title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1796
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Accuracy of conventional identification methods used for Enterobacteriaceae isolates in three Nigerian hospitals
link: https://peerj.com/articles/2511
last-modified: 2016-09-28
description: BackgroundEnterobacteriaceae 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 MethodsIn 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.ResultsOne 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.ConclusionThe 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.
creator: Christiana Jesumirhewe
creator: Peter Oladejo Ogunlowo
creator: Mitsan Olley
creator: Burkhard Springer
creator: Franz Allerberger
creator: Werner Ruppitsch
uri: https://doi.org/10.7717/peerj.2511
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Jesumirhewe et al.

title: An early bothremydid (Testudines, Pleurodira) from the Late Cretaceous (Cenomanian) of Utah, North America
link: https://peerj.com/articles/2502
last-modified: 2016-09-28
description: BackgroundBothremydidae 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.MethodsWe 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.ResultsThe 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.
creator: Walter G. Joyce
creator: Tyler R. Lyson
creator: James I. Kirkland
uri: https://doi.org/10.7717/peerj.2502
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Joyce et al.

title: Dynamics and stability of directional jumps in the desert locust
link: https://peerj.com/articles/2481
last-modified: 2016-09-28
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.
creator: Omer Gvirsman
creator: Gabor Kosa
creator: Amir Ayali
uri: https://doi.org/10.7717/peerj.2481
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Gvirsman et al.

title: Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells
link: https://peerj.com/articles/2478
last-modified: 2016-09-28
description: BackgroundAbnormal 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.MethodsIn 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.ResultsBased 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 DrugBank resources were used to identify potential drugs and targeted genes for vascular diseases involve VSMC proliferation. Our findings are supported by in-vitro experimental IC50, binding activity data and clinical trials.ConclusionThis study provides a systematic strategy to discover potential drugs and target genes, by which we hope to shed light on the treatments of VSMC proliferation associated diseases.
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
uri: https://doi.org/10.7717/peerj.2478
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2016 Huang et al.

title: Investigating the spatial distribution and effects of nearshore topography on Acropora cervicornis abundance in Southeast Florida
link: https://peerj.com/articles/2473
last-modified: 2016-09-28
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 considered for increased management and protection to reduce local stressors.
creator: Nicole L. D’Antonio
creator: David S. Gilliam
creator: Brian K. Walker
uri: https://doi.org/10.7717/peerj.2473
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2016 D’Antonio et al.

title: XA21-specific induction of stress-related genes following Xanthomonas infection of detached rice leaves
link: https://peerj.com/articles/2446
last-modified: 2016-09-28
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.
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
uri: https://doi.org/10.7717/peerj.2446
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Thomas et al.

title: Extremely low genetic variability within and among locations of the greenfish holothurian Stichopus chloronotus Brandt, 1835 in Okinawa, Japan
link: https://peerj.com/articles/2410
last-modified: 2016-09-28
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.
creator: Taha Soliman
creator: Okuto Takama
creator: Iria Fernandez-Silva
creator: James D. Reimer
uri: https://doi.org/10.7717/peerj.2410
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Soliman et al.

title: Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections
link: https://peerj.com/articles/2516
last-modified: 2016-09-27
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.
creator: Saliha Hammoumi
creator: Tatiana Vallaeys
creator: Ayi Santika
creator: Philippe Leleux
creator: Ewa Borzym
creator: Christophe Klopp
creator: Jean-Christophe Avarre
uri: https://doi.org/10.7717/peerj.2516
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Hammoumi et al.

title: Not always a matter of context: direct effects of red on arousal but context-dependent moderations on valence
link: https://peerj.com/articles/2515
last-modified: 2016-09-27
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.
creator: Vanessa L. Buechner
creator: Markus A. Maier
uri: https://doi.org/10.7717/peerj.2515
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Buechner and Maier

title: The origin of widespread species in a poor dispersing lineage (diving beetle genus Deronectes)
link: https://peerj.com/articles/2514
last-modified: 2016-09-27
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 restricted distributions around the Western and Central Mediterranean. The analysis of Wolbachia showed a high prevalence of infection among Deronectes, especially in the D. aubei group, where all sequenced populations were infected with the only exception of the Cantabrian Mountains, the westernmost area of distribution of the lineage. In this group there was a phylogenetic incongruence between the mitochondrial and the nuclear sequence, although no clear pattern links this discordance to the Wolbachia infection. Our results suggest that, in different glacial cycles, populations that happened to be at the edge of the newly deglaciated areas took advantage of the optimal ecological conditions to expand their ranges to central and northern Europe. Once this favourable ecological window ended populations become isolated, resulting in the presence of closely related but distinct species in the Mediterranean peninsulas.
creator: David García-Vázquez
creator: Ignacio Ribera
uri: https://doi.org/10.7717/peerj.2514
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 García-Vázquez and Ribera