PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies
items: Variant profiling of evolving prokaryotic populations
items: Understanding morphological variability in a taxonomic context in Chilean diplomystids (Teleostei: Siluriformes), including the description of a new species
items: High richness of insect herbivory from the early Miocene Hindon Maar crater, Otago, New Zealand
items: Exoskeletons of Bougainvilliidae and other Hydroidolina (Cnidaria, Hydrozoa): structure and composition
items: Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor
items: Risk analysis of colorectal cancer incidence by gene expression analysis
items: Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells
items: ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium
items: Opportunities drive the global distribution of protected areas

Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies
type: item
type: AcademicArticle
description: Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.
format: application/pdf
format: text/html
creator: Cédric Cabau
creator: Frédéric Escudié
creator: Anis Djari
creator: Yann Guiguen
creator: Julien Bobe
creator: Christophe Klopp
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.2988
publisher: PeerJ Inc.
rights: © 2017 Cabau et al.
abstract: Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.
bibliographic citation: Cabau et al. (2017) Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies. PeerJ 5:e2988 https://doi.org/10.7717/peerj.2988
date submitted: 2016-07-11
date accepted: 2017-01-10
issued: 2017-02-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cabau
  given name: Cédric
author list: Agent
  family name: Escudié
  given name: Frédéric
author list: Agent
  family name: Djari
  given name: Anis
author list: Agent
  family name: Guiguen
  given name: Yann
author list: Agent
  family name: Bobe
  given name: Julien
author list: Agent
  family name: Klopp
  given name: Christophe
doi: 10.7717/peerj.2988
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-16
copyright: ©2017 Cabau et al.
attribution name: Cabau et al.

Variant profiling of evolving prokaryotic populations
type: item
type: AcademicArticle
description: Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we…
format: application/pdf
format: text/html
creator: Markus Zojer
creator: Lisa N. Schuster
creator: Frederik Schulz
creator: Alexander Pfundner
creator: Matthias Horn
creator: Thomas Rattei
subject: Bioinformatics
subject: Computational Biology
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.2997
publisher: PeerJ Inc.
rights: © 2017 Zojer et al.
abstract: Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we…
bibliographic citation: Zojer et al. (2017) Variant profiling of evolving prokaryotic populations. PeerJ 5:e2997 https://doi.org/10.7717/peerj.2997
date submitted: 2016-09-13
date accepted: 2017-01-17
issued: 2017-02-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zojer
  given name: Markus
author list: Agent
  family name: Schuster
  given name: Lisa N.
author list: Agent
  family name: Schulz
  given name: Frederik
author list: Agent
  family name: Pfundner
  given name: Alexander
author list: Agent
  family name: Horn
  given name: Matthias
author list: Agent
  family name: Rattei
  given name: Thomas
doi: 10.7717/peerj.2997
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-16
copyright: ©2017 Zojer et al.
attribution name: Zojer et al.

Understanding morphological variability in a taxonomic context in Chilean diplomystids (Teleostei: Siluriformes), including the description of a new species
type: item
type: AcademicArticle
description: Following study of the external morphology and its unmatched variability throughout ontogeny and a re-examination of selected morphological characters based on many specimens of diplomystids from Central and South Chile, we revised and emended previous specific diagnoses and consider Diplomystes chilensis, D. nahuelbutaensis, D. camposensis, and Olivaichthys viedmensis (Baker River) to be valid species. Another group, previously identified as Diplomystes sp., D. spec., D. aff. chilensis, and D. cf. chilensis inhabiting rivers between Rapel and Itata Basins is given a new specific name (Diplomystes incognitus) and is diagnosed. An identification key to the Chilean species, including the new species, is presented. All specific diagnoses are based on external morphological characters, such as aspects of the skin, neuromast lines, and main lateral line, and position of the anus and urogenital pore, as well as certain osteological characters to facilitate the identification of these species that previously was based on many internal characters. Diplomystids below 150 mm standard length (SL) share a similar external morphology and body proportions that make identification difficult; however, specimens over 150 mm SL can be diagnosed by the position of the urogenital pore and anus, and a combination of external and internal morphological characters. According to current knowledge, diplomystid species have an allopatric distribution with each species apparently endemic to particular basins in continental Chile and one species (O. viedmensis) known only from one river in the Chilean Patagonia, but distributed extensively in southern Argentina.
format: application/pdf
format: text/html
creator: Gloria Arratia
creator: Claudio Quezada-Romegialli
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Taxonomy
description: doi:10.7717/peerj.2991
publisher: PeerJ Inc.
rights: © 2017 Arratia and Quezada-Romegialli
abstract: Following study of the external morphology and its unmatched variability throughout ontogeny and a re-examination of selected morphological characters based on many specimens of diplomystids from Central and South Chile, we revised and emended previous specific diagnoses and consider Diplomystes chilensis, D. nahuelbutaensis, D. camposensis, and Olivaichthys viedmensis (Baker River) to be valid species. Another group, previously identified as Diplomystes sp., D. spec., D. aff. chilensis, and D. cf. chilensis inhabiting rivers between Rapel and Itata Basins is given a new specific name (Diplomystes incognitus) and is diagnosed. An identification key to the Chilean species, including the new species, is presented. All specific diagnoses are based on external morphological characters, such as aspects of the skin, neuromast lines, and main lateral line, and position of the anus and urogenital pore, as well as certain osteological characters to facilitate the identification of these species that previously was based on many internal characters. Diplomystids below 150 mm standard length (SL) share a similar external morphology and body proportions that make identification difficult; however, specimens over 150 mm SL can be diagnosed by the position of the urogenital pore and anus, and a combination of external and internal morphological characters. According to current knowledge, diplomystid species have an allopatric distribution with each species apparently endemic to particular basins in continental Chile and one species (O. viedmensis) known only from one river in the Chilean Patagonia, but distributed extensively in southern Argentina.
bibliographic citation: Arratia et al. (2017) Understanding morphological variability in a taxonomic context in Chilean diplomystids (Teleostei: Siluriformes), including the description of a new species. PeerJ 5:e2991 https://doi.org/10.7717/peerj.2991
date submitted: 2016-08-04
date accepted: 2017-01-13
issued: 2017-02-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arratia
  given name: Gloria
author list: Agent
  family name: Quezada-Romegialli
  given name: Claudio
doi: 10.7717/peerj.2991
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-16
copyright: ©2017 Arratia and Quezada-Romegialli
attribution name: Arratia and Quezada-Romegialli

High richness of insect herbivory from the early Miocene Hindon Maar crater, Otago, New Zealand
type: item
type: AcademicArticle
description: Plants and insects are key components of terrestrial ecosystems and insect herbivory is the most important type of interaction in these ecosystems. This study presents the first analysis of associations between plants and insects for the early Miocene Hindon Maar fossil lagerstätte, Otago, New Zealand. A total of 584 fossil angiosperm leaves representing 24 morphotypes were examined to determine the presence or absence of insect damage types. Of these leaves, 73% show signs of insect damage; they comprise 821 occurrences of damage from 87 damage types representing all eight functional feeding groups. In comparison to other fossil localities, the Hindon leaves display a high abundance of insect damage and a high diversity of damage types. Leaves of Nothofagus(southern beech), the dominant angiosperm in the fossil assemblage, exhibit a similar leaf damage pattern to leaves from the nearby mid to late Miocene Dunedin Volcano Group sites but display a more diverse spectrum and much higher percentage of herbivory damage than a comparable dataset of leaves from Palaeocene and Eocene sites in the Antarctic Peninsula.
format: application/pdf
format: text/html
creator: Anna Lena Möller
creator: Uwe Kaulfuss
creator: Daphne E. Lee
creator: Torsten Wappler
subject: Ecology
subject: Paleontology
subject: Plant Science
description: doi:10.7717/peerj.2985
publisher: PeerJ Inc.
rights: © 2017 Möller et al.
abstract: Plants and insects are key components of terrestrial ecosystems and insect herbivory is the most important type of interaction in these ecosystems. This study presents the first analysis of associations between plants and insects for the early Miocene Hindon Maar fossil lagerstätte, Otago, New Zealand. A total of 584 fossil angiosperm leaves representing 24 morphotypes were examined to determine the presence or absence of insect damage types. Of these leaves, 73% show signs of insect damage; they comprise 821 occurrences of damage from 87 damage types representing all eight functional feeding groups. In comparison to other fossil localities, the Hindon leaves display a high abundance of insect damage and a high diversity of damage types. Leaves of Nothofagus(southern beech), the dominant angiosperm in the fossil assemblage, exhibit a similar leaf damage pattern to leaves from the nearby mid to late Miocene Dunedin Volcano Group sites but display a more diverse spectrum and much higher percentage of herbivory damage than a comparable dataset of leaves from Palaeocene and Eocene sites in the Antarctic Peninsula.
bibliographic citation: Möller et al. (2017) High richness of insect herbivory from the early Miocene Hindon Maar crater, Otago, New Zealand. PeerJ 5:e2985 https://doi.org/10.7717/peerj.2985
date submitted: 2016-07-29
date accepted: 2017-01-12
issued: 2017-02-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Möller
  given name: Anna Lena
author list: Agent
  family name: Kaulfuss
  given name: Uwe
author list: Agent
  family name: Lee
  given name: Daphne E.
author list: Agent
  family name: Wappler
  given name: Torsten
doi: 10.7717/peerj.2985
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-16
copyright: ©2017 Möller et al.
attribution name: Möller et al.

Exoskeletons of Bougainvilliidae and other Hydroidolina (Cnidaria, Hydrozoa): structure and composition
type: item
type: AcademicArticle
description: The exoskeleton is an important source of characters for the taxonomy of Hydroidolina. It originates as epidermal secretions and, among other functions, protects the coenosarc of the polypoid stage. However, comparative studies on the exoskeletal tissue origin, development, chemical, and structural characteristics, as well as its evolution and homology, are few and fragmented. This study compares the structure and composition of the exoskeleton and underlying coenosarc in members of “Anthoathecata” and some Leptothecata, but does so mainly in bougainvilliid polyps histological analyses. We also studied the development of the exoskeleton under experimental conditions. We identified three types of glandular epidermal cells related to the origin of the exoskeleton and the secretion of its polysaccharides component. The exoskeleton of the species studied is either bilayered (perisarc and exosarc, especially in bougainvilliids) or corneous (perisarc). The exoskeleton varies in chemical composition, structural rigidity, thickness, extension, and coverage in the different regions of the colony. In bilayered exoskeletons, the exosarc is produced first and appears to be a key step in the formation of the rigid exoskeleton. The exoskeleton contains anchoring structures such as desmocytes and “perisarc extensions.”
format: application/pdf
format: text/html
creator: María A. Mendoza-Becerril
creator: José Eduardo A.R. Marian
creator: Alvaro Esteves Migotto
creator: Antonio Carlos Marques
subject: Cell Biology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.2964
publisher: PeerJ Inc.
rights: © 2017 Mendoza-Becerril et al.
abstract: The exoskeleton is an important source of characters for the taxonomy of Hydroidolina. It originates as epidermal secretions and, among other functions, protects the coenosarc of the polypoid stage. However, comparative studies on the exoskeletal tissue origin, development, chemical, and structural characteristics, as well as its evolution and homology, are few and fragmented. This study compares the structure and composition of the exoskeleton and underlying coenosarc in members of “Anthoathecata” and some Leptothecata, but does so mainly in bougainvilliid polyps histological analyses. We also studied the development of the exoskeleton under experimental conditions. We identified three types of glandular epidermal cells related to the origin of the exoskeleton and the secretion of its polysaccharides component. The exoskeleton of the species studied is either bilayered (perisarc and exosarc, especially in bougainvilliids) or corneous (perisarc). The exoskeleton varies in chemical composition, structural rigidity, thickness, extension, and coverage in the different regions of the colony. In bilayered exoskeletons, the exosarc is produced first and appears to be a key step in the formation of the rigid exoskeleton. The exoskeleton contains anchoring structures such as desmocytes and “perisarc extensions.”
bibliographic citation: Mendoza-Becerril et al. (2017) Exoskeletons of Bougainvilliidae and other Hydroidolina (Cnidaria, Hydrozoa): structure and composition. PeerJ 5:e2964 https://doi.org/10.7717/peerj.2964
date submitted: 2016-09-26
date accepted: 2017-01-06
issued: 2017-02-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza-Becerril
  given name: María A.
author list: Agent
  family name: Marian
  given name: José Eduardo A.R.
author list: Agent
  family name: Migotto
  given name: Alvaro Esteves
author list: Agent
  family name: Marques
  given name: Antonio Carlos
doi: 10.7717/peerj.2964
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-16
copyright: ©2017 Mendoza-Becerril et al.
attribution name: Mendoza-Becerril et al.

Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor
type: item
type: AcademicArticle
description: Management of the few regulated ornamental fisheries relies on inadequate information about the life history of the target species. Herein, we investigated the reproductive biology of the most heavily traded marine invertebrate in the western Atlantic; the blue-legged hermit crab Clibanarius tricolor. We report on density, individual-level, and population-level reproductive parameters in 14 populations spanning the Florida Keys. In C. tricolor, abundance, population-level, and individual-level reproductive parameters exhibited substantial small-scale spatial variation in the Florida Keys. For instance, the proportion of brooding females varied between 10–94% across localities. In females, average (±SD) fecundity varied between 184 (±54) and 614 (±301) embryos crab-1 across populations. Fecundity usually increases with female body size in hermit crabs. However, we found no effect of female body size on fecundity in three of the populations. Altogether, our observations suggest that C. tricolor may fit a source-sink metapopulation dynamic in the Florida Keys with low reproductive intensity and absence of a parental body size—fecundity relationship resulting in net reproductive loses at some localities. We argue in favor of additional studies describing population dynamics and other aspects of the natural history of C. tricolor (e.g., development type, larval duration) to reveal ‘source’ populations, capable of exporting larvae to nearby populations. Our observations imply that future studies aimed at assessing standing stocks or describing other aspects of the life history of this hermit crab need to focus on multiple localities simultaneously. This and future studies on the reproductive biology of this species will form the baseline for models aimed at assessing the stock condition and sustainability of this heavily harvested crustacean.
format: application/pdf
format: text/html
creator: J. Antonio Baeza
creator: Donald C. Behringer
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.3004
publisher: PeerJ Inc.
rights: © 2017 Baeza and Behringer
abstract: Management of the few regulated ornamental fisheries relies on inadequate information about the life history of the target species. Herein, we investigated the reproductive biology of the most heavily traded marine invertebrate in the western Atlantic; the blue-legged hermit crab Clibanarius tricolor. We report on density, individual-level, and population-level reproductive parameters in 14 populations spanning the Florida Keys. In C. tricolor, abundance, population-level, and individual-level reproductive parameters exhibited substantial small-scale spatial variation in the Florida Keys. For instance, the proportion of brooding females varied between 10–94% across localities. In females, average (±SD) fecundity varied between 184 (±54) and 614 (±301) embryos crab-1 across populations. Fecundity usually increases with female body size in hermit crabs. However, we found no effect of female body size on fecundity in three of the populations. Altogether, our observations suggest that C. tricolor may fit a source-sink metapopulation dynamic in the Florida Keys with low reproductive intensity and absence of a parental body size—fecundity relationship resulting in net reproductive loses at some localities. We argue in favor of additional studies describing population dynamics and other aspects of the natural history of C. tricolor (e.g., development type, larval duration) to reveal ‘source’ populations, capable of exporting larvae to nearby populations. Our observations imply that future studies aimed at assessing standing stocks or describing other aspects of the life history of this hermit crab need to focus on multiple localities simultaneously. This and future studies on the reproductive biology of this species will form the baseline for models aimed at assessing the stock condition and sustainability of this heavily harvested crustacean.
bibliographic citation: Baeza et al. (2017) Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor. PeerJ 5:e3004 https://doi.org/10.7717/peerj.3004
date submitted: 2016-10-25
date accepted: 2017-01-19
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baeza
  given name: J. Antonio
author list: Agent
  family name: Behringer
  given name: Donald C.
doi: 10.7717/peerj.3004
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Baeza and Behringer
attribution name: Baeza and Behringer

Risk analysis of colorectal cancer incidence by gene expression analysis
type: item
type: AcademicArticle
description: Background Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction. Objective Microarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples. Methods We collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues. Results Ten genes (ABCG2, AQP8, SPIB, CA7, CLDN8, SCNN1B, SLC30A10, CD177, PADI2, and TGFBI) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method. Conclusions Six genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis.
format: application/pdf
format: text/html
creator: Wei-Chuan Shangkuan
creator: Hung-Che Lin
creator: Yu-Tien Chang
creator: Chen-En Jian
creator: Hueng-Chuen Fan
creator: Kang-Hua Chen
creator: Ya-Fang Liu
creator: Huan-Ming Hsu
creator: Hsiu-Ling Chou
creator: Chung-Tay Yao
creator: Chi-Ming Chu
creator: Sui-Lung Su
creator: Chi-Wen Chang
subject: Bioinformatics
subject: Mathematical Biology
subject: Molecular Biology
subject: Oncology
subject: Statistics
description: doi:10.7717/peerj.3003
publisher: PeerJ Inc.
rights: © 2017 Shangkuan et al.
abstract: Background Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction. Objective Microarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples. Methods We collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues. Results Ten genes (ABCG2, AQP8, SPIB, CA7, CLDN8, SCNN1B, SLC30A10, CD177, PADI2, and TGFBI) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method. Conclusions Six genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis.
bibliographic citation: Shangkuan et al. (2017) Risk analysis of colorectal cancer incidence by gene expression analysis. PeerJ 5:e3003 https://doi.org/10.7717/peerj.3003
date submitted: 2016-09-28
date accepted: 2017-01-19
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shangkuan
  given name: Wei-Chuan
author list: Agent
  family name: Lin
  given name: Hung-Che
author list: Agent
  family name: Chang
  given name: Yu-Tien
author list: Agent
  family name: Jian
  given name: Chen-En
author list: Agent
  family name: Fan
  given name: Hueng-Chuen
author list: Agent
  family name: Chen
  given name: Kang-Hua
author list: Agent
  family name: Liu
  given name: Ya-Fang
author list: Agent
  family name: Hsu
  given name: Huan-Ming
author list: Agent
  family name: Chou
  given name: Hsiu-Ling
author list: Agent
  family name: Yao
  given name: Chung-Tay
author list: Agent
  family name: Chu
  given name: Chi-Ming
author list: Agent
  family name: Su
  given name: Sui-Lung
author list: Agent
  family name: Chang
  given name: Chi-Wen
doi: 10.7717/peerj.3003
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Shangkuan et al.
attribution name: Shangkuan et al.

Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells
type: item
type: AcademicArticle
description: Background Interleukin (IL)-17 produced by mainly T helper 17 (Th17) cells may play an important destructive role in chronic periodontitis (CP). Thus, anti-inflammatory cytokines, such as IL-35, might have a beneficial effect in periodontitis by inhibiting differentiation of Th17 cells. Th17 differentiation is regulated by the retinoic acid receptor-related orphan receptor (ROR) α (encoded by RORA) and RORγt (encoded by RORC). However, the role of IL-35 in periodontitis is not clear and the effect of IL-35 on the function of Th17 cells is still incompletely understood. Therefore, we investigated the effects of IL-35 on Th17 cells. Methods Peripheral blood mononuclear cells (PBMCs) were sampled from three healthy volunteers and three CP patients and were analyzed by flow cytometry for T cell population. Th17 cells differentiated by a cytokine cocktail (recombinant transforming growth factor-β, rIL-6, rIL-1β, anti-interferon (IFN)-γ, anti-IL-2 and anti-IL-4) from PBMCs were cultured with or without rIL-35. IL17A (which usually refers to IL-17), RORA and RORCmRNA expression was analyzed by quantitative polymerase chain reaction, and IL-17A production was determined by enzyme-linked immunosorbent assay. Results The proportion of IL-17A+CD4+ slightly increased in CP patients compared with healthy controls, however, there were no significant differences in the percentage of IL-17A+CD4+ as well as IFN-γ+CD4+ and Foxp3+CD4+ T cells between healthy controls and CP patients. IL17A, RORA and RORC mRNA expression was significantly increased in Th17 cells induced by the cytokine cocktail, and the induction was significantly inhibited by addition of rIL-35 (1 ng/mL). IL-17A production in Th17 cells was significantly inhibited by rIL-35 addition (1 ng/mL). Discussion The present study suggests that IL-35 could directly suppress IL-17 expression via RORα and RORγt inhibition and might play an important role in inflammatory diseases such as periodontitis.
format: application/pdf
format: text/html
creator: Kosuke Okada
creator: Takeki Fujimura
creator: Takeshi Kikuchi
creator: Makoto Aino
creator: Yosuke Kamiya
creator: Ario Izawa
creator: Yuki Iwamura
creator: Hisashi Goto
creator: Iichiro Okabe
creator: Eriko Miyake
creator: Yoshiaki Hasegawa
creator: Makio Mogi
creator: Akio Mitani
subject: Dentistry
subject: Immunology
description: doi:10.7717/peerj.2999
publisher: PeerJ Inc.
rights: © 2017 Okada et al.
abstract: Background Interleukin (IL)-17 produced by mainly T helper 17 (Th17) cells may play an important destructive role in chronic periodontitis (CP). Thus, anti-inflammatory cytokines, such as IL-35, might have a beneficial effect in periodontitis by inhibiting differentiation of Th17 cells. Th17 differentiation is regulated by the retinoic acid receptor-related orphan receptor (ROR) α (encoded by RORA) and RORγt (encoded by RORC). However, the role of IL-35 in periodontitis is not clear and the effect of IL-35 on the function of Th17 cells is still incompletely understood. Therefore, we investigated the effects of IL-35 on Th17 cells. Methods Peripheral blood mononuclear cells (PBMCs) were sampled from three healthy volunteers and three CP patients and were analyzed by flow cytometry for T cell population. Th17 cells differentiated by a cytokine cocktail (recombinant transforming growth factor-β, rIL-6, rIL-1β, anti-interferon (IFN)-γ, anti-IL-2 and anti-IL-4) from PBMCs were cultured with or without rIL-35. IL17A (which usually refers to IL-17), RORA and RORCmRNA expression was analyzed by quantitative polymerase chain reaction, and IL-17A production was determined by enzyme-linked immunosorbent assay. Results The proportion of IL-17A+CD4+ slightly increased in CP patients compared with healthy controls, however, there were no significant differences in the percentage of IL-17A+CD4+ as well as IFN-γ+CD4+ and Foxp3+CD4+ T cells between healthy controls and CP patients. IL17A, RORA and RORC mRNA expression was significantly increased in Th17 cells induced by the cytokine cocktail, and the induction was significantly inhibited by addition of rIL-35 (1 ng/mL). IL-17A production in Th17 cells was significantly inhibited by rIL-35 addition (1 ng/mL). Discussion The present study suggests that IL-35 could directly suppress IL-17 expression via RORα and RORγt inhibition and might play an important role in inflammatory diseases such as periodontitis.
bibliographic citation: Okada et al. (2017) Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells. PeerJ 5:e2999 https://doi.org/10.7717/peerj.2999
date submitted: 2016-09-09
date accepted: 2017-01-17
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Okada
  given name: Kosuke
author list: Agent
  family name: Fujimura
  given name: Takeki
author list: Agent
  family name: Kikuchi
  given name: Takeshi
author list: Agent
  family name: Aino
  given name: Makoto
author list: Agent
  family name: Kamiya
  given name: Yosuke
author list: Agent
  family name: Izawa
  given name: Ario
author list: Agent
  family name: Iwamura
  given name: Yuki
author list: Agent
  family name: Goto
  given name: Hisashi
author list: Agent
  family name: Okabe
  given name: Iichiro
author list: Agent
  family name: Miyake
  given name: Eriko
author list: Agent
  family name: Hasegawa
  given name: Yoshiaki
author list: Agent
  family name: Mogi
  given name: Makio
author list: Agent
  family name: Mitani
  given name: Akio
doi: 10.7717/peerj.2999
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Okada et al.
attribution name: Okada et al.

ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium
type: item
type: AcademicArticle
description: Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the fr…
format: application/pdf
format: text/html
creator: Tomasz Kulik
creator: Kessy Abarenkov
creator: Maciej Buśko
creator: Katarzyna Bilska
creator: Anne D. van Diepeningen
creator: Anna Ostrowska-Kołodziejczak
creator: Katarzyna Krawczyk
creator: Balázs Brankovics
creator: Sebastian Stenglein
creator: Jakub Sawicki
creator: Juliusz Perkowski
subject: Bioinformatics
subject: Mycology
description: doi:10.7717/peerj.2992
publisher: PeerJ Inc.
rights: © 2017 Kulik et al.
abstract: Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the fr…
bibliographic citation: Kulik et al. (2017) ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium. PeerJ 5:e2992 https://doi.org/10.7717/peerj.2992
date submitted: 2016-09-12
date accepted: 2017-01-15
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kulik
  given name: Tomasz
author list: Agent
  family name: Abarenkov
  given name: Kessy
author list: Agent
  family name: Buśko
  given name: Maciej
author list: Agent
  family name: Bilska
  given name: Katarzyna
author list: Agent
  family name: van Diepeningen
  given name: Anne D.
author list: Agent
  family name: Ostrowska-Kołodziejczak
  given name: Anna
author list: Agent
  family name: Krawczyk
  given name: Katarzyna
author list: Agent
  family name: Brankovics
  given name: Balázs
author list: Agent
  family name: Stenglein
  given name: Sebastian
author list: Agent
  family name: Sawicki
  given name: Jakub
author list: Agent
  family name: Perkowski
  given name: Juliusz
doi: 10.7717/peerj.2992
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Kulik et al.
attribution name: Kulik et al.

Opportunities drive the global distribution of protected areas
type: item
type: AcademicArticle
description: Background Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balanced representation of biophysical environments, (ii) a set of preferred conditions (biological, spiritual, economic, or geopolitical), or (iii) existing opportunities for conservation regardless of any representation or preference criteria. Methods We used histograms to describe the distribution of terrestrial protected areas along biophysical, human, and biological independent gradients and linear and non-linear regression and correlation analyses to describe the sign, shape, and strength of the relationships. We used a random forest analysis to rank the importance of different variables related to conservation preferences and opportunity drivers, and an evenness metric to quantify representativeness. Results We find that protection at a global level is primarily driven by the opportunities provided by isolation and a low population density (variable importance = 34.6 and 19.9, respectively). Preferences play a secondary role, with a bias towards tourism attractiveness and proximity to international borders (variable importance = 12.7 and 3.4, respectively). Opportunities shape protection strongly in “North America & Australia–NZ” and “Latin America & Caribbean,” while the importance of the representativeness of biophysical environments is higher in “Sub-Saharan Africa” (1.3 times the average of other regions). Discussion Environmental representativeness and biodiversity protection are top priorities in land conservation agendas. However, our results suggest that they have been minor players driving current protection at both global and regional levels. Attempts to increase their relevance will necessarily have to recognize…
format: application/pdf
format: text/html
creator: Germán Baldi
creator: Marcos Texeira
creator: Osvaldo A. Martin
creator: H. Ricardo Grau
creator: Esteban G. Jobbágy
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.2989
publisher: PeerJ Inc.
rights: © 2017 Baldi et al.
abstract: Background Protected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balanced representation of biophysical environments, (ii) a set of preferred conditions (biological, spiritual, economic, or geopolitical), or (iii) existing opportunities for conservation regardless of any representation or preference criteria. Methods We used histograms to describe the distribution of terrestrial protected areas along biophysical, human, and biological independent gradients and linear and non-linear regression and correlation analyses to describe the sign, shape, and strength of the relationships. We used a random forest analysis to rank the importance of different variables related to conservation preferences and opportunity drivers, and an evenness metric to quantify representativeness. Results We find that protection at a global level is primarily driven by the opportunities provided by isolation and a low population density (variable importance = 34.6 and 19.9, respectively). Preferences play a secondary role, with a bias towards tourism attractiveness and proximity to international borders (variable importance = 12.7 and 3.4, respectively). Opportunities shape protection strongly in “North America & Australia–NZ” and “Latin America & Caribbean,” while the importance of the representativeness of biophysical environments is higher in “Sub-Saharan Africa” (1.3 times the average of other regions). Discussion Environmental representativeness and biodiversity protection are top priorities in land conservation agendas. However, our results suggest that they have been minor players driving current protection at both global and regional levels. Attempts to increase their relevance will necessarily have to recognize…
bibliographic citation: Baldi et al. (2017) Opportunities drive the global distribution of protected areas. PeerJ 5:e2989 https://doi.org/10.7717/peerj.2989
date submitted: 2016-09-20
date accepted: 2017-01-13
issued: 2017-02-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baldi
  given name: Germán
author list: Agent
  family name: Texeira
  given name: Marcos
author list: Agent
  family name: Martin
  given name: Osvaldo A.
author list: Agent
  family name: Grau
  given name: H. Ricardo
author list: Agent
  family name: Jobbágy
  given name: Esteban G.
doi: 10.7717/peerj.2989
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-15
copyright: ©2017 Baldi et al.
attribution name: Baldi et al.

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