis microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing
type: item
type: AcademicArticle
description: Ticks are globally distributed arthropods and a public health concern due to the many human pathogens they carry and transmit, including the causative agent of Lyme disease, Borrelia burgdorferi. As tick species’ ranges increase, so do the number of reported tick related illnesses. The microbiome is a critical part of understanding arthropod biology, and the microbiome of pathogen vectors may provide critical insight into disease transmission and management. Yet we lack a comprehensive understanding of the microbiome of wild ticks, including what effect the presence of multiple tick-borne pathogens (TBPs) has on the microbiome. In this study we chose samples based on life stage (adult or nymph) and which TBPs were present. We used DNA from previously extracted Ixodes scapularis ticks that tested positive for zero, one, two or three common TBPs (B. burgdorferi, B. miyamotoi, Anaplasma phagocytophilum, Babesia microti). We produced 16S rRNA amplicon data for the whole tick microbiome and compared samples across TBPs status, single vs multiple coinfections, and life stages. Focusing on samples with a single TBP, we found no significant differences in microbiome diversity in ticks that were infected with B. burgdorferi and ticks with no TBPs. When comparing multiple TBPs, we found no significant difference in both alpha and beta diversity between ticks with a single TBP and ticks with multiple TBPs. Removal of TBPs from the microbiome did not alter alpha or beta diversity results. Life stage significantly correlated to variation in beta diversity and nymphs had higher alpha diversity than adult ticks. Rickettsia, a common tick endosymbiont, was the most abundant genus. This study confirms that the wild tick microbiome is highly influenced by life stage and much less by the presence of human pathogenic bacteria.
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creator: Joshua C. Gil
creator: Zeinab H. Helal
creator: Guillermo Risatti
creator: Sarah M. Hird
subject: Developmental Biology
subject: Ecology
subject: Entomology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.10424
publisher: PeerJ Inc.
rights: © 2020 Gil et al.
abstract: Ticks are globally distributed arthropods and a public health concern due to the many human pathogens they carry and transmit, including the causative agent of Lyme disease, Borrelia burgdorferi. As tick species’ ranges increase, so do the number of reported tick related illnesses. The microbiome is a critical part of understanding arthropod biology, and the microbiome of pathogen vectors may provide critical insight into disease transmission and management. Yet we lack a comprehensive understanding of the microbiome of wild ticks, including what effect the presence of multiple tick-borne pathogens (TBPs) has on the microbiome. In this study we chose samples based on life stage (adult or nymph) and which TBPs were present. We used DNA from previously extracted Ixodes scapularis ticks that tested positive for zero, one, two or three common TBPs (B. burgdorferi, B. miyamotoi, Anaplasma phagocytophilum, Babesia microti). We produced 16S rRNA amplicon data for the whole tick microbiome and compared samples across TBPs status, single vs multiple coinfections, and life stages. Focusing on samples with a single TBP, we found no significant differences in microbiome diversity in ticks that were infected with B. burgdorferi and ticks with no TBPs. When comparing multiple TBPs, we found no significant difference in both alpha and beta diversity between ticks with a single TBP and ticks with multiple TBPs. Removal of TBPs from the microbiome did not alter alpha or beta diversity results. Life stage significantly correlated to variation in beta diversity and nymphs had higher alpha diversity than adult ticks. Rickettsia, a common tick endosymbiont, was the most abundant genus. This study confirms that the wild tick microbiome is highly influenced by life stage and much less by the presence of human pathogenic bacteria.
bibliographic citation: Gil et al. (2020) Ixodes scapularis microbiome correlates with life stage, not the presence of human pathogens, in ticks submitted for diagnostic testing. PeerJ 8:e10424 https://doi.org/10.7717/peerj.10424
date submitted: 2020-07-06
date accepted: 2020-11-03
issued: 2020-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gil
  given name: Joshua C.
author list: Agent
  family name: Helal
  given name: Zeinab H.
author list: Agent
  family name: Risatti
  given name: Guillermo
author list: Agent
  family name: Hird
  given name: Sarah M.
doi: 10.7717/peerj.10424
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-02
copyright: ©2020 Gil et al.
attribution name: Gil et al.

Phospho-islands and the evolution of phosphorylated amino acids in mammals
type: item
type: AcademicArticle
description: Background Protein phosphorylation is the best studied post-translational modification strongly influencing protein function. Phosphorylated amino acids not only differ in physico-chemical properties from non-phosphorylated counterparts, but also exhibit different evolutionary patterns, tending to mutate to and originate from negatively charged amino acids (NCAs). The distribution of phosphosites along protein sequences is non-uniform, as phosphosites tend to cluster, forming so-called phospho-islands. Methods Here, we have developed a hidden Markov model-based procedure for the identification of phospho-islands and studied the properties of the obtained phosphorylation clusters. To check robustness of evolutionary analysis, we consider different models for the reconstructions of ancestral phosphorylation states. Results Clustered phosphosites differ from individual phosphosites in several functional and evolutionary aspects including underrepresentation of phosphotyrosines, higher conservation, more frequent mutations to NCAs. The spectrum of tissues, frequencies of specific phosphorylation contexts, and mutational patterns observed near clustered sites also are different.
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creator: Mikhail Moldovan
creator: Mikhail S. Gelfand
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.10436
publisher: PeerJ Inc.
rights: © 2020 Moldovan and Gelfand
abstract: Background Protein phosphorylation is the best studied post-translational modification strongly influencing protein function. Phosphorylated amino acids not only differ in physico-chemical properties from non-phosphorylated counterparts, but also exhibit different evolutionary patterns, tending to mutate to and originate from negatively charged amino acids (NCAs). The distribution of phosphosites along protein sequences is non-uniform, as phosphosites tend to cluster, forming so-called phospho-islands. Methods Here, we have developed a hidden Markov model-based procedure for the identification of phospho-islands and studied the properties of the obtained phosphorylation clusters. To check robustness of evolutionary analysis, we consider different models for the reconstructions of ancestral phosphorylation states. Results Clustered phosphosites differ from individual phosphosites in several functional and evolutionary aspects including underrepresentation of phosphotyrosines, higher conservation, more frequent mutations to NCAs. The spectrum of tissues, frequencies of specific phosphorylation contexts, and mutational patterns observed near clustered sites also are different.
bibliographic citation: Moldovan et al. (2020) Phospho-islands and the evolution of phosphorylated amino acids in mammals. PeerJ 8:e10436 https://doi.org/10.7717/peerj.10436
date submitted: 2020-09-03
date accepted: 2020-11-06
issued: 2020-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moldovan
  given name: Mikhail
author list: Agent
  family name: Gelfand
  given name: Mikhail S.
doi: 10.7717/peerj.10436
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-02
copyright: © 2020 Moldovan and Gelfand
attribution name: Moldovan and Gelfand

Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand
type: item
type: AcademicArticle
description: Background Urinary tract infections (UTIs) are the most common bacterial infections and are often caused by uropathogenic Escherichia coli (UPEC). We investigated the distribution of phylogenetic groups, adhesin genes, antimicrobial resistance, and biofilm formation in E. coli isolated from patients with UTIs. Methods In the present study, 208 UPEC isolated from Thai patients were classified into phylogenetic groups and adhesin genes were detected using multiplex PCR. Antimicrobial susceptibility testing was performed using agar disk diffusion. The Congo red agar method was used to determine the ability of the UPEC to form biofilm. Results The most prevalent UPEC strains in this study belonged to phylogenetic group B2 (58.7%), followed by group C (12.5%), group E (12.0%), and the other groups (16.8%). Among adhesin genes, the prevalence of fimH (91.8%) was highest, followed by pap (79.3%), sfa (12.0%), and afa (7.7%). The rates of resistance to fluoroquinolones, trimethoprim-sulfamethoxazole, and amoxicillin-clavulanate were 65%, 54.3%, and 36.5%, respectively. The presence of adhesin genes and antibiotic resistance were more frequent in groups B2 and C compared to the other groups. Of the 129 multidrug-resistant UPEC strains, 54% were biofilm producers. Our findings further indicated that biofilm production was significantly correlated with the pap adhesin gene (p ≤ 0.05). Conclusion These findings provide molecular epidemiologic data, antibiotic resistance profiles, and the potential for biofilm formation among UPEC strains that can inform further development of the appropriate prevention and control strategies for UTIs in this region.
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creator: Nipaporn Tewawong
creator: Siriporn Kowaboot
creator: Yaowaluk Pimainog
creator: Naiyana Watanagul
creator: Thanunrat Thongmee
creator: Yong Poovorawan
subject: Microbiology
subject: Molecular Biology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.10453
publisher: PeerJ Inc.
rights: © 2020 Tewawong et al.
abstract: Background Urinary tract infections (UTIs) are the most common bacterial infections and are often caused by uropathogenic Escherichia coli (UPEC). We investigated the distribution of phylogenetic groups, adhesin genes, antimicrobial resistance, and biofilm formation in E. coli isolated from patients with UTIs. Methods In the present study, 208 UPEC isolated from Thai patients were classified into phylogenetic groups and adhesin genes were detected using multiplex PCR. Antimicrobial susceptibility testing was performed using agar disk diffusion. The Congo red agar method was used to determine the ability of the UPEC to form biofilm. Results The most prevalent UPEC strains in this study belonged to phylogenetic group B2 (58.7%), followed by group C (12.5%), group E (12.0%), and the other groups (16.8%). Among adhesin genes, the prevalence of fimH (91.8%) was highest, followed by pap (79.3%), sfa (12.0%), and afa (7.7%). The rates of resistance to fluoroquinolones, trimethoprim-sulfamethoxazole, and amoxicillin-clavulanate were 65%, 54.3%, and 36.5%, respectively. The presence of adhesin genes and antibiotic resistance were more frequent in groups B2 and C compared to the other groups. Of the 129 multidrug-resistant UPEC strains, 54% were biofilm producers. Our findings further indicated that biofilm production was significantly correlated with the pap adhesin gene (p ≤ 0.05). Conclusion These findings provide molecular epidemiologic data, antibiotic resistance profiles, and the potential for biofilm formation among UPEC strains that can inform further development of the appropriate prevention and control strategies for UTIs in this region.
bibliographic citation: Tewawong et al. (2020) Distribution of phylogenetic groups, adhesin genes, biofilm formation, and antimicrobial resistance of uropathogenic Escherichia coli isolated from hospitalized patients in Thailand. PeerJ 8:e10453 https://doi.org/10.7717/peerj.10453
date submitted: 2020-08-19
date accepted: 2020-11-09
issued: 2020-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tewawong
  given name: Nipaporn
author list: Agent
  family name: Kowaboot
  given name: Siriporn
author list: Agent
  family name: Pimainog
  given name: Yaowaluk
author list: Agent
  family name: Watanagul
  given name: Naiyana
author list: Agent
  family name: Thongmee
  given name: Thanunrat
author list: Agent
  family name: Poovorawan
  given name: Yong
doi: 10.7717/peerj.10453
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-02
copyright: ©2020 Tewawong et al.
attribution name: Tewawong et al.

Genome-wide identification and evolution of HECT genes in wheat
type: item
type: AcademicArticle
description: Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.
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format: text/html
creator: Xianwen Meng
creator: Ting Yang
creator: Jing Liu
creator: Mingde Zhao
creator: Jiuli Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10457
publisher: PeerJ Inc.
rights: © 2020 Meng et al.
abstract: Background As an important class of E3 ubiquitin ligases in the ubiquitin proteasome pathway, proteins containing homologous E6-AP carboxyl terminus (HECT) domains are crucial for growth, development, metabolism, and abiotic and biotic stress responses in plants. However, little is known about HECT genes in wheat (Triticum aestivum L.), one of the most important global crops. Methods Using a genome-wide analysis of high-quality wheat genome sequences, we identified 25 HECT genes classified into six groups based on the phylogenetic relationship among wheat, rice, and Arabidopsis thaliana. Results The predicted HECT genes were distributed evenly in 17 of 21 chromosomes of the three wheat subgenomes. Twenty-one of these genes were hypothesized to be segmental duplication genes, indicating that segmental duplication was significantly associated with the expansion of the wheat HECT gene family. The Ka/Ks ratios of the segmental duplication of these genes were less than 1, suggesting purifying selection within the gene family. The expression profile analysis revealed that the 25 wheat HECT genes were differentially expressed in 15 tissues, and genes in Group II, IV, and VI (UPL8, UPL6, UPL3) were highly expressed in roots, stems, and spikes. This study contributes to further the functional analysis of the HECT gene family in wheat.
bibliographic citation: Meng et al. (2020) Genome-wide identification and evolution of HECT genes in wheat. PeerJ 8:e10457 https://doi.org/10.7717/peerj.10457
date submitted: 2020-06-05
date accepted: 2020-11-10
issued: 2020-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Xianwen
author list: Agent
  family name: Yang
  given name: Ting
author list: Agent
  family name: Liu
  given name: Jing
author list: Agent
  family name: Zhao
  given name: Mingde
author list: Agent
  family name: Wang
  given name: Jiuli
doi: 10.7717/peerj.10457
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-02
copyright: ©2020 Meng et al.
attribution name: Meng et al.

Comparative genomic analysis of the principal Cryptosporidium species that infect humans
type: item
type: AcademicArticle
description: Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.
format: application/pdf
format: text/html
creator: Laura M. Arias-Agudelo
creator: Gisela Garcia-Montoya
creator: Felipe Cabarcas
creator: Ana L. Galvan-Diaz
creator: Juan F. Alzate
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Parasitology
subject: Taxonomy
description: doi:10.7717/peerj.10478
publisher: PeerJ Inc.
rights: © 2020 Arias-Agudelo et al.
abstract: Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.
bibliographic citation: Arias-Agudelo et al. (2020) Comparative genomic analysis of the principal Cryptosporidium species that infect humans. PeerJ 8:e10478 https://doi.org/10.7717/peerj.10478
date submitted: 2020-05-18
date accepted: 2020-11-11
issued: 2020-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arias-Agudelo
  given name: Laura M.
author list: Agent
  family name: Garcia-Montoya
  given name: Gisela
author list: Agent
  family name: Cabarcas
  given name: Felipe
author list: Agent
  family name: Galvan-Diaz
  given name: Ana L.
author list: Agent
  family name: Alzate
  given name: Juan F.
doi: 10.7717/peerj.10478
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-02
copyright: ©2020 Arias-Agudelo et al.
attribution name: Arias-Agudelo et al.

The gut microbiota in the common kestrel (Falco tinnunculus): a report from the Beijing Raptor Rescue Center
type: item
type: AcademicArticle
description: As a complex microecological system, the gut microbiota plays crucial roles in many aspects, including immunology, physiology and development. The specific function and mechanism of the gut microbiota in birds are distinct due to their body structure, physiological attributes and life history. Data on the gut microbiota of the common kestrel, a second-class protected animal species in China, are currently scarce. With high-throughput sequencing technology, we characterized the bacterial community of the gut from nine fecal samples from a wounded common kestrel by sequencing the V3-V4 region of the 16S ribosomal RNA gene. Our results showed that Proteobacteria (41.078%), Firmicutes (40.923%) and Actinobacteria (11.191%) were the most predominant phyla. Lactobacillus (20.563%) was the most dominant genus, followed by Escherichia-Shigella (17.588%) and Acinetobacter (5.956%). Our results would offer fundamental data and direction for the wildlife rescue.
format: application/pdf
format: text/html
creator: Yu Guan
creator: Hongfang Wang
creator: Yinan Gong
creator: Jianping Ge
creator: Lei Bao
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.9970
publisher: PeerJ Inc.
rights: © 2020 Guan et al.
abstract: As a complex microecological system, the gut microbiota plays crucial roles in many aspects, including immunology, physiology and development. The specific function and mechanism of the gut microbiota in birds are distinct due to their body structure, physiological attributes and life history. Data on the gut microbiota of the common kestrel, a second-class protected animal species in China, are currently scarce. With high-throughput sequencing technology, we characterized the bacterial community of the gut from nine fecal samples from a wounded common kestrel by sequencing the V3-V4 region of the 16S ribosomal RNA gene. Our results showed that Proteobacteria (41.078%), Firmicutes (40.923%) and Actinobacteria (11.191%) were the most predominant phyla. Lactobacillus (20.563%) was the most dominant genus, followed by Escherichia-Shigella (17.588%) and Acinetobacter (5.956%). Our results would offer fundamental data and direction for the wildlife rescue.
bibliographic citation: Guan et al. (2020) The gut microbiota in the common kestrel (Falco tinnunculus): a report from the Beijing Raptor Rescue Center. PeerJ 8:e9970 https://doi.org/10.7717/peerj.9970
date submitted: 2020-01-27
date accepted: 2020-08-26
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guan
  given name: Yu
author list: Agent
  family name: Wang
  given name: Hongfang
author list: Agent
  family name: Gong
  given name: Yinan
author list: Agent
  family name: Ge
  given name: Jianping
author list: Agent
  family name: Bao
  given name: Lei
doi: 10.7717/peerj.9970
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: ©2020 Guan et al.
attribution name: Guan et al.

Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration
type: item
type: AcademicArticle
description: Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experimental models. To track the dynamics of individual gut microbiomes during gut regeneration, both caged mariculture and laboratory isolator systems of sea cucumbers (Apostichopus japonicus) were developed and longitudinal meta16S analyses were performed. Under natural environmental conditions in the caged mariculture system, both bacterial and eukaryotic communities in sea cucumbers’ guts appeared to be reconstructed within 4 months after evisceration. Using the laboratory isolator, which can trace daily dynamics, we found that fecal microbiota collected before evisceration were clearly different from those collected after evisceration. We also identified eight key bacteria, belonging to Alteromonadaceae, Rhodobacteraceae, Oceanospirillaceae and family-unassigned Gammaproteobacteria, suggesting that these bacteria might interact with the host during the gut regeneration process. Six of the eight key bacteria were isolated for further bioassay using the isolator developed in this study to test whether these isolates affect gut regeneration.
format: application/pdf
format: text/html
creator: Yohei Yamazaki
creator: Yuichi Sakai
creator: Juanwen Yu
creator: Sayaka Mino
creator: Tomoo Sawabe
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.10260
publisher: PeerJ Inc.
rights: © 2020 Yamazaki et al.
abstract: Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experimental models. To track the dynamics of individual gut microbiomes during gut regeneration, both caged mariculture and laboratory isolator systems of sea cucumbers (Apostichopus japonicus) were developed and longitudinal meta16S analyses were performed. Under natural environmental conditions in the caged mariculture system, both bacterial and eukaryotic communities in sea cucumbers’ guts appeared to be reconstructed within 4 months after evisceration. Using the laboratory isolator, which can trace daily dynamics, we found that fecal microbiota collected before evisceration were clearly different from those collected after evisceration. We also identified eight key bacteria, belonging to Alteromonadaceae, Rhodobacteraceae, Oceanospirillaceae and family-unassigned Gammaproteobacteria, suggesting that these bacteria might interact with the host during the gut regeneration process. Six of the eight key bacteria were isolated for further bioassay using the isolator developed in this study to test whether these isolates affect gut regeneration.
bibliographic citation: Yamazaki et al. (2020) Tracking the dynamics of individual gut microbiome of sea cucumber Apostichopus japonicus during gut regeneration. PeerJ 8:e10260 https://doi.org/10.7717/peerj.10260
date submitted: 2020-03-30
date accepted: 2020-10-06
issued: 2020-12-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yamazaki
  given name: Yohei
author list: Agent
  family name: Sakai
  given name: Yuichi
author list: Agent
  family name: Yu
  given name: Juanwen
author list: Agent
  family name: Mino
  given name: Sayaka
author list: Agent
  family name: Sawabe
  given name: Tomoo
doi: 10.7717/peerj.10260
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-01
copyright: © 2020 Yamazaki et al.
attribution name: Yamazaki et al.

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