PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae
items: LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks
items: Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana
items: An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples
items: Spatial distribution of environmental DNA in a nearshore marine habitat
items: Predatory blue crabs induce stronger nonconsumptive effects in eastern oysters Crassostrea virginica than scavenging blue crabs
items: How conserved are the conserved 16S-rRNA regions?
items: Immediate effects of EVA midsole resilience and upper shoe structure on running biomechanics: a machine learning approach
items: Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod
items: Construction patterns of birds’ nests provide insight into nest-building behaviours

Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae
type: item
type: AcademicArticle
description: Cassiopea xamachana jellyfish are an attractive model system to study metamorphosis and/or cnidarian–dinoflagellate symbiosis due to the ease of cultivation of their planula larvae and scyphistomae through their asexual cycle, in which the latter can bud new larvae and continue the cycle without differentiation into ephyrae. Then, a subsequent induction of metamorphosis and full differentiation into ephyrae is believed to occur when the symbionts are acquired by the scyphistomae. Although strobilation induction and differentiation into ephyrae can be accomplished in various ways, a controlled, reproducible metamorphosis induction has not been reported. Such controlled metamorphosis induction is necessary for an ensured synchronicity and reproducibility of biological, biochemical, and molecular analyses. For this purpose, we tested if differentiation could be pharmacologically stimulated as in Aurelia aurita, by the metamorphic inducers thyroxine, KI, NaI, Lugol’s iodine, H2O2, indomethacin, or retinol. We found reproducibly induced strobilation by 50 μM indomethacin after six days of exposure, and 10–25 μM after 7 days. Strobilation under optimal conditions reached 80–100% with subsequent ephyrae release after exposure. Thyroxine yielded inconsistent results as it caused strobilation occasionally, while all other chemicals had no effect. Thus, indomethacin can be used as a convenient tool for assessment of biological phenomena through a controlled metamorphic process in C. xamachana scyphistomae.
format: application/pdf
format: text/html
creator: Patricia Cabrales-Arellano
creator: Tania Islas-Flores
creator: Patricia E. Thomé
creator: Marco A. Villanueva
subject: Developmental Biology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2979
publisher: PeerJ Inc.
rights: © 2017 Cabrales-Arellano et al.
abstract: Cassiopea xamachana jellyfish are an attractive model system to study metamorphosis and/or cnidarian–dinoflagellate symbiosis due to the ease of cultivation of their planula larvae and scyphistomae through their asexual cycle, in which the latter can bud new larvae and continue the cycle without differentiation into ephyrae. Then, a subsequent induction of metamorphosis and full differentiation into ephyrae is believed to occur when the symbionts are acquired by the scyphistomae. Although strobilation induction and differentiation into ephyrae can be accomplished in various ways, a controlled, reproducible metamorphosis induction has not been reported. Such controlled metamorphosis induction is necessary for an ensured synchronicity and reproducibility of biological, biochemical, and molecular analyses. For this purpose, we tested if differentiation could be pharmacologically stimulated as in Aurelia aurita, by the metamorphic inducers thyroxine, KI, NaI, Lugol’s iodine, H2O2, indomethacin, or retinol. We found reproducibly induced strobilation by 50 μM indomethacin after six days of exposure, and 10–25 μM after 7 days. Strobilation under optimal conditions reached 80–100% with subsequent ephyrae release after exposure. Thyroxine yielded inconsistent results as it caused strobilation occasionally, while all other chemicals had no effect. Thus, indomethacin can be used as a convenient tool for assessment of biological phenomena through a controlled metamorphic process in C. xamachana scyphistomae.
bibliographic citation: Cabrales-Arellano et al. (2017) Indomethacin reproducibly induces metamorphosis in Cassiopea xamachana scyphistomae. PeerJ 5:e2979 https://doi.org/10.7717/peerj.2979
date submitted: 2016-09-20
date accepted: 2017-01-10
issued: 2017-03-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cabrales-Arellano
  given name: Patricia
author list: Agent
  family name: Islas-Flores
  given name: Tania
author list: Agent
  family name: Thomé
  given name: Patricia E.
author list: Agent
  family name: Villanueva
  given name: Marco A.
doi: 10.7717/peerj.2979
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-03-01
copyright: © 2017 Cabrales-Arellano et al.
attribution name: Cabrales-Arellano et al.

LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks
type: item
type: AcademicArticle
description: One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto.
format: application/pdf
format: text/html
creator: Alberto J. Martin
creator: Sebastián Contreras-Riquelme
creator: Calixto Dominguez
creator: Tomas Perez-Acle
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.3052
publisher: PeerJ Inc.
rights: © 2017 Martin et al.
abstract: One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto.
bibliographic citation: Martin et al. (2017) LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks. PeerJ 5:e3052 https://doi.org/10.7717/peerj.3052
date submitted: 2016-09-08
date accepted: 2017-01-31
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martin
  given name: Alberto J.
author list: Agent
  family name: Contreras-Riquelme
  given name: Sebastián
author list: Agent
  family name: Dominguez
  given name: Calixto
author list: Agent
  family name: Perez-Acle
  given name: Tomas
doi: 10.7717/peerj.3052
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Martin et al.
attribution name: Martin et al.

Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana
type: item
type: AcademicArticle
description: Background The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African” CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide. Methods We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages. Results We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol. Discussion This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone.
format: application/pdf
format: text/html
creator: Grace Kpeli
creator: Andrew H. Buultjens
creator: Stefano Giulieri
creator: Evelyn Owusu-Mireku
creator: Samuel Y. Aboagye
creator: Sarah L. Baines
creator: Torsten Seemann
creator: Dieter Bulach
creator: Anders Gonçalves da Silva
creator: Ian R. Monk
creator: Benjamin P. Howden
creator: Gerd Pluschke
creator: Dorothy Yeboah-Manu
creator: Timothy Stinear
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.3047
publisher: PeerJ Inc.
rights: © 2017 Kpeli et al.
abstract: Background The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African” CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide. Methods We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages. Results We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol. Discussion This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone.
bibliographic citation: Kpeli et al. (2017) Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana. PeerJ 5:e3047 https://doi.org/10.7717/peerj.3047
date submitted: 2016-10-21
date accepted: 2017-01-30
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kpeli
  given name: Grace
author list: Agent
  family name: Buultjens
  given name: Andrew H.
author list: Agent
  family name: Giulieri
  given name: Stefano
author list: Agent
  family name: Owusu-Mireku
  given name: Evelyn
author list: Agent
  family name: Aboagye
  given name: Samuel Y.
author list: Agent
  family name: Baines
  given name: Sarah L.
author list: Agent
  family name: Seemann
  given name: Torsten
author list: Agent
  family name: Bulach
  given name: Dieter
author list: Agent
  family name: Gonçalves da Silva
  given name: Anders
author list: Agent
  family name: Monk
  given name: Ian R.
author list: Agent
  family name: Howden
  given name: Benjamin P.
author list: Agent
  family name: Pluschke
  given name: Gerd
author list: Agent
  family name: Yeboah-Manu
  given name: Dorothy
author list: Agent
  family name: Stinear
  given name: Timothy
doi: 10.7717/peerj.3047
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: © 2017 Kpeli et al.
attribution name: Kpeli et al.

An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples
type: item
type: AcademicArticle
description: Background Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings. Methods Here we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples. Results The method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain). Discussion This new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms.
format: application/pdf
format: text/html
creator: Laura Clusa
creator: Alba Ardura
creator: Sara Fernández
creator: Agustín A. Roca
creator: Eva García-Vázquez
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Environmental Sciences
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3045
publisher: PeerJ Inc.
rights: © 2017 Clusa et al.
abstract: Background Salmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings. Methods Here we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples. Results The method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain). Discussion This new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms.
bibliographic citation: Clusa et al. (2017) An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples. PeerJ 5:e3045 https://doi.org/10.7717/peerj.3045
date submitted: 2016-10-19
date accepted: 2017-01-30
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clusa
  given name: Laura
author list: Agent
  family name: Ardura
  given name: Alba
author list: Agent
  family name: Fernández
  given name: Sara
author list: Agent
  family name: Roca
  given name: Agustín A.
author list: Agent
  family name: García-Vázquez
  given name: Eva
doi: 10.7717/peerj.3045
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Clusa et al.
attribution name: Clusa et al.

Spatial distribution of environmental DNA in a nearshore marine habitat
type: item
type: AcademicArticle
description: In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and…
format: application/pdf
format: text/html
creator: James L. O’Donnell
creator: Ryan P. Kelly
creator: Andrew Olaf Shelton
creator: Jameal F. Samhouri
creator: Natalie C. Lowell
creator: Gregory D. Williams
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.3044
publisher: PeerJ Inc.
rights: © 2017
abstract: In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and…
bibliographic citation: O’Donnell et al. (2017) Spatial distribution of environmental DNA in a nearshore marine habitat. PeerJ 5:e3044 https://doi.org/10.7717/peerj.3044
date submitted: 2016-11-28
date accepted: 2017-01-29
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: O’Donnell
  given name: James L.
author list: Agent
  family name: Kelly
  given name: Ryan P.
author list: Agent
  family name: Shelton
  given name: Andrew Olaf
author list: Agent
  family name: Samhouri
  given name: Jameal F.
author list: Agent
  family name: Lowell
  given name: Natalie C.
author list: Agent
  family name: Williams
  given name: Gregory D.
doi: 10.7717/peerj.3044
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28

Predatory blue crabs induce stronger nonconsumptive effects in eastern oysters Crassostrea virginica than scavenging blue crabs
type: item
type: AcademicArticle
description: By influencing critical prey traits such as foraging or habitat selection, predators can affect entire ecosystems, but the nature of cues that trigger prey reactions to predators are not well understood. Predators may scavenge to supplement their energetic needs and scavenging frequency may vary among individuals within a species due to preferences and prey availability. Yet prey reactions to consumers that are primarily scavengers versus those that are active foragers have not been investigated, even though variation in prey reactions to scavengers or predators might influence cascading nonconsumptive effects in food webs. Oysters Crassostrea virginica react to crab predators by growing stronger shells. We exposed oysters to exudates from crabs fed live oysters or fed aged oyster tissue to simulate scavenging, and to controls without crab cues. Oysters grew stronger shells when exposed to either crab exudate, but their shells were significantly stronger when crabs were fed live oysters. The stronger response to predators than scavengers could be due to inherent differences in diet cues representative of reduced risk in the presence of scavengers or to degradation of conspecific alarm cues in aged treatments, which may mask risk from potential predators subsisting by scavenging.
format: application/pdf
format: text/html
creator: Avery E. Scherer
creator: Miranda M. Garcia
creator: Delbert L. Smee
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.3042
publisher: PeerJ Inc.
rights: © 2017 Scherer et al.
abstract: By influencing critical prey traits such as foraging or habitat selection, predators can affect entire ecosystems, but the nature of cues that trigger prey reactions to predators are not well understood. Predators may scavenge to supplement their energetic needs and scavenging frequency may vary among individuals within a species due to preferences and prey availability. Yet prey reactions to consumers that are primarily scavengers versus those that are active foragers have not been investigated, even though variation in prey reactions to scavengers or predators might influence cascading nonconsumptive effects in food webs. Oysters Crassostrea virginica react to crab predators by growing stronger shells. We exposed oysters to exudates from crabs fed live oysters or fed aged oyster tissue to simulate scavenging, and to controls without crab cues. Oysters grew stronger shells when exposed to either crab exudate, but their shells were significantly stronger when crabs were fed live oysters. The stronger response to predators than scavengers could be due to inherent differences in diet cues representative of reduced risk in the presence of scavengers or to degradation of conspecific alarm cues in aged treatments, which may mask risk from potential predators subsisting by scavenging.
bibliographic citation: Scherer et al. (2017) Predatory blue crabs induce stronger nonconsumptive effects in eastern oysters Crassostrea virginica than scavenging blue crabs. PeerJ 5:e3042 https://doi.org/10.7717/peerj.3042
date submitted: 2016-11-16
date accepted: 2017-01-28
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scherer
  given name: Avery E.
author list: Agent
  family name: Garcia
  given name: Miranda M.
author list: Agent
  family name: Smee
  given name: Delbert L.
doi: 10.7717/peerj.3042
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: © 2017 Scherer et al.
attribution name: Scherer et al.

How conserved are the conserved 16S-rRNA regions?
type: item
type: AcademicArticle
description: The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.
format: application/pdf
format: text/html
creator: Marcel Martinez-Porchas
creator: Enrique Villalpando-Canchola
creator: Luis Enrique Ortiz Suarez
creator: Francisco Vargas-Albores
subject: Biodiversity
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.3036
publisher: PeerJ Inc.
rights: © 2017 Martinez-Porchas et al.
abstract: The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker.
bibliographic citation: Martinez-Porchas et al. (2017) How conserved are the conserved 16S-rRNA regions?. PeerJ 5:e3036 https://doi.org/10.7717/peerj.3036
date submitted: 2016-10-17
date accepted: 2017-01-26
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martinez-Porchas
  given name: Marcel
author list: Agent
  family name: Villalpando-Canchola
  given name: Enrique
author list: Agent
  family name: Ortiz Suarez
  given name: Luis Enrique
author list: Agent
  family name: Vargas-Albores
  given name: Francisco
doi: 10.7717/peerj.3036
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Martinez-Porchas et al.
attribution name: Martinez-Porchas et al.

Immediate effects of EVA midsole resilience and upper shoe structure on running biomechanics: a machine learning approach
type: item
type: AcademicArticle
description: Background Resilience of midsole material and the upper structure of the shoe are conceptual characteristics that can interfere in running biomechanics patterns. Artificial intelligence techniques can capture features from the entire waveform, adding new perspective for biomechanical analysis. This study tested the influence of shoe midsole resilience and upper structure on running kinematics and kinetics of non-professional runners by using feature selection, information gain, and artificial neural network analysis. Methods Twenty-seven experienced male runners (63 ± 44 km/week run) ran in four-shoe design that combined two resilience-cushioning materials (low and high) and two uppers (minimalist and structured). Kinematic data was acquired by six infrared cameras at 300 Hz, and ground reaction forces were acquired by two force plates at 1,200 Hz. We conducted a Machine Learning analysis to identify features from the complete kinematic and kinetic time series and from 42 discrete variables that had better discriminate the four shoes studied. For that analysis, we built an input data matrix of dimensions 1,080 (10 trials × 4 shoes × 27 subjects) × 1,254 (3 joints × 3 planes of movement × 101 data points + 3 vectors forces × 101 data points + 42 discrete calculated kinetic and kinematic features). Results The applied feature selection by information gain and artificial neural networks successfully differentiated the two resilience materials using 200(16%) biomechanical variables with an accuracy of 84.8% by detecting alterations of running biomechanics, and the two upper structures with an accuracy of 93.9%. Discussion The discrimination of midsole resilience resulted in lower accuracy levels than did the discrimination of the shoe uppers. In both cases, the ground reaction forces were among the 25 most relevant features. The resilience of the cushioning material caused significant effects on initial heel impact, while the effects of different uppers were distributed…
format: application/pdf
format: text/html
creator: Andrea N. Onodera
creator: Wilson P. Gavião Neto
creator: Maria Isabel Roveri
creator: Wagner R. Oliveira
creator: Isabel CN Sacco
subject: Bioengineering
subject: Kinesiology
description: doi:10.7717/peerj.3026
publisher: PeerJ Inc.
rights: © 2017 Onodera et al.
abstract: Background Resilience of midsole material and the upper structure of the shoe are conceptual characteristics that can interfere in running biomechanics patterns. Artificial intelligence techniques can capture features from the entire waveform, adding new perspective for biomechanical analysis. This study tested the influence of shoe midsole resilience and upper structure on running kinematics and kinetics of non-professional runners by using feature selection, information gain, and artificial neural network analysis. Methods Twenty-seven experienced male runners (63 ± 44 km/week run) ran in four-shoe design that combined two resilience-cushioning materials (low and high) and two uppers (minimalist and structured). Kinematic data was acquired by six infrared cameras at 300 Hz, and ground reaction forces were acquired by two force plates at 1,200 Hz. We conducted a Machine Learning analysis to identify features from the complete kinematic and kinetic time series and from 42 discrete variables that had better discriminate the four shoes studied. For that analysis, we built an input data matrix of dimensions 1,080 (10 trials × 4 shoes × 27 subjects) × 1,254 (3 joints × 3 planes of movement × 101 data points + 3 vectors forces × 101 data points + 42 discrete calculated kinetic and kinematic features). Results The applied feature selection by information gain and artificial neural networks successfully differentiated the two resilience materials using 200(16%) biomechanical variables with an accuracy of 84.8% by detecting alterations of running biomechanics, and the two upper structures with an accuracy of 93.9%. Discussion The discrimination of midsole resilience resulted in lower accuracy levels than did the discrimination of the shoe uppers. In both cases, the ground reaction forces were among the 25 most relevant features. The resilience of the cushioning material caused significant effects on initial heel impact, while the effects of different uppers were distributed…
bibliographic citation: Onodera et al. (2017) Immediate effects of EVA midsole resilience and upper shoe structure on running biomechanics: a machine learning approach. PeerJ 5:e3026 https://doi.org/10.7717/peerj.3026
date submitted: 2016-10-26
date accepted: 2017-01-25
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Onodera
  given name: Andrea N.
author list: Agent
  family name: Gavião Neto
  given name: Wilson P.
author list: Agent
  family name: Roveri
  given name: Maria Isabel
author list: Agent
  family name: Oliveira
  given name: Wagner R.
author list: Agent
  family name: Sacco
  given name: Isabel CN
doi: 10.7717/peerj.3026
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Onodera et al.
attribution name: Onodera et al.

Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod
type: item
type: AcademicArticle
description: Background The Balkans are a major worldwide biodiversity and endemism hotspot. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; (3) given that G. roeselii thrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; (4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification of G. roeselii. Material and Methods DNA was extracted from 177 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors’ occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes. Results We revealed that G. roeselii includes at least 13 cryptic species…
format: application/pdf
format: text/html
creator: Michał Grabowski
creator: Tomasz Mamos
creator: Karolina Bącela-Spychalska
creator: Tomasz Rewicz
creator: Remi A. Wattier
subject: Aquaculture, Fisheries and Fish Science
subject: Biogeography
subject: Evolutionary Studies
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.3016
publisher: PeerJ Inc.
rights: © 2017 Grabowski et al.
abstract: Background The Balkans are a major worldwide biodiversity and endemism hotspot. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; (3) given that G. roeselii thrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; (4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification of G. roeselii. Material and Methods DNA was extracted from 177 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors’ occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes. Results We revealed that G. roeselii includes at least 13 cryptic species…
bibliographic citation: Grabowski et al. (2017) Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod. PeerJ 5:e3016 https://doi.org/10.7717/peerj.3016
date submitted: 2016-06-27
date accepted: 2017-01-23
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grabowski
  given name: Michał
author list: Agent
  family name: Mamos
  given name: Tomasz
author list: Agent
  family name: Bącela-Spychalska
  given name: Karolina
author list: Agent
  family name: Rewicz
  given name: Tomasz
author list: Agent
  family name: Wattier
  given name: Remi A.
doi: 10.7717/peerj.3016
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Grabowski et al.
attribution name: Grabowski et al.

Construction patterns of birds’ nests provide insight into nest-building behaviours
type: item
type: AcademicArticle
description: Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula) nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process.
format: application/pdf
format: text/html
creator: Lucia Biddle
creator: Adrian M. Goodman
creator: D. Charles Deeming
subject: Animal Behavior
subject: Bioengineering
subject: Zoology
description: doi:10.7717/peerj.3010
publisher: PeerJ Inc.
rights: © 2017 Biddle et al.
abstract: Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula) nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process.
bibliographic citation: Biddle et al. (2017) Construction patterns of birds’ nests provide insight into nest-building behaviours. PeerJ 5:e3010 https://doi.org/10.7717/peerj.3010
date submitted: 2016-07-05
date accepted: 2017-01-21
issued: 2017-02-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Biddle
  given name: Lucia
author list: Agent
  family name: Goodman
  given name: Adrian M.
author list: Agent
  family name: Deeming
  given name: D. Charles
doi: 10.7717/peerj.3010
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-02-28
copyright: ©2017 Biddle et al.
attribution name: Biddle et al.

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