PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis
items: First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics
items: Seagrass structural and elemental indicators reveal high nutrient availability within a tropical lagoon in Panama
items: Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines
items: Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum
items: BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains
items: Construction of an immune-related signature with prognostic value for colon cancer
items: Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types
items: Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida
items: Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study

Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis
type: item
type: AcademicArticle
description: Background Even if many schoolchildren in Ethiopia are anemic and stunted, few have studied the co-existence of anemia and stunting among schoolchildren in Ethiopia. In addition, multilevel analysis to explore the variation in prevalence of concurrent anemia and stunting (CAS) across schools and classes is rarely applied. Thus, we aimed to assess the prevalence and risk factors of CAS at the individual, household, and school level among schoolchildren in southern Ethiopia. Methods We recruited 864 students aged 7–14 years from the Wonago district in southern Ethiopia using a three-stage random sampling, assigning four schools to level one, 24 classes to level two. We then randomly selected 36 children from each class, and recorded their weight, height, haemoglobin, intestinal helminthic infections, hygienic practices, dietary practices, household food insecurity, and socio-demographic information. A multivariate, multilevel logistic regression model was applied to detect potential risk factors for CAS. Results The prevalence of CAS was 10.5% (85/810) among schoolchildren, which increased with age in years (adjusted odds ratio [aOR] 1.39 [95% confidence interval 1.13, 1.71, P = 0.002]) and among children who always did not wash their hands with soap after use of latrine (aOR 4.30 [1.21, 15.3, P = 0.02]). Children who walked barefoot (aOR 10.4 [2.77, 39.1, P = 0.001]), were infected with Trichuris trichiura (aOR 1.74 [1.05, 2.88, P = 0.03]), or had head lice infestation (aOR 1.71 [1.01, 2.92, P = 0.04]) had higher CAS prevalence. Prevalence rates of CAS were low in those using treated drinking water (aOR 0.32 [95% CI 0.11, 0.97, P = 0.04]). Most of the risk factors for CAS were identified at the individual level. The clustering effect measured by the intra-cluster correlation coefficient was 6.8% at school level and 19% at class. Conclusion CAS prevalence is a moderate public health problem among schoolchildren in southern Ethiopia and varies across classes and school…
format: application/pdf
format: text/html
creator: Hiwot Hailu Amare
creator: Bernt Lindtjorn
subject: Global Health
subject: Hematology
subject: Nutrition
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.11158
publisher: PeerJ Inc.
rights: © 2021 Amare and Lindtjorn
abstract: Background Even if many schoolchildren in Ethiopia are anemic and stunted, few have studied the co-existence of anemia and stunting among schoolchildren in Ethiopia. In addition, multilevel analysis to explore the variation in prevalence of concurrent anemia and stunting (CAS) across schools and classes is rarely applied. Thus, we aimed to assess the prevalence and risk factors of CAS at the individual, household, and school level among schoolchildren in southern Ethiopia. Methods We recruited 864 students aged 7–14 years from the Wonago district in southern Ethiopia using a three-stage random sampling, assigning four schools to level one, 24 classes to level two. We then randomly selected 36 children from each class, and recorded their weight, height, haemoglobin, intestinal helminthic infections, hygienic practices, dietary practices, household food insecurity, and socio-demographic information. A multivariate, multilevel logistic regression model was applied to detect potential risk factors for CAS. Results The prevalence of CAS was 10.5% (85/810) among schoolchildren, which increased with age in years (adjusted odds ratio [aOR] 1.39 [95% confidence interval 1.13, 1.71, P = 0.002]) and among children who always did not wash their hands with soap after use of latrine (aOR 4.30 [1.21, 15.3, P = 0.02]). Children who walked barefoot (aOR 10.4 [2.77, 39.1, P = 0.001]), were infected with Trichuris trichiura (aOR 1.74 [1.05, 2.88, P = 0.03]), or had head lice infestation (aOR 1.71 [1.01, 2.92, P = 0.04]) had higher CAS prevalence. Prevalence rates of CAS were low in those using treated drinking water (aOR 0.32 [95% CI 0.11, 0.97, P = 0.04]). Most of the risk factors for CAS were identified at the individual level. The clustering effect measured by the intra-cluster correlation coefficient was 6.8% at school level and 19% at class. Conclusion CAS prevalence is a moderate public health problem among schoolchildren in southern Ethiopia and varies across classes and school…
bibliographic citation: Amare et al. (2021) Concurrent anemia and stunting among schoolchildren in Wonago district in southern Ethiopia: a cross-sectional multilevel analysis. PeerJ 9:e11158 https://doi.org/10.7717/peerj.11158
date submitted: 2020-11-10
date accepted: 2021-03-04
issued: 2021-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amare
  given name: Hiwot Hailu
author list: Agent
  family name: Lindtjorn
  given name: Bernt
doi: 10.7717/peerj.11158
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-06
copyright: ©2021 Amare and Lindtjorn
attribution name: Amare and Lindtjorn

First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics
type: item
type: AcademicArticle
description: Background The mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae. Methods Here, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out. Results Mitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae.
format: application/pdf
format: text/html
creator: Chen-Guang Zheng
creator: Xiu-Xiu Zhu
creator: Li-Ping Yan
creator: Yuan Yao
creator: Wen-Jun Bu
creator: Xin-Hua Wang
creator: Xiao-Long Lin
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.11294
publisher: PeerJ Inc.
rights: © 2021 Zheng et al.
abstract: Background The mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae. Methods Here, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out. Results Mitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae.
bibliographic citation: Zheng et al. (2021) First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics. PeerJ 9:e11294 https://doi.org/10.7717/peerj.11294
date submitted: 2020-12-21
date accepted: 2021-03-27
issued: 2021-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Chen-Guang
author list: Agent
  family name: Zhu
  given name: Xiu-Xiu
author list: Agent
  family name: Yan
  given name: Li-Ping
author list: Agent
  family name: Yao
  given name: Yuan
author list: Agent
  family name: Bu
  given name: Wen-Jun
author list: Agent
  family name: Wang
  given name: Xin-Hua
author list: Agent
  family name: Lin
  given name: Xiao-Long
doi: 10.7717/peerj.11294
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-06
copyright: ©2021 Zheng et al.
attribution name: Zheng et al.

Seagrass structural and elemental indicators reveal high nutrient availability within a tropical lagoon in Panama
type: item
type: AcademicArticle
description: Seagrass meadows are valued coastal habitats that provide ecological and economic benefits around the world. Despite their importance, many meadows are in decline, driven by a variety of anthropogenic impacts. While these declines have been well documented in some regions, other locations (particularly within the tropics) lack long-term monitoring programs needed to resolve seagrass trends over time. Effective and spatially-expansive monitoring within under-represented regions is critical to provide an accurate perspective on seagrass status and trends. We present a comprehensive dataset on seagrass coverage and composition across 24 sites in Bahía Almirante, a lagoon along the Caribbean coast of Panama. Using a single survey, we focus on capturing spatial variation in seagrass physical and elemental characteristics and provide data on key seagrass bio-indicators, such as leaf morphology (length and width), elemental content (% nitrogen and phosphorus) and stable isotopic signatures (δ13C and δ15N). We further explore relationships between these variables and water depth (proxy for light availability) and proximity to shore (proxy for terrestrial inputs). The seagrass assemblage was mostly monospecific (dominated by Thalassia testudinum) and restricted to shallow water (<3 m). Above-ground biomass varied widely, averaging 71.7 g dry mass m−2, yet ranging from 24.8 to 139.6 g dry mass m−2. Leaf nitrogen content averaged 2.2%, ranging from 1.76 to 2.57%, while phosphorus content averaged 0.19% and ranged from 0.15 to 0.23%. These values were high compared to other published reports for T. testudinum, indicating elevated nutrient availability within the lagoon. Seagrass stable isotopic characteristics varied slightly and were comparable with other published values. Leaf carbon signatures (δ13C) ranged from −11.74 to −6.70‰ and were positively correlated to shoreline proximity, suggesting a contribution of terrestrial carbon to seagrass biomass. Leaf nitrogen signatures…
format: application/pdf
format: text/html
creator: Julie Gaubert-Boussarie
creator: Andrew H. Altieri
creator: J. Emmett Duffy
creator: Justin E. Campbell
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
description: doi:10.7717/peerj.11308
publisher: PeerJ Inc.
rights: © 2021 Gaubert-Boussarie et al.
abstract: Seagrass meadows are valued coastal habitats that provide ecological and economic benefits around the world. Despite their importance, many meadows are in decline, driven by a variety of anthropogenic impacts. While these declines have been well documented in some regions, other locations (particularly within the tropics) lack long-term monitoring programs needed to resolve seagrass trends over time. Effective and spatially-expansive monitoring within under-represented regions is critical to provide an accurate perspective on seagrass status and trends. We present a comprehensive dataset on seagrass coverage and composition across 24 sites in Bahía Almirante, a lagoon along the Caribbean coast of Panama. Using a single survey, we focus on capturing spatial variation in seagrass physical and elemental characteristics and provide data on key seagrass bio-indicators, such as leaf morphology (length and width), elemental content (% nitrogen and phosphorus) and stable isotopic signatures (δ13C and δ15N). We further explore relationships between these variables and water depth (proxy for light availability) and proximity to shore (proxy for terrestrial inputs). The seagrass assemblage was mostly monospecific (dominated by Thalassia testudinum) and restricted to shallow water (<3 m). Above-ground biomass varied widely, averaging 71.7 g dry mass m−2, yet ranging from 24.8 to 139.6 g dry mass m−2. Leaf nitrogen content averaged 2.2%, ranging from 1.76 to 2.57%, while phosphorus content averaged 0.19% and ranged from 0.15 to 0.23%. These values were high compared to other published reports for T. testudinum, indicating elevated nutrient availability within the lagoon. Seagrass stable isotopic characteristics varied slightly and were comparable with other published values. Leaf carbon signatures (δ13C) ranged from −11.74 to −6.70‰ and were positively correlated to shoreline proximity, suggesting a contribution of terrestrial carbon to seagrass biomass. Leaf nitrogen signatures…
bibliographic citation: Gaubert-Boussarie et al. (2021) Seagrass structural and elemental indicators reveal high nutrient availability within a tropical lagoon in Panama. PeerJ 9:e11308 https://doi.org/10.7717/peerj.11308
date submitted: 2021-01-09
date accepted: 2021-03-29
issued: 2021-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gaubert-Boussarie
  given name: Julie
author list: Agent
  family name: Altieri
  given name: Andrew H.
author list: Agent
  family name: Duffy
  given name: J. Emmett
author list: Agent
  family name: Campbell
  given name: Justin E.
doi: 10.7717/peerj.11308
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-06
copyright: ©2021 Gaubert-Boussarie et al.
attribution name: Gaubert-Boussarie et al.

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines
type: item
type: AcademicArticle
description: Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
format: application/pdf
format: text/html
creator: Elham Karimi
creator: Enora Geslain
creator: Arnaud Belcour
creator: Clémence Frioux
creator: Méziane Aïte
creator: Anne Siegel
creator: Erwan Corre
creator: Simon M. Dittami
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
subject: Computational Science
description: doi:10.7717/peerj.11344
publisher: PeerJ Inc.
rights: © 2021 Karimi et al.
abstract: Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
bibliographic citation: Karimi et al. (2021) Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines. PeerJ 9:e11344 https://doi.org/10.7717/peerj.11344
date submitted: 2020-10-08
date accepted: 2021-04-03
issued: 2021-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karimi
  given name: Elham
author list: Agent
  family name: Geslain
  given name: Enora
author list: Agent
  family name: Belcour
  given name: Arnaud
author list: Agent
  family name: Frioux
  given name: Clémence
author list: Agent
  family name: Aïte
  given name: Méziane
author list: Agent
  family name: Siegel
  given name: Anne
author list: Agent
  family name: Corre
  given name: Erwan
author list: Agent
  family name: Dittami
  given name: Simon M.
doi: 10.7717/peerj.11344
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-06
copyright: ©2021 Karimi et al.
attribution name: Karimi et al.

Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum
type: item
type: AcademicArticle
description: Heat shock transcription factors (HSFs) are critical regulators of plant responses to various abiotic and biotic stresses, including high temperature stress. HSFs are involved in regulating the expression of heat shock proteins (HSPs) by binding with heat stress elements (HSEs) to defend against high-temperature stress. The H. perforatum genome was recently fully sequenced; this provides a valuable resource for genetic and functional analysis. In this study, 23 putative HpHSF genes were identified and divided into three groups (A, B, and C) based on phylogeny and structural features. Gene structure and conserved motif analyses were performed on HpHSFs members; the DNA-binding domain (DBD), hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries exhibited specific phylogenetic relationships. In addition, the presence of various cis-acting elements in the promoter regions of HpHSFs underscored their regulatory function in abiotic stress responses. RT-qPCR analyses showed that most HpHSF genes were expressed in response to heat conditions, suggesting that HpHSFs play potential roles in the heat stress resistance pathway. Our findings are advantageous for the analysis and research of the function of HpHSFs in high temperature stress tolerance in H. perforatum.
format: application/pdf
format: text/html
creator: Li Zhou
creator: Xiaoding Yu
creator: Donghao Wang
creator: Lin Li
creator: Wen Zhou
creator: Qian Zhang
creator: Xinrui Wang
creator: Sumin Ye
creator: Zhezhi Wang
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11345
publisher: PeerJ Inc.
rights: © 2021 Zhou et al.
abstract: Heat shock transcription factors (HSFs) are critical regulators of plant responses to various abiotic and biotic stresses, including high temperature stress. HSFs are involved in regulating the expression of heat shock proteins (HSPs) by binding with heat stress elements (HSEs) to defend against high-temperature stress. The H. perforatum genome was recently fully sequenced; this provides a valuable resource for genetic and functional analysis. In this study, 23 putative HpHSF genes were identified and divided into three groups (A, B, and C) based on phylogeny and structural features. Gene structure and conserved motif analyses were performed on HpHSFs members; the DNA-binding domain (DBD), hydrophobic heptad repeat (HR-A/B), and exon-intron boundaries exhibited specific phylogenetic relationships. In addition, the presence of various cis-acting elements in the promoter regions of HpHSFs underscored their regulatory function in abiotic stress responses. RT-qPCR analyses showed that most HpHSF genes were expressed in response to heat conditions, suggesting that HpHSFs play potential roles in the heat stress resistance pathway. Our findings are advantageous for the analysis and research of the function of HpHSFs in high temperature stress tolerance in H. perforatum.
bibliographic citation: Zhou et al. (2021) Genome-wide identification, classification and expression profile analysis of the HSF gene family in Hypericum perforatum. PeerJ 9:e11345 https://doi.org/10.7717/peerj.11345
date submitted: 2020-09-14
date accepted: 2021-04-03
issued: 2021-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Li
author list: Agent
  family name: Yu
  given name: Xiaoding
author list: Agent
  family name: Wang
  given name: Donghao
author list: Agent
  family name: Li
  given name: Lin
author list: Agent
  family name: Zhou
  given name: Wen
author list: Agent
  family name: Zhang
  given name: Qian
author list: Agent
  family name: Wang
  given name: Xinrui
author list: Agent
  family name: Ye
  given name: Sumin
author list: Agent
  family name: Wang
  given name: Zhezhi
doi: 10.7717/peerj.11345
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-06
copyright: ©2021 Zhou et al.
attribution name: Zhou et al.

BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains
type: item
type: AcademicArticle
description: Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98% greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub (https://github.com/adamhockenberry/bacphlip) and the code used to build and test the classifier is provided in a separate repository (https://github.com/adamhockenberry/bacphlip-model-dev) for users wishing to interrogate and re-train the underlying classification model.
format: application/pdf
format: text/html
creator: Adam J. Hockenberry
creator: Claus O. Wilke
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.11396
publisher: PeerJ Inc.
rights: © 2021 Hockenberry and Wilke
abstract: Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98% greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub (https://github.com/adamhockenberry/bacphlip) and the code used to build and test the classifier is provided in a separate repository (https://github.com/adamhockenberry/bacphlip-model-dev) for users wishing to interrogate and re-train the underlying classification model.
bibliographic citation: Hockenberry et al. (2021) BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains. PeerJ 9:e11396 https://doi.org/10.7717/peerj.11396
date submitted: 2021-03-01
date accepted: 2021-04-12
issued: 2021-05-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hockenberry
  given name: Adam J.
author list: Agent
  family name: Wilke
  given name: Claus O.
doi: 10.7717/peerj.11396
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-06
copyright: ©2021 Hockenberry and Wilke
attribution name: Hockenberry and Wilke

Construction of an immune-related signature with prognostic value for colon cancer
type: item
type: AcademicArticle
description: Background Colon cancer is the third most common malignant tumor in the world. Although immunotherapy has been used in cancer treatment, there is still no first-line immunotherapy method for colon cancer. Therefore, it is essential to search for potential immunotherapy targets and molecular biomarkers for early diagnosis and prognosis. Methods In this study, we downloaded transcriptome data from The Cancer Genome Atlas (TCGA) and immune-related genes from the ImmPort database. Then we filtered genes with prognostic value and constructed an immune-related signature. Patients were classified into low- and high-risk groups, and we exerted a series of analysis between the signature and clinical phenotypes. Additionally, we used protein-protein interaction networks, gene set enrichment analysis (GSEA) and single-sample gene-set enrichment analysis (ssGSEA) to explore the underlying mechanism of this signature. Furthermore, the accuracy of this signature was verified, using two data sets from Gene Expression Omnibus (GEO). Results We selected 12 immune-related genes to construct the immune-related signature. Low-risk group had a higher level of immunity compared to high-risk group. The expression level of HLA genes and checkpoint-related genes were statistically different in low- and high-risk groups. This signature showed its prognostic value in TCGA cohort and 2 GEO data sets. The signature also had strong correlation with TNM classification, stage, survival state and lymphatic invasion. The mechanism of the signature may be related to several transcription factors and CD8+ T cell in the tumor microenvironment. Conclusion In conclusion, this immune-related signature is of great prognosis value for colon cancer and its biofunction might be correlated with HLA genes, checkpoint-related genes and high-infiltrating T cells in tumor tissues.
format: application/pdf
format: text/html
creator: Yunxia Lv
creator: Xinyi Wang
creator: Yu Ren
creator: Xiaorui Fu
creator: Taiyuan Li
creator: Qunguang Jiang
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.10812
publisher: PeerJ Inc.
rights: © 2021 Lv et al.
abstract: Background Colon cancer is the third most common malignant tumor in the world. Although immunotherapy has been used in cancer treatment, there is still no first-line immunotherapy method for colon cancer. Therefore, it is essential to search for potential immunotherapy targets and molecular biomarkers for early diagnosis and prognosis. Methods In this study, we downloaded transcriptome data from The Cancer Genome Atlas (TCGA) and immune-related genes from the ImmPort database. Then we filtered genes with prognostic value and constructed an immune-related signature. Patients were classified into low- and high-risk groups, and we exerted a series of analysis between the signature and clinical phenotypes. Additionally, we used protein-protein interaction networks, gene set enrichment analysis (GSEA) and single-sample gene-set enrichment analysis (ssGSEA) to explore the underlying mechanism of this signature. Furthermore, the accuracy of this signature was verified, using two data sets from Gene Expression Omnibus (GEO). Results We selected 12 immune-related genes to construct the immune-related signature. Low-risk group had a higher level of immunity compared to high-risk group. The expression level of HLA genes and checkpoint-related genes were statistically different in low- and high-risk groups. This signature showed its prognostic value in TCGA cohort and 2 GEO data sets. The signature also had strong correlation with TNM classification, stage, survival state and lymphatic invasion. The mechanism of the signature may be related to several transcription factors and CD8+ T cell in the tumor microenvironment. Conclusion In conclusion, this immune-related signature is of great prognosis value for colon cancer and its biofunction might be correlated with HLA genes, checkpoint-related genes and high-infiltrating T cells in tumor tissues.
bibliographic citation: Lv et al. (2021) Construction of an immune-related signature with prognostic value for colon cancer. PeerJ 9:e10812 https://doi.org/10.7717/peerj.10812
date submitted: 2020-04-14
date accepted: 2020-12-30
issued: 2021-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lv
  given name: Yunxia
author list: Agent
  family name: Wang
  given name: Xinyi
author list: Agent
  family name: Ren
  given name: Yu
author list: Agent
  family name: Fu
  given name: Xiaorui
author list: Agent
  family name: Li
  given name: Taiyuan
author list: Agent
  family name: Jiang
  given name: Qunguang
doi: 10.7717/peerj.10812
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-05
copyright: ©2021 Lv et al.
attribution name: Lv et al.

Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types
type: item
type: AcademicArticle
description: Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here.
format: application/pdf
format: text/html
creator: Kathryn Langenfeld
creator: Kaitlyn Chin
creator: Ariel Roy
creator: Krista Wigginton
creator: Melissa B. Duhaime
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.11111
publisher: PeerJ Inc.
rights: © 2021 Langenfeld et al.
abstract: Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to concentrate and purify viral genomes prior to sequencing is essential for high quality viromes. Using virus spike-and-recovery experiments, we stepwise compared two common approaches for virus concentration, ultrafiltration and iron chloride flocculation, across diverse matrices: wastewater influent, wastewater secondary effluent, river water, and seawater. Viral DNA was purified by removing cellular DNA via chloroform cell lysis, filtration, and enzymatic degradation of extra-viral DNA. We found that viral genomes were concentrated 1-2 orders of magnitude more with ultrafiltration than iron chloride flocculation for all matrices and resulted in higher quality DNA suitable for amplification-free and long-read sequencing. Given its widespread use and utility as an inexpensive field method for virome sampling, we nonetheless sought to optimize iron flocculation. We found viruses were best concentrated in seawater with five-fold higher iron concentrations than the standard used, inhibition of DNase activity reduced purification effectiveness, and five-fold more iron was needed to flocculate viruses from freshwater than seawater—critical knowledge for those seeking to apply this broadly used method to freshwater virome samples. Overall, our results demonstrated that ultrafiltration and purification performed better than iron chloride flocculation and purification in the tested matrices. Given that the method performance depended on the solids content and salinity of the samples, we suggest spike-and-recovery experiments be applied when concentrating and purifying sample types that diverge from those tested here.
bibliographic citation: Langenfeld et al. (2021) Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types. PeerJ 9:e11111 https://doi.org/10.7717/peerj.11111
date submitted: 2020-10-29
date accepted: 2021-02-23
issued: 2021-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Langenfeld
  given name: Kathryn
author list: Agent
  family name: Chin
  given name: Kaitlyn
author list: Agent
  family name: Roy
  given name: Ariel
author list: Agent
  family name: Wigginton
  given name: Krista
author list: Agent
  family name: Duhaime
  given name: Melissa B.
doi: 10.7717/peerj.11111
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-05
copyright: ©2021 Langenfeld et al.
attribution name: Langenfeld et al.

Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida
type: item
type: AcademicArticle
description: Background NAC (NAM, ATAF1/2, and CUC2) transcription factors play an important role in plant growth and development. However, in tumorous stem mustard (Brassica juncea var. tumida), one of the economically important crops cultivated in southwest China and some southeast Asian countries, reports on the identification of NAC family genes are lacking. In this study, we conducted a genome-wide investigation of the NAC family genes in B. juncea var. tumida, based on its recently published genome sequence data. Methods The NAC genes were identified in B. juncea var. tumida using the bioinformatics approach on the whole genome level. Additionally, the expression of BjuNAC genes was analyzed under high- and low-temperature stresses by quantitative real-time PCR (qRT-PCR). Results A total of 300 BjuNAC genes were identified, of which 278 were mapped to specific chromosomes. Phylogenetic analysis of B. juncea var. tumida, Brassica rapa, Brassica nigra, rice and Arabidopsis thaliana NAC proteins revealed that all NAC genes were divided into 18 subgroups. Furthermore, gene structure analysis showed that most of the NAC genes contained two or three exons. Conserved motif analysis revealed that BjuNAC genes contain a conserved NAM domain. Additionally, qRT-PCR data indicated that thirteen BjuNAC genes with a varying degree of up-regulation during high-temperature stress. Conversely, four BjuNAC genes (BjuNAC006, BjuNAC083, BjuNAC170 and BjuNAC223) were up-regulated and two BjuNAC genes (BjuNAC074 and BjuNAC295) down-regulated under low temperature, respectively. Together, the results of this study provide a strong foundation for future investigation of the biological function of NAC genes in B. juncea var. tumida.
format: application/pdf
format: text/html
creator: Longxing Jiang
creator: Quan Sun
creator: Yu Wang
creator: Pingan Chang
creator: Haohuan Kong
creator: Changshu Luo
creator: Xiaohong He
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.11212
publisher: PeerJ Inc.
rights: © 2021 Jiang et al.
abstract: Background NAC (NAM, ATAF1/2, and CUC2) transcription factors play an important role in plant growth and development. However, in tumorous stem mustard (Brassica juncea var. tumida), one of the economically important crops cultivated in southwest China and some southeast Asian countries, reports on the identification of NAC family genes are lacking. In this study, we conducted a genome-wide investigation of the NAC family genes in B. juncea var. tumida, based on its recently published genome sequence data. Methods The NAC genes were identified in B. juncea var. tumida using the bioinformatics approach on the whole genome level. Additionally, the expression of BjuNAC genes was analyzed under high- and low-temperature stresses by quantitative real-time PCR (qRT-PCR). Results A total of 300 BjuNAC genes were identified, of which 278 were mapped to specific chromosomes. Phylogenetic analysis of B. juncea var. tumida, Brassica rapa, Brassica nigra, rice and Arabidopsis thaliana NAC proteins revealed that all NAC genes were divided into 18 subgroups. Furthermore, gene structure analysis showed that most of the NAC genes contained two or three exons. Conserved motif analysis revealed that BjuNAC genes contain a conserved NAM domain. Additionally, qRT-PCR data indicated that thirteen BjuNAC genes with a varying degree of up-regulation during high-temperature stress. Conversely, four BjuNAC genes (BjuNAC006, BjuNAC083, BjuNAC170 and BjuNAC223) were up-regulated and two BjuNAC genes (BjuNAC074 and BjuNAC295) down-regulated under low temperature, respectively. Together, the results of this study provide a strong foundation for future investigation of the biological function of NAC genes in B. juncea var. tumida.
bibliographic citation: Jiang et al. (2021) Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida. PeerJ 9:e11212 https://doi.org/10.7717/peerj.11212
date submitted: 2020-10-20
date accepted: 2021-03-15
issued: 2021-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Longxing
author list: Agent
  family name: Sun
  given name: Quan
author list: Agent
  family name: Wang
  given name: Yu
author list: Agent
  family name: Chang
  given name: Pingan
author list: Agent
  family name: Kong
  given name: Haohuan
author list: Agent
  family name: Luo
  given name: Changshu
author list: Agent
  family name: He
  given name: Xiaohong
doi: 10.7717/peerj.11212
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-05
copyright: ©2021 Jiang et al.
attribution name: Jiang et al.

Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study
type: item
type: AcademicArticle
description: Background Lung adenocarcinoma (LUAD) is the leading histological subtype of non-small cell lung cancer (NSCLC). Methods In the present study, the gene matrixes of LUAD were downloaded from The Cancer Genome Atlas to infer immune and stromal scores with the ‘Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data’ (ESTIMATE) algorithm and identified immune-related differentially expressed genes (DEGs) between the high- and low-stromal/immune score groups. Next, all DEGs were subjected to univariate Cox regression and survival analyses to screen out prognostic biomarkers in the tumor microenvironment (TME), and were validated in the Gene Expression Omnibus database. Single-sample gene set enrichment analysis (ssGSEA) was performed to assess the level of tumor-infiltrating immune cells (TIICs) and immune functions, and GSEA was used to identified pathways altered by prognostic biomarkers. Results Survival analysis showed that LUAD in the high-immune and stromal score group had a better clinical prognosis. A total of 303 immune-related DEGs were detected. Univariate Cox regression and survival analyses revealed that P2Y purinoceptor 13 (P2RY13) was a favorable factor for the prognosis of LUAD. ssGSEA and Spearman correlation analysis demonstrated that P2RY13 was highly correlated with various TIICs and immune functions. Several immune-associated pathways were enriched between the high- and low-expression P2RY13 groups. Conclusion P2RY13 may be a potential prognostic indicator and is highly associated with the TME in LUAD. However, further experimental studies are required to validate the present findings.
format: application/pdf
format: text/html
creator: Jiang Lin
creator: Chunlei Wu
creator: Dehua Ma
creator: Quanteng Hu
subject: Bioinformatics
subject: Computational Biology
subject: Immunology
subject: Oncology
subject: Respiratory Medicine
description: doi:10.7717/peerj.11319
publisher: PeerJ Inc.
rights: © 2021 Lin et al.
abstract: Background Lung adenocarcinoma (LUAD) is the leading histological subtype of non-small cell lung cancer (NSCLC). Methods In the present study, the gene matrixes of LUAD were downloaded from The Cancer Genome Atlas to infer immune and stromal scores with the ‘Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data’ (ESTIMATE) algorithm and identified immune-related differentially expressed genes (DEGs) between the high- and low-stromal/immune score groups. Next, all DEGs were subjected to univariate Cox regression and survival analyses to screen out prognostic biomarkers in the tumor microenvironment (TME), and were validated in the Gene Expression Omnibus database. Single-sample gene set enrichment analysis (ssGSEA) was performed to assess the level of tumor-infiltrating immune cells (TIICs) and immune functions, and GSEA was used to identified pathways altered by prognostic biomarkers. Results Survival analysis showed that LUAD in the high-immune and stromal score group had a better clinical prognosis. A total of 303 immune-related DEGs were detected. Univariate Cox regression and survival analyses revealed that P2Y purinoceptor 13 (P2RY13) was a favorable factor for the prognosis of LUAD. ssGSEA and Spearman correlation analysis demonstrated that P2RY13 was highly correlated with various TIICs and immune functions. Several immune-associated pathways were enriched between the high- and low-expression P2RY13 groups. Conclusion P2RY13 may be a potential prognostic indicator and is highly associated with the TME in LUAD. However, further experimental studies are required to validate the present findings.
bibliographic citation: Lin et al. (2021) Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study. PeerJ 9:e11319 https://doi.org/10.7717/peerj.11319
date submitted: 2020-11-16
date accepted: 2021-03-31
issued: 2021-05-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Jiang
author list: Agent
  family name: Wu
  given name: Chunlei
author list: Agent
  family name: Ma
  given name: Dehua
author list: Agent
  family name: Hu
  given name: Quanteng
doi: 10.7717/peerj.11319
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-05-05
copyright: ©2021 Lin et al.
attribution name: Lin et al.

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