PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Unimodal head-width distribution of the European eel (Anguilla anguilla L.) from the Zeeschelde does not support disruptive selection
items: Sexual dimorphism in the Arachnid orders
items: Genetic population structure of the pelagic mollusk Limacina helicina in the Kara Sea
items: All you can eat: the functional response of the cold-water coral Desmophyllum dianthus feeding on krill and copepods
items: Optimization of the cytogenetic protocol for Pangasianodon hypophthalmus (Sauvage, 1878) and Clarias gariepinus (Burchell, 1822)
items: A trait-based ecology to assess the acclimation of a sperm-dependent clonal fish compared to its sexual host
items: imGLAD: accurate detection and quantification of target organisms in metagenomes
items: Evaluation of soil intervention values in mine tailings in northern Chile
items: Dynamic proteomic changes in soft wheat seeds during accelerated ageing
items: Ontogenetic changes in swimming speed of silver carp, bighead carp, and grass carp larvae: implications for larval dispersal

Unimodal head-width distribution of the European eel (Anguilla anguilla L.) from the Zeeschelde does not support disruptive selection
type: item
type: AcademicArticle
description: Since the early 20th century, European eels (Anguilla anguilla L.) have been dichotomously classified into ‘narrow’ and ‘broad’ heads. These morphs are mainly considered the result of a differential food choice, with narrow heads feeding primarily on small/soft prey and broad heads on large/hard prey. Yet, such a classification implies that head-width variation follows a bimodal distribution, leading to the assumption of disruptive selection. We investigated the head morphology of 272 eels, caught over three consecutive years (2015–2017) at a single location in the Zeeschelde (Belgium). Based on our results, BIC favored a unimodal distribution, while AIC provided equal support for a unimodal and a bimodal distribution. Notably, visualization of the distributions revealed a strong overlap between the two normal distributions under the bimodal model, likely explaining the ambiguity under AIC. Consequently, it is more likely that head-width variation followed a unimodal distribution, indicating there are no disruptive selection pressures for bimodality in the Zeeschelde. As such, eels could not be divided in two distinct head-width groups. Instead, their head widths showed a continuum of narrow to broad with a normal distribution. This pattern was consistent across all maturation stages studied here.
format: application/pdf
format: text/html
creator: Pieterjan Verhelst
creator: Jens De Meyer
creator: Jan Reubens
creator: Johan Coeck
creator: Peter Goethals
creator: Tom Moens
creator: Ans Mouton
subject: Animal Behavior
subject: Developmental Biology
description: doi:10.7717/peerj.5773
publisher: PeerJ Inc.
rights: © 2018 Verhelst et al.
abstract: Since the early 20th century, European eels (Anguilla anguilla L.) have been dichotomously classified into ‘narrow’ and ‘broad’ heads. These morphs are mainly considered the result of a differential food choice, with narrow heads feeding primarily on small/soft prey and broad heads on large/hard prey. Yet, such a classification implies that head-width variation follows a bimodal distribution, leading to the assumption of disruptive selection. We investigated the head morphology of 272 eels, caught over three consecutive years (2015–2017) at a single location in the Zeeschelde (Belgium). Based on our results, BIC favored a unimodal distribution, while AIC provided equal support for a unimodal and a bimodal distribution. Notably, visualization of the distributions revealed a strong overlap between the two normal distributions under the bimodal model, likely explaining the ambiguity under AIC. Consequently, it is more likely that head-width variation followed a unimodal distribution, indicating there are no disruptive selection pressures for bimodality in the Zeeschelde. As such, eels could not be divided in two distinct head-width groups. Instead, their head widths showed a continuum of narrow to broad with a normal distribution. This pattern was consistent across all maturation stages studied here.
bibliographic citation: Verhelst et al. (2018) Unimodal head-width distribution of the European eel (Anguilla anguilla L.) from the Zeeschelde does not support disruptive selection. PeerJ 6:e5773 https://doi.org/10.7717/peerj.5773
date submitted: 2018-06-09
date accepted: 2018-09-17
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Verhelst
  given name: Pieterjan
author list: Agent
  family name: De Meyer
  given name: Jens
author list: Agent
  family name: Reubens
  given name: Jan
author list: Agent
  family name: Coeck
  given name: Johan
author list: Agent
  family name: Goethals
  given name: Peter
author list: Agent
  family name: Moens
  given name: Tom
author list: Agent
  family name: Mouton
  given name: Ans
doi: 10.7717/peerj.5773
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: ©2018 Verhelst et al.
attribution name: Verhelst et al.

Sexual dimorphism in the Arachnid orders
type: item
type: AcademicArticle
description: Sexual differences in size and shape are common across the animal kingdom. The study of sexual dimorphism (SD) can provide insight into the sexual- and natural-selection pressures experienced by males and females in different species. Arachnids are diverse, comprising over 100,000 species, and exhibit some of the more extreme forms of SD in the animal kingdom, with the males and females of some species differing dramatically in body shape and/or size. Despite this, research on arachnid SD has primarily focused on specific clades as opposed to observing traits across arachnid orders, the smallest of which have received comparatively little attention. This review provides an overview of the research to date on the trends and potential evolutionary drivers for SD and sexual size dimorphism (SSD) in individual arachnid orders, and across arachnids as a whole. The most common trends across Arachnida are female-biased SSD in total body size, male-biased SSD in relative leg length and SD in pedipalp length and shape. However, the evolution of sexually dimorphic traits within the group is difficult to elucidate due to uncertainty in arachnid phylogenetic relationships. Based on the dataset we have gathered here, we highlight gaps in our current understanding and suggest areas for future research.
format: application/pdf
format: text/html
creator: Callum J. McLean
creator: Russell J. Garwood
creator: Charlotte A. Brassey
subject: Animal Behavior
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.5751
publisher: PeerJ Inc.
rights: © 2018 McLean et al.
abstract: Sexual differences in size and shape are common across the animal kingdom. The study of sexual dimorphism (SD) can provide insight into the sexual- and natural-selection pressures experienced by males and females in different species. Arachnids are diverse, comprising over 100,000 species, and exhibit some of the more extreme forms of SD in the animal kingdom, with the males and females of some species differing dramatically in body shape and/or size. Despite this, research on arachnid SD has primarily focused on specific clades as opposed to observing traits across arachnid orders, the smallest of which have received comparatively little attention. This review provides an overview of the research to date on the trends and potential evolutionary drivers for SD and sexual size dimorphism (SSD) in individual arachnid orders, and across arachnids as a whole. The most common trends across Arachnida are female-biased SSD in total body size, male-biased SSD in relative leg length and SD in pedipalp length and shape. However, the evolution of sexually dimorphic traits within the group is difficult to elucidate due to uncertainty in arachnid phylogenetic relationships. Based on the dataset we have gathered here, we highlight gaps in our current understanding and suggest areas for future research.
bibliographic citation: McLean et al. (2018) Sexual dimorphism in the Arachnid orders. PeerJ 6:e5751 https://doi.org/10.7717/peerj.5751
date submitted: 2018-03-19
date accepted: 2018-09-14
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McLean
  given name: Callum J.
author list: Agent
  family name: Garwood
  given name: Russell J.
author list: Agent
  family name: Brassey
  given name: Charlotte A.
doi: 10.7717/peerj.5751
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: © 2018 McLean et al.
attribution name: McLean et al.

Genetic population structure of the pelagic mollusk Limacina helicina in the Kara Sea
type: item
type: AcademicArticle
description: Background Pelagic pteropods Limacina helicina are widespread and can play an important role in the food webs and in biosedimentation in Arctic and Subarctic ecosystems. Previous publications have shown differences in the genetic structure of populations of L. helicina from populations found in the Pacific Ocean and Svalbard area. Currently, there are no data on the genetic structure of L. helicina populations in the seas of the Siberian Arctic. We assessed the genetic structure of L. helicina from the Kara Sea populations and compared them with samples from around Svalbard and the North Pacific. Methods We examined genetic differences in L. helicina from three different locations in the Kara Sea via analysis of a fragment of the mitochondrial gene COI. We also compared a subset of samples with L. helicina from previous studies to find connections between populations from the Atlantic and Pacific Oceans. Results 65 individual L. helinica from the Kara Sea were sequenced to produce 19 different haplotypes. This is comparable with numbers of haplotypes found in Svalbard and Pacific samples (24 and 25, respectively). Haplotypes from different locations sampled around the Arctic and Subarctic were combined into two different groups: H1 and H2. The H2 includes sequences from the Kara Sea and Svalbard, was present only in the Atlantic sector of the Arctic. The other genetic group, H1, is widespread and found throughout all L. helicina populations. ϕ ST analyses also indicated significant genetic difference between the Atlantic and Pacific regions, but no differences between Svalbard and the Kara Sea. Discussion The obtained results support our hypothesis about genetic similarity of L. helicina populations from the Kara Sea and Svalbard: the majority of haplotypes belongs to the haplotype group H2, with the H1 group representing a minority of the haplotypes present. In contrast, in the Canadian Arctic and the Pacific Ocean only haplogroup H1 is found. The negative values o…
format: application/pdf
format: text/html
creator: Galina Anatolievna Abyzova
creator: Mikhail Aleksandrovich Nikitin
creator: Olga Vladimirovna Popova
creator: Anna Fedorovna Pasternak
subject: Biodiversity
subject: Biogeography
subject: Marine Biology
subject: Molecular Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.5709
publisher: PeerJ Inc.
rights: © 2018 Abyzova et al.
abstract: Background Pelagic pteropods Limacina helicina are widespread and can play an important role in the food webs and in biosedimentation in Arctic and Subarctic ecosystems. Previous publications have shown differences in the genetic structure of populations of L. helicina from populations found in the Pacific Ocean and Svalbard area. Currently, there are no data on the genetic structure of L. helicina populations in the seas of the Siberian Arctic. We assessed the genetic structure of L. helicina from the Kara Sea populations and compared them with samples from around Svalbard and the North Pacific. Methods We examined genetic differences in L. helicina from three different locations in the Kara Sea via analysis of a fragment of the mitochondrial gene COI. We also compared a subset of samples with L. helicina from previous studies to find connections between populations from the Atlantic and Pacific Oceans. Results 65 individual L. helinica from the Kara Sea were sequenced to produce 19 different haplotypes. This is comparable with numbers of haplotypes found in Svalbard and Pacific samples (24 and 25, respectively). Haplotypes from different locations sampled around the Arctic and Subarctic were combined into two different groups: H1 and H2. The H2 includes sequences from the Kara Sea and Svalbard, was present only in the Atlantic sector of the Arctic. The other genetic group, H1, is widespread and found throughout all L. helicina populations. ϕ ST analyses also indicated significant genetic difference between the Atlantic and Pacific regions, but no differences between Svalbard and the Kara Sea. Discussion The obtained results support our hypothesis about genetic similarity of L. helicina populations from the Kara Sea and Svalbard: the majority of haplotypes belongs to the haplotype group H2, with the H1 group representing a minority of the haplotypes present. In contrast, in the Canadian Arctic and the Pacific Ocean only haplogroup H1 is found. The negative values o…
bibliographic citation: Abyzova et al. (2018) Genetic population structure of the pelagic mollusk Limacina helicina in the Kara Sea. PeerJ 6:e5709 https://doi.org/10.7717/peerj.5709
date submitted: 2018-02-16
date accepted: 2018-09-06
issued: 2018-11-06
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abyzova
  given name: Galina Anatolievna
author list: Agent
  family name: Nikitin
  given name: Mikhail Aleksandrovich
author list: Agent
  family name: Popova
  given name: Olga Vladimirovna
author list: Agent
  family name: Pasternak
  given name: Anna Fedorovna
doi: 10.7717/peerj.5709
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-06
copyright: ©2018 Abyzova et al.
attribution name: Abyzova et al.

All you can eat: the functional response of the cold-water coral Desmophyllum dianthus feeding on krill and copepods
type: item
type: AcademicArticle
description: The feeding behavior of the cosmopolitan cold-water coral (CWC) Desmophyllum dianthus (Cnidaria: Scleractinia) is still poorly known. Its usual deep distribution restricts direct observations, and manipulative experiments are so far limited to prey that do not occur in CWC natural habitat. During a series of replicated incubations, we assessed the functional response of this coral feeding on a medium-sized copepod (Calanoides patagoniensis) and a large euphausiid (Euphausia vallentini). Corals showed a Type I functional response, where feeding rate increased linearly with prey abundance, as predicted for a tentaculate passive suspension feeder. No significant differences in feeding were found between prey items, and corals were able to attain a maximum feeding rate of 10.99 mg C h−1, which represents an ingestion of the 11.4% of the coral carbon biomass per hour. These findings suggest that D. dianthus is a generalist zooplankton predator capable of exploiting dense aggregations of zooplankton over a wide prey size-range.
format: application/pdf
format: text/html
creator: Juan Höfer
creator: Humberto E. González
creator: Jürgen Laudien
creator: Gertraud M. Schmidt
creator: Verena Häussermann
creator: Claudio Richter
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.5872
publisher: PeerJ Inc.
rights: © 2018 Höfer et al.
abstract: The feeding behavior of the cosmopolitan cold-water coral (CWC) Desmophyllum dianthus (Cnidaria: Scleractinia) is still poorly known. Its usual deep distribution restricts direct observations, and manipulative experiments are so far limited to prey that do not occur in CWC natural habitat. During a series of replicated incubations, we assessed the functional response of this coral feeding on a medium-sized copepod (Calanoides patagoniensis) and a large euphausiid (Euphausia vallentini). Corals showed a Type I functional response, where feeding rate increased linearly with prey abundance, as predicted for a tentaculate passive suspension feeder. No significant differences in feeding were found between prey items, and corals were able to attain a maximum feeding rate of 10.99 mg C h−1, which represents an ingestion of the 11.4% of the coral carbon biomass per hour. These findings suggest that D. dianthus is a generalist zooplankton predator capable of exploiting dense aggregations of zooplankton over a wide prey size-range.
bibliographic citation: Höfer et al. (2018) All you can eat: the functional response of the cold-water coral Desmophyllum dianthus feeding on krill and copepods. PeerJ 6:e5872 https://doi.org/10.7717/peerj.5872
date submitted: 2018-08-26
date accepted: 2018-10-04
issued: 2018-11-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Höfer
  given name: Juan
author list: Agent
  family name: González
  given name: Humberto E.
author list: Agent
  family name: Laudien
  given name: Jürgen
author list: Agent
  family name: Schmidt
  given name: Gertraud M.
author list: Agent
  family name: Häussermann
  given name: Verena
author list: Agent
  family name: Richter
  given name: Claudio
doi: 10.7717/peerj.5872
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-05
copyright: © 2018 Höfer et al.
attribution name: Höfer et al.

Optimization of the cytogenetic protocol for Pangasianodon hypophthalmus (Sauvage, 1878) and Clarias gariepinus (Burchell, 1822)
type: item
type: AcademicArticle
description: To obtain well spread chromosomes, the cytogenetic protocol for Pangasianodon hypophthalmus and Clarias gariepinus were optimized. This includes, the colchicine concentration (0.01%, 0.025%, 0.05%)/exposure duration (1, 3, and 5 h), hypotonic solution (distilled water or 0.075M KCl solution)/exposure duration (30 min, 1, and 2 h), the time of cell suspension preparation (at hypotonic treatment or before slide preparation) and chromosome aging period (0, 3, and 7 days in Carnoy’s fixative). In addition, the type (i.e., fin, gill or kidney) and the amount of tissue (10, 50, 100 or 150 mg) were also investigated. Regardless of the species, the result obtained showed that well-spread chromosomes could be obtained using the following optimized protocol: Juveniles are injected with 0.05% colchicine (at one ml kg−1) and allowed to swim for 3 h. Then, 50 mg of gill tissue is made into cell suspension in 0.075M KCl for 1 h. The cell suspension is treated in Carnoy’s fixative (changed three times at 20 min interval) and then aged for 3 days. Finally, chromosome slides are made and stained with 10% Giemsa for 1 h.
format: application/pdf
format: text/html
creator: Victor T. Okomoda
creator: Ivan C.C. Koh
creator: Anuar Hassan
creator: Thumronk Amornsakun
creator: Julia H.Z. Moh
creator: Sheriff Md Shahreza
subject: Aquaculture, Fisheries and Fish Science
description: doi:10.7717/peerj.5712
publisher: PeerJ Inc.
rights: © 2018 Okomoda et al.
abstract: To obtain well spread chromosomes, the cytogenetic protocol for Pangasianodon hypophthalmus and Clarias gariepinus were optimized. This includes, the colchicine concentration (0.01%, 0.025%, 0.05%)/exposure duration (1, 3, and 5 h), hypotonic solution (distilled water or 0.075M KCl solution)/exposure duration (30 min, 1, and 2 h), the time of cell suspension preparation (at hypotonic treatment or before slide preparation) and chromosome aging period (0, 3, and 7 days in Carnoy’s fixative). In addition, the type (i.e., fin, gill or kidney) and the amount of tissue (10, 50, 100 or 150 mg) were also investigated. Regardless of the species, the result obtained showed that well-spread chromosomes could be obtained using the following optimized protocol: Juveniles are injected with 0.05% colchicine (at one ml kg−1) and allowed to swim for 3 h. Then, 50 mg of gill tissue is made into cell suspension in 0.075M KCl for 1 h. The cell suspension is treated in Carnoy’s fixative (changed three times at 20 min interval) and then aged for 3 days. Finally, chromosome slides are made and stained with 10% Giemsa for 1 h.
bibliographic citation: Okomoda et al. (2018) Optimization of the cytogenetic protocol for Pangasianodon hypophthalmus (Sauvage, 1878) and Clarias gariepinus (Burchell, 1822). PeerJ 6:e5712 https://doi.org/10.7717/peerj.5712
date submitted: 2018-05-30
date accepted: 2018-09-10
issued: 2018-11-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Okomoda
  given name: Victor T.
author list: Agent
  family name: Koh
  given name: Ivan C.C.
author list: Agent
  family name: Hassan
  given name: Anuar
author list: Agent
  family name: Amornsakun
  given name: Thumronk
author list: Agent
  family name: Moh
  given name: Julia H.Z.
author list: Agent
  family name: Shahreza
  given name: Sheriff Md
doi: 10.7717/peerj.5712
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-05
copyright: © 2018 Okomoda et al.
attribution name: Okomoda et al.

A trait-based ecology to assess the acclimation of a sperm-dependent clonal fish compared to its sexual host
type: item
type: AcademicArticle
description: Background Survival in temporally or spatially changing environments is a prerequisite for the perpetuation of a given species. In addition to genetic variation, the role of epigenetic processes is crucial in the persistence of organisms. For instance, mechanisms such as developmental flexibility enable the adjustment of the phenotype of a given individual to changing conditions throughout its development. However, the extent of factors other than genetic variability, like epigenetic processes, in the production of alternative phenotype and the consequences in realized ecological niches is still unclear. Methods In this study, we compared the extent of realized niches between asexual and sexual individuals from different environments. We used a trait-based ecology approach exploiting trophic and locomotive structures to infer the environment that each biotype actually used. More specifically, we compared the morphology of the all-female clonal and sperm-dependent fish Chrosomus eos-neogaeus to that of their sexual host species C. eos in common garden and natural conditions. Results Transfer from natural to controlled conditions resulted in a similar shift in measured morphology for clonal and sexual individuals suggesting comparable level of flexibility in both kinds of organisms. However, clonal, but not sexual, individuals displayed a consistent phenotype when reared in uniform conditions indicating that in absence of genetic variation, one phenotype corresponds to one niche. This contrasted with results from natural conditions where clones were morphologically as variable as sexual individuals within a sampled site. In addition, similar phenotypic changes for both clonal and sexual individuals were observed among the majority of sampled sites, indicating that they responded similarly to the same environments. Discussion Our results indicated that clones can efficiently use different niches and may evolve in a range of environmental conditions comparable to that o…
format: application/pdf
format: text/html
creator: Christelle Leung
creator: Sophie Breton
creator: Bernard Angers
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.5896
publisher: PeerJ Inc.
rights: © 2018 Leung et al.
abstract: Background Survival in temporally or spatially changing environments is a prerequisite for the perpetuation of a given species. In addition to genetic variation, the role of epigenetic processes is crucial in the persistence of organisms. For instance, mechanisms such as developmental flexibility enable the adjustment of the phenotype of a given individual to changing conditions throughout its development. However, the extent of factors other than genetic variability, like epigenetic processes, in the production of alternative phenotype and the consequences in realized ecological niches is still unclear. Methods In this study, we compared the extent of realized niches between asexual and sexual individuals from different environments. We used a trait-based ecology approach exploiting trophic and locomotive structures to infer the environment that each biotype actually used. More specifically, we compared the morphology of the all-female clonal and sperm-dependent fish Chrosomus eos-neogaeus to that of their sexual host species C. eos in common garden and natural conditions. Results Transfer from natural to controlled conditions resulted in a similar shift in measured morphology for clonal and sexual individuals suggesting comparable level of flexibility in both kinds of organisms. However, clonal, but not sexual, individuals displayed a consistent phenotype when reared in uniform conditions indicating that in absence of genetic variation, one phenotype corresponds to one niche. This contrasted with results from natural conditions where clones were morphologically as variable as sexual individuals within a sampled site. In addition, similar phenotypic changes for both clonal and sexual individuals were observed among the majority of sampled sites, indicating that they responded similarly to the same environments. Discussion Our results indicated that clones can efficiently use different niches and may evolve in a range of environmental conditions comparable to that o…
bibliographic citation: Leung et al. (2018) A trait-based ecology to assess the acclimation of a sperm-dependent clonal fish compared to its sexual host. PeerJ 6:e5896 https://doi.org/10.7717/peerj.5896
date submitted: 2018-06-20
date accepted: 2018-10-09
issued: 2018-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leung
  given name: Christelle
author list: Agent
  family name: Breton
  given name: Sophie
author list: Agent
  family name: Angers
  given name: Bernard
doi: 10.7717/peerj.5896
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-02
copyright: © 2018 Leung et al.
attribution name: Leung et al.

imGLAD: accurate detection and quantification of target organisms in metagenomes
type: item
type: AcademicArticle
description: Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets. imGLAD achieves high accuracy because it uses the sequence-discrete population concept for discriminating between metagenomic reads originating from the target organism compared to reads from co-occurring close relatives, masks regions of the genome that are not informative using the MyTaxa engine, and models both the sequencing breadth and depth to determine relative abundance and limit of detection. We validated imGLAD by analyzing metagenomic datasets derived from spinach leaves inoculated with the enteric pathogen Escherichia coli O157:H7 and showed that its limit of detection can be comparable to that of PCR-based approaches for these samples (∼1 cell/gram).
format: application/pdf
format: text/html
creator: Juan C. Castro
creator: Luis M. Rodriguez-R
creator: William T. Harvey
creator: Michael R. Weigand
creator: Janet K. Hatt
creator: Michelle Q. Carter
creator: Konstantinos T. Konstantinidis
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.5882
publisher: PeerJ Inc.
rights: © 2018 Castro et al.
abstract: Accurate detection of target microbial species in metagenomic datasets from environmental samples remains limited because the limit of detection of current methods is typically inaccessible and the frequency of false-positives, resulting from inadequate identification of regions of the genome that are either too highly conserved to be diagnostic (e.g., rRNA genes) or prone to frequent horizontal genetic exchange (e.g., mobile elements) remains unknown. To overcome these limitations, we introduce imGLAD, which aims to detect (target) genomic sequences in metagenomic datasets. imGLAD achieves high accuracy because it uses the sequence-discrete population concept for discriminating between metagenomic reads originating from the target organism compared to reads from co-occurring close relatives, masks regions of the genome that are not informative using the MyTaxa engine, and models both the sequencing breadth and depth to determine relative abundance and limit of detection. We validated imGLAD by analyzing metagenomic datasets derived from spinach leaves inoculated with the enteric pathogen Escherichia coli O157:H7 and showed that its limit of detection can be comparable to that of PCR-based approaches for these samples (∼1 cell/gram).
bibliographic citation: Castro et al. (2018) imGLAD: accurate detection and quantification of target organisms in metagenomes. PeerJ 6:e5882 https://doi.org/10.7717/peerj.5882
date submitted: 2018-02-12
date accepted: 2018-10-03
issued: 2018-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castro
  given name: Juan C.
author list: Agent
  family name: Rodriguez-R
  given name: Luis M.
author list: Agent
  family name: Harvey
  given name: William T.
author list: Agent
  family name: Weigand
  given name: Michael R.
author list: Agent
  family name: Hatt
  given name: Janet K.
author list: Agent
  family name: Carter
  given name: Michelle Q.
author list: Agent
  family name: Konstantinidis
  given name: Konstantinos T.
doi: 10.7717/peerj.5882
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-02
copyright: ©2018 Castro et al.
attribution name: Castro et al.

Evaluation of soil intervention values in mine tailings in northern Chile
type: item
type: AcademicArticle
description: The aim of this work is to show a methodological proposal for the analysis of soil intervention values in mine tailings in order to determine the intervention requirements in the commune of Andacollo in northern Chile. The purpose of this analysis is to guide the intervention policies of both private and public organizations. The evaluation method is based on the Dutch legislation. The usability of the proposed methods depends on the available geochemical data from soil samples; in particular, we tackle the case when information regarding clay percentage in the soil is not available. We use the concepts of a threshold factor and an adjusted threshold factor to calculate a weighted intervention ranking. In order to illustrate the utility of this methodological proposal, a case study is carried out with the prescribed approach. In particular, this work presents an analysis of the elements of environmental significance related to the mining activity (Hg, Cd, Pb, As, Cu, Ni, Zn, Cr) in the commune of Andacollo, Coquimbo Region, Chile. The analyzed samples are used to determine where the intervention of tailing deposits is necessary and where a solution to these environmental liabilities is required as soon as possible. Out of the 81 samples evaluated, it was found that 18 require a potential intervention, and of these samples, seven of them are associated with abandoned tailings that, in some cases, are located close to the town center itself, one sample is associated with active tailings and the other 10 with inactive tailings.
format: application/pdf
format: text/html
creator: Elizabeth Lam Esquenazi
creator: Brian Keith Norambuena
creator: Ítalo Montofré Bacigalupo
creator: María Gálvez Estay
subject: Soil Science
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.5879
publisher: PeerJ Inc.
rights: © 2018 Lam Esquenazi et al.
abstract: The aim of this work is to show a methodological proposal for the analysis of soil intervention values in mine tailings in order to determine the intervention requirements in the commune of Andacollo in northern Chile. The purpose of this analysis is to guide the intervention policies of both private and public organizations. The evaluation method is based on the Dutch legislation. The usability of the proposed methods depends on the available geochemical data from soil samples; in particular, we tackle the case when information regarding clay percentage in the soil is not available. We use the concepts of a threshold factor and an adjusted threshold factor to calculate a weighted intervention ranking. In order to illustrate the utility of this methodological proposal, a case study is carried out with the prescribed approach. In particular, this work presents an analysis of the elements of environmental significance related to the mining activity (Hg, Cd, Pb, As, Cu, Ni, Zn, Cr) in the commune of Andacollo, Coquimbo Region, Chile. The analyzed samples are used to determine where the intervention of tailing deposits is necessary and where a solution to these environmental liabilities is required as soon as possible. Out of the 81 samples evaluated, it was found that 18 require a potential intervention, and of these samples, seven of them are associated with abandoned tailings that, in some cases, are located close to the town center itself, one sample is associated with active tailings and the other 10 with inactive tailings.
bibliographic citation: Lam Esquenazi et al. (2018) Evaluation of soil intervention values in mine tailings in northern Chile. PeerJ 6:e5879 https://doi.org/10.7717/peerj.5879
date submitted: 2018-06-09
date accepted: 2018-10-05
issued: 2018-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lam Esquenazi
  given name: Elizabeth
author list: Agent
  family name: Keith Norambuena
  given name: Brian
author list: Agent
  family name: Montofré Bacigalupo
  given name: Ítalo
author list: Agent
  family name: Gálvez Estay
  given name: María
doi: 10.7717/peerj.5879
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-02
copyright: © 2018 Lam Esquenazi et al.
attribution name: Lam Esquenazi et al.

Dynamic proteomic changes in soft wheat seeds during accelerated ageing
type: item
type: AcademicArticle
description: Previous research demonstrated that soft wheat cultivars have better post-harvest storage tolerance than harder cultivars during accelerated ageing. To better understand this phenomenon, a tandem mass tag-based quantitative proteomic analysis of soft wheat seeds was performed at different storage times during accelerated ageing (germination ratios of 97%, 45%, 28%, and 6%). A total of 1,010 proteins were differentially regulated, of which 519 and 491 were up- and downregulated, respectively. Most of the differentially expressed proteins were predicted to be involved in nutrient reservoir, enzyme activity and regulation, energy and metabolism, and response to stimulus functions, consistent with processes occurring in hard wheat during artificial ageing. Notably, defense-associated proteins including wheatwin-2, pathogenesis-related proteins protecting against fungal invasion, and glutathione S-transferase and glutathione synthetase participating in reactive oxygen species (ROS) detoxification, were upregulated compared to levels in hard wheat during accelerated ageing. These upregulated proteins might be responsible for the superior post-harvest storage-tolerance of soft wheat cultivars during accelerated ageing compared with hard wheat. Although accelerated ageing could not fully mimic natural ageing, our findings provided novel dynamic proteomic insight into soft wheat seeds during seed deterioration.
format: application/pdf
format: text/html
creator: Yangyong Lv
creator: Pingping Tian
creator: Shuaibing Zhang
creator: Jinshui Wang
creator: Yuansen Hu
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.5874
publisher: PeerJ Inc.
rights: © 2018 Lv et al.
abstract: Previous research demonstrated that soft wheat cultivars have better post-harvest storage tolerance than harder cultivars during accelerated ageing. To better understand this phenomenon, a tandem mass tag-based quantitative proteomic analysis of soft wheat seeds was performed at different storage times during accelerated ageing (germination ratios of 97%, 45%, 28%, and 6%). A total of 1,010 proteins were differentially regulated, of which 519 and 491 were up- and downregulated, respectively. Most of the differentially expressed proteins were predicted to be involved in nutrient reservoir, enzyme activity and regulation, energy and metabolism, and response to stimulus functions, consistent with processes occurring in hard wheat during artificial ageing. Notably, defense-associated proteins including wheatwin-2, pathogenesis-related proteins protecting against fungal invasion, and glutathione S-transferase and glutathione synthetase participating in reactive oxygen species (ROS) detoxification, were upregulated compared to levels in hard wheat during accelerated ageing. These upregulated proteins might be responsible for the superior post-harvest storage-tolerance of soft wheat cultivars during accelerated ageing compared with hard wheat. Although accelerated ageing could not fully mimic natural ageing, our findings provided novel dynamic proteomic insight into soft wheat seeds during seed deterioration.
bibliographic citation: Lv et al. (2018) Dynamic proteomic changes in soft wheat seeds during accelerated ageing. PeerJ 6:e5874 https://doi.org/10.7717/peerj.5874
date submitted: 2018-06-17
date accepted: 2018-09-30
issued: 2018-11-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lv
  given name: Yangyong
author list: Agent
  family name: Tian
  given name: Pingping
author list: Agent
  family name: Zhang
  given name: Shuaibing
author list: Agent
  family name: Wang
  given name: Jinshui
author list: Agent
  family name: Hu
  given name: Yuansen
doi: 10.7717/peerj.5874
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-02
copyright: ©2018 Lv et al.
attribution name: Lv et al.

Ontogenetic changes in swimming speed of silver carp, bighead carp, and grass carp larvae: implications for larval dispersal
type: item
type: AcademicArticle
description: Bighead, silver, and grass carps are invasive in the waterways of central North America, and grass carp reproduction in tributaries of the Great Lakes has now been documented. Questions about recruitment potential motivate a need for accurate models of egg and larval dispersal. Quantitative data on swimming behaviors and capabilities during early ontogeny are needed to improve these dispersal models. We measured ontogenetic changes in routine and maximum swimming speeds of bighead, grass, and silver carp larvae. Daily measurements of routine swimming speed were taken for two weeks post-hatch using a still camera and the LARVEL program, a custom image-analysis software. Larval swimming speed was calculated using larval locations in subsequent image frames and time between images. Using an endurance chamber, we determined the maximum swimming speed of larvae (post-gas bladder inflation) for four to eight weeks post-hatch. For all species, larval swimming speeds showed similar trends with respect to ontogeny: increases in maximum speed, and decreases in routine speed. Maximum speeds of bighead and grass carp larvae were similar and generally faster than silver carp larvae. Routine swimming speeds of all larvae were highest before gas bladder inflation, most likely because gas bladder inflation allowed the fish to maintain position without swimming. Downward vertical velocities of pre-gas bladder inflation fish were faster than upward velocities. Among the three species, grass carp larvae had the highest swimming speeds in the pre-gas bladder inflation period, and the lowest speeds in the post-gas bladder inflation period. Knowledge of swimming capability of these species, along with hydraulic characteristics of a river, enables further refinement of models of embryonic and larval drift.
format: application/pdf
format: text/html
creator: Amy E. George
creator: Tatiana Garcia
creator: Benjamin H. Stahlschmidt
creator: Duane C. Chapman
subject: Aquaculture, Fisheries and Fish Science
subject: Freshwater Biology
description: doi:10.7717/peerj.5869
publisher: PeerJ Inc.
rights: © 2018
abstract: Bighead, silver, and grass carps are invasive in the waterways of central North America, and grass carp reproduction in tributaries of the Great Lakes has now been documented. Questions about recruitment potential motivate a need for accurate models of egg and larval dispersal. Quantitative data on swimming behaviors and capabilities during early ontogeny are needed to improve these dispersal models. We measured ontogenetic changes in routine and maximum swimming speeds of bighead, grass, and silver carp larvae. Daily measurements of routine swimming speed were taken for two weeks post-hatch using a still camera and the LARVEL program, a custom image-analysis software. Larval swimming speed was calculated using larval locations in subsequent image frames and time between images. Using an endurance chamber, we determined the maximum swimming speed of larvae (post-gas bladder inflation) for four to eight weeks post-hatch. For all species, larval swimming speeds showed similar trends with respect to ontogeny: increases in maximum speed, and decreases in routine speed. Maximum speeds of bighead and grass carp larvae were similar and generally faster than silver carp larvae. Routine swimming speeds of all larvae were highest before gas bladder inflation, most likely because gas bladder inflation allowed the fish to maintain position without swimming. Downward vertical velocities of pre-gas bladder inflation fish were faster than upward velocities. Among the three species, grass carp larvae had the highest swimming speeds in the pre-gas bladder inflation period, and the lowest speeds in the post-gas bladder inflation period. Knowledge of swimming capability of these species, along with hydraulic characteristics of a river, enables further refinement of models of embryonic and larval drift.
bibliographic citation: George et al. (2018) Ontogenetic changes in swimming speed of silver carp, bighead carp, and grass carp larvae: implications for larval dispersal. PeerJ 6:e5869 https://doi.org/10.7717/peerj.5869
date submitted: 2018-04-19
date accepted: 2018-10-03
issued: 2018-11-02
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: George
  given name: Amy E.
author list: Agent
  family name: Garcia
  given name: Tatiana
author list: Agent
  family name: Stahlschmidt
  given name: Benjamin H.
author list: Agent
  family name: Chapman
  given name: Duane C.
doi: 10.7717/peerj.5869
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-02

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