PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Mouse spermatozoa with higher fertilization rates have thinner nuclei
items: Cellobiohydrolase B of Aspergillus niger over-expressed in Pichia pastoris stimulates hydrolysis of oil palm empty fruit bunches
items: Nests of red wood ants (Formica rufa-group) are positively associated with tectonic faults: a double-blind test
items: Seasonal and year-round use of the Kushiro Wetland, Hokkaido, Japan by sika deer (Cervus nippon yesoensis)
items: Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks
items: Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?
items: Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral clearance during 2009 pandemic influenza infection
items: The effects of familiarity on escape responses in the Trinidadian guppy (Poecilia reticulata)
items: Evidence for continual hybridization rather than hybrid speciation between Ligularia duciformis and L. paradoxa (Asteraceae)
items: Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata

Mouse spermatozoa with higher fertilization rates have thinner nuclei
type: item
type: AcademicArticle
description: Background Although spermatozoa with normal morphology are assumed to have uniform fertilization ability, recent data show that even normal spermatozoa have considerable variation in their head shape which is associated with differences in fertilization ability. Appropriate quantitative indicators for good sperm morphology, however, remain unidentified. Methods Therefore, in an effort to identify such an indicator, we compared the nuclear contour of normal mouse spermatozoa by quantitative multivariate analysis using elliptic Fourier descriptors combined with principal component analysis. The spermatozoa were obtained from different strains and collection sites which have been shown to be associated with different fertilization abilities. Results We found that the head was 5.7% thinner in spermatozoa from the B6D2F1 (BDF1) strain, known to have a higher fertilization rate, than in those from the C57BL/6N (B6N) strain, which has a lower fertilization rate. Moreover, zona-penetrated spermatozoa in the perivitelline space consistently had 5.4% thinner heads than those isolated from the epididymis before ejaculation. The aspect ratio, which represents the sperm head thinness, uniquely distinguished these sperm populations, confirming its validity as a morphological indicator. Discussion Because aspect ratio has also been shown to characterize human spermatozoa, this unique morphometric indicator might be applicable to compare normal spermatozoa among multiple patients, which will greatly facilitate and enhance current reproductive technologies.
format: application/pdf
format: text/html
creator: Daisuke Mashiko
creator: Masahito Ikawa
creator: Koichi Fujimoto
subject: Cell Biology
subject: Developmental Biology
subject: Andrology
description: doi:10.7717/peerj.3913
publisher: PeerJ Inc.
rights: © 2017 Mashiko et al.
abstract: Background Although spermatozoa with normal morphology are assumed to have uniform fertilization ability, recent data show that even normal spermatozoa have considerable variation in their head shape which is associated with differences in fertilization ability. Appropriate quantitative indicators for good sperm morphology, however, remain unidentified. Methods Therefore, in an effort to identify such an indicator, we compared the nuclear contour of normal mouse spermatozoa by quantitative multivariate analysis using elliptic Fourier descriptors combined with principal component analysis. The spermatozoa were obtained from different strains and collection sites which have been shown to be associated with different fertilization abilities. Results We found that the head was 5.7% thinner in spermatozoa from the B6D2F1 (BDF1) strain, known to have a higher fertilization rate, than in those from the C57BL/6N (B6N) strain, which has a lower fertilization rate. Moreover, zona-penetrated spermatozoa in the perivitelline space consistently had 5.4% thinner heads than those isolated from the epididymis before ejaculation. The aspect ratio, which represents the sperm head thinness, uniquely distinguished these sperm populations, confirming its validity as a morphological indicator. Discussion Because aspect ratio has also been shown to characterize human spermatozoa, this unique morphometric indicator might be applicable to compare normal spermatozoa among multiple patients, which will greatly facilitate and enhance current reproductive technologies.
bibliographic citation: Mashiko et al. (2017) Mouse spermatozoa with higher fertilization rates have thinner nuclei. PeerJ 5:e3913 https://doi.org/10.7717/peerj.3913
date submitted: 2017-07-31
date accepted: 2017-09-21
issued: 2017-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mashiko
  given name: Daisuke
author list: Agent
  family name: Ikawa
  given name: Masahito
author list: Agent
  family name: Fujimoto
  given name: Koichi
doi: 10.7717/peerj.3913
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-12
copyright: ©2017 Mashiko et al.
attribution name: Mashiko et al.

Cellobiohydrolase B of Aspergillus niger over-expressed in Pichia pastoris stimulates hydrolysis of oil palm empty fruit bunches
type: item
type: AcademicArticle
description: Background Aspergillus niger, along with many other lignocellulolytic fungi, has been widely used as a commercial workhorse for cellulase production. A fungal cellulase system generally includes three major classes of enzymes i.e., β-glucosidases, endoglucanases and cellobiohydrolases. Cellobiohydrolases (CBH) are vital to the degradation of crystalline cellulose present in lignocellulosic biomass. However, A. niger naturally secretes low levels of CBH. Hence, recombinant production of A. niger CBH is desirable to increase CBH production yield and also to allow biochemical characterisation of the recombinant CBH from A. niger. Methods In this study, the gene encoding a cellobiohydrolase B (cbhB) from A. niger ATCC 10574 was cloned and expressed in the methylotrophic yeast Pichia pastoris X-33. The recombinant CBHB was purified and characterised to study its biochemical and kinetic characteristics. To evaluate the potential of CBHB in assisting biomass conversion, CBHB was supplemented into a commercial cellulase preparation (Cellic® CTec2) and was used to hydrolyse oil palm empty fruit bunch (OPEFB), one of the most abundant lignocellulosic waste from the palm oil industry. To attain maximum saccharification, enzyme loadings were optimised by response surface methodology and the optimum point was validated experimentally. Hydrolysed OPEFB samples were analysed using attenuated total reflectance FTIR spectroscopy (ATR-FTIR) to screen for any compositional changes upon enzymatic treatment. Results Recombinant CBHB was over-expressed as a hyperglycosylated protein attached to N-glycans. CBHB was enzymatically active towards soluble substrates such as 4-methylumbelliferyl-β-D-cellobioside (MUC), p-nitrophenyl-cellobioside (pNPC) and p-nitrophenyl-cellobiotrioside (pNPG3) but was not active towards crystalline substrates like Avicel® and Sigmacell cellulose. Characterisation of purified CBHB using MUC as the model substrate revealed that optimum catalysis occurred at 50 …
format: application/pdf
format: text/html
creator: James Sy-Keen Woon
creator: Mukram M. Mackeen
creator: Rosli M. Illias
creator: Nor M. Mahadi
creator: William J. Broughton
creator: Abdul Munir Abdul Murad
creator: Farah Diba Abu Bakar
subject: Biochemistry
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.3909
publisher: PeerJ Inc.
rights: © 2017 Woon et al.
abstract: Background Aspergillus niger, along with many other lignocellulolytic fungi, has been widely used as a commercial workhorse for cellulase production. A fungal cellulase system generally includes three major classes of enzymes i.e., β-glucosidases, endoglucanases and cellobiohydrolases. Cellobiohydrolases (CBH) are vital to the degradation of crystalline cellulose present in lignocellulosic biomass. However, A. niger naturally secretes low levels of CBH. Hence, recombinant production of A. niger CBH is desirable to increase CBH production yield and also to allow biochemical characterisation of the recombinant CBH from A. niger. Methods In this study, the gene encoding a cellobiohydrolase B (cbhB) from A. niger ATCC 10574 was cloned and expressed in the methylotrophic yeast Pichia pastoris X-33. The recombinant CBHB was purified and characterised to study its biochemical and kinetic characteristics. To evaluate the potential of CBHB in assisting biomass conversion, CBHB was supplemented into a commercial cellulase preparation (Cellic® CTec2) and was used to hydrolyse oil palm empty fruit bunch (OPEFB), one of the most abundant lignocellulosic waste from the palm oil industry. To attain maximum saccharification, enzyme loadings were optimised by response surface methodology and the optimum point was validated experimentally. Hydrolysed OPEFB samples were analysed using attenuated total reflectance FTIR spectroscopy (ATR-FTIR) to screen for any compositional changes upon enzymatic treatment. Results Recombinant CBHB was over-expressed as a hyperglycosylated protein attached to N-glycans. CBHB was enzymatically active towards soluble substrates such as 4-methylumbelliferyl-β-D-cellobioside (MUC), p-nitrophenyl-cellobioside (pNPC) and p-nitrophenyl-cellobiotrioside (pNPG3) but was not active towards crystalline substrates like Avicel® and Sigmacell cellulose. Characterisation of purified CBHB using MUC as the model substrate revealed that optimum catalysis occurred at 50 …
bibliographic citation: Woon et al. (2017) Cellobiohydrolase B of Aspergillus niger over-expressed in Pichia pastoris stimulates hydrolysis of oil palm empty fruit bunches. PeerJ 5:e3909 https://doi.org/10.7717/peerj.3909
date submitted: 2017-06-21
date accepted: 2017-09-19
issued: 2017-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Woon
  given name: James Sy-Keen
author list: Agent
  family name: Mackeen
  given name: Mukram M.
author list: Agent
  family name: Illias
  given name: Rosli M.
author list: Agent
  family name: Mahadi
  given name: Nor M.
author list: Agent
  family name: Broughton
  given name: William J.
author list: Agent
  family name: Murad
  given name: Abdul Munir Abdul
author list: Agent
  family name: Abu Bakar
  given name: Farah Diba
doi: 10.7717/peerj.3909
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-12
copyright: ©2017 Woon et al.
attribution name: Woon et al.

Nests of red wood ants (Formica rufa-group) are positively associated with tectonic faults: a double-blind test
type: item
type: AcademicArticle
description: Ecological studies often are subjected to unintentional biases, suggesting that improved research designs for hypothesis testing should be used. Double-blind ecological studies are rare but necessary to minimize sampling biases and omission errors, and improve the reliability of research. We used a double-blind design to evaluate associations between nests of red wood ants (Formica rufa, RWA) and the distribution of tectonic faults. We randomly sampled two regions in western Denmark to map the spatial distribution of RWA nests. We then calculated nest proximity to the nearest active tectonic faults. Red wood ant nests were eight times more likely to be found within 60 m of known tectonic faults than were random points in the same region but without nests. This pattern paralleled the directionality of the fault system, with NNE–SSW faults having the strongest associations with RWA nests. The nest locations were collected without knowledge of the spatial distribution of active faults thus we are confident that the results are neither biased nor artefactual. This example highlights the benefits of double-blind designs in reducing sampling biases, testing controversial hypotheses, and increasing the reliability of the conclusions of research.
format: application/pdf
format: text/html
creator: Israel Del Toro
creator: Gabriele M. Berberich
creator: Relena R. Ribbons
creator: Martin B. Berberich
creator: Nathan J. Sanders
creator: Aaron M. Ellison
subject: Biogeography
subject: Ecology
subject: Entomology
subject: Statistics
description: doi:10.7717/peerj.3903
publisher: PeerJ Inc.
rights: © 2017 Del Toro et al.
abstract: Ecological studies often are subjected to unintentional biases, suggesting that improved research designs for hypothesis testing should be used. Double-blind ecological studies are rare but necessary to minimize sampling biases and omission errors, and improve the reliability of research. We used a double-blind design to evaluate associations between nests of red wood ants (Formica rufa, RWA) and the distribution of tectonic faults. We randomly sampled two regions in western Denmark to map the spatial distribution of RWA nests. We then calculated nest proximity to the nearest active tectonic faults. Red wood ant nests were eight times more likely to be found within 60 m of known tectonic faults than were random points in the same region but without nests. This pattern paralleled the directionality of the fault system, with NNE–SSW faults having the strongest associations with RWA nests. The nest locations were collected without knowledge of the spatial distribution of active faults thus we are confident that the results are neither biased nor artefactual. This example highlights the benefits of double-blind designs in reducing sampling biases, testing controversial hypotheses, and increasing the reliability of the conclusions of research.
bibliographic citation: Del Toro et al. (2017) Nests of red wood ants (Formica rufa-group) are positively associated with tectonic faults: a double-blind test. PeerJ 5:e3903 https://doi.org/10.7717/peerj.3903
date submitted: 2017-07-06
date accepted: 2017-09-18
issued: 2017-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Del Toro
  given name: Israel
author list: Agent
  family name: Berberich
  given name: Gabriele M.
author list: Agent
  family name: Ribbons
  given name: Relena R.
author list: Agent
  family name: Berberich
  given name: Martin B.
author list: Agent
  family name: Sanders
  given name: Nathan J.
author list: Agent
  family name: Ellison
  given name: Aaron M.
doi: 10.7717/peerj.3903
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-12
copyright: © 2017 Del Toro et al.
attribution name: Del Toro et al.

Seasonal and year-round use of the Kushiro Wetland, Hokkaido, Japan by sika deer (Cervus nippon yesoensis)
type: item
type: AcademicArticle
description: The sika deer (Cervus nippon yesoensis) population in the Ramsar-listed Kushiro Wetland has increased in recent years, and the Ministry of the Environment of Japan has decided to take measures to reduce the impact of deer on the ecosystem. However, seasonal movement patterns of the deer (i.e., when and where the deer inhabit the wetland) remain unclear. We examined the seasonal movement patterns of sika deer in the Kushiro Wetland from 2013 to 2015 by analyzing GPS location data for 28 hinds captured at three sites in the wetland. Seasonal movement patterns were quantitatively classified as seasonal migration, mixed, dispersal, nomadic, resident, or atypical, and the degree of wetland utilization for each individual was estimated. The area of overlap for each individual among intra-capture sites and inter-capture sites was calculated for the entire year and for each season. Our results showed that the movement patterns of these deer were classified not only as resident but also as seasonal migration, dispersal, and atypical. Approximately one-third of the individuals moved into and out of the wetland during the year as either seasonal migrants or individuals with atypical movement. Some of the individuals migrated to farmland areas outside the wetland (the farthest being 69.9 km away). Half of the individuals inhabited the wetland all or most of the year, i.e., 81–100% of their annual home range was within the wetland area. Even among individuals captured at the same site, different seasonal movement patterns were identified. The overlap areas of the home ranges of individuals from the same capture sites were larger than those for individuals from different capture sites (e.g., mean of annual home range overlap with intra-capture sites: 47.7% vs. inter-sites: 1.3%). To achieve more effective ecosystem management including deer management in the wetland, management plans should cover inside and outside of the wetland and separate the population into multiple manageme…
format: application/pdf
format: text/html
creator: Hino Takafumi
creator: Tatsuya Kamii
creator: Takunari Murai
creator: Ryoto Yoshida
creator: Atsuki Sato
creator: Yasuyuki Tachiki
creator: Rika Akamatsu
creator: Tsuyoshi Yoshida
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Natural Resource Management
description: doi:10.7717/peerj.3869
publisher: PeerJ Inc.
rights: © 2017 Takafumi et al.
abstract: The sika deer (Cervus nippon yesoensis) population in the Ramsar-listed Kushiro Wetland has increased in recent years, and the Ministry of the Environment of Japan has decided to take measures to reduce the impact of deer on the ecosystem. However, seasonal movement patterns of the deer (i.e., when and where the deer inhabit the wetland) remain unclear. We examined the seasonal movement patterns of sika deer in the Kushiro Wetland from 2013 to 2015 by analyzing GPS location data for 28 hinds captured at three sites in the wetland. Seasonal movement patterns were quantitatively classified as seasonal migration, mixed, dispersal, nomadic, resident, or atypical, and the degree of wetland utilization for each individual was estimated. The area of overlap for each individual among intra-capture sites and inter-capture sites was calculated for the entire year and for each season. Our results showed that the movement patterns of these deer were classified not only as resident but also as seasonal migration, dispersal, and atypical. Approximately one-third of the individuals moved into and out of the wetland during the year as either seasonal migrants or individuals with atypical movement. Some of the individuals migrated to farmland areas outside the wetland (the farthest being 69.9 km away). Half of the individuals inhabited the wetland all or most of the year, i.e., 81–100% of their annual home range was within the wetland area. Even among individuals captured at the same site, different seasonal movement patterns were identified. The overlap areas of the home ranges of individuals from the same capture sites were larger than those for individuals from different capture sites (e.g., mean of annual home range overlap with intra-capture sites: 47.7% vs. inter-sites: 1.3%). To achieve more effective ecosystem management including deer management in the wetland, management plans should cover inside and outside of the wetland and separate the population into multiple manageme…
bibliographic citation: Takafumi et al. (2017) Seasonal and year-round use of the Kushiro Wetland, Hokkaido, Japan by sika deer (Cervus nippon yesoensis). PeerJ 5:e3869 https://doi.org/10.7717/peerj.3869
date submitted: 2017-06-20
date accepted: 2017-09-08
issued: 2017-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Takafumi
  given name: Hino
author list: Agent
  family name: Kamii
  given name: Tatsuya
author list: Agent
  family name: Murai
  given name: Takunari
author list: Agent
  family name: Yoshida
  given name: Ryoto
author list: Agent
  family name: Sato
  given name: Atsuki
author list: Agent
  family name: Tachiki
  given name: Yasuyuki
author list: Agent
  family name: Akamatsu
  given name: Rika
author list: Agent
  family name: Yoshida
  given name: Tsuyoshi
doi: 10.7717/peerj.3869
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-12
copyright: ©2017 Takafumi et al.
attribution name: Takafumi et al.

Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks
type: item
type: AcademicArticle
description: Background The emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks for various organisms is a key outcome of the analysis of these data, giving access to a global view of cell functioning. The analysis of metabolic networks may be carried out by simply considering the architecture of the reaction network or by taking into account the stoichiometry of reactions. In both approaches, this analysis is generally centered on the outcome of the network and considers all metabolic compounds to be equivalent in this respect. As in the case of genes and reactions, about which the concept of essentiality has been developed, it seems, however, that some metabolites play crucial roles in system responses, due to the cell structure or the internal wiring of the metabolic network. Results We propose a classification of metabolic compounds according to their capacity to influence the activation of targeted functions (generally the growth phenotype) in a cell. We generalize the concept of essentiality to metabolites and introduce the concept of the phenotypic essential metabolite (PEM) which influences the growth phenotype according to sustainability, producibility or optimal-efficiency criteria. We have developed and made available a tool, Conquests, which implements a method combining graph-based and flux-based analysis, two approaches that are usually considered separately. The identification of PEMs is made effective by using a logical programming approach. Conclusion The exhaustive study of phenotypic essential metabolites in six genome-scale metabolic models suggests that the combination and the comparison of graph, stoichiometry and optimal flux-based criteria allows some features of the metabolic network functionality to be deciphered by focusing on a small number of compounds…
format: application/pdf
format: text/html
creator: Julie Laniau
creator: Clémence Frioux
creator: Jacques Nicolas
creator: Caroline Baroukh
creator: Maria-Paz Cortes
creator: Jeanne Got
creator: Camille Trottier
creator: Damien Eveillard
creator: Anne Siegel
subject: Bioinformatics
subject: Computational Biology
subject: Artificial Intelligence
description: doi:10.7717/peerj.3860
publisher: PeerJ Inc.
rights: © 2017 Laniau et al.
abstract: Background The emergence of functions in biological systems is a long-standing issue that can now be addressed at the cell level with the emergence of high throughput technologies for genome sequencing and phenotyping. The reconstruction of complete metabolic networks for various organisms is a key outcome of the analysis of these data, giving access to a global view of cell functioning. The analysis of metabolic networks may be carried out by simply considering the architecture of the reaction network or by taking into account the stoichiometry of reactions. In both approaches, this analysis is generally centered on the outcome of the network and considers all metabolic compounds to be equivalent in this respect. As in the case of genes and reactions, about which the concept of essentiality has been developed, it seems, however, that some metabolites play crucial roles in system responses, due to the cell structure or the internal wiring of the metabolic network. Results We propose a classification of metabolic compounds according to their capacity to influence the activation of targeted functions (generally the growth phenotype) in a cell. We generalize the concept of essentiality to metabolites and introduce the concept of the phenotypic essential metabolite (PEM) which influences the growth phenotype according to sustainability, producibility or optimal-efficiency criteria. We have developed and made available a tool, Conquests, which implements a method combining graph-based and flux-based analysis, two approaches that are usually considered separately. The identification of PEMs is made effective by using a logical programming approach. Conclusion The exhaustive study of phenotypic essential metabolites in six genome-scale metabolic models suggests that the combination and the comparison of graph, stoichiometry and optimal flux-based criteria allows some features of the metabolic network functionality to be deciphered by focusing on a small number of compounds…
bibliographic citation: Laniau et al. (2017) Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks. PeerJ 5:e3860 https://doi.org/10.7717/peerj.3860
date submitted: 2017-04-19
date accepted: 2017-09-06
issued: 2017-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laniau
  given name: Julie
author list: Agent
  family name: Frioux
  given name: Clémence
author list: Agent
  family name: Nicolas
  given name: Jacques
author list: Agent
  family name: Baroukh
  given name: Caroline
author list: Agent
  family name: Cortes
  given name: Maria-Paz
author list: Agent
  family name: Got
  given name: Jeanne
author list: Agent
  family name: Trottier
  given name: Camille
author list: Agent
  family name: Eveillard
  given name: Damien
author list: Agent
  family name: Siegel
  given name: Anne
doi: 10.7717/peerj.3860
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-12
copyright: ©2017 Laniau et al.
attribution name: Laniau et al.

Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?
type: item
type: AcademicArticle
description: For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternative topologies were highly divergent (Bayes factor >10) from the molecular topology, with the tree inferred exclusively from morphology being the most divergent. The results of this analysis show that a high degree of morphological convergence from substantial gonopod shape divergence generated spurious phylogenetic relationships. These results indicate the impact that a high degree of morphological homoplasy may have had on prior treatments of the family. Using the results of our phylogenetic analysis, we…
format: application/pdf
format: text/html
creator: Jackson C. Means
creator: Paul E. Marek
subject: Biodiversity
subject: Conservation Biology
subject: Entomology
subject: Evolutionary Studies
subject: Taxonomy
description: doi:10.7717/peerj.3854
publisher: PeerJ Inc.
rights: © 2017 Means and Marek
abstract: For the past several centuries, millipede taxonomists have used the morphology of male copulatory structures (modified legs called gonopods), which are strongly variable and suggestive of species-level differences, as a source to understand taxon relationships. Millipedes in the family Xystodesmidae are blind, dispersal-limited and have narrow habitat requirements. Therefore, geographical proximity may instead be a better predictor of evolutionary relationship than morphology, especially since gonopodal anatomy is extremely divergent and similarities may be masked by evolutionary convergence. Here we provide a phylogenetics-based test of the power of morphological versus geographical character sets for resolving phylogenetic relationships in xystodesmid millipedes. Molecular data from 90 species-group taxa in the family were included in a six-gene phylogenetic analysis to provide the basis for comparing trees generated from these alternative character sets. The molecular phylogeny was compared to topologies representing three hypotheses: (1) a prior classification formulated using morphological and geographical data, (2) hierarchical groupings derived from Euclidean geographical distance, and (3) one based solely on morphological data. Euclidean geographical distance was not found to be a better predictor of evolutionary relationship than the prior classification, the latter of which was the most similar to the molecular topology. However, all three of the alternative topologies were highly divergent (Bayes factor >10) from the molecular topology, with the tree inferred exclusively from morphology being the most divergent. The results of this analysis show that a high degree of morphological convergence from substantial gonopod shape divergence generated spurious phylogenetic relationships. These results indicate the impact that a high degree of morphological homoplasy may have had on prior treatments of the family. Using the results of our phylogenetic analysis, we…
bibliographic citation: Means et al. (2017) Is geography an accurate predictor of evolutionary history in the millipede family Xystodesmidae?. PeerJ 5:e3854 https://doi.org/10.7717/peerj.3854
date submitted: 2017-03-29
date accepted: 2017-09-05
issued: 2017-10-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Means
  given name: Jackson C.
author list: Agent
  family name: Marek
  given name: Paul E.
doi: 10.7717/peerj.3854
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-12
copyright: ©2017 Means and Marek
attribution name: Means and Marek

Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral clearance during 2009 pandemic influenza infection
type: item
type: AcademicArticle
description: Background The interaction between influenza virus and the host response to infection clearly plays an important role in determining the outcome of infection. While much is known on the participation of inflammation on the pathogenesis of severe A (H1N1) pandemic 09-influenza virus, its role in the course of non-fatal pneumonia has not been fully addressed. Methods A systems biology approach was used to define gene expression profiles, histology and viral dynamics in the lungs of healthy immune-competent mice with pneumonia caused by a human influenza A (H1N1) pdm09 virus, which successfully resolved the infection. Results Viral infection activated a marked pro-inflammatory response at the lung level paralleling the emergence of histological changes. Cellular immune response and cytokine signaling were the two signaling pathway categories more representative of our analysis. This transcriptome response was associated to viral clearance, and its resolution was accompanied by resolution of histopathology. Discussion These findings suggest a dual role of pulmonary inflammation in viral clearance and development of pneumonia during non-fatal infection caused by the 2009 pandemic influenza virus. Understanding the dynamics of the host’s transcriptomic and virological changes over the course of the infection caused by A (H1N1) pdm09 virus may help identifying the immune response profiles associated with an effective response against influenza virus.
format: application/pdf
format: text/html
creator: Raquel Almansa
creator: Pamela Martínez-Orellana
creator: Lucía Rico
creator: Verónica Iglesias
creator: Alicia Ortega
creator: Beatriz Vidaña
creator: Jorge Martínez
creator: Ana Expósito
creator: María Montoya
creator: Jesús F. Bermejo-Martin
subject: Global Health
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.3915
publisher: PeerJ Inc.
rights: © 2017 Almansa et al.
abstract: Background The interaction between influenza virus and the host response to infection clearly plays an important role in determining the outcome of infection. While much is known on the participation of inflammation on the pathogenesis of severe A (H1N1) pandemic 09-influenza virus, its role in the course of non-fatal pneumonia has not been fully addressed. Methods A systems biology approach was used to define gene expression profiles, histology and viral dynamics in the lungs of healthy immune-competent mice with pneumonia caused by a human influenza A (H1N1) pdm09 virus, which successfully resolved the infection. Results Viral infection activated a marked pro-inflammatory response at the lung level paralleling the emergence of histological changes. Cellular immune response and cytokine signaling were the two signaling pathway categories more representative of our analysis. This transcriptome response was associated to viral clearance, and its resolution was accompanied by resolution of histopathology. Discussion These findings suggest a dual role of pulmonary inflammation in viral clearance and development of pneumonia during non-fatal infection caused by the 2009 pandemic influenza virus. Understanding the dynamics of the host’s transcriptomic and virological changes over the course of the infection caused by A (H1N1) pdm09 virus may help identifying the immune response profiles associated with an effective response against influenza virus.
bibliographic citation: Almansa et al. (2017) Pulmonary transcriptomic responses indicate a dual role of inflammation in pneumonia development and viral clearance during 2009 pandemic influenza infection. PeerJ 5:e3915 https://doi.org/10.7717/peerj.3915
date submitted: 2017-05-23
date accepted: 2017-09-21
issued: 2017-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almansa
  given name: Raquel
author list: Agent
  family name: Martínez-Orellana
  given name: Pamela
author list: Agent
  family name: Rico
  given name: Lucía
author list: Agent
  family name: Iglesias
  given name: Verónica
author list: Agent
  family name: Ortega
  given name: Alicia
author list: Agent
  family name: Vidaña
  given name: Beatriz
author list: Agent
  family name: Martínez
  given name: Jorge
author list: Agent
  family name: Expósito
  given name: Ana
author list: Agent
  family name: Montoya
  given name: María
author list: Agent
  family name: Bermejo-Martin
  given name: Jesús F.
doi: 10.7717/peerj.3915
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-11
copyright: © 2017 Almansa et al.
attribution name: Almansa et al.

The effects of familiarity on escape responses in the Trinidadian guppy (Poecilia reticulata)
type: item
type: AcademicArticle
description: Predation is the main cause of mortality during early life stages. The ability to avoid and evade potential threats is, therefore, favoured to evolve during the early stages of life. It is also during these early stages that the process of familiarization occurs. It has long been recognized that associating with familiar individuals confers antipredator benefits. Yet gaps in our knowledge remain about how predator evasion is affected by social experience during early stages. In this study, we test the hypothesis that familiarization acquired during early life stages improves escape responses. Using the guppy Poecilia reticulata, we examine the effect of different recent social conditions in the three main components of predator evasion. Using high-speed motion analysis, we compared the number of individuals in each test group that responded to a visual stimulus, their reactive distance and magnitude of their response (maximum speed, maximum acceleration and distance) in groups composed either of familiar or non-familiar individuals. Contrary to the prediction, groups composed of familiar individuals were less responsive than groups of unfamiliar individuals. Reactive distance and magnitude of response were more dependent on individual size rather than on familiarity. Larger individuals reached higher maximum speeds and total distances in their escape response. Our result indicates that familiarity is likely to affect behaviour earlier in a predator-prey interaction, which then affects the behavioural component of the response. Taken together, our study contributes to previous ones by distinguishing which components of an escape response are modulated by familiarity.
format: application/pdf
format: text/html
creator: Hayley L. Wolcott
creator: Alfredo F. Ojanguren
creator: Miguel Barbosa
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
description: doi:10.7717/peerj.3899
publisher: PeerJ Inc.
rights: © 2017 Wolcott et al.
abstract: Predation is the main cause of mortality during early life stages. The ability to avoid and evade potential threats is, therefore, favoured to evolve during the early stages of life. It is also during these early stages that the process of familiarization occurs. It has long been recognized that associating with familiar individuals confers antipredator benefits. Yet gaps in our knowledge remain about how predator evasion is affected by social experience during early stages. In this study, we test the hypothesis that familiarization acquired during early life stages improves escape responses. Using the guppy Poecilia reticulata, we examine the effect of different recent social conditions in the three main components of predator evasion. Using high-speed motion analysis, we compared the number of individuals in each test group that responded to a visual stimulus, their reactive distance and magnitude of their response (maximum speed, maximum acceleration and distance) in groups composed either of familiar or non-familiar individuals. Contrary to the prediction, groups composed of familiar individuals were less responsive than groups of unfamiliar individuals. Reactive distance and magnitude of response were more dependent on individual size rather than on familiarity. Larger individuals reached higher maximum speeds and total distances in their escape response. Our result indicates that familiarity is likely to affect behaviour earlier in a predator-prey interaction, which then affects the behavioural component of the response. Taken together, our study contributes to previous ones by distinguishing which components of an escape response are modulated by familiarity.
bibliographic citation: Wolcott et al. (2017) The effects of familiarity on escape responses in the Trinidadian guppy (Poecilia reticulata). PeerJ 5:e3899 https://doi.org/10.7717/peerj.3899
date submitted: 2017-04-19
date accepted: 2017-09-16
issued: 2017-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wolcott
  given name: Hayley L.
author list: Agent
  family name: Ojanguren
  given name: Alfredo F.
author list: Agent
  family name: Barbosa
  given name: Miguel
doi: 10.7717/peerj.3899
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-11
copyright: ©2017 Wolcott et al.
attribution name: Wolcott et al.

Evidence for continual hybridization rather than hybrid speciation between Ligularia duciformis and L. paradoxa (Asteraceae)
type: item
type: AcademicArticle
description: Background Hybrids possess phenotypic traits that are often intermediate between their parental taxa, which commonly serves as evidence of hybridization in morphological analyses. Natural hybridization has been shown to occur frequently in Ligularia (Asteraceae). In a previous study, Ligularia ×maoniushanensis was demonstrated as a natural hybrid species between L. duciformis and L. paradoxa based on morphological and reproductive traits. Methods We used three chloroplast (cpDNA) fragments (psbA-trnH, trnL-rpl32 and trnQ-5′rps16), the nuclear ribosomal internal transcribed spacer (nrITS), and co-dominant SSR and dominant ISSR markers to study natural hybridization between L. duciformis and L. paradoxa growing sympatrically in two locations. Parental taxa were inferred using network analyses of cpDNA and nrITS haplotypes. Admixture among individuals was examined using the Bayesian clustering programs STRUCTURE and NewHybrids based on the SSR and ISSR data; and potential introgression in the SSR loci was assessed using the INTROGRESS package. Results The putative parental species were clearly distinguished from other sympatric Ligularia species by nrITS data, and L. ×maoniushanensis individuals were confirmed to be the hybrid offspring of L. duciformis and L. paradoxa. Moreover, introgression was detected among several individuals morphologically identified as L. duciformis or L. paradoxa. Analyses of the cpDNA data revealed primarily unidirectional hybridization between L. duciformis and L. paradoxa, with L. paradoxa as the maternal parent in Mt. Maoniu, whereas bidirectional but asymmetrical hybridization was inferred to occur in Heihai Lake. The STRUCTURE analyses based on the SSR data detected two distinct clusters among the three taxa. The NewHybrids analyses showed that individuals circumscribed as L. ×maoniushanensis were dominated by early- and later-generation and backcrossing hybrids. The NewHybrids results based on the ISSR data were congruent with SSR resu…
format: application/pdf
format: text/html
creator: Rong Zhang
creator: Xun Gong
creator: Ryan Folk
subject: Evolutionary Studies
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.3884
publisher: PeerJ Inc.
rights: © 2017 Zhang et al.
abstract: Background Hybrids possess phenotypic traits that are often intermediate between their parental taxa, which commonly serves as evidence of hybridization in morphological analyses. Natural hybridization has been shown to occur frequently in Ligularia (Asteraceae). In a previous study, Ligularia ×maoniushanensis was demonstrated as a natural hybrid species between L. duciformis and L. paradoxa based on morphological and reproductive traits. Methods We used three chloroplast (cpDNA) fragments (psbA-trnH, trnL-rpl32 and trnQ-5′rps16), the nuclear ribosomal internal transcribed spacer (nrITS), and co-dominant SSR and dominant ISSR markers to study natural hybridization between L. duciformis and L. paradoxa growing sympatrically in two locations. Parental taxa were inferred using network analyses of cpDNA and nrITS haplotypes. Admixture among individuals was examined using the Bayesian clustering programs STRUCTURE and NewHybrids based on the SSR and ISSR data; and potential introgression in the SSR loci was assessed using the INTROGRESS package. Results The putative parental species were clearly distinguished from other sympatric Ligularia species by nrITS data, and L. ×maoniushanensis individuals were confirmed to be the hybrid offspring of L. duciformis and L. paradoxa. Moreover, introgression was detected among several individuals morphologically identified as L. duciformis or L. paradoxa. Analyses of the cpDNA data revealed primarily unidirectional hybridization between L. duciformis and L. paradoxa, with L. paradoxa as the maternal parent in Mt. Maoniu, whereas bidirectional but asymmetrical hybridization was inferred to occur in Heihai Lake. The STRUCTURE analyses based on the SSR data detected two distinct clusters among the three taxa. The NewHybrids analyses showed that individuals circumscribed as L. ×maoniushanensis were dominated by early- and later-generation and backcrossing hybrids. The NewHybrids results based on the ISSR data were congruent with SSR resu…
bibliographic citation: Zhang et al. (2017) Evidence for continual hybridization rather than hybrid speciation between Ligularia duciformis and L. paradoxa (Asteraceae). PeerJ 5:e3884 https://doi.org/10.7717/peerj.3884
date submitted: 2016-12-12
date accepted: 2017-09-13
issued: 2017-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Rong
author list: Agent
  family name: Gong
  given name: Xun
author list: Agent
  family name: Folk
  given name: Ryan
doi: 10.7717/peerj.3884
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-11
copyright: ©2017 Zhang et al.
attribution name: Zhang et al.

Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata
type: item
type: AcademicArticle
description: Recent research suggests that prior exposure of several months to elevated irradiance induces enhanced thermal tolerance in scleractinian corals. While this tolerance has been reported at the species level, individual coral colonies may react differently due to individual variability in thermal tolerance. As thermal anomalies are predicted to become common in the upcoming future, intraspecific variation may be key to the survival of coral populations. In order to study light-history based thermal stress responses on individual colonies, we developed a preliminary microcosm experiment where three randomly chosen, aquacultured colonies of the model coral Stylophora pistillata were exposed to two irradiance treatments (200 and 400 μmol photons m−2 s−1) for 31 days, followed by artificially induced heat stress (∼33.4 °C). We found different responses to occur at both the intraspecific and the intracolonial levels, as indicated by either equal, less severe, delayed, and/or even non-necrotic responses of corals previously exposed to the irradiance of 400 compared to 200 μmol photons m−2 s−1. In addition, all individual colonies revealed light-enhanced calcification. Finally, elevated irradiance resulted in a lower chlorophyll a concentration in one colony compared to the control treatment, and the same colony displayed more rapid bleaching compared to the other ones. Taken together, this study highlights the potential importance of intra-individual variability in physiological responses of scleractinian corals and provides recommendations for improving methodological designs for future studies.
format: application/pdf
format: text/html
creator: Arjen Tilstra
creator: Tim Wijgerde
creator: Francisco Dini-Andreote
creator: Britas Klemens Eriksson
creator: Joana Falcão Salles
creator: Ido Pen
creator: Ronald Osinga
creator: Christian Wild
subject: Ecology
subject: Marine Biology
subject: Climate Change Biology
description: doi:10.7717/peerj.3802
publisher: PeerJ Inc.
rights: © 2017 Tilstra et al.
abstract: Recent research suggests that prior exposure of several months to elevated irradiance induces enhanced thermal tolerance in scleractinian corals. While this tolerance has been reported at the species level, individual coral colonies may react differently due to individual variability in thermal tolerance. As thermal anomalies are predicted to become common in the upcoming future, intraspecific variation may be key to the survival of coral populations. In order to study light-history based thermal stress responses on individual colonies, we developed a preliminary microcosm experiment where three randomly chosen, aquacultured colonies of the model coral Stylophora pistillata were exposed to two irradiance treatments (200 and 400 μmol photons m−2 s−1) for 31 days, followed by artificially induced heat stress (∼33.4 °C). We found different responses to occur at both the intraspecific and the intracolonial levels, as indicated by either equal, less severe, delayed, and/or even non-necrotic responses of corals previously exposed to the irradiance of 400 compared to 200 μmol photons m−2 s−1. In addition, all individual colonies revealed light-enhanced calcification. Finally, elevated irradiance resulted in a lower chlorophyll a concentration in one colony compared to the control treatment, and the same colony displayed more rapid bleaching compared to the other ones. Taken together, this study highlights the potential importance of intra-individual variability in physiological responses of scleractinian corals and provides recommendations for improving methodological designs for future studies.
bibliographic citation: Tilstra et al. (2017) Light induced intraspecific variability in response to thermal stress in the hard coral Stylophora pistillata. PeerJ 5:e3802 https://doi.org/10.7717/peerj.3802
date submitted: 2017-02-16
date accepted: 2017-08-23
issued: 2017-10-11
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tilstra
  given name: Arjen
author list: Agent
  family name: Wijgerde
  given name: Tim
author list: Agent
  family name: Dini-Andreote
  given name: Francisco
author list: Agent
  family name: Eriksson
  given name: Britas Klemens
author list: Agent
  family name: Salles
  given name: Joana Falcão
author list: Agent
  family name: Pen
  given name: Ido
author list: Agent
  family name: Osinga
  given name: Ronald
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.3802
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-11
copyright: © 2017 Tilstra et al.
attribution name: Tilstra et al.

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