PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Exploring the socio-emotional factors associated with subjective well-being in the unemployed
items: Effects of elevated CO2 on predator avoidance behaviour by reef fishes is not altered by experimental test water
items: Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment
items: Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions
items: Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator
items: Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda)
items: The ethnobotany of psychoactive plant use: a phylogenetic perspective
items: A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
items: Antibacterial and anti-adherence effects of a plant extract mixture (PEM) and its individual constituent extracts (Psidium sp., Mangifera sp., and Mentha sp.) on single- and dual-species biofilms
items: Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae

Exploring the socio-emotional factors associated with subjective well-being in the unemployed
type: item
type: AcademicArticle
description: In this study, we examined the relations between dimensions of Perceived Emotional Intelligence (PEI) and classic constructs, such as social support, on depression, stress, and subjective well-being indicators (life satisfaction and happiness). The study also sought to determine whether PEI dimensions accounted for a significant portion of the variance beyond that of classic constructs in the study of depression, stress, and well-being outcomes in a sample of 442 unemployed subjects. Results indicated that social support and all PEI dimensions are found to be significant and negatively related to depression and stress, and these variables were also found to be significant and positively associated with life satisfaction and happiness. Additionally, results using regression analysis indicated that PEI, and specifically use of emotions and regulation of emotions, explain a significant amount of the variance of all outcomes after controlling for socio-demographics and social support dimensions. Finally, theoretical and practical implications of these constructs and their relation with psychological adjustment and well-being in unemployed people are discussed.
format: application/pdf
format: text/html
creator: M. Pilar Berrios
creator: Natalio Extremera
creator: M. Pilar Nieto-Flores
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.2506
publisher: PeerJ Inc.
rights: © 2016 Berrios et al.
abstract: In this study, we examined the relations between dimensions of Perceived Emotional Intelligence (PEI) and classic constructs, such as social support, on depression, stress, and subjective well-being indicators (life satisfaction and happiness). The study also sought to determine whether PEI dimensions accounted for a significant portion of the variance beyond that of classic constructs in the study of depression, stress, and well-being outcomes in a sample of 442 unemployed subjects. Results indicated that social support and all PEI dimensions are found to be significant and negatively related to depression and stress, and these variables were also found to be significant and positively associated with life satisfaction and happiness. Additionally, results using regression analysis indicated that PEI, and specifically use of emotions and regulation of emotions, explain a significant amount of the variance of all outcomes after controlling for socio-demographics and social support dimensions. Finally, theoretical and practical implications of these constructs and their relation with psychological adjustment and well-being in unemployed people are discussed.
bibliographic citation: Berrios et al. (2016) Exploring the socio-emotional factors associated with subjective well-being in the unemployed. PeerJ 4:e2506 https://doi.org/10.7717/peerj.2506
date submitted: 2016-06-08
date accepted: 2016-08-30
issued: 2016-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berrios
  given name: M. Pilar
author list: Agent
  family name: Extremera
  given name: Natalio
author list: Agent
  family name: Nieto-Flores
  given name: M. Pilar
doi: 10.7717/peerj.2506
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-06
copyright: © 2016 Berrios et al.
attribution name: Berrios et al.

Effects of elevated CO2 on predator avoidance behaviour by reef fishes is not altered by experimental test water
type: item
type: AcademicArticle
description: Pioneering studies into the effects of elevated CO2 on the behaviour of reef fishes often tested high-CO2 reared fish using control water in the test arena. While subsequent studies using rearing treatment water (control or high CO2) in the test arena have confirmed the effects of high CO2 on a range of reef fish behaviours, a further investigation into the use of different test water in the experimental arena is warranted. Here, we used a fully factorial design to test the effect of rearing treatment water (control or high CO2) and experimental test water (control or high CO2) on antipredator responses of larval reef fishes. We tested antipredator behaviour in larval clownfish Amphiprion percula and ambon damselfish Pomacentrus amboinensis, two species that have been used in previous high CO2 experiments. Specifically, we tested if: (1) using control or high CO2 water in a two channel flume influenced the response of larval clownfish to predator odour; and (2) using control or high CO2 water in the test arena influenced the escape response of larval damselfish to a startle stimulus. Finally, (3) because the effects of high CO2 on fish behaviour appear to be caused by altered function of the GABA-A neurotransmitter we tested if antipredator behaviours were restored in clownfish treated with a GABA antagonist (gabazine) in high CO2 water. Larval clownfish reared from hatching in control water (496 µatm) strongly avoided predator cue whereas larval clownfish reared from hatching in high CO2 (1,022 µatm) were attracted to the predator cue, as has been reported in previous studies. There was no effect on fish responses of using either control or high CO2 water in the flume. Larval damselfish reared for four days in high CO2 (1,051 µatm) exhibited a slower response to a startle stimulus and slower escape speed compared with fish reared in control conditions (464 µatm). There was no effect of test water on escape responses. Treatment of high-CO2 reared clownfish with 4 mg…
format: application/pdf
format: text/html
creator: Philip L. Munday
creator: Megan J. Welch
creator: Bridie J.M. Allan
creator: Sue-Ann Watson
creator: Shannon J. McMahon
creator: Mark I. McCormick
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.2501
publisher: PeerJ Inc.
rights: © 2016 Munday et al.
abstract: Pioneering studies into the effects of elevated CO2 on the behaviour of reef fishes often tested high-CO2 reared fish using control water in the test arena. While subsequent studies using rearing treatment water (control or high CO2) in the test arena have confirmed the effects of high CO2 on a range of reef fish behaviours, a further investigation into the use of different test water in the experimental arena is warranted. Here, we used a fully factorial design to test the effect of rearing treatment water (control or high CO2) and experimental test water (control or high CO2) on antipredator responses of larval reef fishes. We tested antipredator behaviour in larval clownfish Amphiprion percula and ambon damselfish Pomacentrus amboinensis, two species that have been used in previous high CO2 experiments. Specifically, we tested if: (1) using control or high CO2 water in a two channel flume influenced the response of larval clownfish to predator odour; and (2) using control or high CO2 water in the test arena influenced the escape response of larval damselfish to a startle stimulus. Finally, (3) because the effects of high CO2 on fish behaviour appear to be caused by altered function of the GABA-A neurotransmitter we tested if antipredator behaviours were restored in clownfish treated with a GABA antagonist (gabazine) in high CO2 water. Larval clownfish reared from hatching in control water (496 µatm) strongly avoided predator cue whereas larval clownfish reared from hatching in high CO2 (1,022 µatm) were attracted to the predator cue, as has been reported in previous studies. There was no effect on fish responses of using either control or high CO2 water in the flume. Larval damselfish reared for four days in high CO2 (1,051 µatm) exhibited a slower response to a startle stimulus and slower escape speed compared with fish reared in control conditions (464 µatm). There was no effect of test water on escape responses. Treatment of high-CO2 reared clownfish with 4 mg…
bibliographic citation: Munday et al. (2016) Effects of elevated CO2 on predator avoidance behaviour by reef fishes is not altered by experimental test water. PeerJ 4:e2501 https://doi.org/10.7717/peerj.2501
date submitted: 2016-07-05
date accepted: 2016-08-29
issued: 2016-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Munday
  given name: Philip L.
author list: Agent
  family name: Welch
  given name: Megan J.
author list: Agent
  family name: Allan
  given name: Bridie J.M.
author list: Agent
  family name: Watson
  given name: Sue-Ann
author list: Agent
  family name: McMahon
  given name: Shannon J.
author list: Agent
  family name: McCormick
  given name: Mark I.
doi: 10.7717/peerj.2501
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-06
copyright: ©2016 Munday et al.
attribution name: Munday et al.

Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment
type: item
type: AcademicArticle
description: Methanesulfonic acid (MSA) is a relevant intermediate of the biogeochemical cycle of sulfur and environmental microorganisms assume an important role in the mineralization of this compound. Several methylotrophic bacterial strains able to grow on MSA have been isolated from soil or marine water and two conserved operons, msmABCD coding for MSA monooxygenase and msmEFGH coding for a transport system, have been repeatedly encountered in most of these strains. Homologous sequences have also been amplified directly from the environment or observed in marine metagenomic data, but these showed a base composition (G + C content) very different from their counterparts from cultivated bacteria. The aim of this study was to understand which microorganisms within the coastal surface oceanic microflora responded to MSA as a nutrient and how the community evolved in the early phases of an enrichment by means of metagenome and gene-targeted amplicon sequencing. From the phylogenetic point of view, the community shifted significantly with the disappearance of all signals related to the Archaea, the Pelagibacteraceae and phylum SAR406, and the increase in methylotroph-harboring taxa, accompanied by other groups so far not known to comprise methylotrophs such as the Hyphomonadaceae. At the functional level, the abundance of several genes related to sulfur metabolism and methylotrophy increased during the enrichment and the allelic distribution of gene msmA diagnostic for MSA monooxygenase altered considerably. Even more dramatic was the disappearance of MSA import-related gene msmE, which suggests that alternative transporters must be present in the enriched community and illustrate the inadequacy of msmE as an ecofunctional marker for MSA degradation at sea.
format: application/pdf
format: text/html
creator: Ana C. Henriques
creator: Rui M.S. Azevedo
creator: Paolo De Marco
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.2498
publisher: PeerJ Inc.
rights: © 2016 Henriques et al.
abstract: Methanesulfonic acid (MSA) is a relevant intermediate of the biogeochemical cycle of sulfur and environmental microorganisms assume an important role in the mineralization of this compound. Several methylotrophic bacterial strains able to grow on MSA have been isolated from soil or marine water and two conserved operons, msmABCD coding for MSA monooxygenase and msmEFGH coding for a transport system, have been repeatedly encountered in most of these strains. Homologous sequences have also been amplified directly from the environment or observed in marine metagenomic data, but these showed a base composition (G + C content) very different from their counterparts from cultivated bacteria. The aim of this study was to understand which microorganisms within the coastal surface oceanic microflora responded to MSA as a nutrient and how the community evolved in the early phases of an enrichment by means of metagenome and gene-targeted amplicon sequencing. From the phylogenetic point of view, the community shifted significantly with the disappearance of all signals related to the Archaea, the Pelagibacteraceae and phylum SAR406, and the increase in methylotroph-harboring taxa, accompanied by other groups so far not known to comprise methylotrophs such as the Hyphomonadaceae. At the functional level, the abundance of several genes related to sulfur metabolism and methylotrophy increased during the enrichment and the allelic distribution of gene msmA diagnostic for MSA monooxygenase altered considerably. Even more dramatic was the disappearance of MSA import-related gene msmE, which suggests that alternative transporters must be present in the enriched community and illustrate the inadequacy of msmE as an ecofunctional marker for MSA degradation at sea.
bibliographic citation: Henriques et al. (2016) Metagenomic survey of methanesulfonic acid (MSA) catabolic genes in an Atlantic Ocean surface water sample and in a partial enrichment. PeerJ 4:e2498 https://doi.org/10.7717/peerj.2498
date submitted: 2016-02-06
date accepted: 2016-08-28
issued: 2016-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Henriques
  given name: Ana C.
author list: Agent
  family name: Azevedo
  given name: Rui M.S.
author list: Agent
  family name: De Marco
  given name: Paolo
doi: 10.7717/peerj.2498
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-06
copyright: ©2016 Henriques et al.
attribution name: Henriques et al.

Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions
type: item
type: AcademicArticle
description: Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models). Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude) were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species) and taxonomy (amphibians and reptiles). Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural parks.
format: application/pdf
format: text/html
creator: Alberto Muñoz
creator: Xavier Santos
creator: Ángel M. Felicísimo
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.2405
publisher: PeerJ Inc.
rights: © 2016 Muñoz et al.
abstract: Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models). Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude) were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species) and taxonomy (amphibians and reptiles). Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural parks.
bibliographic citation: Muñoz et al. (2016) Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions. PeerJ 4:e2405 https://doi.org/10.7717/peerj.2405
date submitted: 2016-02-23
date accepted: 2016-08-03
issued: 2016-10-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muñoz
  given name: Alberto
author list: Agent
  family name: Santos
  given name: Xavier
author list: Agent
  family name: Felicísimo
  given name: Ángel M.
doi: 10.7717/peerj.2405
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-06
copyright: ©2016 Muñoz et al.
attribution name: Muñoz et al.

Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator
type: item
type: AcademicArticle
description: Background Talitrus saltator is an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean. T. saltator exhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species. Methods We harvested brain tissue from animals expressing robust circadian activity rhythms and used homology cloning and Illumina RNAseq approaches to sequence and identify the core circadian clock and clock-related genes in these samples. We assessed the temporal expression of these genes in time-course samples from rhythmic animals using RNAseq. Results We identified a comprehensive suite of circadian clock gene homologues in T. saltator including the ‘core’ clock genes period (Talper), cryptochrome 2 (Talcry2), timeless (Taltim), clock (Talclk), and bmal1 (Talbmal1). In addition we describe the sequence and putative structures of 23 clock-associated genes including two unusual, extended isoforms of pigment dispersing hormone (Talpdh). We examined time-course RNAseq expression data, derived from tissues harvested from behaviourally rhythmic animals, to reveal rhythmic expression of these genes with approximately circadian period in Talper and Talbmal1. Of the clock-related genes, casein kinase IIβ (TalckIIβ), ebony (Talebony), jetlag (Taljetlag), pigment dispensing hormone (Talpdh), protein phosphatase 1 (Talpp1), shaggy (Talshaggy), sirt1 (Talsirt1), sirt7 (Talsirt7) and supernumerary limbs (Talslimb) show temporal changes in expression. Discussion We report the sequences of principle genes that comprise the circadian clock of T. saltator and highlight the conserved structural and functional domains of their deduced cognate proteins. Our sequencing data …
format: application/pdf
format: text/html
creator: Joseph F. O’Grady
creator: Laura S. Hoelters
creator: Martin T. Swain
creator: David C. Wilcockson
subject: Animal Behavior
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.2555
publisher: PeerJ Inc.
rights: © 2016 O’Grady et al.
abstract: Background Talitrus saltator is an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean. T. saltator exhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species. Methods We harvested brain tissue from animals expressing robust circadian activity rhythms and used homology cloning and Illumina RNAseq approaches to sequence and identify the core circadian clock and clock-related genes in these samples. We assessed the temporal expression of these genes in time-course samples from rhythmic animals using RNAseq. Results We identified a comprehensive suite of circadian clock gene homologues in T. saltator including the ‘core’ clock genes period (Talper), cryptochrome 2 (Talcry2), timeless (Taltim), clock (Talclk), and bmal1 (Talbmal1). In addition we describe the sequence and putative structures of 23 clock-associated genes including two unusual, extended isoforms of pigment dispersing hormone (Talpdh). We examined time-course RNAseq expression data, derived from tissues harvested from behaviourally rhythmic animals, to reveal rhythmic expression of these genes with approximately circadian period in Talper and Talbmal1. Of the clock-related genes, casein kinase IIβ (TalckIIβ), ebony (Talebony), jetlag (Taljetlag), pigment dispensing hormone (Talpdh), protein phosphatase 1 (Talpp1), shaggy (Talshaggy), sirt1 (Talsirt1), sirt7 (Talsirt7) and supernumerary limbs (Talslimb) show temporal changes in expression. Discussion We report the sequences of principle genes that comprise the circadian clock of T. saltator and highlight the conserved structural and functional domains of their deduced cognate proteins. Our sequencing data …
bibliographic citation: O’Grady et al. (2016) Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator. PeerJ 4:e2555 https://doi.org/10.7717/peerj.2555
date submitted: 2016-07-08
date accepted: 2016-09-11
issued: 2016-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: O’Grady
  given name: Joseph F.
author list: Agent
  family name: Hoelters
  given name: Laura S.
author list: Agent
  family name: Swain
  given name: Martin T.
author list: Agent
  family name: Wilcockson
  given name: David C.
doi: 10.7717/peerj.2555
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-05
copyright: ©2016 O’Grady et al.
attribution name: O’Grady et al.

Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda)
type: item
type: AcademicArticle
description: We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10−5 per site per year or μ = 1.99 × 10−4 mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne = 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.
format: application/pdf
format: text/html
creator: Séverine Fourdrilis
creator: Patrick Mardulyn
creator: Olivier J. Hardy
creator: Kurt Jordaens
creator: António Manuel de Frias Martins
creator: Thierry Backeljau
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.2549
publisher: PeerJ Inc.
rights: © 2016 Fourdrilis et al.
abstract: We report the presence of mitochondrial DNA (mtDNA) hyperdiversity in the marine periwinkle Melarhaphe neritoides (Linnaeus, 1758), the first such case among marine gastropods. Our dataset consisted of concatenated 16S-COI-Cytb gene fragments. We used Bayesian analyses to investigate three putative causes underlying genetic variation, and estimated the mtDNA mutation rate, possible signatures of selection and the effective population size of the species in the Azores archipelago. The mtDNA hyperdiversity in M. neritoides is characterized by extremely high haplotype diversity (Hd = 0.999 ± 0.001), high nucleotide diversity (π = 0.013 ± 0.001), and neutral nucleotide diversity above the threshold of 5% (πsyn = 0.0677). Haplotype richness is very high even at spatial scales as small as 100m2. Yet, mtDNA hyperdiversity does not affect the ability of DNA barcoding to identify M. neritoides. The mtDNA hyperdiversity in M. neritoides is best explained by the remarkably high mutation rate at the COI locus (μ = 5.82 × 10−5 per site per year or μ = 1.99 × 10−4 mutations per nucleotide site per generation), whereas the effective population size of this planktonic-dispersing species is surprisingly small (Ne = 5, 256; CI = 1,312–3,7495) probably due to the putative influence of selection. Comparison with COI nucleotide diversity values in other organisms suggests that mtDNA hyperdiversity may be more frequently linked to high μ values and that mtDNA hyperdiversity may be more common across other phyla than currently appreciated.
bibliographic citation: Fourdrilis et al. (2016) Mitochondrial DNA hyperdiversity and its potential causes in the marine periwinkle Melarhaphe neritoides (Mollusca: Gastropoda). PeerJ 4:e2549 https://doi.org/10.7717/peerj.2549
date submitted: 2016-06-23
date accepted: 2016-09-12
issued: 2016-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fourdrilis
  given name: Séverine
author list: Agent
  family name: Mardulyn
  given name: Patrick
author list: Agent
  family name: Hardy
  given name: Olivier J.
author list: Agent
  family name: Jordaens
  given name: Kurt
author list: Agent
  family name: de Frias Martins
  given name: António Manuel
author list: Agent
  family name: Backeljau
  given name: Thierry
doi: 10.7717/peerj.2549
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-05
copyright: ©2016 Fourdrilis et al.
attribution name: Fourdrilis et al.

The ethnobotany of psychoactive plant use: a phylogenetic perspective
type: item
type: AcademicArticle
description: Psychoactive plants contain chemicals that presumably evolved as allelochemicals but target certain neuronal receptors when consumed by humans, altering perception, emotion and cognition. These plants have been used since ancient times as medicines and in the context of religious rituals for their various psychoactive effects (e.g., as hallucinogens, stimulants, sedatives). The ubiquity of psychoactive plants in various cultures motivates investigation of the commonalities among these plants, in which a phylogenetic framework may be insightful. A phylogeny of culturally diverse psychoactive plant taxa was constructed with their psychotropic effects and affected neurotransmitter systems mapped on the phylogeny. The phylogenetic distribution shows multiple evolutionary origins of psychoactive families. The plant families Myristicaceae (e.g., nutmeg), Papaveraceae (opium poppy), Cactaceae (peyote), Convolvulaceae (morning glory), Solanaceae (tobacco), Lamiaceae (mints), Apocynaceae (dogbane) have a disproportionate number of psychoactive genera with various indigenous groups using geographically disparate members of these plant families for the same psychoactive effect, an example of cultural convergence. Pharmacological traits related to hallucinogenic and sedative potential are phylogenetically conserved within families. Unrelated families that exert similar psychoactive effects also modulate similar neurotransmitter systems (i.e., mechanistic convergence). However, pharmacological mechanisms for stimulant effects were varied even within families suggesting that stimulant chemicals may be more evolutionarily labile than those associated with hallucinogenic and sedative effects. Chemically similar psychoactive chemicals may also exist in phylogenetically unrelated lineages, suggesting convergent evolution or differential gene regulation of a common metabolic pathway. Our study has shown that phylogenetic analysis of traditionally used psychoactive plants suggests mult…
format: application/pdf
format: text/html
creator: Nashmiah Aid Alrashedy
creator: Jeanmaire Molina
subject: Anthropology
subject: Biodiversity
subject: Evolutionary Studies
subject: Neuroscience
subject: Plant Science
description: doi:10.7717/peerj.2546
publisher: PeerJ Inc.
rights: © 2016 Alrashedy and Molina
abstract: Psychoactive plants contain chemicals that presumably evolved as allelochemicals but target certain neuronal receptors when consumed by humans, altering perception, emotion and cognition. These plants have been used since ancient times as medicines and in the context of religious rituals for their various psychoactive effects (e.g., as hallucinogens, stimulants, sedatives). The ubiquity of psychoactive plants in various cultures motivates investigation of the commonalities among these plants, in which a phylogenetic framework may be insightful. A phylogeny of culturally diverse psychoactive plant taxa was constructed with their psychotropic effects and affected neurotransmitter systems mapped on the phylogeny. The phylogenetic distribution shows multiple evolutionary origins of psychoactive families. The plant families Myristicaceae (e.g., nutmeg), Papaveraceae (opium poppy), Cactaceae (peyote), Convolvulaceae (morning glory), Solanaceae (tobacco), Lamiaceae (mints), Apocynaceae (dogbane) have a disproportionate number of psychoactive genera with various indigenous groups using geographically disparate members of these plant families for the same psychoactive effect, an example of cultural convergence. Pharmacological traits related to hallucinogenic and sedative potential are phylogenetically conserved within families. Unrelated families that exert similar psychoactive effects also modulate similar neurotransmitter systems (i.e., mechanistic convergence). However, pharmacological mechanisms for stimulant effects were varied even within families suggesting that stimulant chemicals may be more evolutionarily labile than those associated with hallucinogenic and sedative effects. Chemically similar psychoactive chemicals may also exist in phylogenetically unrelated lineages, suggesting convergent evolution or differential gene regulation of a common metabolic pathway. Our study has shown that phylogenetic analysis of traditionally used psychoactive plants suggests mult…
bibliographic citation: Alrashedy et al. (2016) The ethnobotany of psychoactive plant use: a phylogenetic perspective. PeerJ 4:e2546 https://doi.org/10.7717/peerj.2546
date submitted: 2016-06-28
date accepted: 2016-09-09
issued: 2016-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alrashedy
  given name: Nashmiah Aid
author list: Agent
  family name: Molina
  given name: Jeanmaire
doi: 10.7717/peerj.2546
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-05
copyright: ©2016 Alrashedy and Molina
attribution name: Alrashedy and Molina

A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense)
type: item
type: AcademicArticle
description: Background Understanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients. Methods To better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn, Macrobrachium australiense using Illumina deep sequencing technology. This species was targeted because it can complete its life cycle totally in freshwater but, like many Macrobrachium sp., can also tolerate brackish water conditions and hence should have genes associated with tolerance of both FW and saline conditions. Results We obtained between 55.4 and 65.2 million Illumina read pairs from four cDNA libraries. Overall, paired end sequences assembled into a total of 125,196 non-redundant contigs (≥200 bp) with an N50 length of 2,282 bp and an average contig length of 968 bp. Transcriptomic analysis of M. australiense identified 32 different gene families that were potentially involved with osmoregulatory capacity. A total of 32,597 transcripts were specified with gene ontology (GO) terms identified on the basis of GO categories. Abundance estimation of expressed genes based on TPM (transcript per million) ≥20 showed 1625 transcripts commonly expressed in all four libraries. Among the top 10 …
format: application/pdf
format: text/html
creator: Azam Moshtaghi
creator: Md. Lifat Rahi
creator: Viet Tuan Nguyen
creator: Peter B. Mather
creator: David A. Hurwood
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.2520
publisher: PeerJ Inc.
rights: © 2016 Moshtaghi et al.
abstract: Background Understanding the genomic basis of osmoregulation (candidate genes and/or molecular mechanisms controlling the phenotype) addresses one of the fundamental questions in evolutionary ecology. Species distributions and adaptive radiations are thought to be controlled by environmental salinity levels, and efficient osmoregulatory (ionic balance) ability is the main mechanism to overcome the problems related to environmental salinity gradients. Methods To better understand how osmoregulatory performance in freshwater (FW) crustaceans allow individuals to acclimate and adapt to raised salinity conditions, here we (i), reviewed the literature on genes that have been identified to be associated with osmoregulation in FW crustaceans, and (ii), performed a transcriptomic analysis using cDNA libraries developed from mRNA isolated from three important osmoregulatory tissues (gill, antennal gland, hepatopancreas) and total mRNA from post larvae taken from the freshwater prawn, Macrobrachium australiense using Illumina deep sequencing technology. This species was targeted because it can complete its life cycle totally in freshwater but, like many Macrobrachium sp., can also tolerate brackish water conditions and hence should have genes associated with tolerance of both FW and saline conditions. Results We obtained between 55.4 and 65.2 million Illumina read pairs from four cDNA libraries. Overall, paired end sequences assembled into a total of 125,196 non-redundant contigs (≥200 bp) with an N50 length of 2,282 bp and an average contig length of 968 bp. Transcriptomic analysis of M. australiense identified 32 different gene families that were potentially involved with osmoregulatory capacity. A total of 32,597 transcripts were specified with gene ontology (GO) terms identified on the basis of GO categories. Abundance estimation of expressed genes based on TPM (transcript per million) ≥20 showed 1625 transcripts commonly expressed in all four libraries. Among the top 10 …
bibliographic citation: Moshtaghi et al. (2016) A transcriptomic scan for potential candidate genes involved in osmoregulation in an obligate freshwater palaemonid prawn (Macrobrachium australiense). PeerJ 4:e2520 https://doi.org/10.7717/peerj.2520
date submitted: 2016-06-21
date accepted: 2016-09-02
issued: 2016-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moshtaghi
  given name: Azam
author list: Agent
  family name: Rahi
  given name: Md. Lifat
author list: Agent
  family name: Nguyen
  given name: Viet Tuan
author list: Agent
  family name: Mather
  given name: Peter B.
author list: Agent
  family name: Hurwood
  given name: David A.
doi: 10.7717/peerj.2520
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-05
copyright: ©2016 Moshtaghi et al.
attribution name: Moshtaghi et al.

Antibacterial and anti-adherence effects of a plant extract mixture (PEM) and its individual constituent extracts (Psidium sp., Mangifera sp., and Mentha sp.) on single- and dual-species biofilms
type: item
type: AcademicArticle
description: Background Plant extracts mixture (PEM) and its individual constituent plant extracts(Psidium sp., Mangifera sp., Mentha sp.) are known to have an anti-adhering effect towards oral bacteria in the single-species biofilm. To date, the adhering ability of the early and late plaque colonisers (Streptococcus sanguinis and Streptococcus mutans) to PEM-treated experimental pellicle have not been investigated in dual-species biofilms. Methods Fresh leaves of these plants were used in the preparation of the respective aqueous extract decoctions. The minimum inhibitory concentration (MIC) of the extracts towards S. sanguinis ATCC BAA-1455 and S. mutans ATCC 25175 was determined using a two-fold serial microdilution method. The sum of fractional inhibitory concentration (ΣFIC) index of PEM and its constituent plant extracts was calculated using the MIC values of the plants. The minimum bactericidal concentration (MBC) of the plant extracts was also determined. The anti-adherence effect of the plant extracts (individually and mixed) was carried out by developing simulated S. sanguinis and S. mutans respectively in single- and dual-species of biofilms in the Nordini’s Artificial Mouth (NAM) model system in which the experimental pellicle was pretreated with the plant extract before bacterial inoculation. The bacterial population in the respective biofilms was quantified using ten-fold serial dilutions method and expressed as colony forming unit per ml (CFU/ml). The bacterial population was also viewed using Scanning Electron Microscope (SEM). All experiments were done in triplicate. Results The PEM compared with its respective constituent plants showed the lowest MIC towards S. sanguinis (3.81 mg/ml) and S. mutans (1.91 mg/ml) and exhibited a synergistic effect. The Psidium sp. (15.24 mg/ml) and, PEM and Psidium sp. (30.48 mg/ml) showed the lowest MBC towards S. sanguinis and S. mutans respectively. The anti-adherence effect of the PEM and its respective constituent plants (exc…
format: application/pdf
format: text/html
creator: Zaleha Shafiei
creator: Zubaidah Haji Abdul Rahim
creator: Koshy Philip
creator: Nalina Thurairajah
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.2519
publisher: PeerJ Inc.
rights: © 2016 Shafiei et al.
abstract: Background Plant extracts mixture (PEM) and its individual constituent plant extracts(Psidium sp., Mangifera sp., Mentha sp.) are known to have an anti-adhering effect towards oral bacteria in the single-species biofilm. To date, the adhering ability of the early and late plaque colonisers (Streptococcus sanguinis and Streptococcus mutans) to PEM-treated experimental pellicle have not been investigated in dual-species biofilms. Methods Fresh leaves of these plants were used in the preparation of the respective aqueous extract decoctions. The minimum inhibitory concentration (MIC) of the extracts towards S. sanguinis ATCC BAA-1455 and S. mutans ATCC 25175 was determined using a two-fold serial microdilution method. The sum of fractional inhibitory concentration (ΣFIC) index of PEM and its constituent plant extracts was calculated using the MIC values of the plants. The minimum bactericidal concentration (MBC) of the plant extracts was also determined. The anti-adherence effect of the plant extracts (individually and mixed) was carried out by developing simulated S. sanguinis and S. mutans respectively in single- and dual-species of biofilms in the Nordini’s Artificial Mouth (NAM) model system in which the experimental pellicle was pretreated with the plant extract before bacterial inoculation. The bacterial population in the respective biofilms was quantified using ten-fold serial dilutions method and expressed as colony forming unit per ml (CFU/ml). The bacterial population was also viewed using Scanning Electron Microscope (SEM). All experiments were done in triplicate. Results The PEM compared with its respective constituent plants showed the lowest MIC towards S. sanguinis (3.81 mg/ml) and S. mutans (1.91 mg/ml) and exhibited a synergistic effect. The Psidium sp. (15.24 mg/ml) and, PEM and Psidium sp. (30.48 mg/ml) showed the lowest MBC towards S. sanguinis and S. mutans respectively. The anti-adherence effect of the PEM and its respective constituent plants (exc…
bibliographic citation: Shafiei et al. (2016) Antibacterial and anti-adherence effects of a plant extract mixture (PEM) and its individual constituent extracts (Psidium sp., Mangifera sp., and Mentha sp.) on single- and dual-species biofilms. PeerJ 4:e2519 https://doi.org/10.7717/peerj.2519
date submitted: 2016-04-05
date accepted: 2016-09-02
issued: 2016-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shafiei
  given name: Zaleha
author list: Agent
  family name: Haji Abdul Rahim
  given name: Zubaidah
author list: Agent
  family name: Philip
  given name: Koshy
author list: Agent
  family name: Thurairajah
  given name: Nalina
doi: 10.7717/peerj.2519
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-05
copyright: ©2016 Shafiei et al.
attribution name: Shafiei et al.

Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae
type: item
type: AcademicArticle
description: Background The rice receptor kinase XA21 confers robust resistance to the bacterial pathogen Xanthomonas oryzaepv. oryzae(Xoo). We previously reported that XA21 is cleaved in transgenic plants overexpressing XA21 with a GFP tag (Ubi-XA21-GFP) and that the released C-terminal domain is localized to the nucleus. XA21 carries a predicted nuclear localization sequence (NLS) that directs the C-terminal domain to the nucleus in transient assays, whereas alanine substitutions in the NLS disrupt the nuclear localization. Methods To determine if the predicted NLS is required for XA21-mediated immunity in planta, we generated transgenic plants overexpressing an XA21 variant carrying the NLS with the same alanine substitutions (Ubi-XA21nls-GFP). Results Ubi-XA21nls-GFP plants displayed slightly longer lesion lengths, higher Xoobacterial populations after inoculation and lower levels of reactive oxygen species production compared with the Ubi-XA21-GFP control plants. However, the Ubi-XA21nls-GFP plants express lower levels of protein than that observed in Ubi-XA21-GFP. Discussion These results demonstrate that the predicted NLS is not required for XA21-mediated immunity.
format: application/pdf
format: text/html
creator: Tong Wei
creator: Tsung-Chi Chen
creator: Yuen Ting Ho
creator: Pamela C. Ronald
subject: Plant Science
description: doi:10.7717/peerj.2507
publisher: PeerJ Inc.
rights: © 2016 Wei et al.
abstract: Background The rice receptor kinase XA21 confers robust resistance to the bacterial pathogen Xanthomonas oryzaepv. oryzae(Xoo). We previously reported that XA21 is cleaved in transgenic plants overexpressing XA21 with a GFP tag (Ubi-XA21-GFP) and that the released C-terminal domain is localized to the nucleus. XA21 carries a predicted nuclear localization sequence (NLS) that directs the C-terminal domain to the nucleus in transient assays, whereas alanine substitutions in the NLS disrupt the nuclear localization. Methods To determine if the predicted NLS is required for XA21-mediated immunity in planta, we generated transgenic plants overexpressing an XA21 variant carrying the NLS with the same alanine substitutions (Ubi-XA21nls-GFP). Results Ubi-XA21nls-GFP plants displayed slightly longer lesion lengths, higher Xoobacterial populations after inoculation and lower levels of reactive oxygen species production compared with the Ubi-XA21-GFP control plants. However, the Ubi-XA21nls-GFP plants express lower levels of protein than that observed in Ubi-XA21-GFP. Discussion These results demonstrate that the predicted NLS is not required for XA21-mediated immunity.
bibliographic citation: Wei et al. (2016) Mutation of the rice XA21 predicted nuclear localization sequence does not affect resistance to Xanthomonas oryzae pv. oryzae. PeerJ 4:e2507 https://doi.org/10.7717/peerj.2507
date submitted: 2016-08-03
date accepted: 2016-08-30
issued: 2016-10-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Tong
author list: Agent
  family name: Chen
  given name: Tsung-Chi
author list: Agent
  family name: Ho
  given name: Yuen Ting
author list: Agent
  family name: Ronald
  given name: Pamela C.
doi: 10.7717/peerj.2507
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-10-05
copyright: ©2016 Wei et al.
attribution name: Wei et al.

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