PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species
items: Moderately low nitrogen application mitigate the negative effects of salt stress on annual ryegrass seedlings
items: Analysis of 44 Vibrio anguillarum genomes reveals high genetic diversity
items: ARID1A alterations and their clinical significance in cholangiocarcinoma
items: Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs
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

Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species
type: item
type: AcademicArticle
description: Social insects have co-existed with microbial species for millions of years and have evolved a diversity of collective defenses, including the use of antimicrobials. While many studies have revealed strategies that ants use against microbial entomopathogens, and several have shown ant-produced compounds inhibit environmental bacterial growth, few studies have tested whether exposure to environmental bacteria represents a health threat to ants. We compare four ant species’ responses to exposure to Escherichia coli and Staphylococcus epidermidis bacteria in order to broaden our understanding of microbial health-threats to ants and their ability to defend against them. In a first experiment, we measure worker mortality of Solenopsis invicta, Brachymyrmex chinensis, Aphaenogaster rudis, and Dorymyrmex bureni in response to exposure to E. coli and S. epidermidis. We found that exposure to E. coli was lethal for S. invicta and D. bureni, while all other effects of exposure were not different from experimental controls. In a second experiment, we compared the antimicrobial ability of surface extracts from bacteria-exposed and non-exposed S. invicta and B. chinensis worker ants, to see if exposure to E. coli or S. epidermidis led to an increase in antimicrobial compounds. We found no difference in the inhibitory effects from either treatment group in either species. Our results demonstrate the susceptibility to bacteria is varied across ant species. This variation may correlate with an ant species’ use of surface antimicrobials, as we found significant mortality effects in species which also were producing antimicrobials. Further exploration of a wide range of both bacteria and ant species is likely to reveal unique and nuanced antimicrobial strategies and deepen our understanding of how ant societies respond to microbial health threats.
format: application/pdf
format: text/html
creator: Omar Halawani
creator: Robert R. Dunn
creator: Amy M. Grunden
creator: Adrian A. Smith
subject: Ecology
subject: Entomology
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.10412
publisher: PeerJ Inc.
rights: © 2020 Halawani et al.
abstract: Social insects have co-existed with microbial species for millions of years and have evolved a diversity of collective defenses, including the use of antimicrobials. While many studies have revealed strategies that ants use against microbial entomopathogens, and several have shown ant-produced compounds inhibit environmental bacterial growth, few studies have tested whether exposure to environmental bacteria represents a health threat to ants. We compare four ant species’ responses to exposure to Escherichia coli and Staphylococcus epidermidis bacteria in order to broaden our understanding of microbial health-threats to ants and their ability to defend against them. In a first experiment, we measure worker mortality of Solenopsis invicta, Brachymyrmex chinensis, Aphaenogaster rudis, and Dorymyrmex bureni in response to exposure to E. coli and S. epidermidis. We found that exposure to E. coli was lethal for S. invicta and D. bureni, while all other effects of exposure were not different from experimental controls. In a second experiment, we compared the antimicrobial ability of surface extracts from bacteria-exposed and non-exposed S. invicta and B. chinensis worker ants, to see if exposure to E. coli or S. epidermidis led to an increase in antimicrobial compounds. We found no difference in the inhibitory effects from either treatment group in either species. Our results demonstrate the susceptibility to bacteria is varied across ant species. This variation may correlate with an ant species’ use of surface antimicrobials, as we found significant mortality effects in species which also were producing antimicrobials. Further exploration of a wide range of both bacteria and ant species is likely to reveal unique and nuanced antimicrobial strategies and deepen our understanding of how ant societies respond to microbial health threats.
bibliographic citation: Halawani et al. (2020) Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species. PeerJ 8:e10412 https://doi.org/10.7717/peerj.10412
date submitted: 2020-06-05
date accepted: 2020-11-02
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Halawani
  given name: Omar
author list: Agent
  family name: Dunn
  given name: Robert R.
author list: Agent
  family name: Grunden
  given name: Amy M.
author list: Agent
  family name: Smith
  given name: Adrian A.
doi: 10.7717/peerj.10412
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: © 2020 Halawani et al.
attribution name: Halawani et al.

Moderately low nitrogen application mitigate the negative effects of salt stress on annual ryegrass seedlings
type: item
type: AcademicArticle
description: Appropriate application of nitrogen (N) can alleviate the salt stress-induced damage on plants. This study explores the changes of nitrogen requirement in feeding annual ryegrass seedlings under mild salt concentrations (50 mM, 100 mM) plus its underlying mitigation mechanism. Results showed that low salt concentration decreased N requirement as observed from the increment in plant height and biomass at a relative low N level (2.0 mM not 5.0 mM). Under salt treatment, especially at 50 mM NaCl, the OJIP (Chl a fluorescence induction transient) curve and a series of performance indexes (PIABS, RC/CS0, ET0/CS0, ϕE0, ϕ0) peaked whereas DI0/RC, Vj and M0 were the lowest under moderately low N level (2.0 mM). In addition, under salt stress, moderately low N application could maintain the expression of NR (nitrate reductase) and GS (glutamine synthetase) encoding genes at a relatively stable level but had no effect on the expression of detected NRT (nitrate transporter) gene. The seedlings cultured at 2.0 mM N also exhibited the highest activity of CAT and POD antioxidant enzymes and the lowest MDA content and EL under relative low level of salt treatment. These results indicated that mild salt treatment of annual ryegrass seedlings might reduce N requirement while moderately low N application could promote their growth via regulating photosynthesis, alleviating ROS-induced (reactive oxygen species) damage and maintenance of N metabolism. These results also can provide useful reference for nitrogen application in moderation rather than in excess on annual ryegrass in mild or medium salinity areas through understanding the underlying response mechanisms.
format: application/pdf
format: text/html
creator: An Shao
creator: Zhichao Sun
creator: Shugao Fan
creator: Xiao Xu
creator: Wei Wang
creator: Erick Amombo
creator: Yanling Yin
creator: Xiaoning Li
creator: Guangyang Wang
creator: Hongli Wang
creator: Jinmin Fu
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.10427
publisher: PeerJ Inc.
rights: © 2020 Shao et al.
abstract: Appropriate application of nitrogen (N) can alleviate the salt stress-induced damage on plants. This study explores the changes of nitrogen requirement in feeding annual ryegrass seedlings under mild salt concentrations (50 mM, 100 mM) plus its underlying mitigation mechanism. Results showed that low salt concentration decreased N requirement as observed from the increment in plant height and biomass at a relative low N level (2.0 mM not 5.0 mM). Under salt treatment, especially at 50 mM NaCl, the OJIP (Chl a fluorescence induction transient) curve and a series of performance indexes (PIABS, RC/CS0, ET0/CS0, ϕE0, ϕ0) peaked whereas DI0/RC, Vj and M0 were the lowest under moderately low N level (2.0 mM). In addition, under salt stress, moderately low N application could maintain the expression of NR (nitrate reductase) and GS (glutamine synthetase) encoding genes at a relatively stable level but had no effect on the expression of detected NRT (nitrate transporter) gene. The seedlings cultured at 2.0 mM N also exhibited the highest activity of CAT and POD antioxidant enzymes and the lowest MDA content and EL under relative low level of salt treatment. These results indicated that mild salt treatment of annual ryegrass seedlings might reduce N requirement while moderately low N application could promote their growth via regulating photosynthesis, alleviating ROS-induced (reactive oxygen species) damage and maintenance of N metabolism. These results also can provide useful reference for nitrogen application in moderation rather than in excess on annual ryegrass in mild or medium salinity areas through understanding the underlying response mechanisms.
bibliographic citation: Shao et al. (2020) Moderately low nitrogen application mitigate the negative effects of salt stress on annual ryegrass seedlings. PeerJ 8:e10427 https://doi.org/10.7717/peerj.10427
date submitted: 2020-07-29
date accepted: 2020-11-03
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shao
  given name: An
author list: Agent
  family name: Sun
  given name: Zhichao
author list: Agent
  family name: Fan
  given name: Shugao
author list: Agent
  family name: Xu
  given name: Xiao
author list: Agent
  family name: Wang
  given name: Wei
author list: Agent
  family name: Amombo
  given name: Erick
author list: Agent
  family name: Yin
  given name: Yanling
author list: Agent
  family name: Li
  given name: Xiaoning
author list: Agent
  family name: Wang
  given name: Guangyang
author list: Agent
  family name: Wang
  given name: Hongli
author list: Agent
  family name: Fu
  given name: Jinmin
doi: 10.7717/peerj.10427
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: ©2020 Shao et al.
attribution name: Shao et al.

Analysis of 44 Vibrio anguillarum genomes reveals high genetic diversity
type: item
type: AcademicArticle
description: Vibriosis, a hemorrhagic septicemic disease caused by the bacterium Vibrio anguillarum, is an important bacterial infection in Danish sea-reared rainbow trout. Despite of vaccination, outbreaks still occur, likely because the vaccine is based on V. anguillarum strains from abroad/other hosts than rainbow trout. Information about the genetic diversity of V. anguillarum specifically in Danish rainbow trout, is required to investigate this claim. Consequently, the aim of the present investigation was to sequence and to characterize a collection of 44 V. anguillarum strains obtained primarily from vibriosis outbreaks in Danish rainbow trout. The strains were sequenced, de novo assembled, and the genomes examined for the presence of plasmids, virulence, and acquired antibiotic resistance genes. To investigate the phylogeny, single nucleotide polymorphisms were identified, and the pan-genome was calculated. All strains carried tet(34) encoding tetracycline resistance, and 36 strains also contained qnrVC6 for increased fluoroquinolone/quinolone resistance. But interestingly, all strains were phenotypic sensitive to both oxytetracycline and oxolinic acid. Almost all serotype O1 strains contained a pJM1-like plasmid and nine serotype O2A strains carried the plasmid p15. The distribution of virulence genes was rather similar across the strains, although evident variance among serotypes was observed. Most significant, almost all serotype O2 and O3 strains, as well as the serotype O1 strain without a pJM1-like plasmid, carried genes encoding piscibactin biosynthesis. Hence supporting the hypothesis, that piscibactin plays a crucial role in virulence for pathogenic strains lacking the anguibactin system. The phylogenetic analysis and pan-genome calculations revealed great diversity within V. anguillarum. Serotype O1 strains were in general very similar, whereas considerable variation was found among serotype O2A strains. The great diversity within the V. anguillarum serotype O2A…
format: application/pdf
format: text/html
creator: Mie Johanne Hansen
creator: Egle Kudirkiene
creator: Inger Dalsgaard
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.10451
publisher: PeerJ Inc.
rights: © 2020 Hansen et al.
abstract: Vibriosis, a hemorrhagic septicemic disease caused by the bacterium Vibrio anguillarum, is an important bacterial infection in Danish sea-reared rainbow trout. Despite of vaccination, outbreaks still occur, likely because the vaccine is based on V. anguillarum strains from abroad/other hosts than rainbow trout. Information about the genetic diversity of V. anguillarum specifically in Danish rainbow trout, is required to investigate this claim. Consequently, the aim of the present investigation was to sequence and to characterize a collection of 44 V. anguillarum strains obtained primarily from vibriosis outbreaks in Danish rainbow trout. The strains were sequenced, de novo assembled, and the genomes examined for the presence of plasmids, virulence, and acquired antibiotic resistance genes. To investigate the phylogeny, single nucleotide polymorphisms were identified, and the pan-genome was calculated. All strains carried tet(34) encoding tetracycline resistance, and 36 strains also contained qnrVC6 for increased fluoroquinolone/quinolone resistance. But interestingly, all strains were phenotypic sensitive to both oxytetracycline and oxolinic acid. Almost all serotype O1 strains contained a pJM1-like plasmid and nine serotype O2A strains carried the plasmid p15. The distribution of virulence genes was rather similar across the strains, although evident variance among serotypes was observed. Most significant, almost all serotype O2 and O3 strains, as well as the serotype O1 strain without a pJM1-like plasmid, carried genes encoding piscibactin biosynthesis. Hence supporting the hypothesis, that piscibactin plays a crucial role in virulence for pathogenic strains lacking the anguibactin system. The phylogenetic analysis and pan-genome calculations revealed great diversity within V. anguillarum. Serotype O1 strains were in general very similar, whereas considerable variation was found among serotype O2A strains. The great diversity within the V. anguillarum serotype O2A…
bibliographic citation: Hansen et al. (2020) Analysis of 44 Vibrio anguillarum genomes reveals high genetic diversity. PeerJ 8:e10451 https://doi.org/10.7717/peerj.10451
date submitted: 2020-06-19
date accepted: 2020-11-09
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hansen
  given name: Mie Johanne
author list: Agent
  family name: Kudirkiene
  given name: Egle
author list: Agent
  family name: Dalsgaard
  given name: Inger
doi: 10.7717/peerj.10451
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: © 2020 Hansen et al.
attribution name: Hansen et al.

ARID1A alterations and their clinical significance in cholangiocarcinoma
type: item
type: AcademicArticle
description: Background ARID1A is a member of the SWI/SNF chromatin remodeling complex. It functions as a tumor suppressor and several therapeutic targets in ARID1A-mutated cancers are currently under development, including EZH2. A synthetic lethal relationship between ARID1A and EZH2 has been revealed in several tumor entities. Although genomic alterations of ARID1A have been described in various cancers, no study has examined correlations between ARID1A gene mutation and protein expression with clinicopathologic parameters and prognosis, particularly in liver fluke-related cholangiocarcinoma (Ov-CCA). Here, we investigated the clinical significance of ARID1A mutations and protein expression in CCA tissues and determined whether there is a correlation with EZH2 protein expression. Methods We evaluated ARID1A and EZH2 immunoreactivity using immunohistochemistry in 98 Ov-CCA with a wide range of clinicopathological features. Somatic mutations of ARID1A were analyzed using the ICGC sequencing data in 489 of Ov and non Ov-CCA and assessed prognostic values. Results While detecting a loss or reduction of ARID1A expression in 54 cases (55%) in Ov-CCA, ARID1A expression was associated with ARID1A mutations (p < 0.001, adjusted p-value < 0.001). We observed that 12 of 13 tumors (92%) with loss of ARID1A expression had truncating mutations. There were nine of 13 tumors (69%) with loss of ARID1A expression and 25 of 41 tumors (61%) with low ARID1A expression exhibited distant metastasis (p = 0.028, adjusted p-value = 0.168). ARID1A was predominantly mutated in Ov-CCA compared to non Ov-CCA (24% and 14% in Ov-CCA and non Ov-CCA, respectively, p = 0.027). There were 36 of 72 (50%) and 52 of 79 (66%) tumors with ARID1A mutation showed tumor stage IV and T3/T4, respectively. The significant mutual exclusivity and co-occurrence between ARID1A and TP53/KRAS mutations were not found in ICGC cohort. In addition, high EZH2 expression, a potential synthetic lethal target in ARID1A-mutated tumors, …
format: application/pdf
format: text/html
creator: Achira Namjan
creator: Anchalee Techasen
creator: Watcharin Loilome
creator: Prakasit Sa-ngaimwibool
creator: Apinya Jusakul
subject: Genetics
subject: Gastroenterology and Hepatology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.10464
publisher: PeerJ Inc.
rights: © 2020 Namjan et al.
abstract: Background ARID1A is a member of the SWI/SNF chromatin remodeling complex. It functions as a tumor suppressor and several therapeutic targets in ARID1A-mutated cancers are currently under development, including EZH2. A synthetic lethal relationship between ARID1A and EZH2 has been revealed in several tumor entities. Although genomic alterations of ARID1A have been described in various cancers, no study has examined correlations between ARID1A gene mutation and protein expression with clinicopathologic parameters and prognosis, particularly in liver fluke-related cholangiocarcinoma (Ov-CCA). Here, we investigated the clinical significance of ARID1A mutations and protein expression in CCA tissues and determined whether there is a correlation with EZH2 protein expression. Methods We evaluated ARID1A and EZH2 immunoreactivity using immunohistochemistry in 98 Ov-CCA with a wide range of clinicopathological features. Somatic mutations of ARID1A were analyzed using the ICGC sequencing data in 489 of Ov and non Ov-CCA and assessed prognostic values. Results While detecting a loss or reduction of ARID1A expression in 54 cases (55%) in Ov-CCA, ARID1A expression was associated with ARID1A mutations (p < 0.001, adjusted p-value < 0.001). We observed that 12 of 13 tumors (92%) with loss of ARID1A expression had truncating mutations. There were nine of 13 tumors (69%) with loss of ARID1A expression and 25 of 41 tumors (61%) with low ARID1A expression exhibited distant metastasis (p = 0.028, adjusted p-value = 0.168). ARID1A was predominantly mutated in Ov-CCA compared to non Ov-CCA (24% and 14% in Ov-CCA and non Ov-CCA, respectively, p = 0.027). There were 36 of 72 (50%) and 52 of 79 (66%) tumors with ARID1A mutation showed tumor stage IV and T3/T4, respectively. The significant mutual exclusivity and co-occurrence between ARID1A and TP53/KRAS mutations were not found in ICGC cohort. In addition, high EZH2 expression, a potential synthetic lethal target in ARID1A-mutated tumors, …
bibliographic citation: Namjan et al. (2020) ARID1A alterations and their clinical significance in cholangiocarcinoma. PeerJ 8:e10464 https://doi.org/10.7717/peerj.10464
date submitted: 2020-07-28
date accepted: 2020-11-10
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Namjan
  given name: Achira
author list: Agent
  family name: Techasen
  given name: Anchalee
author list: Agent
  family name: Loilome
  given name: Watcharin
author list: Agent
  family name: Sa-ngaimwibool
  given name: Prakasit
author list: Agent
  family name: Jusakul
  given name: Apinya
doi: 10.7717/peerj.10464
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: ©2020 Namjan et al.
attribution name: Namjan et al.

Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs
type: item
type: AcademicArticle
description: The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.
format: application/pdf
format: text/html
creator: Aline Bruna M. Vaz
creator: Paula Luize C. Fonseca
creator: Felipe F. Silva
creator: Gabriel Quintanilha-Peixoto
creator: Inmaculada Sampedro
creator: Jose A. Siles
creator: Anderson Carmo
creator: Rodrigo B. Kato
creator: Vasco Azevedo
creator: Fernanda Badotti
creator: Juan A. Ocampo
creator: Carlos A. Rosa
creator: Aristóteles Góes-Neto
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.10487
publisher: PeerJ Inc.
rights: © 2020 Vaz et al.
abstract: The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.
bibliographic citation: Vaz et al. (2020) Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs. PeerJ 8:e10487 https://doi.org/10.7717/peerj.10487
date submitted: 2020-01-29
date accepted: 2020-11-12
issued: 2020-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vaz
  given name: Aline Bruna M.
author list: Agent
  family name: Fonseca
  given name: Paula Luize C.
author list: Agent
  family name: Silva
  given name: Felipe F.
author list: Agent
  family name: Quintanilha-Peixoto
  given name: Gabriel
author list: Agent
  family name: Sampedro
  given name: Inmaculada
author list: Agent
  family name: Siles
  given name: Jose A.
author list: Agent
  family name: Carmo
  given name: Anderson
author list: Agent
  family name: Kato
  given name: Rodrigo B.
author list: Agent
  family name: Azevedo
  given name: Vasco
author list: Agent
  family name: Badotti
  given name: Fernanda
author list: Agent
  family name: Ocampo
  given name: Juan A.
author list: Agent
  family name: Rosa
  given name: Carlos A.
author list: Agent
  family name: Góes-Neto
  given name: Aristóteles
doi: 10.7717/peerj.10487
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-03
copyright: © 2020 Vaz et al.
attribution name: Vaz et al.

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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format: text/html
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.
format: application/pdf
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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.
format: application/pdf
format: text/html
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

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