PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Accuracy of conventional identification methods used for Enterobacteriaceae isolates in three Nigerian hospitals
items: An early bothremydid (Testudines, Pleurodira) from the Late Cretaceous (Cenomanian) of Utah, North America
items: Dynamics and stability of directional jumps in the desert locust
items: Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells
items: Investigating the spatial distribution and effects of nearshore topography on Acropora cervicornis abundance in Southeast Florida
items: XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves
items: Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan
items: Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections
items: Not always a matter of context: direct effects of red on arousal but context-dependent moderations on valence
items: The origin of widespread species in a poor dispersing lineage (diving beetle genus Deronectes)

Accuracy of conventional identification methods used for Enterobacteriaceae isolates in three Nigerian hospitals
type: item
type: AcademicArticle
description: Background Enterobacteriaceae are ubiquitously present in nature and can be found in the intestinal tract of humans and animals as commensal flora. Multidrug-resistant Enterobacteriaceae are increasingly reported and are a threat to public health implicating a need for accurate identification of the isolates to species level. In developing countries, identification of bacteria basically depends on conventional methods: culture and phenotypic methods that hamper the accurate identification of bacteria. In this study, matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technique was compared to conventional identification techniques. Materials and Methods In total, 147 Enterobacteriaceae isolates were collected from March to May 2015 from three medical microbiology laboratories of hospitals in Edo state, Nigeria, after being tested according to the individual laboratories standard operating procedures. All isolates were stored at −20°C until tested centrally by MALDI-TOF MS. Results One hundred and forty five (98.6%) isolates had a MALDI Biotyper best score > or =2.0, indicating a secure genus and probable species identification; and 2(1.36%) isolates had a best score <2.0 indicating probable genus identification. Isolates with best scores of > or =2.0 comprised nine genera and 10 species, respectively. A total of 57.2% and 33.1% of isolates identified had agreement between MALDI-TOF MS and conventional techniques for identification at genus and species level, respectively, when analyzing bacteria with MALDI Biotyper best scores > or =2.0. Conclusion The results of our study show that the applied conventional identification techniques for Enterobacteriaceae in the investigated Nigerian hospitals are not very accurate. Use of state-of-the-art identification technologies for microorganisms is necessary to guarantee comparability of bacteriological results.
format: application/pdf
format: text/html
creator: Christiana Jesumirhewe
creator: Peter Oladejo Ogunlowo
creator: Mitsan Olley
creator: Burkhard Springer
creator: Franz Allerberger
creator: Werner Ruppitsch
subject: Microbiology
subject: Public Health
description: doi:10.7717/peerj.2511
publisher: PeerJ Inc.
rights: © 2016 Jesumirhewe et al.
abstract: Background Enterobacteriaceae are ubiquitously present in nature and can be found in the intestinal tract of humans and animals as commensal flora. Multidrug-resistant Enterobacteriaceae are increasingly reported and are a threat to public health implicating a need for accurate identification of the isolates to species level. In developing countries, identification of bacteria basically depends on conventional methods: culture and phenotypic methods that hamper the accurate identification of bacteria. In this study, matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technique was compared to conventional identification techniques. Materials and Methods In total, 147 Enterobacteriaceae isolates were collected from March to May 2015 from three medical microbiology laboratories of hospitals in Edo state, Nigeria, after being tested according to the individual laboratories standard operating procedures. All isolates were stored at −20°C until tested centrally by MALDI-TOF MS. Results One hundred and forty five (98.6%) isolates had a MALDI Biotyper best score > or =2.0, indicating a secure genus and probable species identification; and 2(1.36%) isolates had a best score <2.0 indicating probable genus identification. Isolates with best scores of > or =2.0 comprised nine genera and 10 species, respectively. A total of 57.2% and 33.1% of isolates identified had agreement between MALDI-TOF MS and conventional techniques for identification at genus and species level, respectively, when analyzing bacteria with MALDI Biotyper best scores > or =2.0. Conclusion The results of our study show that the applied conventional identification techniques for Enterobacteriaceae in the investigated Nigerian hospitals are not very accurate. Use of state-of-the-art identification technologies for microorganisms is necessary to guarantee comparability of bacteriological results.
bibliographic citation: Jesumirhewe et al. (2016) Accuracy of conventional identification methods used for Enterobacteriaceae isolates in three Nigerian hospitals. PeerJ 4:e2511 https://doi.org/10.7717/peerj.2511
date submitted: 2016-06-03
date accepted: 2016-08-31
issued: 2016-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jesumirhewe
  given name: Christiana
author list: Agent
  family name: Ogunlowo
  given name: Peter Oladejo
author list: Agent
  family name: Olley
  given name: Mitsan
author list: Agent
  family name: Springer
  given name: Burkhard
author list: Agent
  family name: Allerberger
  given name: Franz
author list: Agent
  family name: Ruppitsch
  given name: Werner
doi: 10.7717/peerj.2511
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-28
copyright: ©2016 Jesumirhewe et al.
attribution name: Jesumirhewe et al.

An early bothremydid (Testudines, Pleurodira) from the Late Cretaceous (Cenomanian) of Utah, North America
type: item
type: AcademicArticle
description: Background Bothremydidae is a clade of extinct pleurodiran turtles known from the Cretaceous to Paleogene of Africa, Europe, India, Madagascar, and North and South America. The group is most diverse during the Late Cretaceous to Paleogene of Africa. Little is known, however, about the early evolution of the group. Methods We here figure and describe a fossil turtle from early Late Cretaceous deposits exposed at MacFarlane Mine in Cedar Canyon, southwestern Utah, USA. The sediments associated with the new turtle are utilized to infer its stratigraphic provenience and the depositional settings in which it was deposited. The fossil is compared to previously described fossil pleurodires, integrated into a modified phylogenetic analysis of pelomedusoid turtles, and the biogeography of bothremydid turtles is reassessed. In light of the novel phylogenetic hypotheses, six previously established taxon names are converted to phylogenetically defined clade names to aid communication. Results The new fossil turtle can be inferred with confidence to have originated from a brackish water facies within the late Cenomanian Culver Coal Zone of the Naturita Formation. The fossil can be distinguished from all other previously described pleurodires and is therefore designated as a new taxon, Paiutemys tibert gen. et. sp. nov. Phylogenetic analysis places the new taxon as sister to the European Polysternon provinciale, Foxemys trabanti and Foxemys mechinorum at the base of Bothremydinae. Biogeographic analysis suggests that bothremydids originated as continental turtles in Gondwana, but that bothremydines adapted to near-shore marine conditions and therefore should be seen as having a circum-Atlantic distribution.
format: application/pdf
format: text/html
creator: Walter G. Joyce
creator: Tyler R. Lyson
creator: James I. Kirkland
subject: Paleontology
description: doi:10.7717/peerj.2502
publisher: PeerJ Inc.
rights: © 2016 Joyce et al.
abstract: Background Bothremydidae is a clade of extinct pleurodiran turtles known from the Cretaceous to Paleogene of Africa, Europe, India, Madagascar, and North and South America. The group is most diverse during the Late Cretaceous to Paleogene of Africa. Little is known, however, about the early evolution of the group. Methods We here figure and describe a fossil turtle from early Late Cretaceous deposits exposed at MacFarlane Mine in Cedar Canyon, southwestern Utah, USA. The sediments associated with the new turtle are utilized to infer its stratigraphic provenience and the depositional settings in which it was deposited. The fossil is compared to previously described fossil pleurodires, integrated into a modified phylogenetic analysis of pelomedusoid turtles, and the biogeography of bothremydid turtles is reassessed. In light of the novel phylogenetic hypotheses, six previously established taxon names are converted to phylogenetically defined clade names to aid communication. Results The new fossil turtle can be inferred with confidence to have originated from a brackish water facies within the late Cenomanian Culver Coal Zone of the Naturita Formation. The fossil can be distinguished from all other previously described pleurodires and is therefore designated as a new taxon, Paiutemys tibert gen. et. sp. nov. Phylogenetic analysis places the new taxon as sister to the European Polysternon provinciale, Foxemys trabanti and Foxemys mechinorum at the base of Bothremydinae. Biogeographic analysis suggests that bothremydids originated as continental turtles in Gondwana, but that bothremydines adapted to near-shore marine conditions and therefore should be seen as having a circum-Atlantic distribution.
bibliographic citation: Joyce et al. (2016) An early bothremydid (Testudines, Pleurodira) from the Late Cretaceous (Cenomanian) of Utah, North America. PeerJ 4:e2502 https://doi.org/10.7717/peerj.2502
date submitted: 2016-04-28
date accepted: 2016-08-29
issued: 2016-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Joyce
  given name: Walter G.
author list: Agent
  family name: Lyson
  given name: Tyler R.
author list: Agent
  family name: Kirkland
  given name: James I.
doi: 10.7717/peerj.2502
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-28
copyright: ©2016 Joyce et al.
attribution name: Joyce et al.

Dynamics and stability of directional jumps in the desert locust
type: item
type: AcademicArticle
description: Locusts are known for their ability to jump large distances to avoid predation. The jump also serves to launch the adult locust into the air in order to initiate flight. Various aspects of this important behavior have been studied extensively, from muscle physiology and biomechanics, to the energy storage systems involved in powering the jump, and more. Less well understood are the mechanisms participating in control of the jump trajectory. Here we utilise video monitoring and careful analysis of experimental directional jumps by adult desert locusts, together with dynamic computer simulation, in order to understand how the locusts control the direction and elevation of the jump, the residual angular velocities resulting from the jump and the timing of flapping-flight initiation. Our study confirms and expands early findings regarding the instrumental role of the initial body position and orientation. Both real-jump video analysis and simulations based on our expanded dynamical model demonstrate that the initial body coordinates of position (relative to the hind-legs ground-contact points) are dominant in predicting the jumps’ azimuth and elevation angles. We also report a strong linear correlation between the jumps’ pitch-angular-velocity and flight initiation timing, such that head downwards rotations lead to earlier wing opening. In addition to offering important insights into the bio-mechanical principles of locust jumping and flight initiation, the findings from this study will be used in designing future prototypes of a bio-inspired miniature jumping robot that will be employed in animal behaviour studies and environmental monitoring applications.
format: application/pdf
format: text/html
creator: Omer Gvirsman
creator: Gabor Kosa
creator: Amir Ayali
subject: Animal Behavior
subject: Bioengineering
subject: Biophysics
subject: Entomology
description: doi:10.7717/peerj.2481
publisher: PeerJ Inc.
rights: © 2016 Gvirsman et al.
abstract: Locusts are known for their ability to jump large distances to avoid predation. The jump also serves to launch the adult locust into the air in order to initiate flight. Various aspects of this important behavior have been studied extensively, from muscle physiology and biomechanics, to the energy storage systems involved in powering the jump, and more. Less well understood are the mechanisms participating in control of the jump trajectory. Here we utilise video monitoring and careful analysis of experimental directional jumps by adult desert locusts, together with dynamic computer simulation, in order to understand how the locusts control the direction and elevation of the jump, the residual angular velocities resulting from the jump and the timing of flapping-flight initiation. Our study confirms and expands early findings regarding the instrumental role of the initial body position and orientation. Both real-jump video analysis and simulations based on our expanded dynamical model demonstrate that the initial body coordinates of position (relative to the hind-legs ground-contact points) are dominant in predicting the jumps’ azimuth and elevation angles. We also report a strong linear correlation between the jumps’ pitch-angular-velocity and flight initiation timing, such that head downwards rotations lead to earlier wing opening. In addition to offering important insights into the bio-mechanical principles of locust jumping and flight initiation, the findings from this study will be used in designing future prototypes of a bio-inspired miniature jumping robot that will be employed in animal behaviour studies and environmental monitoring applications.
bibliographic citation: Gvirsman et al. (2016) Dynamics and stability of directional jumps in the desert locust. PeerJ 4:e2481 https://doi.org/10.7717/peerj.2481
date submitted: 2016-06-20
date accepted: 2016-08-23
issued: 2016-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gvirsman
  given name: Omer
author list: Agent
  family name: Kosa
  given name: Gabor
author list: Agent
  family name: Ayali
  given name: Amir
doi: 10.7717/peerj.2481
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-28
copyright: ©2016 Gvirsman et al.
attribution name: Gvirsman et al.

Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells
type: item
type: AcademicArticle
description: Background Abnormal proliferation of vascular smooth muscle cells (VSMC) is a major cause of cardiovascular diseases (CVDs). Many studies suggest that vascular injury triggers VSMC dedifferentiation, which results in VSMC changes from a contractile to a synthetic phenotype; however, the underlying molecular mechanisms are still unclear. Methods In this study, we examined how VSMC responds under mechanical stress by using time-course microarray data. A three-phase study was proposed to investigate the stress-induced differentially expressed genes (DEGs) in VSMC. First, DEGs were identified by using the moderated t-statistics test. Second, more DEGs were inferred by using the Gaussian Graphical Model (GGM). Finally, the topological parameters-based method and cluster analysis approach were employed to predict the last batch of DEGs. To identify the potential drugs for vascular diseases involve VSMC proliferation, the drug-gene interaction database, Connectivity Map (cMap) was employed. Success of the predictions were determined using in-vitro data, i.e. MTT and clonogenic assay. Results Based on the differential expression calculation, at least 23 DEGs were found, and the findings were qualified by previous studies on VSMC. The results of gene set enrichment analysis indicated that the most often found enriched biological processes are cell-cycle-related processes. Furthermore, more stress-induced genes, well supported by literature, were found by applying graph theory to the gene association network (GAN). Finally, we showed that by processing the cMap input queries with a cluster algorithm, we achieved a substantial increase in the number of potential drugs with experimental IC50 measurements. With this novel approach, we have not only successfully identified the DEGs, but also improved the DEGs prediction by performing the topological and cluster analysis. Moreover, the findings are remarkably validated and in line with the literature. Furthermore, the cMap and Dru…
format: application/pdf
format: text/html
creator: Chien-Hung Huang
creator: Jin-Shuei Ciou
creator: Shun-Tsung Chen
creator: Victor C. Kok
creator: Yi Chung
creator: Jeffrey J. P. Tsai
creator: Nilubon Kurubanjerdjit
creator: Chi-Ying F. Huang
creator: Ka-Lok Ng
subject: Bioinformatics
subject: Molecular Biology
subject: Drugs and Devices
description: doi:10.7717/peerj.2478
publisher: PeerJ Inc.
rights: © 2016 Huang et al.
abstract: Background Abnormal proliferation of vascular smooth muscle cells (VSMC) is a major cause of cardiovascular diseases (CVDs). Many studies suggest that vascular injury triggers VSMC dedifferentiation, which results in VSMC changes from a contractile to a synthetic phenotype; however, the underlying molecular mechanisms are still unclear. Methods In this study, we examined how VSMC responds under mechanical stress by using time-course microarray data. A three-phase study was proposed to investigate the stress-induced differentially expressed genes (DEGs) in VSMC. First, DEGs were identified by using the moderated t-statistics test. Second, more DEGs were inferred by using the Gaussian Graphical Model (GGM). Finally, the topological parameters-based method and cluster analysis approach were employed to predict the last batch of DEGs. To identify the potential drugs for vascular diseases involve VSMC proliferation, the drug-gene interaction database, Connectivity Map (cMap) was employed. Success of the predictions were determined using in-vitro data, i.e. MTT and clonogenic assay. Results Based on the differential expression calculation, at least 23 DEGs were found, and the findings were qualified by previous studies on VSMC. The results of gene set enrichment analysis indicated that the most often found enriched biological processes are cell-cycle-related processes. Furthermore, more stress-induced genes, well supported by literature, were found by applying graph theory to the gene association network (GAN). Finally, we showed that by processing the cMap input queries with a cluster algorithm, we achieved a substantial increase in the number of potential drugs with experimental IC50 measurements. With this novel approach, we have not only successfully identified the DEGs, but also improved the DEGs prediction by performing the topological and cluster analysis. Moreover, the findings are remarkably validated and in line with the literature. Furthermore, the cMap and Dru…
bibliographic citation: Huang et al. (2016) Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells. PeerJ 4:e2478 https://doi.org/10.7717/peerj.2478
date submitted: 2016-03-29
date accepted: 2016-08-23
issued: 2016-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Chien-Hung
author list: Agent
  family name: Ciou
  given name: Jin-Shuei
author list: Agent
  family name: Chen
  given name: Shun-Tsung
author list: Agent
  family name: Kok
  given name: Victor C.
author list: Agent
  family name: Chung
  given name: Yi
author list: Agent
  family name: Tsai
  given name: Jeffrey J. P.
author list: Agent
  family name: Kurubanjerdjit
  given name: Nilubon
author list: Agent
  family name: Huang
  given name: Chi-Ying F.
author list: Agent
  family name: Ng
  given name: Ka-Lok
doi: 10.7717/peerj.2478
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-28
copyright: © 2016 Huang et al.
attribution name: Huang et al.

Investigating the spatial distribution and effects of nearshore topography on Acropora cervicornis abundance in Southeast Florida
type: item
type: AcademicArticle
description: Dense Acropora cervicornis aggregations, or patches, have been documented within nearshore habitats in Southeast Florida (SE FL) despite close proximity to numerous anthropogenic stressors and subjection to frequent natural disturbance events. Limited information has been published concerning the distribution and abundance of A. cervicornis outside of these known dense patches. The first goal of this study was to conduct a spatially extensive and inclusive survey (9.78 km2) to determine whether A. cervicornis distribution in the nearshore habitat of SE FL was spatially uniform or clustered. The second goal was to investigate potential relationships between broad-scale seafloor topography and A. cervicornis abundance using high resolution bathymetric data. Acropora cervicornis was distributed throughout the study area, and the Getis-Ord Gi* statistic and Anselin Local Moran’s I spatial cluster analysis showed significant clustering along topographic features termed ridge crests. Significant clustering was further supported by the inverse distance weighted surface model. Ordinal logistic regression indicated 1) as distance from a ridge increases, odds of reduced A. cervicornis abundance increases; 2) as topographic elevation increases, odds of increased abundance increases; and 3) as mean depth increases, odds of increased abundance increases. This study provides detailed information on A. cervicornis distribution and abundance at a regional scale and supports modeling its distributions in similar habitats elsewhere throughout the western Atlantic and Caribbean. Acropora cervicornis is frequently observed and in areas an abundant species within the nearshore habitat along the SE FL portion of the Florida Reef Tract (FRT). This study provides a better understanding of local habitat associations thus facilitating appropriate management of the nearshore environment and species conservation. The portion of the FRT between Hillsboro and Port Everglades inlets should be con…
format: application/pdf
format: text/html
creator: Nicole L. D’Antonio
creator: David S. Gilliam
creator: Brian K. Walker
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.2473
publisher: PeerJ Inc.
rights: © 2016 D’Antonio et al.
abstract: Dense Acropora cervicornis aggregations, or patches, have been documented within nearshore habitats in Southeast Florida (SE FL) despite close proximity to numerous anthropogenic stressors and subjection to frequent natural disturbance events. Limited information has been published concerning the distribution and abundance of A. cervicornis outside of these known dense patches. The first goal of this study was to conduct a spatially extensive and inclusive survey (9.78 km2) to determine whether A. cervicornis distribution in the nearshore habitat of SE FL was spatially uniform or clustered. The second goal was to investigate potential relationships between broad-scale seafloor topography and A. cervicornis abundance using high resolution bathymetric data. Acropora cervicornis was distributed throughout the study area, and the Getis-Ord Gi* statistic and Anselin Local Moran’s I spatial cluster analysis showed significant clustering along topographic features termed ridge crests. Significant clustering was further supported by the inverse distance weighted surface model. Ordinal logistic regression indicated 1) as distance from a ridge increases, odds of reduced A. cervicornis abundance increases; 2) as topographic elevation increases, odds of increased abundance increases; and 3) as mean depth increases, odds of increased abundance increases. This study provides detailed information on A. cervicornis distribution and abundance at a regional scale and supports modeling its distributions in similar habitats elsewhere throughout the western Atlantic and Caribbean. Acropora cervicornis is frequently observed and in areas an abundant species within the nearshore habitat along the SE FL portion of the Florida Reef Tract (FRT). This study provides a better understanding of local habitat associations thus facilitating appropriate management of the nearshore environment and species conservation. The portion of the FRT between Hillsboro and Port Everglades inlets should be con…
bibliographic citation: D’Antonio et al. (2016) Investigating the spatial distribution and effects of nearshore topography on Acropora cervicornis abundance in Southeast Florida. PeerJ 4:e2473 https://doi.org/10.7717/peerj.2473
date submitted: 2016-01-21
date accepted: 2016-08-23
issued: 2016-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: D’Antonio
  given name: Nicole L.
author list: Agent
  family name: Gilliam
  given name: David S.
author list: Agent
  family name: Walker
  given name: Brian K.
doi: 10.7717/peerj.2473
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-28
copyright: © 2016 D’Antonio et al.
attribution name: D’Antonio et al.

XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves
type: item
type: AcademicArticle
description: The rice XA21 receptor kinase confers robust resistance to the bacterial pathogen Xanthomonas oryzaepv. oryzae (Xoo). We developed a detached leaf infection assay to quickly and reliably measure activation of the XA21-mediated immune response using genetic markers. We used RNA sequencing of elf18 treated EFR:XA21:GFP plants to identify candidate genes that could serve as markers for XA21 activation. From this analysis, we identified eight genes that are up-regulated in both in elf18 treated EFR:XA21:GFP rice leaves and Xoo infected XA21 rice leaves. These results provide a rapid and reliable method to assess bacterial-rice interactions.
format: application/pdf
format: text/html
creator: Nicholas C. Thomas
creator: Benjamin Schwessinger
creator: Furong Liu
creator: Huamin Chen
creator: Tong Wei
creator: Yen P. Nguyen
creator: Isaac W.F. Shaker
creator: Pamela C. Ronald
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.2446
publisher: PeerJ Inc.
rights: © 2016 Thomas et al.
abstract: The rice XA21 receptor kinase confers robust resistance to the bacterial pathogen Xanthomonas oryzaepv. oryzae (Xoo). We developed a detached leaf infection assay to quickly and reliably measure activation of the XA21-mediated immune response using genetic markers. We used RNA sequencing of elf18 treated EFR:XA21:GFP plants to identify candidate genes that could serve as markers for XA21 activation. From this analysis, we identified eight genes that are up-regulated in both in elf18 treated EFR:XA21:GFP rice leaves and Xoo infected XA21 rice leaves. These results provide a rapid and reliable method to assess bacterial-rice interactions.
bibliographic citation: Thomas et al. (2016) XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves. PeerJ 4:e2446 https://doi.org/10.7717/peerj.2446
date submitted: 2016-07-14
date accepted: 2016-08-14
issued: 2016-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thomas
  given name: Nicholas C.
author list: Agent
  family name: Schwessinger
  given name: Benjamin
author list: Agent
  family name: Liu
  given name: Furong
author list: Agent
  family name: Chen
  given name: Huamin
author list: Agent
  family name: Wei
  given name: Tong
author list: Agent
  family name: Nguyen
  given name: Yen P.
author list: Agent
  family name: Shaker
  given name: Isaac W.F.
author list: Agent
  family name: Ronald
  given name: Pamela C.
doi: 10.7717/peerj.2446
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-28
copyright: ©2016 Thomas et al.
attribution name: Thomas et al.

Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan
type: item
type: AcademicArticle
description: The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan.
format: application/pdf
format: text/html
creator: Taha Soliman
creator: Okuto Takama
creator: Iria Fernandez-Silva
creator: James D. Reimer
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
description: doi:10.7717/peerj.2410
publisher: PeerJ Inc.
rights: © 2016 Soliman et al.
abstract: The greenfish sea cucumber Stichopus chloronotus is an economically and ecologically important sea cucumber species throughout its range. This species is widely distributed, inhabiting coral reefs of the Indo-Pacific Ocean. Our study evaluated population genetic structure and levels of genetic diversity in southern Japan. A total of 180 individuals were collected from eight locations from Okinawa and Okinoerabu Islands and sequenced using mitochondrial 16S ribosomal DNA (16S) and nuclear histone H3 (H3) gene. Only three 16S haplotypes were detected (518 bp) with haplotype diversity ranging from 0 to 0.56 and nucleotide diversity from 0 to 0.1%. H3 showed no variation among the studied locations. It is plausible that such results could be due to a shift to asexual reproduction. Additionally, the presence of the species on the east coast of Okinawa could only be detected in one location and all individuals consisted of a single haplotype. Genetic differences between the east and west coasts of Okinawa have been noticed in other coral reef organisms, and attributed to either ecological or biogeographical historical differences between the coasts due to differing levels of isolation during Pleistocene ice ages. Results from the present study should inform management and conservation policies of S. chloronotus in southern Japan.
bibliographic citation: Soliman et al. (2016) Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan. PeerJ 4:e2410 https://doi.org/10.7717/peerj.2410
date submitted: 2016-03-17
date accepted: 2016-08-04
issued: 2016-09-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soliman
  given name: Taha
author list: Agent
  family name: Takama
  given name: Okuto
author list: Agent
  family name: Fernandez-Silva
  given name: Iria
author list: Agent
  family name: Reimer
  given name: James D.
doi: 10.7717/peerj.2410
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-28
copyright: ©2016 Soliman et al.
attribution name: Soliman et al.

Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections
type: item
type: AcademicArticle
description: Koi herpesvirus disease (KHVD) is an emerging disease that causes mass mortality in koi and common carp, Cyprinus carpio L. Its causative agent is Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV). Although data on the pathogenesis of this deadly virus is relatively abundant in the literature, still little is known about its genomic diversity and about the molecular mechanisms that lead to such a high virulence. In this context, we developed a new strategy for sequencing full-length CyHV-3 genomes directly from infected fish tissues. Total genomic DNA extracted from carp gill tissue was specifically enriched with CyHV-3 sequences through hybridization to a set of nearly 2 million overlapping probes designed to cover the entire genome length, using KHV-J sequence (GenBank accession number AP008984) as reference. Applied to 7 CyHV-3 specimens from Poland and Indonesia, this targeted genomic enrichment enabled recovery of the full genomes with >99.9% reference coverage. The enrichment rate was directly correlated to the estimated number of viral copies contained in the DNA extracts used for library preparation, which varied between ∼5000 and ∼2×107. The average sequencing depth was >200 for all samples, thus allowing the search for variants with high confidence. Sequence analyses highlighted a significant proportion of intra-specimen sequence heterogeneity, suggesting the presence of mixed infections in all investigated fish. They also showed that inter-specimen genetic diversity at the genome scale was very low (>99.95% of sequence identity). By enabling full genome comparisons directly from infected fish tissues, this new method will be valuable to trace outbreaks rapidly and at a reasonable cost, and in turn to understand the transmission routes of CyHV-3.
format: application/pdf
format: text/html
creator: Saliha Hammoumi
creator: Tatiana Vallaeys
creator: Ayi Santika
creator: Philippe Leleux
creator: Ewa Borzym
creator: Christophe Klopp
creator: Jean-Christophe Avarre
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.2516
publisher: PeerJ Inc.
rights: © 2016 Hammoumi et al.
abstract: Koi herpesvirus disease (KHVD) is an emerging disease that causes mass mortality in koi and common carp, Cyprinus carpio L. Its causative agent is Cyprinid herpesvirus 3 (CyHV-3), also known as koi herpesvirus (KHV). Although data on the pathogenesis of this deadly virus is relatively abundant in the literature, still little is known about its genomic diversity and about the molecular mechanisms that lead to such a high virulence. In this context, we developed a new strategy for sequencing full-length CyHV-3 genomes directly from infected fish tissues. Total genomic DNA extracted from carp gill tissue was specifically enriched with CyHV-3 sequences through hybridization to a set of nearly 2 million overlapping probes designed to cover the entire genome length, using KHV-J sequence (GenBank accession number AP008984) as reference. Applied to 7 CyHV-3 specimens from Poland and Indonesia, this targeted genomic enrichment enabled recovery of the full genomes with >99.9% reference coverage. The enrichment rate was directly correlated to the estimated number of viral copies contained in the DNA extracts used for library preparation, which varied between ∼5000 and ∼2×107. The average sequencing depth was >200 for all samples, thus allowing the search for variants with high confidence. Sequence analyses highlighted a significant proportion of intra-specimen sequence heterogeneity, suggesting the presence of mixed infections in all investigated fish. They also showed that inter-specimen genetic diversity at the genome scale was very low (>99.95% of sequence identity). By enabling full genome comparisons directly from infected fish tissues, this new method will be valuable to trace outbreaks rapidly and at a reasonable cost, and in turn to understand the transmission routes of CyHV-3.
bibliographic citation: Hammoumi et al. (2016) Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections. PeerJ 4:e2516 https://doi.org/10.7717/peerj.2516
date submitted: 2016-05-05
date accepted: 2016-09-01
issued: 2016-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hammoumi
  given name: Saliha
author list: Agent
  family name: Vallaeys
  given name: Tatiana
author list: Agent
  family name: Santika
  given name: Ayi
author list: Agent
  family name: Leleux
  given name: Philippe
author list: Agent
  family name: Borzym
  given name: Ewa
author list: Agent
  family name: Klopp
  given name: Christophe
author list: Agent
  family name: Avarre
  given name: Jean-Christophe
doi: 10.7717/peerj.2516
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-27
copyright: ©2016 Hammoumi et al.
attribution name: Hammoumi et al.

Not always a matter of context: direct effects of red on arousal but context-dependent moderations on valence
type: item
type: AcademicArticle
description: The arousal theory of color proposes that red is associated with arousal. Research on the color-in-context theory, in turn, states that the context in which red is perceived influences its valence-related meaning and behavioral responses to it. This study faces and integrates these theories by examining the influence of red on both arousal and valence perceptions of test-relevant and neutral stimuli, rendering a color 2 (red vs. blue) × context 2 (test vs. neutral) between-subjects design. Participants rated different pictures regarding their arousal and valence component, respectively. In line with the assumptions of both theories, red increased arousal perceptions of stimuli irrespective of their valence but a context × color interaction was found for valence perceptions: for participants viewing test-relevant pictures, red increased their perceptions of negativity compared to neutral pictures. The present study shows that both theories are actually compatible when differentiating the arousal and valence component.
format: application/pdf
format: text/html
creator: Vanessa L. Buechner
creator: Markus A. Maier
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2515
publisher: PeerJ Inc.
rights: © 2016 Buechner and Maier
abstract: The arousal theory of color proposes that red is associated with arousal. Research on the color-in-context theory, in turn, states that the context in which red is perceived influences its valence-related meaning and behavioral responses to it. This study faces and integrates these theories by examining the influence of red on both arousal and valence perceptions of test-relevant and neutral stimuli, rendering a color 2 (red vs. blue) × context 2 (test vs. neutral) between-subjects design. Participants rated different pictures regarding their arousal and valence component, respectively. In line with the assumptions of both theories, red increased arousal perceptions of stimuli irrespective of their valence but a context × color interaction was found for valence perceptions: for participants viewing test-relevant pictures, red increased their perceptions of negativity compared to neutral pictures. The present study shows that both theories are actually compatible when differentiating the arousal and valence component.
bibliographic citation: Buechner et al. (2016) Not always a matter of context: direct effects of red on arousal but context-dependent moderations on valence. PeerJ 4:e2515 https://doi.org/10.7717/peerj.2515
date submitted: 2016-06-01
date accepted: 2016-09-01
issued: 2016-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buechner
  given name: Vanessa L.
author list: Agent
  family name: Maier
  given name: Markus A.
doi: 10.7717/peerj.2515
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-27
copyright: ©2016 Buechner and Maier
attribution name: Buechner and Maier

The origin of widespread species in a poor dispersing lineage (diving beetle genus Deronectes)
type: item
type: AcademicArticle
description: In most lineages, most species have restricted geographic ranges, with only few reaching widespread distributions. How these widespread species reached their current ranges is an intriguing biogeographic and evolutionary question, especially in groups known to be poor dispersers. We reconstructed the biogeographic and temporal origin of the widespread species in a lineage with particularly poor dispersal capabilities, the diving beetle genus Deronectes (Dytiscidae). Most of the ca. 60 described species of Deronectes have narrow ranges in the Mediterranean area, with only four species with widespread European distributions. We sequenced four mitochondrial and two nuclear genes of 297 specimens of 109 different populations covering the entire distribution of the four lineages of Deronectes, including widespread species. Using Bayesian probabilities with an a priori evolutionary rate, we performed (1) a global phylogeny/phylogeography to estimate the relationships of the main lineages within each group and root them, and (2) demographic analyses of the best population coalescent model for each species group, including a reconstruction of the geographical history estimated from the distribution of the sampled localities. We also selected 56 specimens to test for the presence of Wolbachia, a maternally transmitted parasite that can alter the patterns of mtDNA variability. All species of the four studied groups originated in the southern Mediterranean peninsulas and were estimated to be of Pleistocene origin. In three of the four widespread species, the central and northern European populations were nested within those in the northern areas of the Anatolian, Balkan and Iberian peninsulas respectively, suggesting a range expansion at the edge of the southern refugia. In the Mediterranean peninsulas the widespread European species were replaced by vicariant taxa of recent origin. The fourth species (D. moestus) was proven to be a composite of unrecognised lineages with more…
format: application/pdf
format: text/html
creator: David García-Vázquez
creator: Ignacio Ribera
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.2514
publisher: PeerJ Inc.
rights: © 2016 García-Vázquez and Ribera
abstract: In most lineages, most species have restricted geographic ranges, with only few reaching widespread distributions. How these widespread species reached their current ranges is an intriguing biogeographic and evolutionary question, especially in groups known to be poor dispersers. We reconstructed the biogeographic and temporal origin of the widespread species in a lineage with particularly poor dispersal capabilities, the diving beetle genus Deronectes (Dytiscidae). Most of the ca. 60 described species of Deronectes have narrow ranges in the Mediterranean area, with only four species with widespread European distributions. We sequenced four mitochondrial and two nuclear genes of 297 specimens of 109 different populations covering the entire distribution of the four lineages of Deronectes, including widespread species. Using Bayesian probabilities with an a priori evolutionary rate, we performed (1) a global phylogeny/phylogeography to estimate the relationships of the main lineages within each group and root them, and (2) demographic analyses of the best population coalescent model for each species group, including a reconstruction of the geographical history estimated from the distribution of the sampled localities. We also selected 56 specimens to test for the presence of Wolbachia, a maternally transmitted parasite that can alter the patterns of mtDNA variability. All species of the four studied groups originated in the southern Mediterranean peninsulas and were estimated to be of Pleistocene origin. In three of the four widespread species, the central and northern European populations were nested within those in the northern areas of the Anatolian, Balkan and Iberian peninsulas respectively, suggesting a range expansion at the edge of the southern refugia. In the Mediterranean peninsulas the widespread European species were replaced by vicariant taxa of recent origin. The fourth species (D. moestus) was proven to be a composite of unrecognised lineages with more…
bibliographic citation: García-Vázquez et al. (2016) The origin of widespread species in a poor dispersing lineage (diving beetle genus Deronectes). PeerJ 4:e2514 https://doi.org/10.7717/peerj.2514
date submitted: 2016-06-23
date accepted: 2016-09-01
issued: 2016-09-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Vázquez
  given name: David
author list: Agent
  family name: Ribera
  given name: Ignacio
doi: 10.7717/peerj.2514
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-27
copyright: ©2016 García-Vázquez and Ribera
attribution name: García-Vázquez and Ribera

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