PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback
items: Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations
items: RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)
items: Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill
items: Microbiome succession during ammonification in eelgrass bed sediments
items: RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages
items: Changes in zooplankton community, and seston and zooplankton fatty acid profiles at the freshwater/saltwater interface of the Chowan River, North Carolina
items: RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus
items: Germination of dimorphic seeds of Suaeda aralocaspica in response to light and salinity conditions during and after cold stratification
items: Aura-biomes are present in the water layer above coral reef benthic macro-organisms

Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback
type: item
type: AcademicArticle
description: The polyphagous shot hole borer and Kuroshio shot hole borer, two members of the Euwallacea fornicatus species complex (Coleoptera: Curculionidae: Scolytinae), are invasive ambrosia beetles that harbor distinct species of Fusarium fungal symbionts. Together with the damage caused by gallery construction, these two phytopathogenic Fusarium species are responsible for the emerging tree disease Fusarium dieback, which affects over 50 common tree species in Southern California. Host trees suffer branch dieback as the xylem is blocked by invading beetles and fungi, forcing the costly removal of dead and dying trees in urban areas. The beetles are also threatening natural riparian habitats, and avocado is susceptible to Fusarium dieback as well, resulting in damage to the avocado industries in California and Israel. Currently there are no adequate control mechanisms for shot hole borers. This paper summarizes efforts to find a suitable lure to monitor shot hole borer invasions and dispersal. Field trials were conducted in two counties in Southern California over a span of two years. We find that the chemical quercivorol is highly attractive to these beetles, and perform subsequent field experiments attempting to optimize this lure. We also explore other methods of increasing trap catch and effects of other potential attractants, as well as the deterrents verbenone and piperitone.
format: application/pdf
format: text/html
creator: Christine Dodge
creator: Jessica Coolidge
creator: Miriam Cooperband
creator: Allard Cossé
creator: Daniel Carrillo
creator: Richard Stouthamer
subject: Agricultural Science
subject: Animal Behavior
subject: Entomology
description: doi:10.7717/peerj.3656
publisher: PeerJ Inc.
rights: © 2017 Dodge et al.
abstract: The polyphagous shot hole borer and Kuroshio shot hole borer, two members of the Euwallacea fornicatus species complex (Coleoptera: Curculionidae: Scolytinae), are invasive ambrosia beetles that harbor distinct species of Fusarium fungal symbionts. Together with the damage caused by gallery construction, these two phytopathogenic Fusarium species are responsible for the emerging tree disease Fusarium dieback, which affects over 50 common tree species in Southern California. Host trees suffer branch dieback as the xylem is blocked by invading beetles and fungi, forcing the costly removal of dead and dying trees in urban areas. The beetles are also threatening natural riparian habitats, and avocado is susceptible to Fusarium dieback as well, resulting in damage to the avocado industries in California and Israel. Currently there are no adequate control mechanisms for shot hole borers. This paper summarizes efforts to find a suitable lure to monitor shot hole borer invasions and dispersal. Field trials were conducted in two counties in Southern California over a span of two years. We find that the chemical quercivorol is highly attractive to these beetles, and perform subsequent field experiments attempting to optimize this lure. We also explore other methods of increasing trap catch and effects of other potential attractants, as well as the deterrents verbenone and piperitone.
bibliographic citation: Dodge et al. (2017) Quercivorol as a lure for the polyphagous and Kuroshio shot hole borers, Euwallacea spp. nr. fornicatus (Coleoptera: Scolytinae), vectors of Fusarium dieback. PeerJ 5:e3656 https://doi.org/10.7717/peerj.3656
date submitted: 2017-06-19
date accepted: 2017-07-14
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dodge
  given name: Christine
author list: Agent
  family name: Coolidge
  given name: Jessica
author list: Agent
  family name: Cooperband
  given name: Miriam
author list: Agent
  family name: Cossé
  given name: Allard
author list: Agent
  family name: Carrillo
  given name: Daniel
author list: Agent
  family name: Stouthamer
  given name: Richard
doi: 10.7717/peerj.3656
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: © 2017 Dodge et al.
attribution name: Dodge et al.

Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations
type: item
type: AcademicArticle
description: The prevalence of Type II Diabetes (T2D) has been increasing and has become a disease of significant public health burden in Jordan. None of the previous genome-wide association studies (GWAS) have specifically investigated the Middle East populations. The Circassian and Chechen communities in Jordan represent unique populations that are genetically distinct from the Arab population and other populations in the Caucasus. Prevalence of T2D is very high in both the Circassian and Chechen communities in Jordan despite low obesity prevalence. We conducted GWAS on T2D in these two populations and further performed meta-analysis of the results. We identified a novel T2D locus at chr20p12.2 at genome-wide significance (rs6134031, P = 1.12 × 10−8) and we replicated the results in the Wellcome Trust Case Control Consortium (WTCCC) dataset. Another locus at chr12q24.31 is associated with T2D at suggestive significance level (top SNP rs4758690, P = 4.20 × 10−5) and it is a robust eQTL for the gene, MLXIP (P = 1.10 × 10−14), and is significantly associated with methylation level in MLXIP, the functions of which involves cellular glucose response. Therefore, in this first GWAS of T2D in Jordan subpopulations, we identified novel and unique susceptibility loci which may help inform the genetic underpinnings of T2D in other populations.
format: application/pdf
format: text/html
creator: Rana Dajani
creator: Jin Li
creator: Zhi Wei
creator: Michael E. March
creator: Qianghua Xia
creator: Yousef Khader
creator: Nancy Hakooz
creator: Raja Fatahallah
creator: Mohammed El-Khateeb
creator: Ala Arafat
creator: Tareq Saleh
creator: Abdel Rahman Dajani
creator: Zaid Al-Abbadi
creator: Mohamed Abdul Qader
creator: Abdel Halim Shiyab
creator: Anwar Bateiha
creator: Kamel Ajlouni
creator: Hakon Hakonarson
subject: Genetics
subject: Genomics
subject: Diabetes and Endocrinology
subject: Medical Genetics
description: doi:10.7717/peerj.3618
publisher: PeerJ Inc.
rights: © 2017 Dajani et al.
abstract: The prevalence of Type II Diabetes (T2D) has been increasing and has become a disease of significant public health burden in Jordan. None of the previous genome-wide association studies (GWAS) have specifically investigated the Middle East populations. The Circassian and Chechen communities in Jordan represent unique populations that are genetically distinct from the Arab population and other populations in the Caucasus. Prevalence of T2D is very high in both the Circassian and Chechen communities in Jordan despite low obesity prevalence. We conducted GWAS on T2D in these two populations and further performed meta-analysis of the results. We identified a novel T2D locus at chr20p12.2 at genome-wide significance (rs6134031, P = 1.12 × 10−8) and we replicated the results in the Wellcome Trust Case Control Consortium (WTCCC) dataset. Another locus at chr12q24.31 is associated with T2D at suggestive significance level (top SNP rs4758690, P = 4.20 × 10−5) and it is a robust eQTL for the gene, MLXIP (P = 1.10 × 10−14), and is significantly associated with methylation level in MLXIP, the functions of which involves cellular glucose response. Therefore, in this first GWAS of T2D in Jordan subpopulations, we identified novel and unique susceptibility loci which may help inform the genetic underpinnings of T2D in other populations.
bibliographic citation: Dajani et al. (2017) Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations. PeerJ 5:e3618 https://doi.org/10.7717/peerj.3618
date submitted: 2017-04-03
date accepted: 2017-07-06
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dajani
  given name: Rana
author list: Agent
  family name: Li
  given name: Jin
author list: Agent
  family name: Wei
  given name: Zhi
author list: Agent
  family name: March
  given name: Michael E.
author list: Agent
  family name: Xia
  given name: Qianghua
author list: Agent
  family name: Khader
  given name: Yousef
author list: Agent
  family name: Hakooz
  given name: Nancy
author list: Agent
  family name: Fatahallah
  given name: Raja
author list: Agent
  family name: El-Khateeb
  given name: Mohammed
author list: Agent
  family name: Arafat
  given name: Ala
author list: Agent
  family name: Saleh
  given name: Tareq
author list: Agent
  family name: Dajani
  given name: Abdel Rahman
author list: Agent
  family name: Al-Abbadi
  given name: Zaid
author list: Agent
  family name: Abdul Qader
  given name: Mohamed
author list: Agent
  family name: Shiyab
  given name: Abdel Halim
author list: Agent
  family name: Bateiha
  given name: Anwar
author list: Agent
  family name: Ajlouni
  given name: Kamel
author list: Agent
  family name: Hakonarson
  given name: Hakon
doi: 10.7717/peerj.3618
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: ©2017 Dajani et al.
attribution name: Dajani et al.

RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis)
type: item
type: AcademicArticle
description: The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology. A total of 174,208,078 paired end 70 base pair sequencing reads were obtained from the Illumina Hi-Seq 2500 sequencer. The overall mapping percentage of the sequencing reads to the M. fascicularis reference genome ranged from 53–63%. Categorisation of expressed genes to Gene Ontology (GO) and KEGG pathway categories revealed that GO terms with the highest number of associated expressed genes include Cellular process, Catalytic activity, and Cell part, while for pathway categorisation, the majority of expressed genes in lymph node, spleen, and thymus fall under the Global overview and maps pathway category, while 266, 221, and 138 genes from lymph node, spleen, and thymus were respectively enriched in the Immune system category. Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production. Differential gene expression analysis among the three tissues revealed 574 differentially expressed genes (DEG) between lymph and spleen, 5402 DEGs between lymph and thymus, and 7008 DEGs between spleen and thymus. Venn diagram analysis of expressed genes revealed a total of 2,630, 253, and 279 tissue-specific genes respectively for lymph node, spleen, and thymus tissues. This is the first time the lymph node, spleen, and thymus transcriptome of the Peninsular Malaysian…
format: application/pdf
format: text/html
creator: Joey Ee Uli
creator: Christina Seok Yien Yong
creator: Swee Keong Yeap
creator: Jeffrine J. Rovie-Ryan
creator: Nurulfiza Mat Isa
creator: Soon Guan Tan
creator: Noorjahan Banu Alitheen
subject: Bioinformatics
subject: Genomics
subject: Zoology
subject: Immunology
description: doi:10.7717/peerj.3566
publisher: PeerJ Inc.
rights: © 2017 Ee Uli et al.
abstract: The cynomolgus macaque (Macaca fascicularis) is an extensively utilised nonhuman primate model for biomedical research due to its biological, behavioural, and genetic similarities to humans. Genomic information of cynomolgus macaque is vital for research in various fields; however, there is presently a shortage of genomic information on the Malaysian cynomolgus macaque. This study aimed to sequence, assemble, annotate, and profile the Peninsular Malaysian cynomolgus macaque transcriptome derived from three tissues (lymph node, spleen, and thymus) using RNA sequencing (RNA-Seq) technology. A total of 174,208,078 paired end 70 base pair sequencing reads were obtained from the Illumina Hi-Seq 2500 sequencer. The overall mapping percentage of the sequencing reads to the M. fascicularis reference genome ranged from 53–63%. Categorisation of expressed genes to Gene Ontology (GO) and KEGG pathway categories revealed that GO terms with the highest number of associated expressed genes include Cellular process, Catalytic activity, and Cell part, while for pathway categorisation, the majority of expressed genes in lymph node, spleen, and thymus fall under the Global overview and maps pathway category, while 266, 221, and 138 genes from lymph node, spleen, and thymus were respectively enriched in the Immune system category. Enriched Immune system pathways include Platelet activation pathway, Antigen processing and presentation, B cell receptor signalling pathway, and Intestinal immune network for IgA production. Differential gene expression analysis among the three tissues revealed 574 differentially expressed genes (DEG) between lymph and spleen, 5402 DEGs between lymph and thymus, and 7008 DEGs between spleen and thymus. Venn diagram analysis of expressed genes revealed a total of 2,630, 253, and 279 tissue-specific genes respectively for lymph node, spleen, and thymus tissues. This is the first time the lymph node, spleen, and thymus transcriptome of the Peninsular Malaysian…
bibliographic citation: Ee Uli et al. (2017) RNA sequencing (RNA-Seq) of lymph node, spleen, and thymus transcriptome from wild Peninsular Malaysian cynomolgus macaque (Macaca fascicularis). PeerJ 5:e3566 https://doi.org/10.7717/peerj.3566
date submitted: 2017-03-02
date accepted: 2017-06-21
issued: 2017-08-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ee Uli
  given name: Joey
author list: Agent
  family name: Yong
  given name: Christina Seok Yien
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Rovie-Ryan
  given name: Jeffrine J.
author list: Agent
  family name: Mat Isa
  given name: Nurulfiza
author list: Agent
  family name: Tan
  given name: Soon Guan
author list: Agent
  family name: Alitheen
  given name: Noorjahan Banu
doi: 10.7717/peerj.3566
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-17
copyright: ©2017 Ee Uli et al.
attribution name: Ee Uli et al.

Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill
type: item
type: AcademicArticle
description: Salt marshes in northern Barataria Bay, Louisiana, USA were oiled, sometimes heavily, in the aftermath of the Deepwater Horizon oil spill. Previous studies indicate that fiddler crabs (in the genus Uca) and the salt marsh periwinkle (Littoraria irrorata) were negatively impacted in the short term by the spill. Here, we detail longer-term effects and recovery from moderate and heavy oiling over a 3-year span, beginning 30 months after the spill. Although neither fiddler crab burrow density nor diameter differed between oiled and reference sites when combined across all sampling events, these traits differed among some individual sampling periods consistent with a pattern of lingering oiling impacts. Periwinkle density, however, increased in all oiling categories and shell-length groups during our sampling period, and periwinkle densities were consistently highest at moderately oiled sites where Spartina alterniflora aboveground biomass was highest. Periwinkle shell length linearly increased from a mean of 16.5 to 19.2 mm over the study period at reference sites. In contrast, shell lengths at moderately oiled and heavily oiled sites increased through month 48 after the spill, but then decreased. This decrease was associated with a decline in the relative abundance of large adults (shell length 21–26 mm) at oiled sites which was likely caused by chronic hydrocarbon toxicity or oil-induced effects on habitat quality or food resources. Overall, the recovery of S. alterniflora facilitated the recovery of fiddler crabs and periwinkles. However, our long-term record not only indicates that variation in periwinkle mean shell length and length-frequency distributions are sensitive indicators of the health and recovery of the marsh, but agrees with synoptic studies of vegetation and infaunal communities that full recovery of heavily oiled sites will take longer than 66 months.
format: application/pdf
format: text/html
creator: Donald R. Deis
creator: John W. Fleeger
creator: Stefan M. Bourgoin
creator: Irving A. Mendelssohn
creator: Qianxin Lin
creator: Aixin Hou
subject: Ecology
subject: Environmental Sciences
subject: Zoology
subject: Biosphere Interactions
subject: Ecotoxicology
description: doi:10.7717/peerj.3680
publisher: PeerJ Inc.
rights: © 2017 Deis et al.
abstract: Salt marshes in northern Barataria Bay, Louisiana, USA were oiled, sometimes heavily, in the aftermath of the Deepwater Horizon oil spill. Previous studies indicate that fiddler crabs (in the genus Uca) and the salt marsh periwinkle (Littoraria irrorata) were negatively impacted in the short term by the spill. Here, we detail longer-term effects and recovery from moderate and heavy oiling over a 3-year span, beginning 30 months after the spill. Although neither fiddler crab burrow density nor diameter differed between oiled and reference sites when combined across all sampling events, these traits differed among some individual sampling periods consistent with a pattern of lingering oiling impacts. Periwinkle density, however, increased in all oiling categories and shell-length groups during our sampling period, and periwinkle densities were consistently highest at moderately oiled sites where Spartina alterniflora aboveground biomass was highest. Periwinkle shell length linearly increased from a mean of 16.5 to 19.2 mm over the study period at reference sites. In contrast, shell lengths at moderately oiled and heavily oiled sites increased through month 48 after the spill, but then decreased. This decrease was associated with a decline in the relative abundance of large adults (shell length 21–26 mm) at oiled sites which was likely caused by chronic hydrocarbon toxicity or oil-induced effects on habitat quality or food resources. Overall, the recovery of S. alterniflora facilitated the recovery of fiddler crabs and periwinkles. However, our long-term record not only indicates that variation in periwinkle mean shell length and length-frequency distributions are sensitive indicators of the health and recovery of the marsh, but agrees with synoptic studies of vegetation and infaunal communities that full recovery of heavily oiled sites will take longer than 66 months.
bibliographic citation: Deis et al. (2017) Shoreline oiling effects and recovery of salt marsh macroinvertebrates from the Deepwater Horizon Oil Spill. PeerJ 5:e3680 https://doi.org/10.7717/peerj.3680
date submitted: 2015-11-01
date accepted: 2017-07-22
issued: 2017-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deis
  given name: Donald R.
author list: Agent
  family name: Fleeger
  given name: John W.
author list: Agent
  family name: Bourgoin
  given name: Stefan M.
author list: Agent
  family name: Mendelssohn
  given name: Irving A.
author list: Agent
  family name: Lin
  given name: Qianxin
author list: Agent
  family name: Hou
  given name: Aixin
doi: 10.7717/peerj.3680
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-16
copyright: ©2017 Deis et al.
attribution name: Deis et al.

Microbiome succession during ammonification in eelgrass bed sediments
type: item
type: AcademicArticle
description: Background Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA. Methods Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n = 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification. Results Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers (Desulfobacterales) and corresponding increases in predicted sulfide oxidizers (Thiotrichales). None of these changes in composition or richness were associated with variation in ammonification ra…
format: application/pdf
format: text/html
creator: Cassandra L. Ettinger
creator: Susan L. Williams
creator: Jessica M. Abbott
creator: John J. Stachowicz
creator: Jonathan A. Eisen
subject: Marine Biology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.3674
publisher: PeerJ Inc.
rights: © 2017 Ettinger et al.
abstract: Background Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, also known as diagenesis, from plots at a field site in Bodega Bay, CA. Methods Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n = 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 °C) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at seven, 13 and 19 days to characterize changes in the relative abundances of microbial taxa throughout ammonification. Results Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in predicted sulfur reducers (Desulfobacterales) and corresponding increases in predicted sulfide oxidizers (Thiotrichales). None of these changes in composition or richness were associated with variation in ammonification ra…
bibliographic citation: Ettinger et al. (2017) Microbiome succession during ammonification in eelgrass bed sediments. PeerJ 5:e3674 https://doi.org/10.7717/peerj.3674
date submitted: 2017-04-29
date accepted: 2017-07-21
issued: 2017-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ettinger
  given name: Cassandra L.
author list: Agent
  family name: Williams
  given name: Susan L.
author list: Agent
  family name: Abbott
  given name: Jessica M.
author list: Agent
  family name: Stachowicz
  given name: John J.
author list: Agent
  family name: Eisen
  given name: Jonathan A.
doi: 10.7717/peerj.3674
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-16
copyright: ©2017 Ettinger et al.
attribution name: Ettinger et al.

RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages
type: item
type: AcademicArticle
description: Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by transposons of TRAS and Jockey families represented separate brunches in a phylogenetic tree of helicase domains and thus could be considered as independently originated in the evolution of insect transposons. Transcriptome database analyses revealed that both TRAS and Jockey transposons encoding the helicase domain represented transcribed genome sequences. Moreover, the transposon-encoded helicases were found to contain the full set of conserved motifs essential for their enzymatic activities. Taking into account the previously reported ability of RNA helicase encoded by TRAS ORF2 to suppress post-transcriptional RNA silencing, we propose possible scenarios of evolutionary fixation of actively expressed functional helicases of viral origin in insect retrotransposons as genetic elements advantageous for both transposons and their insect hosts.
format: application/pdf
format: text/html
creator: Sergey Y. Morozov
creator: Ekaterina A. Lazareva
creator: Andrey G. Solovyev
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.3673
publisher: PeerJ Inc.
rights: © 2017 Morozov et al.
abstract: Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by transposons of TRAS and Jockey families represented separate brunches in a phylogenetic tree of helicase domains and thus could be considered as independently originated in the evolution of insect transposons. Transcriptome database analyses revealed that both TRAS and Jockey transposons encoding the helicase domain represented transcribed genome sequences. Moreover, the transposon-encoded helicases were found to contain the full set of conserved motifs essential for their enzymatic activities. Taking into account the previously reported ability of RNA helicase encoded by TRAS ORF2 to suppress post-transcriptional RNA silencing, we propose possible scenarios of evolutionary fixation of actively expressed functional helicases of viral origin in insect retrotransposons as genetic elements advantageous for both transposons and their insect hosts.
bibliographic citation: Morozov et al. (2017) RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages. PeerJ 5:e3673 https://doi.org/10.7717/peerj.3673
date submitted: 2017-06-29
date accepted: 2017-07-21
issued: 2017-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morozov
  given name: Sergey Y.
author list: Agent
  family name: Lazareva
  given name: Ekaterina A.
author list: Agent
  family name: Solovyev
  given name: Andrey G.
doi: 10.7717/peerj.3673
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-16
copyright: ©2017 Morozov et al.
attribution name: Morozov et al.

Changes in zooplankton community, and seston and zooplankton fatty acid profiles at the freshwater/saltwater interface of the Chowan River, North Carolina
type: item
type: AcademicArticle
description: The variability in zooplankton fatty acid composition may be an indicator of larval fish habitat quality as fatty acids are linked to fish larval growth and survival. We sampled an anadromous fish nursery, the Chowan River, during spring of 2013 in order to determine how the seston fatty acid composition varied in comparison with the zooplankton community composition and fatty acid composition during the period of anadromous larval fish residency. The seston fatty acid profiles showed no distinct pattern in relation to sampling time or location. The mesozooplankton community composition varied spatially and the fatty acid profiles were typical of freshwater species in April. The Chowan River experienced a saltwater intrusion event during May, which resulted in brackish water species dominating the zooplankton community and the fatty acid profile showed an increase in polyunsaturated fatty acids (PUFA), in particular eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The saltwater intrusion event was followed by an influx of freshwater due to high precipitation levels in June. The zooplankton community composition once again became dominated by freshwater species and the fatty acid profiles shifted to reflect this change; however, EPA levels remained high, particularly in the lower river. We found correlations between the seston, microzooplankton and mesozooplankton fatty acid compositions. Salinity was the main factor correlated to the observed pattern in species composition, and fatty acid changes in the mesozooplankton. These data suggest that anadromous fish nursery habitat likely experiences considerable spatial variability in fatty acid profiles of zooplankton prey and that are correlated to seston community composition and hydrodynamic changes. Our results also suggest that sufficient prey density as well as a diverse fatty acid composition is present in the Chowan River to support larval fish production.
format: application/pdf
format: text/html
creator: Deborah A. Lichti
creator: Jacques Rinchard
creator: David G. Kimmel
subject: Aquaculture, Fisheries and Fish Science
subject: Biochemistry
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.3667
publisher: PeerJ Inc.
rights: © 2017 Lichti et al.
abstract: The variability in zooplankton fatty acid composition may be an indicator of larval fish habitat quality as fatty acids are linked to fish larval growth and survival. We sampled an anadromous fish nursery, the Chowan River, during spring of 2013 in order to determine how the seston fatty acid composition varied in comparison with the zooplankton community composition and fatty acid composition during the period of anadromous larval fish residency. The seston fatty acid profiles showed no distinct pattern in relation to sampling time or location. The mesozooplankton community composition varied spatially and the fatty acid profiles were typical of freshwater species in April. The Chowan River experienced a saltwater intrusion event during May, which resulted in brackish water species dominating the zooplankton community and the fatty acid profile showed an increase in polyunsaturated fatty acids (PUFA), in particular eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The saltwater intrusion event was followed by an influx of freshwater due to high precipitation levels in June. The zooplankton community composition once again became dominated by freshwater species and the fatty acid profiles shifted to reflect this change; however, EPA levels remained high, particularly in the lower river. We found correlations between the seston, microzooplankton and mesozooplankton fatty acid compositions. Salinity was the main factor correlated to the observed pattern in species composition, and fatty acid changes in the mesozooplankton. These data suggest that anadromous fish nursery habitat likely experiences considerable spatial variability in fatty acid profiles of zooplankton prey and that are correlated to seston community composition and hydrodynamic changes. Our results also suggest that sufficient prey density as well as a diverse fatty acid composition is present in the Chowan River to support larval fish production.
bibliographic citation: Lichti et al. (2017) Changes in zooplankton community, and seston and zooplankton fatty acid profiles at the freshwater/saltwater interface of the Chowan River, North Carolina. PeerJ 5:e3667 https://doi.org/10.7717/peerj.3667
date submitted: 2017-03-15
date accepted: 2017-07-19
issued: 2017-08-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lichti
  given name: Deborah A.
author list: Agent
  family name: Rinchard
  given name: Jacques
author list: Agent
  family name: Kimmel
  given name: David G.
doi: 10.7717/peerj.3667
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-16
copyright: ©2017 Lichti et al.
attribution name: Lichti et al.

RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus
type: item
type: AcademicArticle
description: An overdominant mutation in an intron of the elongation factor 1-α (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to “sea star wasting disease”, a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences in constitutive expression of gene regions that may help explain this tolerance phenotype. Our results show that individuals carrying this mutation have lower expression at a large contingent of gene regions. Individuals without this mutation also appear to have a greater cellular response to temperature stress, which has been implicated in the outbreak of sea star wasting disease. Given the ecological significance of P. ochraceus, these results may be useful in predicting the evolutionary and demographic future for Pacific intertidal communities.
format: application/pdf
format: text/html
creator: V. Katelyn Chandler
creator: John P. Wares
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.3696
publisher: PeerJ Inc.
rights: © 2017 Chandler Wares
abstract: An overdominant mutation in an intron of the elongation factor 1-α (EF1A) gene in the sea star Pisaster ochraceus has shown itself to mediate tolerance to “sea star wasting disease”, a pandemic that has significantly reduced sea star populations on the Pacific coast of North America. Here we use RNA sequencing of healthy individuals to identify differences in constitutive expression of gene regions that may help explain this tolerance phenotype. Our results show that individuals carrying this mutation have lower expression at a large contingent of gene regions. Individuals without this mutation also appear to have a greater cellular response to temperature stress, which has been implicated in the outbreak of sea star wasting disease. Given the ecological significance of P. ochraceus, these results may be useful in predicting the evolutionary and demographic future for Pacific intertidal communities.
bibliographic citation: Chandler et al. (2017) RNA expression and disease tolerance are associated with a “keystone mutation” in the ochre sea star Pisaster ochraceus. PeerJ 5:e3696 https://doi.org/10.7717/peerj.3696
date submitted: 2017-05-23
date accepted: 2017-07-26
issued: 2017-08-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chandler
  given name: V. Katelyn
author list: Agent
  family name: Wares
  given name: John P.
doi: 10.7717/peerj.3696
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-15
copyright: ©2017 Chandler and Wares
attribution name: Chandler Wares

Germination of dimorphic seeds of Suaeda aralocaspica in response to light and salinity conditions during and after cold stratification
type: item
type: AcademicArticle
description: Cold stratification is a requirement for seed dormancy breaking in many species, and thus it is one of the important factors for the regulation of timing of germination. However, few studies have examined the influence of various environmental conditions during cold stratification on subsequent germination, and no study has compared such effects on the performance of dormant versus non-dormant seeds. Seeds of halophytes in the cold desert might experience different light and salinity conditions during and after cold stratification. As such, dimorphic seeds (non-dormant brown seeds and black seeds with non-deep physiological dormancy) of Suaeda aralocaspica were cold stratified under different light (12 h light–12 h darkness photoperiod or continuous darkness) or salinity (0, 200 or 1,000 mmol L-1 NaCl) conditions for 20 or 40 days. Then stratified seeds were incubated under different light or salinity conditions at daily (12/12 h) temperature regime of 10:25 °C for 20 days. For brown seeds, cold stratification was also part of the germination period. In contrast, almost no black seeds germinated during cold stratification. The longer the cold stratification, the better the subsequent germination of black seeds, regardless of light or salinity conditions. Light did not influence germination of brown seeds. Germination of cold-stratified black seeds was inhibited by darkness, especially when they were stratified in darkness. With an increase in salinity at the stage of cold stratification or germination, germination percentages of both seed morphs decreased. Combinational pre-treatments of cold stratification and salinity did not increase salt tolerance of dimorphic seeds in germination phase. Thus, light and salinity conditions during cold stratification partly interact with these conditions during germination stage and differentially affect germination of dimorphic seeds of S. aralocaspica.
format: application/pdf
format: text/html
creator: Hong-Ling Wang
creator: Chang-Yan Tian
creator: Lei Wang
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.3671
publisher: PeerJ Inc.
rights: © 2017 Wang et al.
abstract: Cold stratification is a requirement for seed dormancy breaking in many species, and thus it is one of the important factors for the regulation of timing of germination. However, few studies have examined the influence of various environmental conditions during cold stratification on subsequent germination, and no study has compared such effects on the performance of dormant versus non-dormant seeds. Seeds of halophytes in the cold desert might experience different light and salinity conditions during and after cold stratification. As such, dimorphic seeds (non-dormant brown seeds and black seeds with non-deep physiological dormancy) of Suaeda aralocaspica were cold stratified under different light (12 h light–12 h darkness photoperiod or continuous darkness) or salinity (0, 200 or 1,000 mmol L-1 NaCl) conditions for 20 or 40 days. Then stratified seeds were incubated under different light or salinity conditions at daily (12/12 h) temperature regime of 10:25 °C for 20 days. For brown seeds, cold stratification was also part of the germination period. In contrast, almost no black seeds germinated during cold stratification. The longer the cold stratification, the better the subsequent germination of black seeds, regardless of light or salinity conditions. Light did not influence germination of brown seeds. Germination of cold-stratified black seeds was inhibited by darkness, especially when they were stratified in darkness. With an increase in salinity at the stage of cold stratification or germination, germination percentages of both seed morphs decreased. Combinational pre-treatments of cold stratification and salinity did not increase salt tolerance of dimorphic seeds in germination phase. Thus, light and salinity conditions during cold stratification partly interact with these conditions during germination stage and differentially affect germination of dimorphic seeds of S. aralocaspica.
bibliographic citation: Wang et al. (2017) Germination of dimorphic seeds of Suaeda aralocaspica in response to light and salinity conditions during and after cold stratification. PeerJ 5:e3671 https://doi.org/10.7717/peerj.3671
date submitted: 2015-01-20
date accepted: 2017-07-20
issued: 2017-08-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hong-Ling
author list: Agent
  family name: Tian
  given name: Chang-Yan
author list: Agent
  family name: Wang
  given name: Lei
doi: 10.7717/peerj.3671
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-15
copyright: ©2017 Wang et al.
attribution name: Wang et al.

Aura-biomes are present in the water layer above coral reef benthic macro-organisms
type: item
type: AcademicArticle
description: As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific “aura-biome”. The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.
format: application/pdf
format: text/html
creator: Kevin Walsh
creator: J. Matthew Haggerty
creator: Michael P. Doane
creator: John J. Hansen
creator: Megan M. Morris
creator: Ana Paula B. Moreira
creator: Louisi de Oliveira
creator: Luciana Leomil
creator: Gizele D. Garcia
creator: Fabiano Thompson
creator: Elizabeth A. Dinsdale
subject: Biodiversity
subject: Ecology
subject: Genomics
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.3666
publisher: PeerJ Inc.
rights: © 2017 Walsh et al.
abstract: As coral reef habitats decline worldwide, some reefs are transitioning from coral- to algal-dominated benthos with the exact cause for this shift remaining elusive. Increases in the abundance of microbes in the water column has been correlated with an increase in coral disease and reduction in coral cover. Here we investigated how multiple reef organisms influence microbial communities in the surrounding water column. Our study consisted of a field assessment of microbial communities above replicate patches dominated by a single macro-organism. Metagenomes were constructed from 20 L of water above distinct macro-organisms, including (1) the coral Mussismilia braziliensis, (2) fleshy macroalgae (Stypopodium, Dictota and Canistrocarpus), (3) turf algae, and (4) the zoanthid Palythoa caribaeorum and were compared to the water microbes collected 3 m above the reef. Microbial genera and functional potential were annotated using MG-RAST and showed that the dominant benthic macro-organisms influence the taxa and functions of microbes in the water column surrounding them, developing a specific “aura-biome”. The coral aura-biome reflected the open water column, and was associated with Synechococcus and functions suggesting oligotrophic growth, while the fleshy macroalgae aura-biome was associated with Ruegeria, Pseudomonas, and microbial functions suggesting low oxygen conditions. The turf algae aura-biome was associated with Vibrio, Flavobacterium, and functions suggesting pathogenic activity, while zoanthids were associated with Alteromonas and functions suggesting a stressful environment. Because each benthic organism has a distinct aura-biome, a change in benthic cover will change the microbial community of the water, which may lead to either the stimulation or suppression of the recruitment of benthic organisms.
bibliographic citation: Walsh et al. (2017) Aura-biomes are present in the water layer above coral reef benthic macro-organisms. PeerJ 5:e3666 https://doi.org/10.7717/peerj.3666
date submitted: 2016-10-17
date accepted: 2017-07-19
issued: 2017-08-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Walsh
  given name: Kevin
author list: Agent
  family name: Haggerty
  given name: J. Matthew
author list: Agent
  family name: Doane
  given name: Michael P.
author list: Agent
  family name: Hansen
  given name: John J.
author list: Agent
  family name: Morris
  given name: Megan M.
author list: Agent
  family name: Moreira
  given name: Ana Paula B.
author list: Agent
  family name: de Oliveira
  given name: Louisi
author list: Agent
  family name: Leomil
  given name: Luciana
author list: Agent
  family name: Garcia
  given name: Gizele D.
author list: Agent
  family name: Thompson
  given name: Fabiano
author list: Agent
  family name: Dinsdale
  given name: Elizabeth A.
doi: 10.7717/peerj.3666
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-15
copyright: ©2017 Walsh et al.
attribution name: Walsh et al.

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