PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients
items: Uncovering unseen fungal diversity from plant DNA banks
items: New insights into Mesozoic cycad evolution: an exploration of anatomically preserved Cycadaceae seeds from the Jurassic Oxford Clay biota
items: PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages
items: Mutation detection and prenatal diagnosis of XLHED pedigree
items: BioFuelDB: a database and prediction server of enzymes involved in biofuels production
items: Gene expression profiling and functional analysis reveals that p53 pathway-related gene expression is highly activated in cancer cells treated by cold atmospheric plasma-activated medium
items: Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoid Eutreptiella pomquetensis
items: Fluctuating selection across years and phenotypic variation in food-deceptive orchids
items: Comparison of chemical compounds associated with sclerites from healthy and diseased sea fan corals (Gorgonia ventalina)

Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients
type: item
type: AcademicArticle
description: Host-associated microbial communities are ubiquitous among animals, and serve important functions. For example, the bacterial skin microbiome of amphibians can play a role in preventing or reducing infection by the amphibian chytrid fungus, Batrachochytrium dendrobatidis. Evidence suggests that environmental bacteria likely serve as a source pool for at least some of the members of the amphibian skin bacterial community, underscoring the potential for local environmental changes to disrupt microbial community source pools that could be critical to the health of host organisms. However, few studies have assessed variation in the amphibian skin microbiome along clear environmental gradients, and so we know relatively little about how local environmental conditions influence microbiome diversity. We sampled the skin bacterial communities of Coqui frogs, Eleutherodactylus coqui (N = 77), along an elevational gradient in eastern Puerto Rico (0–875 m), with transects in two land use types: intact forest (N = 4 sites) and disturbed (N = 3 sites) forest. We found that alpha diversity (as assessed by Shannon, Simpson, and Phylogenetic Diversity indices) varied across sites, but this variation was not correlated with elevation or land use. Beta diversity (community structure), on the other hand, varied with site, elevation and land use, primarily due to changes in the relative abundance of certain bacterial OTUs (∼species) within these communities. Importantly, although microbiome diversity varied, E. coqui maintained a common core microbiota across all sites. Thus, our findings suggest that environmental conditions can influence the composition of the skin microbiome of terrestrial amphibians, but that some aspects of the microbiome remain consistent despite environmental variation.
format: application/pdf
format: text/html
creator: Myra C. Hughey
creator: Janelle A. Pena
creator: Roberto Reyes
creator: Daniel Medina
creator: Lisa K. Belden
creator: Patricia A. Burrowes
subject: Ecology
subject: Environmental Impacts
subject: Environmental Sciences
subject: Microbiology
description: doi:10.7717/peerj.3688
publisher: PeerJ Inc.
rights: © 2017 Hughey et al.
abstract: Host-associated microbial communities are ubiquitous among animals, and serve important functions. For example, the bacterial skin microbiome of amphibians can play a role in preventing or reducing infection by the amphibian chytrid fungus, Batrachochytrium dendrobatidis. Evidence suggests that environmental bacteria likely serve as a source pool for at least some of the members of the amphibian skin bacterial community, underscoring the potential for local environmental changes to disrupt microbial community source pools that could be critical to the health of host organisms. However, few studies have assessed variation in the amphibian skin microbiome along clear environmental gradients, and so we know relatively little about how local environmental conditions influence microbiome diversity. We sampled the skin bacterial communities of Coqui frogs, Eleutherodactylus coqui (N = 77), along an elevational gradient in eastern Puerto Rico (0–875 m), with transects in two land use types: intact forest (N = 4 sites) and disturbed (N = 3 sites) forest. We found that alpha diversity (as assessed by Shannon, Simpson, and Phylogenetic Diversity indices) varied across sites, but this variation was not correlated with elevation or land use. Beta diversity (community structure), on the other hand, varied with site, elevation and land use, primarily due to changes in the relative abundance of certain bacterial OTUs (∼species) within these communities. Importantly, although microbiome diversity varied, E. coqui maintained a common core microbiota across all sites. Thus, our findings suggest that environmental conditions can influence the composition of the skin microbiome of terrestrial amphibians, but that some aspects of the microbiome remain consistent despite environmental variation.
bibliographic citation: Hughey et al. (2017) Skin bacterial microbiome of a generalist Puerto Rican frog varies along elevation and land use gradients. PeerJ 5:e3688 https://doi.org/10.7717/peerj.3688
date submitted: 2017-05-27
date accepted: 2017-07-24
issued: 2017-08-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hughey
  given name: Myra C.
author list: Agent
  family name: Pena
  given name: Janelle A.
author list: Agent
  family name: Reyes
  given name: Roberto
author list: Agent
  family name: Medina
  given name: Daniel
author list: Agent
  family name: Belden
  given name: Lisa K.
author list: Agent
  family name: Burrowes
  given name: Patricia A.
doi: 10.7717/peerj.3688
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-29
copyright: ©2017 Hughey et al.
attribution name: Hughey et al.

Uncovering unseen fungal diversity from plant DNA banks
type: item
type: AcademicArticle
description: Throughout the world DNA banks are used as storage repositories for genetic diversity of organisms ranging from plants to insects to mammals. Designed to preserve the genetic information for organisms of interest, these banks also indirectly preserve organisms’ associated microbiomes, including fungi associated with plant tissues. Studies of fungal biodiversity lag far behind those of macroorganisms, such as plants, and estimates of global fungal richness are still widely debated. Utilizing previously collected specimens to study patterns of fungal diversity could significantly increase our understanding of overall patterns of biodiversity from snapshots in time. Here, we investigated the fungi inhabiting the phylloplane among species of the endemic Hawaiian plant genus, Clermontia (Campanulaceae). Utilizing next generation DNA amplicon sequencing, we uncovered approximately 1,780 fungal operational taxonomic units from just 20 DNA bank samples collected throughout the main Hawaiian Islands. Using these historical samples, we tested the macroecological pattern of decreasing community similarity with decreasing geographic proximity. We found a significant distance decay pattern among Clermontia associated fungal communities. This study provides the first insights into elucidating patterns of microbial diversity through the use of DNA bank repository samples.
format: application/pdf
format: text/html
creator: Erin M. Datlof
creator: Anthony S. Amend
creator: Kamala Earl
creator: Jeremy Hayward
creator: Clifford W. Morden
creator: Rachael Wade
creator: Geoffrey Zahn
creator: Nicole A. Hynson
subject: Biodiversity
subject: Biogeography
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.3730
publisher: PeerJ Inc.
rights: © 2017 Datlof et al.
abstract: Throughout the world DNA banks are used as storage repositories for genetic diversity of organisms ranging from plants to insects to mammals. Designed to preserve the genetic information for organisms of interest, these banks also indirectly preserve organisms’ associated microbiomes, including fungi associated with plant tissues. Studies of fungal biodiversity lag far behind those of macroorganisms, such as plants, and estimates of global fungal richness are still widely debated. Utilizing previously collected specimens to study patterns of fungal diversity could significantly increase our understanding of overall patterns of biodiversity from snapshots in time. Here, we investigated the fungi inhabiting the phylloplane among species of the endemic Hawaiian plant genus, Clermontia (Campanulaceae). Utilizing next generation DNA amplicon sequencing, we uncovered approximately 1,780 fungal operational taxonomic units from just 20 DNA bank samples collected throughout the main Hawaiian Islands. Using these historical samples, we tested the macroecological pattern of decreasing community similarity with decreasing geographic proximity. We found a significant distance decay pattern among Clermontia associated fungal communities. This study provides the first insights into elucidating patterns of microbial diversity through the use of DNA bank repository samples.
bibliographic citation: Datlof et al. (2017) Uncovering unseen fungal diversity from plant DNA banks. PeerJ 5:e3730 https://doi.org/10.7717/peerj.3730
date submitted: 2017-05-06
date accepted: 2017-08-03
issued: 2017-08-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Datlof
  given name: Erin M.
author list: Agent
  family name: Amend
  given name: Anthony S.
author list: Agent
  family name: Earl
  given name: Kamala
author list: Agent
  family name: Hayward
  given name: Jeremy
author list: Agent
  family name: Morden
  given name: Clifford W.
author list: Agent
  family name: Wade
  given name: Rachael
author list: Agent
  family name: Zahn
  given name: Geoffrey
author list: Agent
  family name: Hynson
  given name: Nicole A.
doi: 10.7717/peerj.3730
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-28
copyright: ©2017 Datlof et al.
attribution name: Datlof et al.

New insights into Mesozoic cycad evolution: an exploration of anatomically preserved Cycadaceae seeds from the Jurassic Oxford Clay biota
type: item
type: AcademicArticle
description: Most knowledge concerning Mesozoic Era floras has come from compression fossils. This has been augmented in the last 20 years by rarer permineralized material showing cellular preservation. Here, we describe a new genus of anatomically preserved gymnosperm seed from the Callovian–Oxfordian (Jurassic) Oxford Clay Formation (UK), using a combination of traditional sectioning and synchrotron radiation X-ray micro-tomography (SRXMT). Oxfordiana motturii gen. et sp. nov. is large and bilaterally symmetrical. It has prominent external ribs, and has a three-layered integument comprising: a narrow outer layer of thick walled cells; a thick middle parenchymatous layer; and innermost a thin fleshy layer. The integument has a longitudinal interior groove and micropyle, enveloping a nucellus with a small pollen chamber. The large size, bilateral symmetry and integumentary groove demonstrate an affinity for the new species within the cycads. Moreover, the internal groove in extant taxa is an autapomorphy of the genus Cycas, where it facilitates seed germination. Based upon the unique seed germination mechanism shared with living species of the Cycadaceae, we conclude that O. motturii is a member of the stem-group lineage leading to Cycas after the Jurassic divergence of the Cycadaceae from other extant cycads. SRXMT—for the first time successfully applied to fossils already prepared as slides—reveals the distribution of different mineral phases within the fossil, and allows us to evaluate the taphonomy of Oxfordiana. An early pyrite phase replicates the external surfaces of individual cells, a later carbonate component infilling void spaces. The resulting taphonomic model suggests that the relatively small size of the fossils was key to their exceptional preservation, concentrating sulfate-reducing bacteria in a locally closed microenvironment and thus facilitating soft-tissue permineralization.
format: application/pdf
format: text/html
creator: Alan R.T. Spencer
creator: Russell J. Garwood
creator: Andrew R. Rees
creator: Robert J. Raine
creator: Gar W. Rothwell
creator: Neville T.J. Hollingworth
creator: Jason Hilton
subject: Paleontology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.3723
publisher: PeerJ Inc.
rights: © 2017 Spencer et al.
abstract: Most knowledge concerning Mesozoic Era floras has come from compression fossils. This has been augmented in the last 20 years by rarer permineralized material showing cellular preservation. Here, we describe a new genus of anatomically preserved gymnosperm seed from the Callovian–Oxfordian (Jurassic) Oxford Clay Formation (UK), using a combination of traditional sectioning and synchrotron radiation X-ray micro-tomography (SRXMT). Oxfordiana motturii gen. et sp. nov. is large and bilaterally symmetrical. It has prominent external ribs, and has a three-layered integument comprising: a narrow outer layer of thick walled cells; a thick middle parenchymatous layer; and innermost a thin fleshy layer. The integument has a longitudinal interior groove and micropyle, enveloping a nucellus with a small pollen chamber. The large size, bilateral symmetry and integumentary groove demonstrate an affinity for the new species within the cycads. Moreover, the internal groove in extant taxa is an autapomorphy of the genus Cycas, where it facilitates seed germination. Based upon the unique seed germination mechanism shared with living species of the Cycadaceae, we conclude that O. motturii is a member of the stem-group lineage leading to Cycas after the Jurassic divergence of the Cycadaceae from other extant cycads. SRXMT—for the first time successfully applied to fossils already prepared as slides—reveals the distribution of different mineral phases within the fossil, and allows us to evaluate the taphonomy of Oxfordiana. An early pyrite phase replicates the external surfaces of individual cells, a later carbonate component infilling void spaces. The resulting taphonomic model suggests that the relatively small size of the fossils was key to their exceptional preservation, concentrating sulfate-reducing bacteria in a locally closed microenvironment and thus facilitating soft-tissue permineralization.
bibliographic citation: Spencer et al. (2017) New insights into Mesozoic cycad evolution: an exploration of anatomically preserved Cycadaceae seeds from the Jurassic Oxford Clay biota. PeerJ 5:e3723 https://doi.org/10.7717/peerj.3723
date submitted: 2017-06-02
date accepted: 2017-07-31
issued: 2017-08-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spencer
  given name: Alan R.T.
author list: Agent
  family name: Garwood
  given name: Russell J.
author list: Agent
  family name: Rees
  given name: Andrew R.
author list: Agent
  family name: Raine
  given name: Robert J.
author list: Agent
  family name: Rothwell
  given name: Gar W.
author list: Agent
  family name: Hollingworth
  given name: Neville T.J.
author list: Agent
  family name: Hilton
  given name: Jason
doi: 10.7717/peerj.3723
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-28
copyright: © 2017 Spencer et al.
attribution name: Spencer et al.

PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages
type: item
type: AcademicArticle
description: Direct and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here we present a highly scalable and time-efficient computational framework for predicting linkages within the whole human proteome. We have validated this method through analysis of 3,697 human pathways and molecular complexes and a comparison of our results with the prediction outcomes of previously published co-occurrency model-based and normalization methods. Here we also introduce PrePhyloPro, a web-based software that uses our method for accurately predicting proteome-wide linkages. We present data on interactions of human mitochondrial proteins, verifying the performance of this software. PrePhyloPro is freely available at http://prephylopro.org/phyloprofile/.
format: application/pdf
format: text/html
creator: Yulong Niu
creator: Chengcheng Liu
creator: Shayan Moghimyfiroozabad
creator: Yi Yang
creator: Kambiz N. Alavian
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.3712
publisher: PeerJ Inc.
rights: © 2017 Niu et al.
abstract: Direct and indirect functional links between proteins as well as their interactions as part of larger protein complexes or common signaling pathways may be predicted by analyzing the correlation of their evolutionary patterns. Based on phylogenetic profiling, here we present a highly scalable and time-efficient computational framework for predicting linkages within the whole human proteome. We have validated this method through analysis of 3,697 human pathways and molecular complexes and a comparison of our results with the prediction outcomes of previously published co-occurrency model-based and normalization methods. Here we also introduce PrePhyloPro, a web-based software that uses our method for accurately predicting proteome-wide linkages. We present data on interactions of human mitochondrial proteins, verifying the performance of this software. PrePhyloPro is freely available at http://prephylopro.org/phyloprofile/.
bibliographic citation: Niu et al. (2017) PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages. PeerJ 5:e3712 https://doi.org/10.7717/peerj.3712
date submitted: 2017-04-13
date accepted: 2017-07-28
issued: 2017-08-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Yulong
author list: Agent
  family name: Liu
  given name: Chengcheng
author list: Agent
  family name: Moghimyfiroozabad
  given name: Shayan
author list: Agent
  family name: Yang
  given name: Yi
author list: Agent
  family name: Alavian
  given name: Kambiz N.
doi: 10.7717/peerj.3712
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-28
copyright: ©2017 Niu et al.
attribution name: Niu et al.

Mutation detection and prenatal diagnosis of XLHED pedigree
type: item
type: AcademicArticle
description: Background The phenotypic characters of X -linked Hypohidrotic Ectodermal Dysplasia (XLHED) are the dysplasia of epithelial- and mesenchymal-derived organs. Ectodysplasin (EDA) is the causative gene of XLHED. Methods The current study reported a large Chinese XLHED pedigree. The genomic DNA of adult and fetus was extracted from peripheral blood and shed chorion cell respectively. The nucleotide variation in EDA gene was screened through direct sequencing the coding sequence. The methylation state of EDA gene’s promoter was evaluated by pyrosequencing. Results This Chinese XLHED family had two male patients and three carriers. All of them were with a novel EDA frameshift mutation. The mutation, c.172-173insGG, which leads to an immediate premature stop codon in exon one caused severe structural changes of EDA. Prenatal diagnosis suggested that the fetus was a female carrier. The follow-up observation of this child indicated that she had mild hypodontia of deciduous teeth at age six. The methylation level of EDA gene’s promoter was not related to carriers’ phenotype changes in this family. Discussion We reported a new frameshift mutation of EDA gene in a Chinese family. Prenatal diagnosis can help to predict the disease status of the fetus.
format: application/pdf
format: text/html
creator: Yao Lin
creator: Wei Yin
creator: Zhuan Bian
subject: Genetics
subject: Dentistry
description: doi:10.7717/peerj.3691
publisher: PeerJ Inc.
rights: © 2017 Lin et al.
abstract: Background The phenotypic characters of X -linked Hypohidrotic Ectodermal Dysplasia (XLHED) are the dysplasia of epithelial- and mesenchymal-derived organs. Ectodysplasin (EDA) is the causative gene of XLHED. Methods The current study reported a large Chinese XLHED pedigree. The genomic DNA of adult and fetus was extracted from peripheral blood and shed chorion cell respectively. The nucleotide variation in EDA gene was screened through direct sequencing the coding sequence. The methylation state of EDA gene’s promoter was evaluated by pyrosequencing. Results This Chinese XLHED family had two male patients and three carriers. All of them were with a novel EDA frameshift mutation. The mutation, c.172-173insGG, which leads to an immediate premature stop codon in exon one caused severe structural changes of EDA. Prenatal diagnosis suggested that the fetus was a female carrier. The follow-up observation of this child indicated that she had mild hypodontia of deciduous teeth at age six. The methylation level of EDA gene’s promoter was not related to carriers’ phenotype changes in this family. Discussion We reported a new frameshift mutation of EDA gene in a Chinese family. Prenatal diagnosis can help to predict the disease status of the fetus.
bibliographic citation: Lin et al. (2017) Mutation detection and prenatal diagnosis of XLHED pedigree. PeerJ 5:e3691 https://doi.org/10.7717/peerj.3691
date submitted: 2017-06-07
date accepted: 2017-07-25
issued: 2017-08-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Yao
author list: Agent
  family name: Yin
  given name: Wei
author list: Agent
  family name: Bian
  given name: Zhuan
doi: 10.7717/peerj.3691
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-28
copyright: ©2017 Lin et al.
attribution name: Lin et al.

BioFuelDB: a database and prediction server of enzymes involved in biofuels production
type: item
type: AcademicArticle
description: Background In light of the rapid decrease in fossils fuel reserves and an increasing demand for energy, novel methods are required to explore alternative biofuel production processes to alleviate these pressures. A wide variety of molecules which can either be used as biofuels or as biofuel precursors are produced using microbial enzymes. However, the common challenges in the industrial implementation of enzyme catalysis for biofuel production are the unavailability of a comprehensive biofuel enzyme resource, low efficiency of known enzymes, and limited availability of enzymes which can function under extreme conditions in the industrial processes. Methods We have developed a comprehensive database of known enzymes with proven or potential applications in biofuel production through text mining of PubMed abstracts and other publicly available information. A total of 131 enzymes with a role in biofuel production were identified and classified into six enzyme classes and four broad application categories namely ‘Alcohol production’, ‘Biodiesel production’, ‘Fuel Cell’ and ‘Alternate biofuels’. A prediction tool ‘Benz’ was developed to identify and classify novel homologues of the known biofuel enzyme sequences from sequenced genomes and metagenomes. ‘Benz’ employs a hybrid approach incorporating HMMER 3.0 and RAPSearch2 programs to provide high accuracy and high speed for prediction. Results Using the Benz tool, 153,754 novel homologues of biofuel enzymes were identified from 23 diverse metagenomic sources. The comprehensive data of curated biofuel enzymes, their novel homologs identified from diverse metagenomes, and the hybrid prediction tool Benz are presented as a web server which can be used for the prediction of biofuel enzymes from genomic and metagenomic datasets. The database and the Benz tool is publicly available at http://metabiosys.iiserb.ac.in/biofueldb& http://metagenomics.iiserb.ac.in/biofueldb.
format: application/pdf
format: text/html
creator: Nikhil Chaudhary
creator: Ankit Gupta
creator: Sudheer Gupta
creator: Vineet K. Sharma
subject: Bioinformatics
subject: Computational Science
description: doi:10.7717/peerj.3497
publisher: PeerJ Inc.
rights: © 2017 Chaudhary et al.
abstract: Background In light of the rapid decrease in fossils fuel reserves and an increasing demand for energy, novel methods are required to explore alternative biofuel production processes to alleviate these pressures. A wide variety of molecules which can either be used as biofuels or as biofuel precursors are produced using microbial enzymes. However, the common challenges in the industrial implementation of enzyme catalysis for biofuel production are the unavailability of a comprehensive biofuel enzyme resource, low efficiency of known enzymes, and limited availability of enzymes which can function under extreme conditions in the industrial processes. Methods We have developed a comprehensive database of known enzymes with proven or potential applications in biofuel production through text mining of PubMed abstracts and other publicly available information. A total of 131 enzymes with a role in biofuel production were identified and classified into six enzyme classes and four broad application categories namely ‘Alcohol production’, ‘Biodiesel production’, ‘Fuel Cell’ and ‘Alternate biofuels’. A prediction tool ‘Benz’ was developed to identify and classify novel homologues of the known biofuel enzyme sequences from sequenced genomes and metagenomes. ‘Benz’ employs a hybrid approach incorporating HMMER 3.0 and RAPSearch2 programs to provide high accuracy and high speed for prediction. Results Using the Benz tool, 153,754 novel homologues of biofuel enzymes were identified from 23 diverse metagenomic sources. The comprehensive data of curated biofuel enzymes, their novel homologs identified from diverse metagenomes, and the hybrid prediction tool Benz are presented as a web server which can be used for the prediction of biofuel enzymes from genomic and metagenomic datasets. The database and the Benz tool is publicly available at http://metabiosys.iiserb.ac.in/biofueldb& http://metagenomics.iiserb.ac.in/biofueldb.
bibliographic citation: Chaudhary et al. (2017) BioFuelDB: a database and prediction server of enzymes involved in biofuels production. PeerJ 5:e3497 https://doi.org/10.7717/peerj.3497
date submitted: 2017-03-30
date accepted: 2017-06-02
issued: 2017-08-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chaudhary
  given name: Nikhil
author list: Agent
  family name: Gupta
  given name: Ankit
author list: Agent
  family name: Gupta
  given name: Sudheer
author list: Agent
  family name: Sharma
  given name: Vineet K.
doi: 10.7717/peerj.3497
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-28
copyright: ©2017 Chaudhary et al.
attribution name: Chaudhary et al.

Gene expression profiling and functional analysis reveals that p53 pathway-related gene expression is highly activated in cancer cells treated by cold atmospheric plasma-activated medium
type: item
type: AcademicArticle
description: Background Cold atmospheric-pressure plasma (CAP) has been considered a promising strategy for anti-cancer treatment. Traditionally, CAP was employed to kill cancer cells or tumor tissues by direct irradiation. However, CAP has some disadvantages such as infiltration capacity and storage convenience. Recently, plasma-activated medium (PAM) was used as an alternative strategy to treat cancer cells or tumors. The novel PAM approach has potential as an anti-cancer therapy. Objective To reveal the global activation of signaling pathways in oral cancer cells induced by PAM. Methods Oral squamous cell line SCC15 were treated by PAM and gene expression profiles were evaluated by using RNA-seq. Functional analyses were employed to reveal the global responses of SCC15 cells with PAM stimulation. QRT-PCR and Western blot were carried out to validate the expression levels of selected genes. Results More than 6G clean data per sample were obtained in PAM-treated SCC15 cells. A total of 934 differentially expressed genes (DEGs) were identified and GO analysis implicated the deep involvement of biological process. KEGG mapping further clustered 40 pathways, revealing that “p53 pathway” was significantly enriched. SCC15 cells were commonly used as a p53-null cell line. Therefore, the enriched p53 pathway-related genes in our analysis might be activated by other stimulators, in a p53-independent manner. Gene set enrichment analysis (GSEA) was also performed to evaluate changes at the gene-sets level. The results demonstrated not only the high engagement of “p53 pathway” but also the involvement of novel pathways such as hypoxia pathway. Conclusions The present study elucidates the transcriptomic changes of PAM treated SCC15 cells, containing highly enriched DEGs involved in “p53 pathway”. Our analysis in this work not only provides genomic resources for future studies but also gives novel insights to uncover the molecular mechanism of PAM stimulation.
format: application/pdf
format: text/html
creator: Lei Shi
creator: Lihua Yu
creator: Fagui Zou
creator: Huimin Hu
creator: Kun Liu
creator: Zhenghong Lin
subject: Oncology
description: doi:10.7717/peerj.3751
publisher: PeerJ Inc.
rights: © 2017 Shi et al.
abstract: Background Cold atmospheric-pressure plasma (CAP) has been considered a promising strategy for anti-cancer treatment. Traditionally, CAP was employed to kill cancer cells or tumor tissues by direct irradiation. However, CAP has some disadvantages such as infiltration capacity and storage convenience. Recently, plasma-activated medium (PAM) was used as an alternative strategy to treat cancer cells or tumors. The novel PAM approach has potential as an anti-cancer therapy. Objective To reveal the global activation of signaling pathways in oral cancer cells induced by PAM. Methods Oral squamous cell line SCC15 were treated by PAM and gene expression profiles were evaluated by using RNA-seq. Functional analyses were employed to reveal the global responses of SCC15 cells with PAM stimulation. QRT-PCR and Western blot were carried out to validate the expression levels of selected genes. Results More than 6G clean data per sample were obtained in PAM-treated SCC15 cells. A total of 934 differentially expressed genes (DEGs) were identified and GO analysis implicated the deep involvement of biological process. KEGG mapping further clustered 40 pathways, revealing that “p53 pathway” was significantly enriched. SCC15 cells were commonly used as a p53-null cell line. Therefore, the enriched p53 pathway-related genes in our analysis might be activated by other stimulators, in a p53-independent manner. Gene set enrichment analysis (GSEA) was also performed to evaluate changes at the gene-sets level. The results demonstrated not only the high engagement of “p53 pathway” but also the involvement of novel pathways such as hypoxia pathway. Conclusions The present study elucidates the transcriptomic changes of PAM treated SCC15 cells, containing highly enriched DEGs involved in “p53 pathway”. Our analysis in this work not only provides genomic resources for future studies but also gives novel insights to uncover the molecular mechanism of PAM stimulation.
bibliographic citation: Shi et al. (2017) Gene expression profiling and functional analysis reveals that p53 pathway-related gene expression is highly activated in cancer cells treated by cold atmospheric plasma-activated medium. PeerJ 5:e3751 https://doi.org/10.7717/peerj.3751
date submitted: 2017-05-22
date accepted: 2017-08-08
issued: 2017-08-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Lei
author list: Agent
  family name: Yu
  given name: Lihua
author list: Agent
  family name: Zou
  given name: Fagui
author list: Agent
  family name: Hu
  given name: Huimin
author list: Agent
  family name: Liu
  given name: Kun
author list: Agent
  family name: Lin
  given name: Zhenghong
doi: 10.7717/peerj.3751
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-25
copyright: ©2017 Shi et al.
attribution name: Shi et al.

Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoid Eutreptiella pomquetensis
type: item
type: AcademicArticle
description: Background Over the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast genome evolution in early evolving Eutreptiales, this study focused on the cpGenome of Eutreptiella pomquetensis, and the spread and peculiarities of introns. Methods The Etl. pomquetensis cpGenome was sequenced, annotated and afterwards examined in structure, size, gene order and intron content. These features were compared with other euglenoid cpGenomes as well as those of prasinophyte green algae, including Pyramimonas parkeae. Results and Discussion With about 130,561 bp the chloroplast genome of Etl. pomquetensis, a basal taxon in the phototrophic euglenoids, was considerably larger than the two other Eutreptiales cpGenomes sequenced so far. Although the detected quadripartite structure resembled most green algae and plant chloroplast genomes, the gene content of the single copy regions in Etl. pomquetensis was completely different from those observed in green algae and plants. The gene composition of Etl. pomquetensis was extensively changed and turned out to be almost identical to other Eutreptiales and Euglenales, and not to P. parkeae. Furthermore, the cpGenome of Etl. pomquetensis was unexpectedly permeated by a high number of introns, which led to a substantially larger genome. The 51 identified introns of Etl. pomquetensis showed two major unique features: (i) more than half of the introns displayed a high level of pairwise identities; (ii) no group III introns could be identified in the protein coding genes. These findings support the hypothesis that group III int…
format: application/pdf
format: text/html
creator: Nadja Dabbagh
creator: Matthew S. Bennett
creator: Richard E. Triemer
creator: Angelika Preisfeld
subject: Cell Biology
subject: Evolutionary Studies
subject: Genomics
description: doi:10.7717/peerj.3725
publisher: PeerJ Inc.
rights: © 2017 Dabbagh et al.
abstract: Background Over the last few years multiple studies have been published showing a great diversity in size of chloroplast genomes (cpGenomes), and in the arrangement of gene clusters, in the Euglenales. However, while these genomes provided important insights into the evolution of cpGenomes across the Euglenales and within their genera, only two genomes were analyzed in regard to genomic variability between and within Euglenales and Eutreptiales. To better understand the dynamics of chloroplast genome evolution in early evolving Eutreptiales, this study focused on the cpGenome of Eutreptiella pomquetensis, and the spread and peculiarities of introns. Methods The Etl. pomquetensis cpGenome was sequenced, annotated and afterwards examined in structure, size, gene order and intron content. These features were compared with other euglenoid cpGenomes as well as those of prasinophyte green algae, including Pyramimonas parkeae. Results and Discussion With about 130,561 bp the chloroplast genome of Etl. pomquetensis, a basal taxon in the phototrophic euglenoids, was considerably larger than the two other Eutreptiales cpGenomes sequenced so far. Although the detected quadripartite structure resembled most green algae and plant chloroplast genomes, the gene content of the single copy regions in Etl. pomquetensis was completely different from those observed in green algae and plants. The gene composition of Etl. pomquetensis was extensively changed and turned out to be almost identical to other Eutreptiales and Euglenales, and not to P. parkeae. Furthermore, the cpGenome of Etl. pomquetensis was unexpectedly permeated by a high number of introns, which led to a substantially larger genome. The 51 identified introns of Etl. pomquetensis showed two major unique features: (i) more than half of the introns displayed a high level of pairwise identities; (ii) no group III introns could be identified in the protein coding genes. These findings support the hypothesis that group III int…
bibliographic citation: Dabbagh et al. (2017) Chloroplast genome expansion by intron multiplication in the basal psychrophilic euglenoid Eutreptiella pomquetensis. PeerJ 5:e3725 https://doi.org/10.7717/peerj.3725
date submitted: 2017-03-10
date accepted: 2017-08-01
issued: 2017-08-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dabbagh
  given name: Nadja
author list: Agent
  family name: Bennett
  given name: Matthew S.
author list: Agent
  family name: Triemer
  given name: Richard E.
author list: Agent
  family name: Preisfeld
  given name: Angelika
doi: 10.7717/peerj.3725
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-25
copyright: ©2017 Dabbagh et al.
attribution name: Dabbagh et al.

Fluctuating selection across years and phenotypic variation in food-deceptive orchids
type: item
type: AcademicArticle
description: Nectarless flowers that deceive pollinators offer an opportunity to study asymmetric plant-insect interactions. Orchids are a widely used model for studying these interactions because they encompass several thousand species adopting deceptive pollination systems. High levels of intra-specific phenotypic variation have been reported in deceptive orchids, suggesting a reduced consistency of pollinator-mediated selection on their floral traits. Nevertheless, several studies report on widespread directional selection mediated by pollinators even in these deceptive orchids. In this study we test the hypothesis that the observed selection can fluctuate across years in strength and direction thus likely contributing to the phenotypic variability of this orchid group. We performed a three-year study estimating selection differentials and selection gradients for nine phenotypic traits involved in insect attraction in two Mediterranean orchid species, namely Orchis mascula and O. pauciflora, both relying on a well-described food-deceptive pollination strategy. We found weak directional selection and marginally significant selection gradients in the two investigated species with significant intra-specific differences in selection differentials across years. Our data do not link this variation with a specific environmental cause, but our results suggest that pollinator-mediated selection in food-deceptive orchids can change in strength and in direction over time. In perennial plants, such as orchids, different selection differentials in the same populations in different flowering seasons can contribute to the maintenance of phenotypic variation often reported in deceptive orchids.
format: application/pdf
format: text/html
creator: Giovanni Scopece
creator: Nicolas Juillet
creator: Christian Lexer
creator: Salvatore Cozzolino
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.3704
publisher: PeerJ Inc.
rights: © 2017 Scopece et al.
abstract: Nectarless flowers that deceive pollinators offer an opportunity to study asymmetric plant-insect interactions. Orchids are a widely used model for studying these interactions because they encompass several thousand species adopting deceptive pollination systems. High levels of intra-specific phenotypic variation have been reported in deceptive orchids, suggesting a reduced consistency of pollinator-mediated selection on their floral traits. Nevertheless, several studies report on widespread directional selection mediated by pollinators even in these deceptive orchids. In this study we test the hypothesis that the observed selection can fluctuate across years in strength and direction thus likely contributing to the phenotypic variability of this orchid group. We performed a three-year study estimating selection differentials and selection gradients for nine phenotypic traits involved in insect attraction in two Mediterranean orchid species, namely Orchis mascula and O. pauciflora, both relying on a well-described food-deceptive pollination strategy. We found weak directional selection and marginally significant selection gradients in the two investigated species with significant intra-specific differences in selection differentials across years. Our data do not link this variation with a specific environmental cause, but our results suggest that pollinator-mediated selection in food-deceptive orchids can change in strength and in direction over time. In perennial plants, such as orchids, different selection differentials in the same populations in different flowering seasons can contribute to the maintenance of phenotypic variation often reported in deceptive orchids.
bibliographic citation: Scopece et al. (2017) Fluctuating selection across years and phenotypic variation in food-deceptive orchids. PeerJ 5:e3704 https://doi.org/10.7717/peerj.3704
date submitted: 2017-05-23
date accepted: 2017-07-27
issued: 2017-08-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scopece
  given name: Giovanni
author list: Agent
  family name: Juillet
  given name: Nicolas
author list: Agent
  family name: Lexer
  given name: Christian
author list: Agent
  family name: Cozzolino
  given name: Salvatore
doi: 10.7717/peerj.3704
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-25
copyright: ©2017 Scopece et al.
attribution name: Scopece et al.

Comparison of chemical compounds associated with sclerites from healthy and diseased sea fan corals (Gorgonia ventalina)
type: item
type: AcademicArticle
description: Background The roles of gorgonian sclerites as structural components and predator deterrents have been widely studied. Yet their role as barriers against microbes has only recently been investigated, and even less is known about the diversity and roles of the chemical compounds associated with sclerites. Methods Here, we examine the semi-volatile organic compound fraction (SVOCs) associated with sclerites from healthy and diseased Gorgonia ventalina sea fan corals to understand their possible role as a stress response or in defense of infection. We also measured the oxidative potential of compounds from diseased and healthy G. ventalina colonies. Results The results showed that sclerites harbor a great diversity of SVOCs. Overall, 70 compounds were identified, the majority of which are novel with unknown biological roles. The majority of SVOCs identified exhibit multiple immune-related roles including antimicrobial and radical scavenging functions. The free radical activity assays further confirmed the anti-oxidative potential of some these compounds. The anti-oxidative activity was, nonetheless, similar across sclerites regardless of the health condition of the colony, although sclerites from diseased sea fans display slightly higher anti-oxidative activity than the healthy ones. Discussion Sclerites harbor great SVOCs diversity, the majority of which are novel to sea fans or any other corals. Yet the scientific literature consulted showed that the roles of compounds found in sclerites vary from antioxidant to antimicrobial compounds. However, this study fell short in determine the origin of the SVOCs identified, undermining our capacity to determine the biological roles of the SVOCs on sclerites and sea fans.
format: application/pdf
format: text/html
creator: Carlos Toledo-Hernández
creator: Claudia P. Ruiz-Diaz
creator: Liz M. Díaz-Vázquez
creator: Vanessa Santiago-Cárdenas
creator: Derick N. Rosario-Berrios
creator: Derek M. García-Almedina
creator: Loretta M. Roberson
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3677
publisher: PeerJ Inc.
rights: © 2017 Toledo-Hernández et al.
abstract: Background The roles of gorgonian sclerites as structural components and predator deterrents have been widely studied. Yet their role as barriers against microbes has only recently been investigated, and even less is known about the diversity and roles of the chemical compounds associated with sclerites. Methods Here, we examine the semi-volatile organic compound fraction (SVOCs) associated with sclerites from healthy and diseased Gorgonia ventalina sea fan corals to understand their possible role as a stress response or in defense of infection. We also measured the oxidative potential of compounds from diseased and healthy G. ventalina colonies. Results The results showed that sclerites harbor a great diversity of SVOCs. Overall, 70 compounds were identified, the majority of which are novel with unknown biological roles. The majority of SVOCs identified exhibit multiple immune-related roles including antimicrobial and radical scavenging functions. The free radical activity assays further confirmed the anti-oxidative potential of some these compounds. The anti-oxidative activity was, nonetheless, similar across sclerites regardless of the health condition of the colony, although sclerites from diseased sea fans display slightly higher anti-oxidative activity than the healthy ones. Discussion Sclerites harbor great SVOCs diversity, the majority of which are novel to sea fans or any other corals. Yet the scientific literature consulted showed that the roles of compounds found in sclerites vary from antioxidant to antimicrobial compounds. However, this study fell short in determine the origin of the SVOCs identified, undermining our capacity to determine the biological roles of the SVOCs on sclerites and sea fans.
bibliographic citation: Toledo-Hernández et al. (2017) Comparison of chemical compounds associated with sclerites from healthy and diseased sea fan corals (Gorgonia ventalina). PeerJ 5:e3677 https://doi.org/10.7717/peerj.3677
date submitted: 2017-04-09
date accepted: 2017-07-22
issued: 2017-08-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Toledo-Hernández
  given name: Carlos
author list: Agent
  family name: Ruiz-Diaz
  given name: Claudia P.
author list: Agent
  family name: Díaz-Vázquez
  given name: Liz M.
author list: Agent
  family name: Santiago-Cárdenas
  given name: Vanessa
author list: Agent
  family name: Rosario-Berrios
  given name: Derick N.
author list: Agent
  family name: García-Almedina
  given name: Derek M.
author list: Agent
  family name: Roberson
  given name: Loretta M.
doi: 10.7717/peerj.3677
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-25
copyright: ©2017 Toledo-Hernández et al.
attribution name: Toledo-Hernández et al.

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