title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2017-02 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: LoTo: a graphlet based method for the comparison of local topology between gene regulatory networks link: https://peerj.com/articles/3052 last-modified: 2017-02-28 description: One of the main challenges of the post-genomic era is the understanding of how gene expression is controlled. Changes in gene expression lay behind diverse biological phenomena such as development, disease and the adaptation to different environmental conditions. Despite the availability of well-established methods to identify these changes, tools to discern how gene regulation is orchestrated are still required. The regulation of gene expression is usually depicted as a Gene Regulatory Network (GRN) where changes in the network structure (i.e., network topology) represent adjustments of gene regulation. Like other networks, GRNs are composed of basic building blocks; small induced subgraphs called graphlets. Here we present LoTo, a novel method that using Graphlet Based Metrics (GBMs) identifies topological variations between different states of a GRN. Under our approach, different states of a GRN are analyzed to determine the types of graphlet formed by all triplets of nodes in the network. Subsequently, graphlets occurring in a state of the network are compared to those formed by the same three nodes in another version of the network. Once the comparisons are performed, LoTo applies metrics from binary classification problems calculated on the existence and absence of graphlets to assess the topological similarity between both network states. Experiments performed on randomized networks demonstrate that GBMs are more sensitive to topological variation than the same metrics calculated on single edges. Additional comparisons with other common metrics demonstrate that our GBMs are capable to identify nodes whose local topology changes between different states of the network. Notably, due to the explicit use of graphlets, LoTo captures topological variations that are disregarded by other approaches. LoTo is freely available as an online web server at http://dlab.cl/loto. creator: Alberto J. Martin creator: Sebastián Contreras-Riquelme creator: Calixto Dominguez creator: Tomas Perez-Acle uri: https://doi.org/10.7717/peerj.3052 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Martin et al. title: Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana link: https://peerj.com/articles/3047 last-modified: 2017-02-28 description: BackgroundThe emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African” CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide.MethodsWe first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages.ResultsWe show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol.DiscussionThis study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone. creator: Grace Kpeli creator: Andrew H. Buultjens creator: Stefano Giulieri creator: Evelyn Owusu-Mireku creator: Samuel Y. Aboagye creator: Sarah L. Baines creator: Torsten Seemann creator: Dieter Bulach creator: Anders Gonçalves da Silva creator: Ian R. Monk creator: Benjamin P. Howden creator: Gerd Pluschke creator: Dorothy Yeboah-Manu creator: Timothy Stinear uri: https://doi.org/10.7717/peerj.3047 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Kpeli et al. title: An extremely sensitive nested PCR-RFLP mitochondrial marker for detection and identification of salmonids in eDNA from water samples link: https://peerj.com/articles/3045 last-modified: 2017-02-28 description: BackgroundSalmonids are native from the North Hemisphere but have been introduced for aquaculture and sport fishing in the South Hemisphere and inhabit most rivers and lakes in temperate and cold regions worldwide. Five species are included in the Global Invasive Species Database: rainbow trout Oncorhynchus mykiss, Atlantic salmon Salmo salar, brown trout Salmo trutta, brook trout Salvelinus fontinalis, and lake trout Salvelinus namaycush. In contrast, other salmonids are endangered in their native settings.MethodsHere we have developed a method to identify salmonid species directly from water samples, focusing on the Iberian Peninsula as a case study. We have designed nested Salmonidae-specific primers within the 16S rDNA region. From these primers and a PCR-RFLP procedure the target species can be unequivocally identified from DNA extracted from water samples.ResultsThe method was validated in aquarium experiments and in the field with water from watersheds with known salmonid populations. Finally, the method was applied to obtain a global view of the Salmonidae community in Nalón River (north coast of Spain).DiscussionThis new powerful, very sensitive (identifying the species down to 10 pg DNA/ml water) and economical tool can be applied for monitoring the presence of salmonids in a variety of situations, from checking upstream colonization after removal of river barriers to monitoring potential escapes from fish farms. creator: Laura Clusa creator: Alba Ardura creator: Sara Fernández creator: Agustín A. Roca creator: Eva García-Vázquez uri: https://doi.org/10.7717/peerj.3045 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Clusa et al. title: Spatial distribution of environmental DNA in a nearshore marine habitat link: https://peerj.com/articles/3044 last-modified: 2017-02-28 description: In the face of increasing threats to biodiversity, the advancement of methods for surveying biological communities is a major priority for ecologists. Recent advances in molecular biological technologies have made it possible to detect and sequence DNA from environmental samples (environmental DNA or eDNA); however, eDNA techniques have not yet seen widespread adoption as a routine method for biological surveillance primarily due to gaps in our understanding of the dynamics of eDNA in space and time. In order to identify the effective spatial scale of this approach in a dynamic marine environment, we collected marine surface water samples from transects ranging from the intertidal zone to four kilometers from shore. Using PCR primers that target a diverse assemblage of metazoans, we amplified a region of mitochondrial 16S rDNA from the samples and sequenced the products on an Illumina platform in order to detect communities and quantify their spatial patterns using a variety of statistical tools. We find evidence for multiple, discrete eDNA communities in this habitat, and show that these communities decrease in similarity as they become further apart. Offshore communities tend to be richer but less even than those inshore, though diversity was not spatially autocorrelated. Taxon-specific relative abundance coincided with our expectations of spatial distribution in taxa lacking a microscopic, pelagic life-history stage, though most of the taxa detected do not meet these criteria. Finally, we use carefully replicated laboratory procedures to show that laboratory treatments were remarkably similar in most cases, while allowing us to detect a faulty replicate, emphasizing the importance of replication to metabarcoding studies. While there is much work to be done before eDNA techniques can be confidently deployed as a standard method for ecological monitoring, this study serves as a first analysis of diversity at the fine spatial scales relevant to marine ecologists and confirms the promise of eDNA in dynamic environments. creator: James L. O’Donnell creator: Ryan P. Kelly creator: Andrew Olaf Shelton creator: Jameal F. Samhouri creator: Natalie C. Lowell creator: Gregory D. Williams uri: https://doi.org/10.7717/peerj.3044 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Predatory blue crabs induce stronger nonconsumptive effects in eastern oysters Crassostrea virginica than scavenging blue crabs link: https://peerj.com/articles/3042 last-modified: 2017-02-28 description: By influencing critical prey traits such as foraging or habitat selection, predators can affect entire ecosystems, but the nature of cues that trigger prey reactions to predators are not well understood. Predators may scavenge to supplement their energetic needs and scavenging frequency may vary among individuals within a species due to preferences and prey availability. Yet prey reactions to consumers that are primarily scavengers versus those that are active foragers have not been investigated, even though variation in prey reactions to scavengers or predators might influence cascading nonconsumptive effects in food webs. Oysters Crassostrea virginica react to crab predators by growing stronger shells. We exposed oysters to exudates from crabs fed live oysters or fed aged oyster tissue to simulate scavenging, and to controls without crab cues. Oysters grew stronger shells when exposed to either crab exudate, but their shells were significantly stronger when crabs were fed live oysters. The stronger response to predators than scavengers could be due to inherent differences in diet cues representative of reduced risk in the presence of scavengers or to degradation of conspecific alarm cues in aged treatments, which may mask risk from potential predators subsisting by scavenging. creator: Avery E. Scherer creator: Miranda M. Garcia creator: Delbert L. Smee uri: https://doi.org/10.7717/peerj.3042 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Scherer et al. title: How conserved are the conserved 16S-rRNA regions? link: https://peerj.com/articles/3036 last-modified: 2017-02-28 description: The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker. creator: Marcel Martinez-Porchas creator: Enrique Villalpando-Canchola creator: Luis Enrique Ortiz Suarez creator: Francisco Vargas-Albores uri: https://doi.org/10.7717/peerj.3036 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Martinez-Porchas et al. title: Immediate effects of EVA midsole resilience and upper shoe structure on running biomechanics: a machine learning approach link: https://peerj.com/articles/3026 last-modified: 2017-02-28 description: BackgroundResilience of midsole material and the upper structure of the shoe are conceptual characteristics that can interfere in running biomechanics patterns. Artificial intelligence techniques can capture features from the entire waveform, adding new perspective for biomechanical analysis. This study tested the influence of shoe midsole resilience and upper structure on running kinematics and kinetics of non-professional runners by using feature selection, information gain, and artificial neural network analysis.MethodsTwenty-seven experienced male runners (63 ± 44 km/week run) ran in four-shoe design that combined two resilience-cushioning materials (low and high) and two uppers (minimalist and structured). Kinematic data was acquired by six infrared cameras at 300 Hz, and ground reaction forces were acquired by two force plates at 1,200 Hz. We conducted a Machine Learning analysis to identify features from the complete kinematic and kinetic time series and from 42 discrete variables that had better discriminate the four shoes studied. For that analysis, we built an input data matrix of dimensions 1,080 (10 trials × 4 shoes × 27 subjects) × 1,254 (3 joints × 3 planes of movement × 101 data points + 3 vectors forces × 101 data points + 42 discrete calculated kinetic and kinematic features).ResultsThe applied feature selection by information gain and artificial neural networks successfully differentiated the two resilience materials using 200(16%) biomechanical variables with an accuracy of 84.8% by detecting alterations of running biomechanics, and the two upper structures with an accuracy of 93.9%.DiscussionThe discrimination of midsole resilience resulted in lower accuracy levels than did the discrimination of the shoe uppers. In both cases, the ground reaction forces were among the 25 most relevant features. The resilience of the cushioning material caused significant effects on initial heel impact, while the effects of different uppers were distributed along the stance phase of running. Biomechanical changes due to shoe midsole resilience seemed to be subject-dependent, while those due to upper structure seemed to be subject-independent. creator: Andrea N. Onodera creator: Wilson P. Gavião Neto creator: Maria Isabel Roveri creator: Wagner R. Oliveira creator: Isabel CN Sacco uri: https://doi.org/10.7717/peerj.3026 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Onodera et al. title: Neogene paleogeography provides context for understanding the origin and spatial distribution of cryptic diversity in a widespread Balkan freshwater amphipod link: https://peerj.com/articles/3016 last-modified: 2017-02-28 description: BackgroundThe Balkans are a major worldwide biodiversity and endemism hotspot. Among the freshwater biota, amphipods are known for their high cryptic diversity. However, little is known about the temporal and paleogeographic aspects of their evolutionary history. We used paleogeography as a framework for understanding the onset of diversification in Gammarus roeselii: (1) we hypothesised that, given the high number of isolated waterbodies in the Balkans, the species is characterised by high level of cryptic diversity, even on a local scale; (2) the long geological history of the region might promote pre-Pleistocene divergence between lineages; (3) given that G. roeselii thrives both in lakes and rivers, its evolutionary history could be linked to the Balkan Neogene paleolake system; (4) we inspected whether the Pleistocene decline of hydrological networks could have any impact on the diversification of G. roeselii.Material and MethodsDNA was extracted from 177 individuals collected from 26 sites all over Balkans. All individuals were amplified for ca. 650 bp long fragment of the mtDNA cytochrome oxidase subunit I (COI). After defining molecular operational taxonomic units (MOTU) based on COI, 50 individuals were amplified for ca. 900 bp long fragment of the nuclear 28S rDNA. Molecular diversity, divergence, differentiation and historical demography based on COI sequences were estimated for each MOTU. The relative frequency, geographic distribution and molecular divergence between COI haplotypes were presented as a median-joining network. COI was used also to reconstruct time-calibrated phylogeny with Bayesian inference. Probabilities of ancestors’ occurrence in riverine or lacustrine habitats, as well their possible geographic locations, were estimated with the Bayesian method. A Neighbour Joining tree was constructed to illustrate the phylogenetic relationships between 28S rDNA haplotypes.ResultsWe revealed that G. roeselii includes at least 13 cryptic species or molecular operational taxonomic units (MOTUs), mostly of Miocene origin. A substantial Pleistocene diversification within-MOTUs was observed in several cases. We evidenced secondary contacts between very divergent MOTUs and introgression of nDNA. The Miocene ancestors could live in either lacustrine or riverine habitats yet their presumed geographic localisations overlapped with those of the Neogene lakes. Several extant riverine populations had Pleistocene lacustrine ancestors.DiscussionNeogene divergence of lineages resulting in substantial cryptic diversity may be a common phenomenon in extant freshwater benthic crustaceans occupying areas that were not glaciated during the Pleistocene. Evolution of G. roeselii could be associated with gradual deterioration of the paleolakes. The within-MOTU diversification might be driven by fragmentation of river systems during the Pleistocene. Extant ancient lakes could serve as local microrefugia during that time. creator: Michał Grabowski creator: Tomasz Mamos creator: Karolina Bącela-Spychalska creator: Tomasz Rewicz creator: Remi A. Wattier uri: https://doi.org/10.7717/peerj.3016 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Grabowski et al. title: Construction patterns of birds’ nests provide insight into nest-building behaviours link: https://peerj.com/articles/3010 last-modified: 2017-02-28 description: Previous studies have suggested that birds and mammals select materials needed for nest building based on their thermal or structural properties, although the amounts or properties of the materials used have been recorded for only a very small number of species. Some of the behaviours underlying the construction of nests can be indirectly determined by careful deconstruction of the structure and measurement of the biomechanical properties of the materials used. Here we examined this idea in an investigation of Bullfinch (Pyrrhula pyrrhula) nests as a model for open-nesting songbird species that construct a “twig” nest, and tested the hypothesis that materials in different parts of nests serve different functions. The quantities of materials present in the nest base, sides and cup were recorded before structural analysis. Structural analysis showed that the base of the outer nests were composed of significantly thicker, stronger and more rigid materials compared to the side walls, which in turn were significantly thicker, stronger and more rigid than materials used in the cup. These results suggest that the placement of particular materials in nests may not be random, but further work is required to determine if the final structure of a nest accurately reflects the construction process. creator: Lucia Biddle creator: Adrian M. Goodman creator: D. Charles Deeming uri: https://doi.org/10.7717/peerj.3010 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Biddle et al. title: Effects of enhanced hydrological connectivity on Mediterranean salt marsh fish assemblages with emphasis on the endangered Spanish toothcarp (Aphanius iberus) link: https://peerj.com/articles/3009 last-modified: 2017-02-28 description: The hydrological connectivity between the salt marsh and the sea was partially restored in a Mediterranean wetland containing isolated ponds resulting from former salt extraction and aquaculture activities. A preliminary assessment provided evidence that ponds farther from the sea hosted very large numbers of the endangered Spanish toothcarp, Aphanius iberus, suggesting that individuals had been trapped and consequently reach unnaturally high densities. In order to achieve both habitat rehabilitation and toothcarp conservation, efforts were made to create a gradient of hydrologically connected areas, including isolated fish reservoirs, semi-isolated, and connected salt marsh-sea areas that could allow migratory movements of fish and provide some protection for A. iberus. The fish community was monitored prior to, and for three years after rehabilitation. Results showed an increase in the number of fish species within semi-isolated areas (Zone A), whereas areas adjacent to the sea (Zone B) increased the number of marine species and decreased that of estuarine species (ES). Yet overall differences in fish assemblages were much higher between zones than among study years. Generalized linear models (GLMs) evidenced that distance to the sea was the most important variable explaining the local diversity of the fish community after restoration, with occasional influence of other factors such as temperature, and depth. The abundance of A. iberus was consistently higher in semi-isolated areas at greater distances from the sea, but a decline occurred in both zones and in isolated reservoir ponds after restoration efforts, which may be attributable to interannual differences in recruitment success and, to a lesser extent, to dispersal into adjacent habitats. A negative effect of restoration works on fish population cannot be excluded, but the final outcome of the intervention likely needs a longer period. creator: Patricia Prado creator: Carles Alcaraz creator: Lluis Jornet creator: Nuno Caiola creator: Carles Ibáñez uri: https://doi.org/10.7717/peerj.3009 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Prado et al. title: Limited effects of source population identity and number on seagrass transplant performance link: https://peerj.com/articles/2972 last-modified: 2017-02-28 description: Global declines in coastal foundation species highlight the importance of effective restoration. In this study, we examined the effects of source population identity and diversity (one vs. three sources per plot) on seagrass (Zostera marina) transplant success. The field experiment was replicated at two locations in Massachusetts with adjacent natural Zostera marina beds to test for local adaptation and source diversity effects on shoot density. We also collected morphological and genetic data to characterize variation within and among source populations, and evaluate whether they were related to performance. Transplants grew and expanded until six months post-transplantation, but then steadily declined at both sites. Prior to declines, we observed variation in performance among source populations at one site that was related to morphological traits: the populations with the longest leaves had the highest shoot densities, whereas the population with the shortest leaves performed the worst at six months post-transplantation. In addition, multiple source plots at this same transplant site consistently had similar or higher shoot densities than single source plots, and shoots from weak-performing populations showed improved performance in multiple source plots. We found no evidence for home site advantage or benefits of population-level genetic variation in early transplant performance at either site. Our results show limited effects of source population on early transplant performance and suggest that factors (e.g., morphology) other than home site advantage and population genetic variation serve a role. Based on our overall findings that transplant success varied among source populations and that population diversity at the plot level had positive but limited effects on individual and plot performance, we support planting shoots from multiple source sites in combination to enhance transplant success, particularly in the absence of detailed information on individual source characteristics. creator: Alyssa B. Novak creator: Holly K. Plaisted creator: Cynthia G. Hays creator: Randall A. Hughes uri: https://doi.org/10.7717/peerj.2972 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Novak et al. title: Purification and biochemical characterization of recombinant Persicaria minor β-sesquiphellandrene synthase link: https://peerj.com/articles/2961 last-modified: 2017-02-28 description: BackgroundSesquiterpenes are 15-carbon terpenes synthesized by sesquiterpene synthases using farnesyl diphosphate (FPP) as a substrate. Recently, a sesquiterpene synthase gene that encodes a 65 kDa protein was isolated from the aromatic plant Persicaria minor. Here, we report the expression, purification and characterization of recombinant P. minor sesquiterpene synthase protein (PmSTS). Insights into the catalytic active site were further provided by structural analysis guided by multiple sequence alignment.MethodsThe enzyme was purified in two steps using affinity and size exclusion chromatography. Enzyme assays were performed using the malachite green assay and enzymatic product was identified using gas chromatography-mass spectrometry (GC-MS) analysis. Sequence analysis of PmSTS was performed using multiple sequence alignment (MSA) against plant sesquiterpene synthase sequences. The homology model of PmSTS was generated using I-TASSER server.ResultsOur findings suggest that the recombinant PmSTS is mainly expressed as inclusion bodies and soluble aggregate in the E. coli protein expression system. However, the addition of 15% (v/v) glycerol to the protein purification buffer and the removal of N-terminal 24 amino acids of PmSTS helped to produce homogenous recombinant protein. Enzyme assay showed that recombinant PmSTS is active and specific to the C15 substrate FPP. The optimal temperature and pH for the recombinant PmSTS are 30 °C and pH 8.0, respectively. The GC-MS analysis further showed that PmSTS produces β-sesquiphellandrene as a major product and β-farnesene as a minor product. MSA analysis revealed that PmSTS adopts a modified conserved metal binding motif (NSE/DTE motif). Structural analysis suggests that PmSTS may binds to its substrate similarly to other plant sesquiterpene synthases.DiscussionThe study has revealed that homogenous PmSTS protein can be obtained with the addition of glycerol in the protein buffer. The N-terminal truncation dramatically improved the homogeneity of PmSTS during protein purification, suggesting that the disordered N-terminal region may have caused the formation of soluble aggregate. We further show that the removal of the N-terminus disordered region of PmSTS does not affect the product specificity. The optimal temperature, optimal pH, Km and kcat values of PmSTS suggests that PmSTS shares similar enzyme characteristics with other plant sesquiterpene synthases. The discovery of an altered conserved metal binding motif in PmSTS through MSA analysis shows that the NSE/DTE motif commonly found in terpene synthases is able to accommodate certain level of plasticity to accept variant amino acids. Finally, the homology structure of PmSTS that allows good fitting of substrate analog into the catalytic active site suggests that PmSTS may adopt a sesquiterpene biosynthesis mechanism similar to other plant sesquiterpene synthases. creator: De-Sheng Ker creator: Sze Lei Pang creator: Noor Farhan Othman creator: Sekar Kumaran creator: Ee Fun Tan creator: Thiba Krishnan creator: Kok Gan Chan creator: Roohaida Othman creator: Maizom Hassan creator: Chyan Leong Ng uri: https://doi.org/10.7717/peerj.2961 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ker et al. title: Transcriptome analysis of Polygonum minus reveals candidate genes involved in important secondary metabolic pathways of phenylpropanoids and flavonoids link: https://peerj.com/articles/2938 last-modified: 2017-02-28 description: BackgroundPolygonum minus is an herbal plant in the Polygonaceae family which is rich in ethnomedicinal plants. The chemical composition and characteristic pungent fragrance of Polygonum minus have been extensively studied due to its culinary and medicinal properties. There are only a few transcriptome sequences available for species from this important family of medicinal plants. The limited genetic information from the public expressed sequences tag (EST) library hinders further study on molecular mechanisms underlying secondary metabolite production.MethodsIn this study, we performed a hybrid assembly of 454 and Illumina sequencing reads from Polygonum minus root and leaf tissues, respectively, to generate a combined transcriptome library as a reference.ResultsA total of 34.37 million filtered and normalized reads were assembled into 188,735 transcripts with a total length of 136.67 Mbp. We performed a similarity search against all the publicly available genome sequences and found similarity matches for 163,200 (86.5%) of Polygonum minus transcripts, largely from Arabidopsis thaliana (58.9%). Transcript abundance in the leaf and root tissues were estimated and validated through RT-qPCR of seven selected transcripts involved in the biosynthesis of phenylpropanoids and flavonoids. All the transcripts were annotated against KEGG pathways to profile transcripts related to the biosynthesis of secondary metabolites.DiscussionThis comprehensive transcriptome profile will serve as a useful sequence resource for molecular genetics and evolutionary research on secondary metabolite biosynthesis in Polygonaceae family. Transcriptome assembly of Polygonum minus can be accessed at http://prims.researchfrontier.org/index.php/dataset/transcriptome. creator: Kok-Keong Loke creator: Reyhaneh Rahnamaie-Tajadod creator: Chean-Chean Yeoh creator: Hoe-Han Goh creator: Zeti-Azura Mohamed-Hussein creator: Zamri Zainal creator: Ismanizan Ismail creator: Normah Mohd Noor uri: https://doi.org/10.7717/peerj.2938 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Loke et al. title: Evidence for high inter-generational individual quality in yellow-eyed penguins link: https://peerj.com/articles/2935 last-modified: 2017-02-28 description: Longitudinal studies focusing on lifetime reproductive success (LRS) have been used to measure individual breeding performance and identify commonalities among successful breeders. By extending the focus to subsequent generations we identify a proportion of high-quality individuals that contribute disproportionately to the population over multiple generations. We used 23 years of yellow-eyed penguin (Megadyptes antipodes) breeding data from one breeding area to identify the proportion of individual birds that raised successful breeders, which in turn raised offspring. We explored which life-history components influenced LRS, as this knowledge would enable conservation resources to be focused on high-performing individuals in this endangered population. From 2,147 birds marked as chicks, 370 (17.2%) survived to adulthood and recruited to their natal location, of which 219 (10.2%) fledged offspring: 124 (56.6%) of the 219 birds produced offspring that recruited as breeders. Only 102 birds (4.8% of 2,147) fledged first-generation offspring that in turn fledged offspring (second-generation offspring, or grand-offspring). We found that ∼25% of the birds that survived to breed had above-average LRS as well as above-average numbers of grand-offspring, and were more likely to have produced first-generation chicks that recruited and also produced above-average numbers of second-generation chicks. Our findings suggest that there is a core of “super-breeders” that contribute disproportionately to the population over successive generations. Lifespan and age-at-first-breeding were correlated with LRS. We suggest that traits of birds relating to longevity, health (e.g., immunocompetence) and fitness could be examined to identify potential links with high LRS and inter-generational fecundity. “Super-breeders” appear to consistently achieve high LRS and long lifespans in a stochastic environment, demonstrating greater resilience in the face of extreme events. creator: Aviva M. Stein creator: Melanie J. Young creator: John T. Darby creator: Philip J. Seddon creator: Yolanda van Heezik uri: https://doi.org/10.7717/peerj.2935 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Stein et al. title: FUCHS—towards full circular RNA characterization using RNAseq link: https://peerj.com/articles/2934 last-modified: 2017-02-28 description: Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5′ splice site is linked to an upstream 3′ splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs could act as miRNA-sponges, the function of most circRNAs remains unknown. To expand our understanding of possible roles of circular RNAs, we propose a new pipeline that could fully characterizes candidate circRNA structure from RNAseq data—FUCHS: FUll CHaracterization of circular RNA using RNA-Sequencing. Currently, most computational prediction pipelines use back-spliced reads to identify circular RNAs. FUCHS extends this concept by considering all RNA-seq information from long reads (typically >150 bp) to learn more about the exon coverage, the number of double break point fragments, the different circular isoforms arising from one host-gene, and the alternatively spliced exons within the same circRNA boundaries. This new knowledge will enable the user to carry out differential motif enrichment and miRNA seed analysis to determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-use Python based pipeline that contributes a new aspect to the circRNA research. creator: Franziska Metge creator: Lisa F. Czaja-Hasse creator: Richard Reinhardt creator: Chistoph Dieterich uri: https://doi.org/10.7717/peerj.2934 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Metge et al. title: Facilitating permeability of landscapes impacted by roads for protected amphibians: patterns of movement for the great crested newt link: https://peerj.com/articles/2922 last-modified: 2017-02-28 description: Amphibian populations are highly vulnerable to road mortality and habitat fragmentation caused by road networks. Wildlife road tunnels are considered the most promising road mitigation measure for amphibians yet generally remain inadequately monitored, resulting in mixed success rates in the short-term and uncertain conservation benefits in the long-term. We monitored a complex multi-tunnel and fence system over five years and investigated the impact of the scheme on movement patterns of two newt species, including the largest known UK population of the great crested newt (Triturus cristatus), a European Protected Species. We used a stage descriptive approach based on capture positions to quantify newt movement patterns. Newt species successfully used the mitigation but the system constituted a bottleneck to movements from the fences to the tunnels. Crossing rates varied widely among years and were skewed towards autumn dispersal rather than spring breeding migration. There was a substantial negative bias against adult male great crested newts using the system. This study indicates that road tunnels could partially mitigate wider connectivity loss and fragmentation at the landscape scale for newt species. However, the observed bottleneck effects and seasonal bias could have population-level effects which must be better understood, especially for small populations, so that improvements can be made. Current requirements for monitoring mitigation schemes post-implementation are probably too short to assess their effectiveness in maintaining connectivity and to adequately understand their population-level impacts. creator: Cátia Matos creator: Silviu Petrovan creator: Alastair I. Ward creator: Philip Wheeler uri: https://doi.org/10.7717/peerj.2922 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Matos et al. title: Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary link: https://peerj.com/articles/2804 last-modified: 2017-02-28 description: Since three bullhead catfish species were introduced to Europe in the late 19th century, they have spread to most European countries. In Hungary, the brown bullhead (Ameiurus nebulosus) was more widespread in the 1970s–1980s, but the black bullhead (Ameiurus melas) has gradually supplanted since their second introduction in 1980. The introgressive hybridization of the two species has been presumed based on morphological examinations, but it has not previously been supported by genetic evidence. In this study, 11 different Hungarian habitats were screened with a new species-specific nuclear genetic, duplex PCR based, marker system to distinguish the introduced catfish species, Ameiurus nebulosus, Ameiurus melas, and Ameiurus natalis, as well as the hybrids of the first two. More than 460 specimens were analyzed using the above markers and additional mitochondrial sequence analyses were also conducted on >25% of the individuals from each habitat sampled. The results showed that only 7.9% of the specimens from two habitats belonged to Ameiurus nebulosus, and 92.1% were classified as Ameiurus melas of all habitats, whereas the presence of Ameiurus natalis was not detected. Two specimens (>0.4%) showed the presence of both nuclear genomes and they were identified as hybrids of Ameiurus melas and Ameiurus nebulosus. An additional two individuals showed contradicting results from the nuclear and mitochondrial assays as a sign of a possible footprint of introgressive hybridization that might have happened two or more generations before. Surprisingly, the level of hybridization was much smaller than expected based on the analyses of the North American continent’s indigenous stock from the hybrid zones. This phenomenon has been observed in several invasive fish species and it is regarded as an added level of complexity in the management of their rapid adaptation. creator: Beatrix Béres creator: Dóra Kánainé Sipos creator: Tamás Müller creator: Ádám Staszny creator: Milán Farkas creator: Katalin Bakos creator: László Orbán creator: Béla Urbányi creator: Balázs Kovács uri: https://doi.org/10.7717/peerj.2804 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Béres et al. title: Effects of shepherds and dogs on livestock depredation by leopards (Panthera pardus) in north-eastern Iran link: https://peerj.com/articles/3049 last-modified: 2017-02-23 description: Human-carnivore conflicts over livestock depredation are increasingly common, yet little is understood about the role of husbandry in conflict mitigation. As shepherds and guarding dogs are most commonly used to curb carnivore attacks on grazing livestock, evaluation and improvement of these practices becomes an important task. We addressed this issue by studying individual leopard (Panthera pardus) attacks on sheep and goats in 34 villages near Golestan National Park, Iran. We obtained and analyzed data on 39 attacks, which included a total loss of 31 sheep and 36 goats in 17 villages. We applied non-parametric testing, Poisson Generalized Linear Modelling (GLM) and model selection to assess how numbers of sheep and goats killed per attack are associated with the presence and absence of shepherds and dogs during attacks, depredation in previous years, villages, seasons, ethnic groups, numbers of sheep and goats kept in villages, and distances from villages to the nearest protected areas. We found that 95.5% of losses were inflicted in forests when sheep and goats were accompanied by shepherds (92.5% of losses) and dogs (77.6%). Leopards tended to kill more sheep and goats per attack (surplus killing) when dogs were absent in villages distant from protected areas, but still inflicted most losses when dogs were present, mainly in villages near protected areas. No other variables affected numbers of sheep and goats killed per attack. These results indicate that local husbandry practices are ineffectual and the mere presence of shepherds and guarding dogs is not enough to secure protection. Shepherds witnessed leopard attacks, but could not deter them while dogs did not exhibit guarding behavior and were sometimes killed by leopards. In an attempt to make practical, low-cost and socially acceptable improvements in local husbandry, we suggest that dogs are raised to create a strong social bond with livestock, shepherds use only best available dogs, small flocks are aggregated into larger ones and available shepherds herd these larger flocks together. Use of deterrents and avoidance of areas close to Golestan and in central, core areas of neighboring protected areas is also essential to keep losses down. creator: Igor Khorozyan creator: Mahmood Soofi creator: Mobin Soufi creator: Amirhossein Khaleghi Hamidi creator: Arash Ghoddousi creator: Matthias Waltert uri: https://doi.org/10.7717/peerj.3049 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Khorozyan et al. title: Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment link: https://peerj.com/articles/3046 last-modified: 2017-02-23 description: The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screen’s high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers. creator: Valentina S. Vysotskaia creator: Gregory J. Hogan creator: Genevieve M. Gould creator: Xin Wang creator: Alex D. Robertson creator: Kevin R. Haas creator: Mark R. Theilmann creator: Lindsay Spurka creator: Peter V. Grauman creator: Henry H. Lai creator: Diana Jeon creator: Genevieve Haliburton creator: Matt Leggett creator: Clement S. Chu creator: Kevin Iori creator: Jared R. Maguire creator: Kaylene Ready creator: Eric A. Evans creator: Hyunseok P. Kang creator: Imran S. Haque uri: https://doi.org/10.7717/peerj.3046 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vysotskaia et al. title: Effectiveness of removals of the invasive lionfish: how many dives are needed to deplete a reef? link: https://peerj.com/articles/3043 last-modified: 2017-02-23 description: Introduced Indo-Pacific red lionfish (Pterois volitans/miles) have spread throughout the greater Caribbean and are associated with a number of negative impacts on reef ecosystems. Human interventions, in the form of culling activities, are becoming common to reduce their numbers and mitigate the negative effects associated with the invasion. However, marine managers must often decide how to best allocate limited resources. Previous work has identified the population size thresholds needed to limit the negative impacts of lionfish. Here we develop a framework that allows managers to predict the removal effort required to achieve specific targets (represented as the percent of lionfish remaining on the reef). We found an important trade-off between time spent removing and achieving an increasingly smaller lionfish density. The model used in our suggested framework requires relatively little data to parameterize, allowing its use with already existing data, permitting managers to tailor their culling strategy to maximize efficiency and rate of success. creator: Paolo Usseglio creator: Jason D. Selwyn creator: Alan M. Downey-Wall creator: J. Derek Hogan uri: https://doi.org/10.7717/peerj.3043 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Usseglio et al. title: Tartrazine induces structural and functional aberrations and genotoxic effects in vivo link: https://peerj.com/articles/3041 last-modified: 2017-02-23 description: Tartrazine is a synthetic organic azo dye widely used in food and pharmaceutical products. The current study aimed to evaluate the possible adverse effect of this coloring food additive on renal and hepatic structures and functions. Also, the genotoxic potential of tartrazine on white blood cells was investigated using comet assay. Twenty adult male Wistar rats were grouped into two groups of 10 each, control- and tartrazine-treated groups. The control group was administered orally with water alone. The experimental group was administered orally with tartrazine (7.5 mg/kg, b.wt.). Our results showed a marked increase in the levels of ALT, AST, ALP, urea, uric acid, creatinine, MDA and NO, and a decreased level of total antioxidants in the serum of rats dosed with tartrazine compared to controls. On the other hand, administration of tartrazine was associated with severe histopathological and cellular alterations of rat liver and kidney tissues and induced DNA damage in leucocytes as detected by comet assay. Taken together, the results showed that tartrazine intake may lead to adverse health effects. creator: Latifa Khayyat creator: Amina Essawy creator: Jehan Sorour creator: Ahmed Soffar uri: https://doi.org/10.7717/peerj.3041 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Khayyat et al. title: Retrospective observation of drug susceptibility of Candida strains in the years 1999, 2004, and 2015 link: https://peerj.com/articles/3038 last-modified: 2017-02-23 description: IntroductionThere is much literature devoted to the problem of drug resistance and decreased susceptibility of fungi to commonly used antifungals.AimTo analyze drug susceptibility of Candida albicans and non-Candida albicans strains isolated from the hands of people without any symptoms of disease over a 16-year period.Materials and MethodsThe study included a total of 1,274 Candida-type strains isolated from the hands of people without any symptoms of disease, including: in 1999, 432 strains; in 2004, 368; and in 2015, 454 strains. Biological monitoring of hand surface contamination was performed using the Count-TactTM applicator with Count-Tact plates (bioMerieux). Drug susceptibility was evaluated using FUNGITEST®.ResultsIn 1999, the most strains showed resistance to fluconazole (53.2%), in 2004 to itraconazole (52.9%), and in 2015 to fluconazole (85.8%). Resistance to more than one drug was 35.8% in 1999, 64.7% in 2004, and 92% in 2015. Mean resistance to azole antifungals significantly increased from 98 ± 39.7 strains in 1999 to 118.3 ± 29.6 in 2015 (p < 0.001). In 1999, the most strains showed resistance to fluconazole (50.6%), in 2004 to itraconazole (52.9%), and in 2015 to fluconazole (44.9%). Resistance to more than one drug was 52.9% in 1999, 64.3% in 2004, and 88.1% in 2015. Mean resistance to azole antifungals significantly increased from a mean of 76 ± 9.7 strains in 1999, to 95.3 ± 24.2 in 2004, and to 97.3 ± 16.6 in 2015 (p < 0.001).ConclusionsWe showed increased C. albicans and non-Candida albicans strain resistance to commonly used antifungal chemotherapeutics, mainly imidazole. We found a clear rise in susceptibility of C. albicans and non-Candida albicans strains to several studied antifungals. creator: Cecylia Łukaszuk creator: Elżbieta Krajewska-Kułak creator: Wojciech Kułak uri: https://doi.org/10.7717/peerj.3038 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Łukaszuk et al. title: Inhibition of calcineurin by FK506 stimulates germinal vesicle breakdown of mouse oocytes in hypoxanthine-supplemented medium link: https://peerj.com/articles/3032 last-modified: 2017-02-23 description: Calcineurin (CN) is a serine/threonine phosphatase which plays important roles in meiosis maturation in invertebrate oocytes; however, the role of CN in mouse oocytes is relatively unexplored. In this study, we examined the expression, localization and functional roles of CN in mouse oocytes and granulosa cells. The RT-PCR results showed that the β isoform of calcineurin A subunit (Cn A) expressed significantly higher than α and γ isoforms, and the expression of Cn Aβ mRNA obviously decreased in oocytes in which germinal vesicle breakdown (GVBD) occurred, while only B1 of calcineurin B subunit (Cn B) was detected in oocytes and stably expressed during oocytes maturation. The following fluorescence experiment showed that Cn A was mainly located in the nucleus of germinal vesicle (GV) stage oocytes and gruanlosa cells, and subsequently dispersed into the entire cytoplasm after GVBD. The decline of Cn A in oocytes suggested that it may play an important role in GVBD. To further clarify the role of calcineurin during meiotic maturation, FK506 (a calcineurin inhibitor) was used in the culture medium contained hypoxanthine (HX) which could keep mouse oocytes staying at GV stage. As expected, FK506 could induce a significant elevation of GVBD rate and increase the MPF level of denuded oocytes (DOs). Furthermore, FK506 could also play an induction role of GVBD of oocytes in COCs and follicles, and the process could be counteracted by MAPK kinase inhibitor (U0126). Above all, the results implied that calcineurin might play a crucial role in development of mouse oocytes and MPF and MAPK pathways are involved in this process. creator: Li Wang creator: Yan-Hong Zhen creator: Xiao-Ming Liu creator: Jing Cao creator: Yan-Ling Wang creator: Li-Jun Huo uri: https://doi.org/10.7717/peerj.3032 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Eotaria citrica, sp. nov., a new stem otariid from the “Topanga” formation of Southern California link: https://peerj.com/articles/3022 last-modified: 2017-02-23 description: A new taxon of stem otariid, Eotaria citrica sp. nov., is described from the upper Burdigalian to lower Langhian “Topanga” formation of Orange County, California. The new species is described from mandibular and dental remains that show a unique combination of plesiomorphic and derived characters. Specifically, it is characterized by having trenchant and prominent paraconid cusps in p3–m1, lingual cingula of p2–4 with faint crenulations, premolars and molars with vestigial metaconid, bilobed root of m2 and a genial tuberosity located under p3. Furthermore, additional material of the contemporaneous Eotaria crypta is described, providing new information on the morphology of this taxon. Both species of Eotaria represent the earliest stem otariids, reinforcing the hypothesis that the group originated in the north Eastern Pacific Region. At present, the “Topanga” Fm. pinniped fauna includes Eotaria citrica, Eotaria crypta, the desmatophocid Allodesmus sp., the odobenids Neotherium sp., Pelagiarctos sp. and includes the oldest records of crown pinnipeds in California. Overall this pinniped fauna is similar to the nearly contemporaneous Sharktooth Hill bonebed. However, unambiguous records of Eotaria are still missing from Sharktooth Hill. This absence may be due to taphonomic or paleoenvironmental factors. The new “Topanga” record presented here was integrated into an overview of the late Oligocene through early Pleistocene pinniped faunas of Southern California. The results show an overall increase in body size over time until the Pleistocene. Furthermore, desmatophocids were the largest pinnipeds during the middle Miocene, but were extinct by the beginning of the late Miocene. Odobenids diversified and became the dominant pinnipeds in late Miocene through Pleistocene assemblages, usually approaching or exceeding 3 m in body length, while otariids remained as the smallest taxa. This pattern contrasts with modern assemblages, in which the phocid Mirounga angustirostris is the largest pinniped taxon in the region, odobenids are extinct and medium and small size ranges are occupied by otariids or other phocids. creator: Jorge Velez-Juarbe uri: https://doi.org/10.7717/peerj.3022 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Velez-Juarbe title: Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci link: https://peerj.com/articles/2936 last-modified: 2017-02-23 description: Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs. creator: Caroline E. Dubé creator: Serge Planes creator: Yuxiang Zhou creator: Véronique Berteaux-Lecellier creator: Emilie Boissin uri: https://doi.org/10.7717/peerj.2936 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dubé et al. title: Using visuo-kinetic virtual reality to induce illusory spinal movement: the MoOVi Illusion link: https://peerj.com/articles/3023 last-modified: 2017-02-22 description: BackgroundIllusions that alter perception of the body provide novel opportunities to target brain-based contributions to problems such as persistent pain. One example of this, mirror therapy, uses vision to augment perceived movement of a painful limb to treat pain. Since mirrors can’t be used to induce augmented neck or other spinal movement, we aimed to test whether such an illusion could be achieved using virtual reality, in advance of testing its potential therapeutic benefit. We hypothesised that perceived head rotation would depend on visually suggested movement.MethodIn a within-subjects repeated measures experiment, 24 healthy volunteers performed neck movements to 50o of rotation, while a virtual reality system delivered corresponding visual feedback that was offset by a factor of 50%–200%—the Motor Offset Visual Illusion (MoOVi)—thus simulating more or less movement than that actually occurring. At 50o of real-world head rotation, participants pointed in the direction that they perceived they were facing. The discrepancy between actual and perceived direction was measured and compared between conditions. The impact of including multisensory (auditory and visual) feedback, the presence of a virtual body reference, and the use of 360o immersive virtual reality with and without three-dimensional properties, was also investigated.ResultsPerception of head movement was dependent on visual-kinaesthetic feedback (p = 0.001, partial eta squared = 0.17). That is, altered visual feedback caused a kinaesthetic drift in the direction of the visually suggested movement. The magnitude of the drift was not moderated by secondary variables such as the addition of illusory auditory feedback, the presence of a virtual body reference, or three-dimensionality of the scene.DiscussionVirtual reality can be used to augment perceived movement and body position, such that one can perform a small movement, yet perceive a large one. The MoOVi technique tested here has clear potential for assessment and therapy of people with spinal pain. creator: Daniel S. Harvie creator: Ross T. Smith creator: Estin V. Hunter creator: Miles G. Davis creator: Michele Sterling creator: G. Lorimer Moseley uri: https://doi.org/10.7717/peerj.3023 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Harvie et al. title: Making inference from wildlife collision data: inferring predator absence from prey strikes link: https://peerj.com/articles/3014 last-modified: 2017-02-22 description: Wildlife collision data are ubiquitous, though challenging for making ecological inference due to typically irreducible uncertainty relating to the sampling process. We illustrate a new approach that is useful for generating inference from predator data arising from wildlife collisions. By simply conditioning on a second prey species sampled via the same collision process, and by using a biologically realistic numerical response functions, we can produce a coherent numerical response relationship between predator and prey. This relationship can then be used to make inference on the population size of the predator species, including the probability of extinction. The statistical conditioning enables us to account for unmeasured variation in factors influencing the runway strike incidence for individual airports and to enable valid comparisons. A practical application of the approach for testing hypotheses about the distribution and abundance of a predator species is illustrated using the hypothesized red fox incursion into Tasmania, Australia. We estimate that conditional on the numerical response between fox and lagomorph runway strikes on mainland Australia, the predictive probability of observing no runway strikes of foxes in Tasmania after observing 15 lagomorph strikes is 0.001. We conclude there is enough evidence to safely reject the null hypothesis that there is a widespread red fox population in Tasmania at a population density consistent with prey availability. The method is novel and has potential wider application. creator: Peter Caley creator: Geoffrey R. Hosack creator: Simon C. Barry uri: https://doi.org/10.7717/peerj.3014 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Caley et al. title: Gait changes in a line of mice artificially selected for longer limbs link: https://peerj.com/articles/3008 last-modified: 2017-02-22 description: In legged terrestrial locomotion, the duration of stance phase, i.e., when limbs are in contact with the substrate, is positively correlated with limb length, and negatively correlated with the metabolic cost of transport. These relationships are well documented at the interspecific level, across a broad range of body sizes and travel speeds. However, such relationships are harder to evaluate within species (i.e., where natural selection operates), largely for practical reasons, including low population variance in limb length, and the presence of confounding factors such as body mass, or training. Here, we compared spatiotemporal kinematics of gait in Longshanks, a long-legged mouse line created through artificial selection, and in random-bred, mass-matched Control mice raised under identical conditions. We used a gait treadmill to test the hypothesis that Longshanks have longer stance phases and stride lengths, and decreased stride frequencies in both fore- and hind limbs, compared with Controls. Our results indicate that gait differs significantly between the two groups. Specifically, and as hypothesized, stance duration and stride length are 8–10% greater in Longshanks, while stride frequency is 8% lower than in Controls. However, there was no difference in the touch-down timing and sequence of the paws between the two lines. Taken together, these data suggest that, for a given speed, Longshanks mice take significantly fewer, longer steps to cover the same distance or running time compared to Controls, with important implications for other measures of variation among individuals in whole-organism performance, such as the metabolic cost of transport. creator: Leah M. Sparrow creator: Emily Pellatt creator: Sabrina S. Yu creator: David A. Raichlen creator: Herman Pontzer creator: Campbell Rolian uri: https://doi.org/10.7717/peerj.3008 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sparrow et al. title: Seven new species of Night Frogs (Anura, Nyctibatrachidae) from the Western Ghats Biodiversity Hotspot of India, with remarkably high diversity of diminutive forms link: https://peerj.com/articles/3007 last-modified: 2017-02-21 description: The Night Frog genus Nyctibatrachus (Family Nyctibatrachidae) represents an endemic anuran lineage of the Western Ghats Biodiversity Hotspot, India. Until now, it included 28 recognised species, of which more than half were described recently over the last five years. Our amphibian explorations have further revealed the presence of undescribed species of Nights Frogs in the southern Western Ghats. Based on integrated molecular, morphological and bioacoustic evidence, seven new species are formally described here as Nyctibatrachus athirappillyensis sp. nov., Nyctibatrachus manalari sp. nov., Nyctibatrachus pulivijayani sp. nov., Nyctibatrachus radcliffei sp. nov., Nyctibatrachus robinmoorei sp. nov., Nyctibatrachus sabarimalai sp. nov. and Nyctibatrachus webilla sp. nov., thereby bringing the total number of valid Nyctibatrachus species to 35 and increasing the former diversity estimates by a quarter. Detailed morphological descriptions, comparisons with other members of the genus, natural history notes, and genetic relationships inferred from phylogenetic analyses of a mitochondrial dataset are presented for all the new species. Additionally, characteristics of male advertisement calls are described for four new and three previously known species. Among the new species, six are currently known to be geographically restricted to low and mid elevation regions south of Palghat gap in the states of Kerala and Tamil Nadu, and one is probably endemic to high-elevation mountain streams slightly northward of the gap in Tamil Nadu. Interestingly, four new species are also among the smallest known Indian frogs. Hence, our discovery of several new species, particularly of easily overlooked miniaturized forms, reiterates that the known amphibian diversity of the Western Ghats of India still remains underestimated. creator: Sonali Garg creator: Robin Suyesh creator: Sandeep Sukesan creator: SD Biju uri: https://doi.org/10.7717/peerj.3007 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Garg et al. title: On Prophoca and Leptophoca (Pinnipedia, Phocidae) from the Miocene of the North Atlantic realm: redescription, phylogenetic affinities and paleobiogeographic implications link: https://peerj.com/articles/3024 last-modified: 2017-02-21 description: BackgroundProphoca and Leptophoca represent the oldest known genera of phocine seals, dating from the latest early to middle Miocene. Originally, Prophoca rousseaui and Prophoca proxima were described based on fragmentary remains from the Miocene of Belgium. However, several researchers contested the union of Prophoca rousseaui and Prophoca proxima into one genus, without providing evidence. The stratigraphic context of Prophoca remained poorly constrained due to the lack of precise data associated with the original specimens collected in the area of Antwerp (north of Belgium).MethodsProphoca and Leptophoca are redescribed and their phylogenetic position among Phocidae is reassessed using PAUP. Dinoflagellate biostratigraphy has been carried out on sediment samples associated with specimens from Prophoca and Leptophoca to elucidate their approximate ages.ResultsWhereas the species Prophoca rousseaui is redescribed, Prophoca proxima is considered synonymous to Leptophoca lenis, with the proposal of a new combination Leptophoca proxima (Van Beneden, 1877). Sediment samples from specimens of both taxa have been dated to the late Langhian–early Serravallian (middle Miocene). Following a reinvestigation of Leptophoca amphiatlantica, characters from the original diagnosis are questioned and the specimens of Leptophoca amphiatlantica are considered Leptophoca cf. L. proxima. In a phylogenetic analysis, Prophoca rousseaui and Leptophoca proxima constitute early branching stem-phocines.DiscussionLeptophoca proxima from the North Sea Basin is younger than the oldest known find of Leptophoca proxima from North America, which does not contradict the hypothesis that Phocinae originated along the east coast of North America during the late early Miocene, followed by dispersal to Europe shortly after. Morphological features of the appendicular skeleton indicate that Prophoca rousseaui and Leptophoca proxima have archaic locomotory modes, retaining a more prominent use of the fore flipper for aquatic propulsion than extant Phocidae. creator: Leonard Dewaele creator: Olivier Lambert creator: Stephen Louwye uri: https://doi.org/10.7717/peerj.3024 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Dewaele et al. title: Modeling using clinical examination indicators predicts interstitial lung disease among patients with rheumatoid arthritis link: https://peerj.com/articles/3021 last-modified: 2017-02-21 description: Interstitial lung disease (ILD) is a severe extra-articular manifestation of rheumatoid arthritis (RA) that is well-defined as a chronic systemic autoimmune disease. A proportion of patients with RA-associated ILD (RA-ILD) develop pulmonary fibrosis (PF), resulting in poor prognosis and increased lifetime risk. We investigated whether routine clinical examination indicators (CEIs) could be used to identify RA patients with high PF risk. A total of 533 patients with established RA were recruited in this study for model building and 32 CEIs were measured for each of them. To identify PF risk, a new artificial neural network (ANN) was built, in which inputs were generated by calculating Euclidean distance of CEIs between patients. Receiver operating characteristic curve analysis indicated that the ANN performed well in predicting the PF risk (Youden index = 0.436) by only incorporating four CEIs including age, eosinophil count, platelet count, and white blood cell count. A set of 218 RA patients with healthy lungs or suffering from ILD and a set of 87 RA patients suffering from PF were used for independent validation. Results showed that the model successfully identified ILD and PF with a true positive rate of 84.9% and 82.8%, respectively. The present study suggests that model integration of multiple routine CEIs contributes to identification of potential PF risk among patients with RA. creator: Yao Wang creator: Wuqi Song creator: Jing Wu creator: Zhangming Li creator: Fengyun Mu creator: Yang Li creator: He Huang creator: Wenliang Zhu creator: Fengmin Zhang uri: https://doi.org/10.7717/peerj.3021 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Molecular and morphological data reveal three new cryptic species of Chiasmocleis (Mehely 1904) (Anura, Microhylidae) endemic to the Atlantic Forest, Brazil link: https://peerj.com/articles/3005 last-modified: 2017-02-21 description: Three new cryptic species of Chiasmocleis from the Atlantic Forest of Brazil are described. Two of these species occur in the northeastern states of Sergipe and Bahia, whereas the third species is found in the southeastern state of São Paulo. The new species can be distinguished from other congeneric species by the molecular data, as evidenced in the phylogeny, and by a combination of morphological characters including: size, foot webbing, dermal spines, and coloration patterns. Chiasmocleis species differ in osteological traits, therefore we also provide an osteological description of each new species and comparsions with data reported for other species in the genus. creator: Mauricio C. Forlani creator: João F.R. Tonini creator: Carlos A.G. Cruz creator: Hussam Zaher creator: Rafael O. de Sá uri: https://doi.org/10.7717/peerj.3005 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Forlani et al. title: A detailed observation of the ejection and retraction of defense tissue acontia in sea anemone (Exaiptasia pallida) link: https://peerj.com/articles/2996 last-modified: 2017-02-21 description: Acontia, located in the gastrovascular cavity of anemone, are thread-like tissue containing numerous stinging cells which serve as a unique defense tissue against predators of the immobile acontiarian sea anemone. Although its morphology and biological functions, such as defense and digestion, have been studied, the defense behavior and the specific events of acontia ejection and retraction are unclear. The aim of this study is to observe and record the detailed process of acontia control in anemones. Observations reveal that the anemone, Exaiptasia pallida, possibly controls a network of body muscles and manipulates water pressure in the gastrovascular cavity to eject and retract acontia. Instead of resynthesizing acontia after each ejection, the retraction and reuse of acontia enables the anemone to respond quickly at any given time, thus increasing its overall survivability. Since the Exaiptasia anemone is an emerging model for coral biology, this study provides a foundation to further investigate the biophysics, neuroscience, and defense biology of this marine model organism. creator: Julie Lam creator: Ya-Wen Cheng creator: Wan-Nan U. Chen creator: Hsing-Hui Li creator: Chii-Shiarng Chen creator: Shao-En Peng uri: https://doi.org/10.7717/peerj.2996 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lam et al. title: How patch size and refuge availability change interaction strength and population dynamics: a combined individual- and population-based modeling experiment link: https://peerj.com/articles/2993 last-modified: 2017-02-21 description: Knowledge on how functional responses (a measurement of feeding interaction strength) are affected by patch size and habitat complexity (represented by refuge availability) is crucial for understanding food-web stability and subsequently biodiversity. Due to their laborious character, it is almost impossible to carry out systematic empirical experiments on functional responses across wide gradients of patch sizes and refuge availabilities. Here we overcame this issue by using an individual-based model (IBM) to simulate feeding experiments. The model is based on empirically measured traits such as body-mass dependent speed and capture success. We simulated these experiments in patches ranging from sizes of petri dishes to natural patches in the field. Moreover, we varied the refuge availability within the patch independently of patch size, allowing for independent analyses of both variables. The maximum feeding rate (the maximum number of prey a predator can consume in a given time frame) is independent of patch size and refuge availability, as it is the physiological upper limit of feeding rates. Moreover, the results of these simulations revealed that a type III functional response, which is known to have a stabilizing effect on population dynamics, fitted the data best. The half saturation density (the prey density where a predator consumes half of its maximum feeding rate) increased with refuge availability but was only marginally influenced by patch size. Subsequently, we investigated how patch size and refuge availability influenced stability and coexistence of predator-prey systems. Following common practice, we used an allometric scaled Rosenzweig–MacArthur predator-prey model based on results from our in silico IBM experiments. The results suggested that densities of both populations are nearly constant across the range of patch sizes simulated, resulting from the constant interaction strength across the patch sizes. However, constant densities with decreasing patch sizes mean a decrease of absolute number of individuals, consequently leading to extinction of predators in the smallest patches. Moreover, increasing refuge availabilities also allowed predator and prey to coexist by decreased interaction strengths. Our results underline the need for protecting large patches with high habitat complexity to sustain biodiversity. creator: Yuanheng Li creator: Ulrich Brose creator: Katrin Meyer creator: Björn C. Rall uri: https://doi.org/10.7717/peerj.2993 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Li et al. title: Counting complete? Finalising the plant inventory of a global biodiversity hotspot link: https://peerj.com/articles/2984 last-modified: 2017-02-21 description: The Cape Floristic Region—the world’s smallest and third richest botanical hotspot—has benefited from sustained levels of taxonomic effort and exploration for almost three centuries, but how close is this to resulting in a near-complete plant species inventory? We analyse a core component of this flora over a 250-year period for trends in taxonomic effort and species discovery linked to ecological and conservation attributes. We show that >40% of the current total of species was described within the first 100 years of exploration, followed by a continued steady rate of description. We propose that <1% of the flora is still to be described. We document a relatively constant cohort of taxonomists, working over 250 years at what we interpret to be their ‘taxonomic maximum.’ Rates of description of new species were independent of plant growth-form but narrow-range taxa have constituted a significantly greater proportion of species discoveries since 1950. This suggests that the fraction of undiscovered species predominantly comprises localised endemics that are thus of high conservation concern. Our analysis provides important real-world insights for other hotspots in the context of global strategic plans for biodiversity in informing considerations of the likely effort required in attaining set targets of comprehensive plant inventories. In a time of unprecedented biodiversity loss, we argue for a focused research agenda across disciplines to increase the rate of species descriptions in global biodiversity hotspots. creator: Martina Treurnicht creator: Jonathan F. Colville creator: Lucas N. Joppa creator: Onno Huyser creator: John Manning uri: https://doi.org/10.7717/peerj.2984 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Treurnicht et al. title: Patient satisfaction with doctor-patient interaction and its association with modifiable cardiovascular risk factors among moderately-high risk patients in primary healthcare link: https://peerj.com/articles/2983 last-modified: 2017-02-21 description: BackgroundThe outcomes of the physician-patient discussion intervene in the satisfaction of cardiovascular disease risk patients. Adherence to treatment, provision of continuous care, clinical management of the illness and patients’ adjustment are influenced by satisfaction with physician-patient interaction. This study aims to determine patient satisfaction with doctor-patient interactions and, over six months after following prevention counselling, its associations with modifiable cardiovascular risk factors amongst moderately-high risk patients in a primary healthcare clinic in Kelantan, Malaysia.MethodsA prospective survey was conducted amongst patients with moderately-high cardiovascular risk. A total of 104 moderately-high risk patients were recruited and underwent structured prevention counselling based on the World Health Organization guideline, and their satisfaction with the doctor-patient interaction was assessed using ‘Skala Kepuasan Interaksi Perubatan-11,’ the Malay version of the Medical Interview Satisfaction Scale-21. Systolic blood pressure, total cholesterol and high-density lipoprotein cholesterol were measured at baseline and at a follow-up visit at six months. Descriptive analysis, paired t test and linear regression analyses were performed.ResultsA total of 102 patients responded, giving a response rate of 98.1%. At baseline, 76.5% of the respondents were satisfied with the relation with their doctor, with the favourable domain of distress relief (85.3%) and rapport/confidence (91.2%). The unfavourable domain was interaction outcome, with satisfaction in only 67.6% of the respondents. Between the two visits, changes had occurred in total cholesterol (P = 0.022) and in systolic blood pressure (P < 0.001). Six months after the initial visits, no relationship existed between patient satisfaction scores and changes in modifiable cardiovascular risks.DiscussionThe ‘Skala Kepuasan Interaksi Perubatan-11’ which represents a component of the interpersonal doctor-patient relationship can be used to assess improvements of the medical skills and in medical training to enhance the quality of therapeutic communication. creator: Mohd Noor Norhayati creator: Abd Aziz Masseni creator: Ishak Azlina uri: https://doi.org/10.7717/peerj.2983 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Norhayati et al. title: Bax-inhibitor-1 knockdown phenotypes are suppressed by Buffy and exacerbate degeneration in a Drosophila model of Parkinson disease link: https://peerj.com/articles/2974 last-modified: 2017-02-21 description: BackgroundBax inhibitor-1 (BI-1) is an evolutionarily conserved cytoprotective transmembrane protein that acts as a suppressor of Bax-induced apoptosis by regulation of endoplasmic reticulum stress-induced cell death. We knocked down BI-1 in the sensitive dopa decarboxylase (Ddc) expressing neurons of Drosophila melanogaster to investigate its neuroprotective functions. We additionally sought to rescue the BI-1-induced phenotypes by co-expression with the pro-survival Buffy and determined the effect of BI-1 knockdown on the neurodegenerative α-synuclein-induced Parkinson disease (PD) model.MethodsWe used organismal assays to assess longevity of the flies to determine the effect of the altered expression of BI-1 in the Ddc-Gal4-expressing neurons by employing two RNAi transgenic fly lines. We measured the locomotor ability of these RNAi lines by computing the climbing indices of the climbing ability and compared them to a control line that expresses the lacZ transgene. Finally, we performed biometric analysis of the developing eye, where we counted the number of ommatidia and calculated the area of ommatidial disruption.ResultsThe knockdown of BI-1 in these neurons was achieved under the direction of the Ddc-Gal4 transgene and resulted in shortened lifespan and precocious loss of locomotor ability. The co-expression of Buffy, the Drosophila anti-apoptotic Bcl-2 homologue, with BI-1-RNAi resulted in suppression of the reduced lifespan and impaired climbing ability. Expression of human α-synuclein in Drosophila dopaminergic neurons results in neuronal degeneration, accompanied by the age-dependent loss in climbing ability. We exploited this neurotoxic system to investigate possible BI-1 neuroprotective function. The co-expression of α-synuclein with BI-1-RNAi results in a slight decrease in lifespan coupled with an impairment in climbing ability. In supportive experiments, we employed the neuron-rich Drosophila compound eye to investigate subtle phenotypes that result from altered gene expression. The knockdown of BI-1 in the Drosophila developing eye under the direction of the GMR-Gal4 transgene results in reduced ommatidia number and increased disruption of the ommatidial array. Similarly, the co-expression of BI-1-RNAi with Buffy results in the suppression of the eye phenotypes. The expression of α-synuclein along with the knockdown of BI-1 resulted in reduction of ommatidia number and more disruption of the ommatidial array.ConclusionKnockdown of BI-1 in the dopaminergic neurons of Drosophila results in a shortened lifespan and premature loss in climbing ability, phenotypes that appear to be strongly associated with models of PD in Drosophila, and which are suppressed upon overexpression of Buffy and worsened by co-expression with α-synuclein. This suggests that BI-1 is neuroprotective and its knockdown can be counteracted by the overexpression of the pro-survival Bcl-2 homologue. creator: P. Githure M’Angale creator: Brian E. Staveley uri: https://doi.org/10.7717/peerj.2974 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 M’Angale & Staveley title: Intersexual differences of heat shock response between two amphipods (Eulimnogammarus verrucosus and Eulimnogammarus cyaneus) in Lake Baikal link: https://peerj.com/articles/2864 last-modified: 2017-02-21 description: Acute temperature fluctuations are common in surface waters, and aquatic organisms may manifest physiological responses to punctuated temperature spikes long before behavioral responses. Ectotherms, especially cryophilic stenotherms such as those endemic to Lake Baikal (Siberia), may demonstrate specialized physiological responses to acute temperature increases because their proteomes have evolved to function most efficiently at lower temperatures (e.g., <10 °C). Therefore, our study questioned the nature and degree of variation in physiological response to acute thermal stress in two congenerous, endemic Baikal amphipod species, Eulimnogammarus verrucosus and Eulimnogammarus cyaneus. We hypothesized that because interspecific and intersexual thermosensitivity varies significantly among ectotherms, there would be divergent intersexual and interspecific strategies to withstand acute thermal stress, manifested in different protein compositions and concentrations. We exposed individuals to the species’ respective LT50 for one hour followed by a three-hour recovery period. We then performed 1D-PAGE, Western blotting, 2D-PAGE, and Mass Spectrometry techniques and assessed relative intersexual and interspecific changes in proteomic composition and heat shock protein 70 level. Our results demonstrate that females tend to be more sensitive to an acute thermal stimulus than males, most likely because females allocate significant energy to reproduction and less to heat shock response, evidenced by females’ significantly lower LT50time. Lower level of Hsp70 was found in females of the thermosensitive E. verrucosus compared to males of this species. No intersexual differences were found in Hsp70 level in thermotolerant E. cyaneus. Higher levels of hemocyanin subunits and arginine kinase were found in E. cyaneus females after heat shock and recovery compared to males, which was not found for E. verrucosus, suggesting interspecific mechanisms for E. cyaneus’s higher thermotolerance. These differing responses between species and sexes of Baikal amphipods may reflect more general strategies for maintaining homeostatic conditions during acute thermal stress. As mean surface water temperatures increase worldwide, the net efficiency and efficacy of these strategies could give rise to long term changes in physiology, behavior, and interactions with other species, potentially precipitating population and community level alterations. creator: Daria Bedulina creator: Michael F. Meyer creator: Anton Gurkov creator: Ekaterina Kondratjeva creator: Boris Baduev creator: Roman Gusdorf creator: Maxim A. Timofeyev uri: https://doi.org/10.7717/peerj.2864 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bedulina et al. title: Species coexistence and the superior ability of an invasive species to exploit a facilitation cascade habitat link: https://peerj.com/articles/2848 last-modified: 2017-02-21 description: Facilitation cascades generated by co-occurring foundation species can enhance the abundance and diversity of associated organisms. However, it remains poorly understood how differences among native and invasive species in their ability to exploit these positive interactions contribute to emergent patterns of community structure and biotic acceptance. On intertidal shorelines in New England, we examined the patterns of coexistence between the native mud crabs and the invasive Asian shore crab in and out of a facilitation cascade habitat generated by mid intertidal cordgrass and ribbed mussels. These crab species co-occurred in low intertidal cobbles adjacent to the cordgrass–mussel beds, despite experimental findings that the dominant mud crabs can kill and displace Asian shore crabs and thereby limit their successful recruitment to their shared habitat. A difference between the native and invasive species in their utilization of the facilitation cascade likely contributes to this pattern. Only the Asian shore crabs inhabit the cordgrass–mussel beds, despite experimental evidence that both species can similarly benefit from stress amelioration in the beds. Moreover, only Asian shore crabs settle in the beds, which function as a nursery habitat free of lethal mud crabs, and where their recruitment rates are particularly high (nearly an order of magnitude higher than outside beds). Persistence of invasive adult Asian shore crabs among the dominant native mud crabs in the low cobble zone is likely enhanced by a spillover effect of the facilitation cascade in which recruitment-limited Asian shore crabs settle in the mid intertidal cordgrass–mussel beds and subsidize their vulnerable populations in the adjacent low cobble zone. This would explain why the abundances of Asian shore crabs in cobbles are doubled when adjacent to facilitation cascade habitats. The propensity for this exotic species to utilize habitats created by facilitation cascades, despite the lack of a shared evolutionary history, contributes to species coexistence and the acceptance of invasives into a diverse community. creator: Andrew H. Altieri creator: Andrew D. Irving uri: https://doi.org/10.7717/peerj.2848 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Altieri and Irving title: Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies link: https://peerj.com/articles/2988 last-modified: 2017-02-16 description: BackgroundDe novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved.ResultsWe built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts.ConclusionTranscriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap. creator: Cédric Cabau creator: Frédéric Escudié creator: Anis Djari creator: Yann Guiguen creator: Julien Bobe creator: Christophe Klopp uri: https://doi.org/10.7717/peerj.2988 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cabau et al. title: Variant profiling of evolving prokaryotic populations link: https://peerj.com/articles/2997 last-modified: 2017-02-16 description: Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes. However, false positive variant predictions due to sequencing errors and mapping artifacts of short reads need to be prevented. We therefore created VarCap, a workflow for the reliable prediction of different types of variants even at low frequencies. In order to predict SNPs, InDels and structural variations, we evaluated the sensitivity and accuracy of different software tools using synthetic read data. The results suggested that the best sensitivity could be reached by a union of different tools, however at the price of increased false positives. We identified possible reasons for false predictions and used this knowledge to improve the accuracy by post-filtering the predicted variants according to properties such as frequency, coverage, genomic environment/localization and co-localization with other variants. We observed that best precision was achieved by using an intersection of at least two tools per variant. This resulted in the reliable prediction of variants above a minimum relative abundance of 2%. VarCap is designed for being routinely used within experimental evolution experiments or for clinical diagnostics. The detected variants are reported as frequencies within a VCF file and as a graphical overview of the distribution of the different variant/allele/haplotype frequencies. The source code of VarCap is available at https://github.com/ma2o/VarCap. In order to provide this workflow to a broad community, we implemeted VarCap on a Galaxy webserver, which is accessible at http://galaxy.csb.univie.ac.at. creator: Markus Zojer creator: Lisa N. Schuster creator: Frederik Schulz creator: Alexander Pfundner creator: Matthias Horn creator: Thomas Rattei uri: https://doi.org/10.7717/peerj.2997 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zojer et al. title: Understanding morphological variability in a taxonomic context in Chilean diplomystids (Teleostei: Siluriformes), including the description of a new species link: https://peerj.com/articles/2991 last-modified: 2017-02-16 description: Following study of the external morphology and its unmatched variability throughout ontogeny and a re-examination of selected morphological characters based on many specimens of diplomystids from Central and South Chile, we revised and emended previous specific diagnoses and consider Diplomystes chilensis, D. nahuelbutaensis, D. camposensis, and Olivaichthys viedmensis (Baker River) to be valid species. Another group, previously identified as Diplomystes sp., D. spec., D. aff. chilensis, and D. cf. chilensis inhabiting rivers between Rapel and Itata Basins is given a new specific name (Diplomystes incognitus) and is diagnosed. An identification key to the Chilean species, including the new species, is presented. All specific diagnoses are based on external morphological characters, such as aspects of the skin, neuromast lines, and main lateral line, and position of the anus and urogenital pore, as well as certain osteological characters to facilitate the identification of these species that previously was based on many internal characters. Diplomystids below 150 mm standard length (SL) share a similar external morphology and body proportions that make identification difficult; however, specimens over 150 mm SL can be diagnosed by the position of the urogenital pore and anus, and a combination of external and internal morphological characters. According to current knowledge, diplomystid species have an allopatric distribution with each species apparently endemic to particular basins in continental Chile and one species (O. viedmensis) known only from one river in the Chilean Patagonia, but distributed extensively in southern Argentina. creator: Gloria Arratia creator: Claudio Quezada-Romegialli uri: https://doi.org/10.7717/peerj.2991 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Arratia and Quezada-Romegialli title: High richness of insect herbivory from the early Miocene Hindon Maar crater, Otago, New Zealand link: https://peerj.com/articles/2985 last-modified: 2017-02-16 description: Plants and insects are key components of terrestrial ecosystems and insect herbivory is the most important type of interaction in these ecosystems. This study presents the first analysis of associations between plants and insects for the early Miocene Hindon Maar fossil lagerstätte, Otago, New Zealand. A total of 584 fossil angiosperm leaves representing 24 morphotypes were examined to determine the presence or absence of insect damage types. Of these leaves, 73% show signs of insect damage; they comprise 821 occurrences of damage from 87 damage types representing all eight functional feeding groups. In comparison to other fossil localities, the Hindon leaves display a high abundance of insect damage and a high diversity of damage types. Leaves of Nothofagus(southern beech), the dominant angiosperm in the fossil assemblage, exhibit a similar leaf damage pattern to leaves from the nearby mid to late Miocene Dunedin Volcano Group sites but display a more diverse spectrum and much higher percentage of herbivory damage than a comparable dataset of leaves from Palaeocene and Eocene sites in the Antarctic Peninsula. creator: Anna Lena Möller creator: Uwe Kaulfuss creator: Daphne E. Lee creator: Torsten Wappler uri: https://doi.org/10.7717/peerj.2985 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Möller et al. title: Exoskeletons of Bougainvilliidae and other Hydroidolina (Cnidaria, Hydrozoa): structure and composition link: https://peerj.com/articles/2964 last-modified: 2017-02-16 description: The exoskeleton is an important source of characters for the taxonomy of Hydroidolina. It originates as epidermal secretions and, among other functions, protects the coenosarc of the polypoid stage. However, comparative studies on the exoskeletal tissue origin, development, chemical, and structural characteristics, as well as its evolution and homology, are few and fragmented. This study compares the structure and composition of the exoskeleton and underlying coenosarc in members of “Anthoathecata” and some Leptothecata, but does so mainly in bougainvilliid polyps histological analyses. We also studied the development of the exoskeleton under experimental conditions. We identified three types of glandular epidermal cells related to the origin of the exoskeleton and the secretion of its polysaccharides component. The exoskeleton of the species studied is either bilayered (perisarc and exosarc, especially in bougainvilliids) or corneous (perisarc). The exoskeleton varies in chemical composition, structural rigidity, thickness, extension, and coverage in the different regions of the colony. In bilayered exoskeletons, the exosarc is produced first and appears to be a key step in the formation of the rigid exoskeleton. The exoskeleton contains anchoring structures such as desmocytes and “perisarc extensions.” creator: María A. Mendoza-Becerril creator: José Eduardo A.R. Marian creator: Alvaro Esteves Migotto creator: Antonio Carlos Marques uri: https://doi.org/10.7717/peerj.2964 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Mendoza-Becerril et al. title: Small-scale spatial variation in population- and individual-level reproductive parameters of the blue-legged hermit crab Clibanarius tricolor link: https://peerj.com/articles/3004 last-modified: 2017-02-15 description: Management of the few regulated ornamental fisheries relies on inadequate information about the life history of the target species. Herein, we investigated the reproductive biology of the most heavily traded marine invertebrate in the western Atlantic; the blue-legged hermit crab Clibanarius tricolor. We report on density, individual-level, and population-level reproductive parameters in 14 populations spanning the Florida Keys. In C. tricolor, abundance, population-level, and individual-level reproductive parameters exhibited substantial small-scale spatial variation in the Florida Keys. For instance, the proportion of brooding females varied between 10–94% across localities. In females, average (±SD) fecundity varied between 184 (±54) and 614 (±301) embryos crab-1 across populations. Fecundity usually increases with female body size in hermit crabs. However, we found no effect of female body size on fecundity in three of the populations. Altogether, our observations suggest that C. tricolor may fit a source-sink metapopulation dynamic in the Florida Keys with low reproductive intensity and absence of a parental body size—fecundity relationship resulting in net reproductive loses at some localities. We argue in favor of additional studies describing population dynamics and other aspects of the natural history of C. tricolor (e.g., development type, larval duration) to reveal ‘source’ populations, capable of exporting larvae to nearby populations. Our observations imply that future studies aimed at assessing standing stocks or describing other aspects of the life history of this hermit crab need to focus on multiple localities simultaneously. This and future studies on the reproductive biology of this species will form the baseline for models aimed at assessing the stock condition and sustainability of this heavily harvested crustacean. creator: J. Antonio Baeza creator: Donald C. Behringer uri: https://doi.org/10.7717/peerj.3004 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Baeza and Behringer title: Risk analysis of colorectal cancer incidence by gene expression analysis link: https://peerj.com/articles/3003 last-modified: 2017-02-15 description: BackgroundColorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction.ObjectiveMicroarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples.MethodsWe collected microarray data from the GEO database to establish colorectal cancer microarray gene expression datasets for a combined analysis. Using the Prediction Analysis for Microarrays (PAM) method and the GSEA MSigDB resource, we analyzed the 14,698 genes that were identified through an examination of their expression values between normal and tumor tissues.ResultsTen genes (ABCG2, AQP8, SPIB, CA7, CLDN8, SCNN1B, SLC30A10, CD177, PADI2, and TGFBI) were found to be good indicators of the candidate genes that correlate with CRC. From these selected genes, an average of six significant genes were obtained using the PAM method, with an accuracy rate of 95%. The results demonstrate the potential of utilizing a model with the PAM method for data mining. After a detailed review of the published reports, the results confirmed that the screened candidate genes are good indicators for cancer risk analysis using the PAM method.ConclusionsSix genes were selected with 95% accuracy to effectively classify normal and colorectal cancer tissues. We hope that these results will provide the basis for new research projects in clinical practice that aim to rapidly assess colorectal cancer risk using microarray gene expression analysis. creator: Wei-Chuan Shangkuan creator: Hung-Che Lin creator: Yu-Tien Chang creator: Chen-En Jian creator: Hueng-Chuen Fan creator: Kang-Hua Chen creator: Ya-Fang Liu creator: Huan-Ming Hsu creator: Hsiu-Ling Chou creator: Chung-Tay Yao creator: Chi-Ming Chu creator: Sui-Lung Su creator: Chi-Wen Chang uri: https://doi.org/10.7717/peerj.3003 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shangkuan et al. title: Effect of interleukin (IL)-35 on IL-17 expression and production by human CD4+ T cells link: https://peerj.com/articles/2999 last-modified: 2017-02-15 description: BackgroundInterleukin (IL)-17 produced by mainly T helper 17 (Th17) cells may play an important destructive role in chronic periodontitis (CP). Thus, anti-inflammatory cytokines, such as IL-35, might have a beneficial effect in periodontitis by inhibiting differentiation of Th17 cells. Th17 differentiation is regulated by the retinoic acid receptor-related orphan receptor (ROR) α (encoded by RORA) and RORγt (encoded by RORC). However, the role of IL-35 in periodontitis is not clear and the effect of IL-35 on the function of Th17 cells is still incompletely understood. Therefore, we investigated the effects of IL-35 on Th17 cells.MethodsPeripheral blood mononuclear cells (PBMCs) were sampled from three healthy volunteers and three CP patients and were analyzed by flow cytometry for T cell population. Th17 cells differentiated by a cytokine cocktail (recombinant transforming growth factor-β, rIL-6, rIL-1β, anti-interferon (IFN)-γ, anti-IL-2 and anti-IL-4) from PBMCs were cultured with or without rIL-35. IL17A (which usually refers to IL-17), RORA and RORCmRNA expression was analyzed by quantitative polymerase chain reaction, and IL-17A production was determined by enzyme-linked immunosorbent assay.ResultsThe proportion of IL-17A+CD4+ slightly increased in CP patients compared with healthy controls, however, there were no significant differences in the percentage of IL-17A+CD4+ as well as IFN-γ+CD4+ and Foxp3+CD4+ T cells between healthy controls and CP patients. IL17A, RORA and RORC mRNA expression was significantly increased in Th17 cells induced by the cytokine cocktail, and the induction was significantly inhibited by addition of rIL-35 (1 ng/mL). IL-17A production in Th17 cells was significantly inhibited by rIL-35 addition (1 ng/mL).DiscussionThe present study suggests that IL-35 could directly suppress IL-17 expression via RORα and RORγt inhibition and might play an important role in inflammatory diseases such as periodontitis. creator: Kosuke Okada creator: Takeki Fujimura creator: Takeshi Kikuchi creator: Makoto Aino creator: Yosuke Kamiya creator: Ario Izawa creator: Yuki Iwamura creator: Hisashi Goto creator: Iichiro Okabe creator: Eriko Miyake creator: Yoshiaki Hasegawa creator: Makio Mogi creator: Akio Mitani uri: https://doi.org/10.7717/peerj.2999 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Okada et al. title: ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in Fusarium link: https://peerj.com/articles/2992 last-modified: 2017-02-15 description: Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22 Fusarium species were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the freely available annotation effort. creator: Tomasz Kulik creator: Kessy Abarenkov creator: Maciej Buśko creator: Katarzyna Bilska creator: Anne D. van Diepeningen creator: Anna Ostrowska-Kołodziejczak creator: Katarzyna Krawczyk creator: Balázs Brankovics creator: Sebastian Stenglein creator: Jakub Sawicki creator: Juliusz Perkowski uri: https://doi.org/10.7717/peerj.2992 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kulik et al. title: Opportunities drive the global distribution of protected areas link: https://peerj.com/articles/2989 last-modified: 2017-02-15 description: BackgroundProtected areas, regarded today as a cornerstone of nature conservation, result from an array of multiple motivations and opportunities. We explored at global and regional levels the current distribution of protected areas along biophysical, human, and biological gradients, and assessed to what extent protection has pursued (i) a balanced representation of biophysical environments, (ii) a set of preferred conditions (biological, spiritual, economic, or geopolitical), or (iii) existing opportunities for conservation regardless of any representation or preference criteria.MethodsWe used histograms to describe the distribution of terrestrial protected areas along biophysical, human, and biological independent gradients and linear and non-linear regression and correlation analyses to describe the sign, shape, and strength of the relationships. We used a random forest analysis to rank the importance of different variables related to conservation preferences and opportunity drivers, and an evenness metric to quantify representativeness.ResultsWe find that protection at a global level is primarily driven by the opportunities provided by isolation and a low population density (variable importance = 34.6 and 19.9, respectively). Preferences play a secondary role, with a bias towards tourism attractiveness and proximity to international borders (variable importance = 12.7 and 3.4, respectively). Opportunities shape protection strongly in “North America & Australia–NZ” and “Latin America & Caribbean,” while the importance of the representativeness of biophysical environments is higher in “Sub-Saharan Africa” (1.3 times the average of other regions).DiscussionEnvironmental representativeness and biodiversity protection are top priorities in land conservation agendas. However, our results suggest that they have been minor players driving current protection at both global and regional levels. Attempts to increase their relevance will necessarily have to recognize the predominant opportunistic nature that the establishment of protected areas has had until present times. creator: Germán Baldi creator: Marcos Texeira creator: Osvaldo A. Martin creator: H. Ricardo Grau creator: Esteban G. Jobbágy uri: https://doi.org/10.7717/peerj.2989 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Baldi et al. title: The preventive effect of dexmedetomidine on paroxysmal sympathetic hyperactivity in severe traumatic brain injury patients who have undergone surgery: a retrospective study link: https://peerj.com/articles/2986 last-modified: 2017-02-15 description: BackgroundParoxysmal sympathetic hyperactivity (PSH) results and aggravates in secondary brain injury, which seriously affects the prognosis of severe traumatic brain injury patients. Although several studies have focused on the treatment of PSH, few have concentrated on its prevention.MethodsNinety post-operation (post-op) severe traumatic brain injury (sTBI) patients admitted from October 2014 to April 2016 were chosen to participate in this study. Fifty of the post-op sTBI patients were sedated with dexmedetomidine and were referred as the “dexmedetomidine group” (admitted from May 2015 to April 2016). The other 40 patients (admitted from October 2014 to May 2015) received other sedations and were referred as the “control group.” The two groups were then compared based on their PSH scores and the scores and ratios of those patients who met the criteria of “probable,” “possible” and “unlikely” using the PSH assessment measure (PSH-AM) designed by Baguley et al. (2014). The durations of the neurosurgery intensive care unit (NICU) and hospital stays and the Glasgow outcome scale (GOS) values for the two groups were also compared to evaluate the therapeutic effects and the patients’ prognosis.ResultsThe overall PSH score for the dexmedetomidine group was 5.26 ± 4.66, compared with 8.58 ± 8.09 for the control group. The difference between the two groups’ PSH scores was significant (P = 0.017). The score of the patients who met the criterion of “probable” was 18.33 ± 1.53 in the dexmedetomidine group and 22.63 ± 2.97 in the control group, and the difference was statistically significant (P = 0.045). The ratio of patients who were classified as “unlikely” between the two groups was statistically significant (P = 0.028); that is, 42 (84%) in the dexmedetomidine group and 25 (62.5%) in the control group. The differences in NICU, hospital stays and GOS values between the two groups were not significant.ConclusionDexmedetomidine has a preventive effect on PSH in sTBI patients who have undergone surgery. creator: Qilin Tang creator: Xiang Wu creator: Weiji Weng creator: Hongpeng Li creator: Junfeng Feng creator: Qing Mao creator: Guoyi Gao creator: Jiyao Jiang uri: https://doi.org/10.7717/peerj.2986 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tang et al. title: Is there a relation between dental anxiety, fear and general psychological status? link: https://peerj.com/articles/2978 last-modified: 2017-02-15 description: BackgroundDental anxiety is a widespread problem in many populations. This problem can be a barrier to dental care and may lead to poor oral health. Dental anxiety may be related to psychological status.AimsThe aim of the present study was to assess the levels of dental anxiety, dental fear, Beck Depression, and state-trait anxiety according to age, gender and education level in patients at the periodontology clinic in the Diyarbakır Mouth and Dental Health Center.Study DesignA total of 231 patients (115 males, 116 females) filled out dental fear scale (DFS), dental anxiety scale (DAS), Beck Depression Inventory (BDI), state-trait anxiety inventory-state (STAI-S), and state-trait anxiety inventory–trait (STAI-T) questionnaires, and evaluations of DFS, DAS, BDI, STAI-S, and STAI-T were conducted according to age, gender, and education level.ResultsThe mean DFS, DAS, BDI, STAI-T, and STAI –S were 45.64, 9.15, 13.16, 38.90, and 40.18, respectively. There was a significant association among DFS, DAS, BDI, STAI-S, and STAI-T (p < 0.05). These surveys scores were significantly higher in females than males (p < 0.05). The results of this study indicated that gender age and education level have important effects on DFS, DAS, BDI, STAI-S, and STAI-T (p < 0.05).ConclusionDental anxiety and dental fear were found to be related to psychological status (BDI, STAI-S, and STAI-T) over time. There are some patients with unaddressed psychological distress. creator: Tuba Talo Yildirim creator: Serkan Dundar creator: Alihan Bozoglan creator: Tahir Karaman creator: Neval Dildes creator: Filiz Acun Kaya creator: Eyyup Altintas creator: Faruk Oztekin creator: Osman Atas creator: Hilal Alan uri: https://doi.org/10.7717/peerj.2978 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Talo Yildirim et al. title: Spawning aggregation of white-streaked grouper Epinephelus ongus: spatial distribution and annual variation in the fish density within a spawning ground link: https://peerj.com/articles/3000 last-modified: 2017-02-14 description: White-streaked grouper (Epinephelus ongus) is an important fisheries target and forms spawning aggregations at particular spawning grounds. The aims of the present study were to investigate the ecological characteristics of annual spawning aggregations such as (1) spatial variations in the density of E. ongus at the spawning ground, (2) the relationship between fish density and environmental variables, (3) inter-annual variations in the spawning aggregation, (4) the proportion of males to females at the spawning ground for several days pre—and post-spawning and (5) the relationship between male density and female density at the protected spawning ground, based on observations over five years at an Okinawan coral reef. Although the protected spawning ground area was large (ca. 2,500 m × 700 m), high density of E. ongus (over 25 individuals per 100 m2) was found in a limited area (within c.a. 750 m × 50 m). Current velocity and coverage of rocks had significant positive effects on the spatial distribution of E. ongus at the spawning ground. Inter-annual variation in the degree of aggregation was found and this variation was explained by the annual variation of mean seawater temperature during 40 days before the spawning day. The male–female ratio (male:female) at the spawning ground was ca. 3:1 for three years (May 2012, May 2014 and May 2015) whereas >13:1 for one year (May 2013). Significant positive relationships between male density and female density were found at the aggregation sites. It is suggested that E. ongus use aggregation sites with greater current velocity to reduce the risk of egg predation and seawater temperature is one of the main factors that is responsible for determining the degree of aggregation. It is also suggested that females possibly select sites with a greater density of males and this selection behavior might be the reason why females arrived at the spawning ground after the arrival of the males. For effective management of spawning grounds, precise site selection as well as the duration of the protection period are suggested to be key aspects to protect the spawning aggregations of E. ongus, which have been currently achieved at the spawning ground. creator: Atsushi Nanami creator: Taku Sato creator: Yuuki Kawabata creator: Junichi Okuyama uri: https://doi.org/10.7717/peerj.3000 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nanami et al. title: Modafinil decreases anxiety-like behaviour in zebrafish link: https://peerj.com/articles/2994 last-modified: 2017-02-14 description: Modafinil (2-((diphenylmethyl)sulfinyl)acetamide), a selective dopamine and norepinephrine transporter inhibitor, is most commonly prescribed for narcolepsy but has gained recent interest for treating a variety of disorders. Zebrafish (Danio rerio) are becoming a model of choice for pharmacological and behavioural research. To investigate the behavioural effects of modafinil on anxiety, we administered doses of 0, 2, 20, and 200 mg/L for 30 minutes then tested zebrafish in the novel approach test. In this test, the fish was placed into a circular arena with a novel object in the center and motion-tracking software was used to quantify the time the fish spent in the outer area of the arena (thigmotaxis zone), middle third of the arena (transition zone) and center of the arena, as well as total distance traveled, immobility and meandering. Modafinil caused a decrease in time spent in the thigmotaxis zone and increased time spent in the transition zone across all doses. Modafinil did not significantly alter the time spent in the center zone (near the novel object), the distance moved, meandering, or the duration of time spent immobile. We also validated this test as a measure of anxiety with the administration of ethanol (1%) which decreased time spent in the thigmotaxis zone and increased time spent in the transition zone. These results suggest that modafinil decreases anxiety-like behaviour in zebrafish. creator: Adrian Johnson creator: Trevor James Hamilton uri: https://doi.org/10.7717/peerj.2994 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Johnson and and Hamilton title: An open source device for operant licking in rats link: https://peerj.com/articles/2981 last-modified: 2017-02-14 description: We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior. creator: Matthew Longley creator: Ethan L. Willis creator: Cindy X. Tay creator: Hao Chen uri: https://doi.org/10.7717/peerj.2981 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Longley et al. title: ­Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis link: https://peerj.com/articles/2912 last-modified: 2017-02-14 description: Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment. creator: Agustina Undabarrena creator: Juan A. Ugalde creator: Michael Seeger creator: Beatriz Cámara uri: https://doi.org/10.7717/peerj.2912 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Undabarrena et al. title: Comparison of hand grip strength and upper limb pressure pain threshold between older adults with or without non-specific shoulder pain link: https://peerj.com/articles/2995 last-modified: 2017-02-09 description: BackgroundThere is a high prevalence of non-specific shoulder pain associated with upper limb functional limitations in older adults. The purpose of this study was to determine the minimal clinically important differences (MCID) of grip strength and pressure pain threshold (PPT) in the upper limb between older adults with or without non-specific shoulder pain.MethodsA case-control study was carried out following the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) criteria. A sample of 132 shoulders (mean ± SD years) with (n = 66; 76.04 ± 7.58) and without (n = 66; 75.05 ± 6.26) non-specific pain were recruited. The grip strength and PPT of the anterior deltoid and extensor carpi radialis brevis (ECRB) muscles were assessed.ResultsThere were statistically significant differences (mean ± SD; P-value) for anterior deltoid PPT (2.51 ± 0.69 vs 3.68 ± 0.65, kg/cm2; P < .001), ECRB PPT (2.20 ± 0.60 vs 3.35 ± 0.38 kg/cm2; P < .001) and grip strength (20.78 ± 10.94 vs 24.63 ± 9.38 kg; P = .032) between shoulders with and without non-specific pain, respectively.DiscussionThe MCID of 1.17 kg/cm2, 1.15 kg/cm2 and 3.84 kg were proposed for anterior deltoid PPT, ECRB PPT and grip strength, respectively, to assess the upper limb of older adults with non-specific shoulder pain after treatment. In addition, univariate and multivariate (linear regression and regression trees) analyses may be used to consider age distribution, sex, pain intensity, grip strength and PPT in older adults including clinical and epidemiological studies with non-specific shoulder pain. creator: Cesar Calvo Lobo creator: Carlos Romero Morales creator: David Rodríguez Sanz creator: Irene Sanz Corbalán creator: Eleuterio A. Sánchez Romero creator: Josué Fernández Carnero creator: Daniel López López uri: https://doi.org/10.7717/peerj.2995 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Calvo Lobo et al. title: Pattern analysis of total item score and item response of the Kessler Screening Scale for Psychological Distress (K6) in a nationally representative sample of US adults link: https://peerj.com/articles/2987 last-modified: 2017-02-09 description: BackgroundSeveral recent studies have shown that total scores on depressive symptom measures in a general population approximate an exponential pattern except for the lower end of the distribution. Furthermore, we confirmed that the exponential pattern is present for the individual item responses on the Center for Epidemiologic Studies Depression Scale (CES-D). To confirm the reproducibility of such findings, we investigated the total score distribution and item responses of the Kessler Screening Scale for Psychological Distress (K6) in a nationally representative study.MethodsData were drawn from the National Survey of Midlife Development in the United States (MIDUS), which comprises four subsamples: (1) a national random digit dialing (RDD) sample, (2) oversamples from five metropolitan areas, (3) siblings of individuals from the RDD sample, and (4) a national RDD sample of twin pairs. K6 items are scored using a 5-point scale: “none of the time,” “a little of the time,” “some of the time,” “most of the time,” and “all of the time.” The pattern of total score distribution and item responses were analyzed using graphical analysis and exponential regression model.ResultsThe total score distributions of the four subsamples exhibited an exponential pattern with similar rate parameters. The item responses of the K6 approximated a linear pattern from “a little of the time” to “all of the time” on log-normal scales, while “none of the time” response was not related to this exponential pattern.DiscussionThe total score distribution and item responses of the K6 showed exponential patterns, consistent with other depressive symptom scales. creator: Shinichiro Tomitaka creator: Yohei Kawasaki creator: Kazuki Ide creator: Maiko Akutagawa creator: Hiroshi Yamada creator: Ono Yutaka creator: Toshiaki A. Furukawa uri: https://doi.org/10.7717/peerj.2987 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tomitaka et al. title: Comparison of 3D laser-based photonic scans and manual anthropometric measurements of body size and shape in a validation study of 123 young Swiss men link: https://peerj.com/articles/2980 last-modified: 2017-02-09 description: BackgroundManual anthropometric measurements are time-consuming and challenging to perform within acceptable intra- and inter-individual error margins in large studies. Three-dimensional (3D) laser body scanners provide a fast and precise alternative: within a few seconds the system produces a 3D image of the body topography and calculates some 150 standardised body size measurements.ObjectiveThe aim was to enhance the small number of existing validation studies and compare scan and manual techniques based on five selected measurements. We assessed the agreement between two repeated measurements within the two methods, analysed the direct agreement between the two methods, and explored the differences between the techniques when used in regressions assessing the effect of health related determinants on body shape indices.MethodsWe performed two repeated body scans on 123 volunteering young men using a Vitus Smart XXL body scanner. We manually measured height, waist, hip, buttock, and chest circumferences twice for each participant according to the WHO guidelines. The participants also filled in a basic questionnaire.ResultsMean differences between the two scan measurements were smaller than between the two manual measurements, and precision as well as intra-class correlation coefficients were higher. Both techniques were strongly correlated. When comparing means between both techniques we found significant differences: Height was systematically shorter by 2.1 cm, whereas waist, hip and bust circumference measurements were larger in the scans by 1.17–4.37 cm. In consequence, body shape indices also became larger and the prevalence of overweight was greater when calculated from the scans. Between 4.1% and 7.3% of the probands changed risk category from normal to overweight when classified based on the scans. However, when employing regression analyses the two measurement techniques resulted in very similar coefficients, confidence intervals, and p-values.ConclusionFor performing a large number of measurements in a large group of probands in a short time, body scans generally showed good feasibility, reliability, and validity in comparison to manual measurements. The systematic differences between the methods may result from their technical nature (contact vs. non-contact). creator: Nikola Koepke creator: Marcel Zwahlen creator: Jonathan C. Wells creator: Nicole Bender creator: Maciej Henneberg creator: Frank J. Rühli creator: Kaspar Staub uri: https://doi.org/10.7717/peerj.2980 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Koepke et al. title: Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets link: https://peerj.com/articles/2969 last-modified: 2017-02-09 description: Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, “phylofactorization,” to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen. creator: Alex D. Washburne creator: Justin D. Silverman creator: Jonathan W. Leff creator: Dominic J. Bennett creator: John L. Darcy creator: Sayan Mukherjee creator: Noah Fierer creator: Lawrence A. David uri: https://doi.org/10.7717/peerj.2969 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Washburne et al. title: Acoustic monitoring indicates a correlation between calling and spawning in captive spotted seatrout (Cynoscion nebulosus) link: https://peerj.com/articles/2944 last-modified: 2017-02-09 description: BackgroundFish sound production is widespread throughout many families. Territorial displays and courtship are the most common reasons for fish sound production. Yet, there is still some questions on how acoustic signaling and reproduction are correlated in many sound-producing species. In the present study, our aim was to determine if a quantitative relationship exists between calling and egg deposition in captive spotted seatrout (Cynoscion nebulosus). This type of data is essential if passive acoustics is to be used to identify spawning aggregations over large spatial scales and monitor reproductive activity over annual and decadal timeframes.MethodsAcoustic recorders (i.e., DSG-Oceans) were placed in three laboratory tanks to record underwater sound over an entire, simulated reproductive season. We enumerated the number of calls, calculated the received sound pressure level, and counted the number of eggs every morning in each tank.ResultsSpotted seatrout produced three distinct call types characterized as “drums,” “grunts,” and “staccatos.” Spotted seatrout calling increased as the light cycle shifted from 13.5 to 14.5 h of light, and the temperature increased to 27.7 °C. Calling decreased once the temperature fell below 27.7 °C, and the light cycle shifted to 12 h of light. These temperature and light patterns followed the natural reproductive season observed in wild spotted seatrout in the Southeast United States. Spotted seatrout exhibited daily rhythms in calling. Acoustic signaling began once the lights turned off, and calling reached maximum activity approximately 3 h later. Eggs were released only on evenings in which spotted seatrout were calling. In all tanks, spotted seatrout were more likely to spawn when male fish called more frequently. A positive relationship between SPL and the number of eggs collected was found in Tanks 1 and 3.DiscussionOur findings indicate that acoustic metrics can predict spawning potential. These findings are important because plankton tows may not accurately reflect spawning locations since egg capture is likely affected by predator activity and water currents. Instead, passive acoustics could be used to monitor spotted seatrout reproduction. Future studies can use this captive study as a model to record the estuarine soundscape precisely over long time periods to better understand how human-made stressors (e.g., climate change, noise pollution, and chemical pollutants) may affect spawning patterns. creator: Eric W. Montie creator: Matt Hoover creator: Christopher Kehrer creator: Justin Yost creator: Karl Brenkert creator: Tim O’Donnell creator: Michael R. Denson uri: https://doi.org/10.7717/peerj.2944 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Montie et al. title: Molecular characterization and genetic diversity of Jatropha curcas L. in Costa Rica link: https://peerj.com/articles/2931 last-modified: 2017-02-09 description: We estimated the genetic diversity of 50 Jatropha curcas samples from the Costa Rican germplasm bank using 18 EST-SSR, one G-SSR and nrDNA-ITS markers. We also evaluated the phylogenetic relationships among samples using nuclear ribosomal ITS markers. Non-toxicity was evaluated using G-SSRs and SCARs markers. A Neighbor-Joining (NJ) tree and a Maximum Likelihood (ML) tree were constructed using SSR markers and ITS sequences, respectively. Heterozygosity was moderate (He = 0.346), but considerable compared to worldwide values for J. curcas. The PIC (PIC = 0.274) and inbreeding coefficient (f =  − 0.102) were both low. Clustering was not related to the geographical origin of accessions. International accessions clustered independently of collection sites, suggesting a lack of genetic structure, probably due to the wide distribution of this crop and ample gene flow. Molecular markers identified only one non-toxic accession (JCCR-24) from Mexico. This work is part of a countrywide effort to characterize the genetic diversity of the Jatropha curcas germplasm bank in Costa Rica. creator: Marcela Vásquez-Mayorga creator: Eric J. Fuchs creator: Eduardo J. Hernández creator: Franklin Herrera creator: Jesús Hernández creator: Ileana Moreira creator: Elizabeth Arnáez creator: Natalia M. Barboza uri: https://doi.org/10.7717/peerj.2931 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vásquez-Mayorga et al. title: Candidate genes that have facilitated freshwater adaptation by palaemonid prawns in the genus Macrobrachium: identification and expression validation in a model species (M. koombooloomba) link: https://peerj.com/articles/2977 last-modified: 2017-02-08 description: BackgroundThe endemic Australian freshwater prawn, Macrobrachium koombooloomba, provides a model for exploring genes involved with freshwater adaptation because it is one of the relatively few Macrobrachium species that can complete its entire life cycle in freshwater.MethodsThe present study was conducted to identify potential candidate genes that are likely to contribute to effective freshwater adaptation by M. koombooloomba using a transcriptomics approach. De novo assembly of 75 bp paired end 227,564,643 high quality Illumina raw reads from 6 different cDNA libraries revealed 125,917 contigs of variable lengths (200–18,050 bp) with an N50 value of 1597.ResultsIn total, 31,272 (24.83%) of the assembled contigs received significant blast hits, of which 27,686 and 22,560 contigs were mapped and functionally annotated, respectively. CEGMA (Core Eukaryotic Genes Mapping Approach) based transcriptome quality assessment revealed 96.37% completeness. We identified 43 different potential genes that are likely to be involved with freshwater adaptation in M. koombooloomba. Identified candidate genes included: 25 genes for osmoregulation, five for cell volume regulation, seven for stress tolerance, three for body fluid (haemolymph) maintenance, eight for epithelial permeability and water channel regulation, nine for egg size control and three for larval development. RSEM (RNA-Seq Expectation Maximization) based abundance estimation revealed that 6,253, 5,753 and 3,795 transcripts were expressed (at TPM value ≥10) in post larvae, juveniles and adults, respectively. Differential gene expression (DGE) analysis showed that 15 genes were expressed differentially in different individuals but these genes apparently were not involved with freshwater adaptation but rather were involved in growth, development and reproductive maturation.DiscussionThe genomic resources developed here will be useful for better understanding the molecular basis of freshwater adaptation in Macrobrachium prawns and other crustaceans more broadly. creator: Md Lifat Rahi creator: Shorash Amin creator: Peter B. Mather creator: David A. Hurwood uri: https://doi.org/10.7717/peerj.2977 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Rahi et al. title: Cropping system diversification for food production in Mindanao rubber plantations: a rice cultivar mixture and rice intercropped with mungbean link: https://peerj.com/articles/2975 last-modified: 2017-02-08 description: Including food production in non-food systems, such as rubber plantations and biofuel or bioenergy crops, may contribute to household food security. We evaluated the potential for planting rice, mungbean, rice cultivar mixtures, and rice intercropped with mungbean in young rubber plantations in experiments in the Arakan Valley of Mindanao in the Philippines. Rice mixtures consisted of two- or three-row strips of cultivar Dinorado, a cultivar with higher value but lower yield, and high-yielding cultivar UPL Ri-5. Rice and mungbean intercropping treatments consisted of different combinations of two- or three-row strips of rice and mungbean. We used generalized linear mixed models to evaluate the yield of each crop alone and in the mixture or intercropping treatments. We also evaluated a land equivalent ratio for yield, along with weed biomass (where Ageratum conyzoides was particularly abundant), the severity of disease caused by Magnaporthe oryzae and Cochliobolus miyabeanus, and rice bug (Leptocorisa acuta) abundance. We analyzed the yield ranking of each cropping system across site-year combinations to determine mean relative performance and yield stability. When weighted by their relative economic value, UPL Ri-5 had the highest mean performance, but with decreasing performance in low-yielding environments. A rice and mungbean intercropping system had the second highest performance, tied with high-value Dinorado but without decreasing relative performance in low-yielding environments. Rice and mungbean intercropped with rubber have been adopted by farmers in the Arakan Valley. creator: Rosa Fe Hondrade creator: Edwin Hondrade creator: Lianqing Zheng creator: Francisco Elazegui creator: Jo-Anne Lynne Joy E. Duque creator: Christopher C. Mundt creator: Casiana M. Vera Cruz creator: Karen A. Garrett uri: https://doi.org/10.7717/peerj.2975 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hondrade et al. title: Pull-down combined with proteomic strategy reveals functional diversity of synaptotagmin I link: https://peerj.com/articles/2973 last-modified: 2017-02-08 description: Synaptotagmin I (Syt I) is most abundant in the brain and is involved in multiple cellular processes. Its two C2 domains, C2A and C2B, are the main functional regions. Our present study employed a pull-down combined with proteomic strategy to identify the C2 domain-interacting proteins to comprehensively understand the biological roles of the C2 domains and thus the functional diversity of Syt I. A total of 135 non-redundant proteins interacting with the C2 domains of Syt I were identified. Out of them, 32 and 64 proteins only bound to C2A or C2B domains, respectively, and 39 proteins bound to both of them. Compared with C2A, C2B could bind to many more proteins particularly those involved in synaptic transmission and metabolic regulation. Functional analysis indicated that Syt I may exert impacts by interacting with other proteins on multiple cellular processes, including vesicular membrane trafficking, synaptic transmission, metabolic regulation, catalysis, transmembrane transport and structure formation, etc. These results demonstrate that the functional diversity of Syt I is higher than previously expected, that its two domains may mediate the same and different cellular processes cooperatively or independently, and that C2B domain may play even more important roles than C2A in the functioning of Syt I. This work not only further deepened our understanding of the functional diversity of Syt I and the functional differences between its two C2 domains, but also provided important clues for the further related researches. creator: Tianyao Guo creator: Zhigui Duan creator: Jia Chen creator: Chunliang Xie creator: Ying Wang creator: Ping Chen creator: Xianchun Wang uri: https://doi.org/10.7717/peerj.2973 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Guo et al. title: Screening of faba bean (Vicia faba L.) accessions to acidity and aluminium stresses link: https://peerj.com/articles/2963 last-modified: 2017-02-08 description: BackgroundFaba bean is an important starch-based protein crop produced worldwide. Soil acidity and aluminium toxicity are major abiotic stresses affecting its production, so in regions where soil acidity is a problem, there is a gap between the potential and actual productivity of the crop. Hence, we set out to evaluate acidity and aluminium tolerance in a range of faba bean germplasm using solution culture and pot experiments.MethodsA set of 30 accessions was collected from regions where acidity and aluminium are or are not problems. The accessions were grown in solution culture and a subset of 10 was grown first in peat and later in perlite potting media. In solution culture, morphological parameters including taproot length, root regrowth and root tolerance index were measured, and in the pot experiments the key measurements were taproot length, plant biomass, chlorophyll concentration and stomatal conductance.ResultResponses to acidity and aluminium were apparently independent. Accessions Dosha and NC 58 were tolerant to both stress. Kassa and GLA 1103 were tolerant to acidity showing less than 3% reduction in taproot length. Aurora and Messay were tolerant to aluminium. Babylon was sensitive to both, with up to 40% reduction in taproot length from acidity and no detectable recovery from Al3+ challenge.DiscussionThe apparent independence of the responses to acidity and aluminium is in agreement with the previous research findings, suggesting that crop accessions separately adapt to H+ and Al3+ toxicity as a result of the difference in the nature of soil parent materials where the accession originated. Differences in rankings between experiments were minor and attributable to heterogeneity of seed materials and the specific responses of accessions to the rooting media. Use of perlite as a potting medium offers an ideal combination of throughput, inertness of support medium, access to leaves for detection of their stress responses, and harvest of clean roots for evaluation of their growth. creator: Kiflemariam Y. Belachew creator: Frederick L. Stoddard uri: https://doi.org/10.7717/peerj.2963 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Belachew and Stoddard title: Will you swim into my parlour? In situ observations of Atlantic cod (Gadus morhua) interactions with baited pots, with implications for gear design link: https://peerj.com/articles/2953 last-modified: 2017-02-08 description: Pots (also known as traps) are baited fishing gears widely used in commercial fisheries, and are being considered as a tool for harvesting Atlantic cod (Gadus morhua) in Newfoundland and Labrador, Canada. Pots produce lower environmental impacts than many other fishing gears, but they will only be a viable fishing strategy if they are efficient and selective at catching their target species. To study the behaviour of cod in and around pots, and how those behaviours affect pot efficiency, we used long-duration underwater video cameras to assess two models of cod pot deployed in the nearshore waters of Fogo Island, NL. We examined the number of cod that approached the pot, the number and proportion that successfully completed entries into the pot openings, and the number that exited, and related these factors to the direction of water movement. We observed very few entry attempts relative to the number of approaches by cod, and only 22% of all entry attempts were successful. We observed that 50% of approaches, 70% of entry attempts, and 73% of successful entrances occurred against the current, and 25% of cod were able to exit the pot following capture. Based on our observations, we suggest that future cod pots should have a greater number of entrances, or a mechanism to ensure that entrances rotate in line with the current, in order to maximize their catch efficiency for cod. creator: Phillip Meintzer creator: Philip Walsh creator: Brett Favaro uri: https://doi.org/10.7717/peerj.2953 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Meintzer et al. title: Tracking the virus-like particles of Macrobrachium rosenbergii nodavirus in insect cells link: https://peerj.com/articles/2947 last-modified: 2017-02-08 description: Macrobrachium rosenbergii nodavirus (MrNv) poses a major threat to the prawn industry. Currently, no effective vaccine and treatment are available to prevent the spread of MrNv. Its infection mechanism and localisation in a host cell are also not well characterised. The MrNv capsid protein (MrNvc) produced in Escherichia coli self-assembled into virus-like particles (VLPs) resembling the native virus. Thus, fluorescein labelled MrNvc VLPs were employed as a model to study the virus entry and localisation in Spodoptera frugiperda, Sf9 cells. Through fluorescence microscopy and sub-cellular fractionation, the MrNvc was shown to enter Sf9 cells, and eventually arrived at the nucleus. The presence of MrNvc within the cytoplasm and nucleus of Sf9 cells was further confirmed by the Z-stack imaging. The presence of ammonium chloride (NH4Cl), genistein, methyl-β-cyclodextrin or chlorpromazine (CPZ) inhibited the entry of MrNvc into Sf9 cells, but cytochalasin D did not inhibit this process. This suggests that the internalisation of MrNvc VLPs is facilitated by caveolae- and clathrin-mediated endocytosis. The whole internalisation process of MrNvc VLPs into a Sf9 cell was recorded with live cell imaging. We have also identified a potential nuclear localisation signal (NLS) of MrNvc through deletion mutagenesis and verified by classical-NLS mapping. Overall, this study provides an insight into the journey of MrNvc VLPs in insect cells. creator: Ummi Fairuz Hanapi creator: Chean Yeah Yong creator: Zee Hong Goh creator: Noorjahan Banu Alitheen creator: Swee Keong Yeap creator: Wen Siang Tan uri: https://doi.org/10.7717/peerj.2947 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hanapi et al. title: Trace elements during primordial plexiform network formation in human cerebral organoids link: https://peerj.com/articles/2927 last-modified: 2017-02-08 description: Systematic studies of micronutrients during brain formation are hindered by restrictions to animal models and adult post-mortem tissues. Recently, advances in stem cell biology have enabled recapitulation of the early stages of human telencephalon development in vitro. In the present work, we analyzed cerebral organoids derived from human pluripotent stem cells by synchrotron radiation X-ray fluorescence in order to measure biologically valuable micronutrients incorporated and distributed into the exogenously developing brain. Our findings indicate that elemental inclusion in organoids is consistent with human brain tissue and involves P, S, K, Ca, Fe and Zn. Occurrence of different concentration gradients also suggests active regulation of elemental transmembrane transport. Finally, the analysis of pairs of elements shows interesting elemental interaction patterns that change from 30 to 45 days of development, suggesting short- or long-term associations, such as storage in similar compartments or relevance for time-dependent biological processes. These findings shed light on which trace elements are important during human brain development and will support studies aimed to unravel the consequences of disrupted metal homeostasis for neurodevelopmental diseases, including those manifested in adulthood. creator: Rafaela C. Sartore creator: Simone C. Cardoso creator: Yury V.M. Lages creator: Julia M. Paraguassu creator: Mariana P. Stelling creator: Rodrigo F. Madeiro da Costa creator: Marilia Z. Guimaraes creator: Carlos A. Pérez creator: Stevens K. Rehen uri: https://doi.org/10.7717/peerj.2927 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sartore et al. title: Off the scale: a new species of fish-scale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales link: https://peerj.com/articles/2955 last-modified: 2017-02-07 description: The gecko genus Geckolepis, endemic to Madagascar and the Comoro archipelago, is taxonomically challenging. One reason is its members ability to autotomize a large portion of their scales when grasped or touched, most likely to escape predation. Based on an integrative taxonomic approach including external morphology, morphometrics, genetics, pholidosis, and osteology, we here describe the first new species from this genus in 75 years: Geckolepis megalepissp. nov. from the limestone karst of Ankarana in northern Madagascar. The new species has the largest known body scales of any gecko (both relatively and absolutely), which come off with exceptional ease. We provide a detailed description of the skeleton of the genus Geckolepis based on micro-Computed Tomography (micro-CT) analysis of the new species, the holotype of G. maculata, the recently resurrected G. humbloti, and a specimen belonging to an operational taxonomic unit (OTU) recently suggested to represent G. maculata. Geckolepis is characterized by highly mineralized, imbricated scales, paired frontals, and unfused subolfactory processes of the frontals, among other features. We identify diagnostic characters in the osteology of these geckos that help define our new species and show that the OTU assigned to G. maculata is probably not conspecific with it, leaving the taxonomic identity of this species unclear. We discuss possible reasons for the extremely enlarged scales of G. megalepis in the context of an anti-predator defence mechanism, and the future of Geckolepis taxonomy. creator: Mark D. Scherz creator: Juan D. Daza creator: Jörn Köhler creator: Miguel Vences creator: Frank Glaw uri: https://doi.org/10.7717/peerj.2955 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Scherz et al. title: Large-scale gene flow in the barnacle Jehlius cirratus and contrasts with other broadly-distributed taxa along the Chilean coast link: https://peerj.com/articles/2971 last-modified: 2017-02-07 description: We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3,000 km of the linear range of this species, there is only slight regional structure indicated, with overall Φ CT of 0.036 (p < 0.001) yet no support for isolation by distance. While these results suggest greater structure than previous studies of J. cirratus had indicated, the pattern of diversity is still far more subtle than in other similarly-distributed species with similar larval and life history traits. We compare these data and results with recent findings in four other intertidal species that have planktotrophic larvae. There are no clear patterns among these taxa that can be associated with intertidal depth or other known life history traits. creator: Baoying Guo creator: John P. Wares uri: https://doi.org/10.7717/peerj.2971 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Guo and Wares title: Evolutionary and functional implications of hypervariable loci within the skin virome link: https://peerj.com/articles/2959 last-modified: 2017-02-07 description: Localized genomic variability is crucial for the ongoing conflicts between infectious microbes and their hosts. An understanding of evolutionary and adaptive patterns associated with genomic variability will help guide development of vaccines and antimicrobial agents. While most analyses of the human microbiome have focused on taxonomic classification and gene annotation, we investigated genomic variation of skin-associated viral communities. We evaluated patterns of viral genomic variation across 16 healthy human volunteers. Human papillomavirus (HPV) and Staphylococcus phages contained 106 and 465 regions of diversification, or hypervariable loci, respectively. Propionibacterium phage genomes were minimally divergent and contained no hypervariable loci. Genes containing hypervariable loci were involved in functions including host tropism and immune evasion. HPV and Staphylococcus phage hypervariable loci were associated with purifying selection. Amino acid substitution patterns were virus dependent, as were predictions of their phenotypic effects. We identified diversity generating retroelements as one likely mechanism driving hypervariability. We validated these findings in an independently collected skin metagenomic sequence dataset, suggesting that these features of skin virome genomic variability are widespread. Our results highlight the genomic variation landscape of the skin virome and provide a foundation for better understanding community viral evolution and the functional implications of genomic diversification of skin viruses. creator: Geoffrey D. Hannigan creator: Qi Zheng creator: Jacquelyn S. Meisel creator: Samuel S. Minot creator: Frederick D. Bushman creator: Elizabeth A. Grice uri: https://doi.org/10.7717/peerj.2959 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Hannigan et al. title: The concept of Watson’s carative factors in nursing and their (dis)harmony with patient satisfaction link: https://peerj.com/articles/2940 last-modified: 2017-02-07 description: BackgroundConstant reviews of the caring behavior of nurses and patient satisfaction help to improve the quality of nursing. The aim of our research was to explore relationships between the level of nursing education, the perception of nurses and nursing assistants of Watson’s carative factors, and patient satisfaction.MethodsA questionnaire survey using a convenience sample of 1,098 members of nursing teams and a purposive sample of 1,123 patients in four health care institutions in Slovenia was conducted in August 2012. A demographic questionnaire and the Caring Nurse-Patient Interactions Scale (nurse version) were delivered to the nurses. A Hospital Consumer Assessment of Health Plans Survey was delivered to discharged patients. Data were analyzed using descriptive and inferential statistics.ResultsCarative factor sensibility was related to the level of nursing education. Patients were satisfied with the care received from nurses, nursing assistants and hospitals, although we found differences between the perceptions of nurses and nursing assistants of carative factors and patient satisfaction. By comparing only the perceptions of nurses and nursing assistants of carative factors in health care institutions, differences were found for seven out of ten carative factors.DiscussionWe did not find major significant differences between carative factors and level of nurse education, except in one carative factor. Differences in perceptions of carative factors between health care institutions are probably the result of different institutional factors. The results can be of great benefit to nurse administrators and educators, indicating the factors that must be taken into account for enhancing patient satisfaction. Emphasis on caring theories should be placed in nursing education and their application in nursing practice. creator: Majda Pajnkihar creator: Gregor Štiglic creator: Dominika Vrbnjak uri: https://doi.org/10.7717/peerj.2940 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pajnkihar et al. title: Differences in pollination success between local and foreign flower color phenotypes: a translocation experiment with Gentiana lutea (Gentianaceae) link: https://peerj.com/articles/2882 last-modified: 2017-02-07 description: BackgroundThe adaptive maintenance of flower color variation is frequently attributed to pollinators partly because they preferentially visit certain flower phenotypes. We tested whether Gentiana lutea—which shows a flower color variation (from orange to yellow) in the Cantabrian Mountains range (north of Spain)—is locally adapted to the pollinator community.MethodsWe transplanted orange-flowering individuals to a population with yellow-flowering individuals and vice versa, in order to assess whether there is a pollination advantage in the local morph by comparing its visitation rate with the foreign morph.ResultsOur reciprocal transplant experiment did not show clear local morph advantage in overall visitation rate: local orange flowers received more visits than foreign yellow flowers in the orange population, while both local and foreign flowers received the same visits in the yellow population; thus, there is no evidence of local adaptation in Gentiana lutea to the pollinator assemblage. However, some floral visitor groups (such as Bombus pratorum, B. soroensis ancaricus and B. lapidarius decipiens) consistently preferred the local morph to the foreign morph whereas others (such as Bombus terrestris) consistently preferred the foreign morph.DiscussionWe concluded that there is no evidence of local adaptation to the pollinator community in each of the two G. lutea populations studied. The consequences for local adaptation to pollinator on G. lutea flower color would depend on the variation along the Cantabrian Mountains range in morph frequency and pollinator community composition. creator: Javier A. Guitián creator: Mar Sobral creator: Tania Veiga creator: María Losada creator: Pablo Guitián creator: José M. Guitián uri: https://doi.org/10.7717/peerj.2882 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Guitián et al. title: Vascular plant biodiversity of the lower Coppermine River valley and vicinity (Nunavut, Canada): an annotated checklist of an Arctic flora link: https://peerj.com/articles/2835 last-modified: 2017-02-07 description: The Coppermine River in western Nunavut is one of Canada’s great Arctic rivers, yet its vascular plant flora is poorly known. Here, we report the results of a floristic inventory of the lower Coppermine River valley and vicinity, including Kugluk (Bloody Falls) Territorial Park and the hamlet of Kugluktuk. The study area is approximately 1,200 km2, extending from the forest-tundra south of the treeline to the Arctic coast. Vascular plant floristic data are based on a review of all previous collections from the area and more than 1,200 new collections made in 2014. Results are presented in an annotated checklist, including citation of all specimens examined, comments on taxonomy and distribution, and photographs for a subset of taxa. The vascular plant flora comprises 300 species (311 taxa), a 36.6% increase from the 190 species documented by previous collections made in the area over the last century, and is considerably more diverse than other local floras on mainland Nunavut. We document 207 taxa for Kugluk (Bloody Falls) Territorial Park, an important protected area for plants on mainland Nunavut. A total of 190 taxa are newly recorded for the study area. Of these, 14 taxa (13 species and one additional variety) are newly recorded for Nunavut (Allium schoenoprasum, Carex capitata, Draba lonchocarpa, Eremogone capillaris subsp. capillaris, Sabulina elegans, Eleocharis quinqueflora, Epilobium cf. anagallidifolium, Botrychium neolunaria, Botrychium tunux, Festuca altaica, Polygonum aviculare, Salix ovalifolia var. arctolitoralis, Salix ovalifolia var. ovalifolia and Stuckenia pectinata), seven species are newly recorded for mainland Nunavut (Carex gynocrates, Carex livida, Cryptogramma stelleri, Draba simmonsii, Festuca viviparoidea subsp. viviparoidea, Juncus alpinoarticulatus subsp. americanus and Salix pseudomyrsinites) and 56 range extensions are reported. The psbA-trnH and rbcL DNA sequence data were used to help identify the three Botrychium taxa recorded in the study area. Three new combinations are proposed: Petasites frigidus subsp. sagittatus (Banks ex Pursh) Saarela, Carex petricosa subsp. misandroides (Fernald) Saarela and Carex simpliciuscula subsp. subholarctica (T. V. Egorova) Saarela. creator: Jeffery M. Saarela creator: Paul C. Sokoloff creator: Roger D. Bull uri: https://doi.org/10.7717/peerj.2835 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Saarela et al. title: Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands link: https://peerj.com/articles/2968 last-modified: 2017-02-02 description: BackgroundThe páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants.MethodsField expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogenies based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny.ResultsPhylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species. Results from the Monte Carlo permutation test suggests a very strong influence of the geography on the phylogenetic relationships. Venezuelan páramos tend to hold taxa that are more distantly-related to each other than Colombian páramos, where taxa are more closely-related to each other.ConclusionsOur data suggest the presence of two independent radiations: one in Venezuela and the other in Colombia. In addition, the current generic classification will need to be deeply revised. Analyses show a strong geographic structure in the phylogeny, with large clades grouped in hotspots of diversity at a regional scale, and in páramo localities at a local scale. Differences in the degrees of relatedness between sympatric species of Venezuelan and Colombian páramos may be explained because of the younger age of the latter páramos, and the lesser time for speciation of Espeletiinae in them. creator: Mauricio Diazgranados creator: Janet C. Barber uri: https://doi.org/10.7717/peerj.2968 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Diazgranados and Barber title: A new glimpse on Mesozoic zooplankton—150 million-year-old lobster larvae link: https://peerj.com/articles/2966 last-modified: 2017-02-02 description: Larvae of malacostracan crustaceans represent a large fraction of modern day zooplankton. Plankton is not only a major part of the modern marine ecosystem, but must have played an important role in the ecosystems of the past as well. Unfortunately, our knowledge about plankton composition of the past is still quite limited. As an important part of today’s zooplankton, malacostracan larvae are still a rarity in the fossil record; many types of malacostracan larvae dominating the modern plankton have so far not been found as fossils. Here we report a new type of fossil malacostracan larva, found in the 150 million years old lithographic limestones of southern Germany (Solnhofen Lithographic Limestones). The three rather incomplete specimens mainly preserve the telson. A pronounced middle spine on the posterior edge of these specimens indicates that they are either larval forms of a clawed lobster or of an axiidean lobster, or of a closer relative to one of the two groups. The tergo-pleura are drawn out into distinct spines in one specimen, further supporting the interpretation as a larva of a clawed lobster or an early relative. The telson morphology also shows adaptations to a prolonged planktic life style, the latero-posterior edges are drawn out into distinct spines. Similar adaptations are known in larvae of the modern homarid lobster Nephrops norvegicus, not necessarily indicating a closer relationship, but convergent life styles. The new finds provide an important new insight into the composition of Mesozoic zooplankton and demonstrate the preservation potential of lithographic limestones. creator: Joachim T. Haug creator: Carolin Haug uri: https://doi.org/10.7717/peerj.2966 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Haug and Haug title: Effects of rhodomyrtone on Gram-positive bacterial tubulin homologue FtsZ link: https://peerj.com/articles/2962 last-modified: 2017-02-02 description: Rhodomyrtone, a natural antimicrobial compound, displays potent activity against many Gram-positive pathogenic bacteria, comparable to last-defence antibiotics including vancomycin and daptomycin. Our previous studies pointed towards effects of rhodomyrtone on the bacterial membrane and cell wall. In addition, a recent molecular docking study suggested that the compound could competitively bind to the main bacterial cell division protein FtsZ. In this study, we applied a computational approach (in silico), in vitro, and in vivo experiments to investigate molecular interactions of rhodomyrtone with FtsZ. Using molecular simulation, FtsZ conformational changes were observed in both (S)- and (R)-rhodomyrtone binding states, compared with the three natural states of FtsZ (ligand-free, GDP-, and GTP-binding states). Calculations of free binding energy showed a higher affinity of FtsZ to (S)-rhodomyrtone (−35.92 ± 0.36 kcal mol−1) than the GDP substrate (−23.47 ± 0.25 kcal mol−1) while less affinity was observed in the case of (R)-rhodomyrtone (−18.11 ± 0.11 kcal mol−1). In vitro experiments further revealed that rhodomyrtone reduced FtsZ polymerization by 36% and inhibited GTPase activity by up to 45%. However, the compound had no effect on FtsZ localization in Bacillus subtilis at inhibitory concentrations and cells also did not elongate after treatment. Higher concentrations of rhodomyrtone did affect localization of FtsZ and also affected localization of its membrane anchor proteins FtsA and SepF, showing that the compound did not specifically inhibit FtsZ but rather impaired multiple divisome proteins. Furthermore, a number of cells adopted a bean-like shape suggesting that rhodomyrtone possibly possesses further targets involved in cell envelope synthesis and/or maintenance. creator: Dennapa Saeloh creator: Michaela Wenzel creator: Thanyada Rungrotmongkol creator: Leendert Willem Hamoen creator: Varomyalin Tipmanee creator: Supayang Piyawan Voravuthikunchai uri: https://doi.org/10.7717/peerj.2962 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Saeloh et al. title: Medial knee joint contact force in the intact limb during walking in recently ambulatory service members with unilateral limb loss: a cross-sectional study link: https://peerj.com/articles/2960 last-modified: 2017-02-02 description: BackgroundIndividuals with unilateral lower limb amputation have a high risk of developing knee osteoarthritis (OA) in their intact limb as they age. This risk may be related to joint loading experienced earlier in life. We hypothesized that loading during walking would be greater in the intact limb of young US military service members with limb loss than in controls with no limb loss.MethodsCross-sectional instrumented gait analysis at self-selected walking speeds with a limb loss group (N = 10, age 27 ± 5 years, 170 ± 36 days since last surgery) including five service members with transtibial limb loss and five with transfemoral limb loss, all walking independently with their first prosthesis for approximately two months. Controls (N = 10, age 30 ± 4 years) were service members with no overt demographical risk factors for knee OA. 3D inverse dynamics modeling was performed to calculate joint moments and medial knee joint contact forces (JCF) were calculated using a reduction-based musculoskeletal modeling method and expressed relative to body weight (BW).ResultsPeak JCF and maximum JCF loading rate were significantly greater in limb loss (184% BW, 2,469% BW/s) vs. controls (157% BW, 1,985% BW/s), with large effect sizes. Results were robust to probabilistic perturbations to the knee model parameters.DiscussionAssuming these data are reflective of joint loading experienced in daily life, they support a “mechanical overloading” hypothesis for the risk of developing knee OA in the intact limb of limb loss subjects. Examination of the evolution of gait mechanics, joint loading, and joint health over time, as well as interventions to reduce load or strengthen the ability of the joint to withstand loads, is warranted. creator: Ross H. Miller creator: Rebecca L. Krupenevich creator: Alison L. Pruziner creator: Erik J. Wolf creator: Barri L. Schnall uri: https://doi.org/10.7717/peerj.2960 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Miller et al. title: Demographic, ecological, and physiological responses of ringed seals to an abrupt decline in sea ice availability link: https://peerj.com/articles/2957 last-modified: 2017-02-02 description: To assess whether demographic declines of Arctic species at the southern limit of their range will be gradual or punctuated, we compared large-scale environmental patterns including sea ice dynamics to ringed seal (Pusa hispida) reproduction, body condition, recruitment, and stress in Hudson Bay from 2003 to 2013. Aerial surveys suggested a gradual decline in seal density from 1995 to 2013, with the lowest density occurring in 2013. Body condition decreased and stress (cortisol) increased over time in relation to longer open water periods. The 2010 open water period in Hudson Bay coincided with extremes in large-scale atmospheric patterns (North Atlantic Oscillation, Arctic Oscillation, El Nino-Southern Oscillation) resulting in the earliest spring breakup and the latest ice formation on record. The warming event was coincident with high stress level, low ovulation rate, low pregnancy rate, few pups in the Inuit harvest, and observations of sick seals. Results provide evidence of changes in the condition of Arctic marine mammals in relation to climate mediated sea ice dynamics. We conclude that although negative demographic responses of Hudson Bay seals are occurring gradually with diminishing sea ice, a recent episodic environmental event played a significant role in a punctuated population decline. creator: Steven H. Ferguson creator: Brent G. Young creator: David J. Yurkowski creator: Randi Anderson creator: Cornelia Willing creator: Ole Nielsen uri: https://doi.org/10.7717/peerj.2957 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Ferguson et al. title: Are sawfishes still present in Mozambique? A baseline ecological study link: https://peerj.com/articles/2950 last-modified: 2017-02-02 description: Sawfishes (Pristidae) were formerly abundant in the western Indian Ocean, but current data on sawfish presence and distribution are lacking for most of the region. This paper summarises historical records of sawfishes in Mozambican waters and presents the findings of the first assessment of the presence and status of sawfishes in Mozambique. A countrywide baseline assessment was undertaken between May and July 2014, using interviews with artisanal, semi-industrial and industrial fishers, fish traders and fisheries monitoring staff as the primary source of information on sawfish distribution, recent catches, socio-economic value and cultural importance. Additional interviews were conducted via email or telephone with individuals running sport fishing operations or who otherwise had considerable experience interacting with the fishing sectors or the marine environment in Mozambique. Where encountered, sawfish rostra were photographed and a series of measurements and associated data were collected. In total, 200 questionnaire surveys and seven interviews with recreational fishing and dive operators were conducted, and 19 rostra were documented from museum archives and private collections, belonging to two sawfish species, the Largetooth Sawfish (Pristis pristis) and Green Sawfish (P. zijsron). The most recent captures of sawfishes were reported to have occurred in 2014. Two key sites were identified where both recent encounters were reported and numerous Largetooth Sawfish rostra were documented. Gill nets were the fishing gear most commonly attributed to sawfish catches. Sawfishes did not hold any cultural importance in Mozambique, but they have at least some socio-economic importance to artisanal fishers, primarily through the sale of their fins. The meat did not appear to be held in high regard and was usually consumed locally. Sampling and further research is now required to confirm the presence of sawfishes and to assess the primary threats to sawfishes in those areas. At one site where a number of rostra were present and where fishers stated that they still catch sawfish, gill nets are being provided to fishers as an alternative to beach seining. This may have a serious impact on the local sawfish population and more broadly for other elasmobranchs in the area. Immediate action is required to develop a landings monitoring programme in this and other key habitats, and to encourage fishers to release sawfishes alive. creator: Ruth H. Leeney uri: https://doi.org/10.7717/peerj.2950 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Leeney title: Comparison of admission random glucose, fasting glucose, and glycated hemoglobin in predicting the neurological outcome of acute ischemic stroke: a retrospective study link: https://peerj.com/articles/2948 last-modified: 2017-02-02 description: BackgroundHyperglycemia is a known predictor of negative outcomes in stroke. Several glycemic measures, including admission random glucose, fasting glucose, and glycated hemoglobin (HbA1c), have been associated with bad neurological outcomes in acute ischemic stroke, particularly in nondiabetic patients. However, the predictive power of these glycemic measures is yet to be investigated.MethodsThis retrospective study enrolled 484 patients with acute ischemic stroke from January 2009 to March 2013, and complete records of initial stroke severity, neurological outcomes at three months, and glycemic measures were evaluated. We examined the predictive power of admission random glucose, fasting glucose, and HbA1c for neurological outcomes in acute ischemic stroke. Furthermore, subgroup analyses of nondiabetic patients and patients with diabetes were performed separately.ResultsReceiver operating characteristic (ROC) analysis revealed that admission random glucose and fasting glucose were significant predictors of poor neurological outcomes, whereas HbA1c was not (areas under the ROC curve (AUCs): admission random glucose = 0.564, p = 0.026; fasting glucose = 0.598, p = 0.001; HbA1c = 0.510, p = 0.742). Subgroup analyses of nondiabetic patients and those with diabetes revealed that only fasting glucose predicts neurological outcomes in patients with diabetes, and the AUCs of these three glycemic measures did not differ between the two groups. A multivariate logistic regression analysis of the study patients indicated that only age, initial stroke severity, and fasting glucose were independent predictors of poor neurological outcomes, whereas admission random glucose and HbA1c were not (adjusted odds ratio: admission random glucose = 1.002, p = 0.228; fasting glucose = 1.005, p = 0.039; HbA1c = 1.160, p = 0.076). Furthermore, subgroup multivariate logistic regression analyses of nondiabetic patients and those with diabetes indicated that none of the three glycemic measures were associated with poor neurological outcomes.DiscussionFasting glucose is an independent predictor of poor neurological outcomes in patients with acute ischemic stroke and had greater predictive power than that of admission random glucose and HbA1c. The predictive power of glycemic measures for poor neurological outcomes did not differ significantly between the nondiabetic patients and those with diabetes. creator: Jia-Ying Sung creator: Chin-I Chen creator: Yi-Chen Hsieh creator: Yih-Ru Chen creator: Hsin-Chiao Wu creator: Lung Chan creator: Chaur-Jong Hu creator: Han-Hwa Hu creator: Hung-Yi Chiou creator: Nai-Fang Chi uri: https://doi.org/10.7717/peerj.2948 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sung et al. title: Do syntopic host species harbour similar symbiotic communities? The case of Chaetopterus spp. (Annelida: Chaetopteridae) link: https://peerj.com/articles/2930 last-modified: 2017-02-02 description: To assess whether closely related host species harbour similar symbiotic communities, we studied two polychaetes, Chaetopterus sp. (n = 11) and Chaetopterus cf. appendiculatus (n = 83) living in soft sediments of Nhatrang Bay (South China Sea, Vietnam). The former harboured the porcellanid crabs Polyonyx cf. heok and Polyonyx sp., the pinnotherid crab Tetrias sp. and the tergipedid nudibranch Phestilla sp. The latter harboured the polynoid polychaete Ophthalmonoe pettiboneae, the carapid fish Onuxodon fowleri and the porcellanid crab Eulenaios cometes, all of which, except O. fowleri, seemed to be specialized symbionts. The species richness and mean intensity of the symbionts were higher in Chaetopterus sp. than in C. cf. appendiculatus (1.8 and 1.02 species and 3.0 and 1.05 individuals per host respectively). We suggest that the lower density of Chaetopterus sp. may explain the higher number of associated symbionts observed, as well as the 100% prevalence (69.5% in C. cf. appenciculatus). Most Chaetopterus sp. harboured two symbiotic species, which was extremely rare in C. cf. appendiculatus, suggesting lower interspecific interactions in the former. The crab and nudibranch symbionts of Chaetopterus sp. often shared a host and lived in pairs, thus partitioning resources. This led to the species coexisting in the tubes of Chaetopterus sp., establishing a tightly packed community, indicating high species richness and mean intensity, together with a low species dominance. In contrast, the aggressive, strictly territorial species associated with C. cf. appendiculatus established a symbiotic community strongly dominated by single species and, thus, low species richness and mean intensity. Therefore, we suggest that interspecific interactions are determining species richness, intensity and dominance, while intraspecific interactions are influencing only intensity and abundance. It is possible that species composition may have influenced the differences in community structure observed. We hypothesize that both host species could originally be allopatric. The evolutionary specialization of the symbiotic communities would occur in separated geographical areas, while the posterior disappearance of the existing geographical barriers would lead to the overlapped distribution. creator: Temir A. Britayev creator: Elena Mekhova creator: Yury Deart creator: Daniel Martin uri: https://doi.org/10.7717/peerj.2930 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Britayev et al. title: The embryonic life history of the tropical sea hare Stylocheilus striatus (Gastropoda: Opisthobranchia) under ambient and elevated ocean temperatures link: https://peerj.com/articles/2956 last-modified: 2017-02-01 description: Ocean warming represents a major threat to marine biota worldwide, and forecasting ecological ramifications is a high priority as atmospheric carbon dioxide (CO2) emissions continue to rise. Fitness of marine species relies critically on early developmental and reproductive stages, but their sensitivity to environmental stressors may be a bottleneck in future warming oceans. The present study focuses on the tropical sea hare, Stylocheilus striatus (Gastropoda: Opisthobranchia), a common species found throughout the Indo-West Pacific and Atlantic Oceans. Its ecological importance is well-established, particularly as a specialist grazer of the toxic cyanobacterium, Lyngbya majuscula. Although many aspects of its biology and ecology are well-known, description of its early developmental stages is lacking. First, a detailed account of this species’ life history is described, including reproductive behavior, egg mass characteristics and embryonic development phases. Key developmental features are then compared between embryos developed in present-day (ambient) and predicted end-of-century elevated ocean temperatures (+3 °C). Results showed developmental stages of embryos reared at ambient temperature were typical of other opisthobranch species, with hatching of planktotrophic veligers occurring 4.5 days post-oviposition. However, development times significantly decreased under elevated temperature, with key embryonic features such as the velum, statocysts, operculum, eyespots and protoconch developing approximately 24 h earlier when compared to ambient temperature. Although veligers hatched one day earlier under elevated temperature, their shell size decreased by approximately 20%. Our findings highlight how an elevated thermal environment accelerates planktotrophic development of this important benthic invertebrate, possibly at the cost of reducing fitness and increasing mortality. creator: Rael Horwitz creator: Matthew D. Jackson creator: Suzanne C. Mills uri: https://doi.org/10.7717/peerj.2956 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Horwitz et al. title: What has been missed for predicting human attention in viewing driving clips? link: https://peerj.com/articles/2946 last-modified: 2017-02-01 description: Recent research progress on the topic of human visual attention allocation in scene perception and its simulation is based mainly on studies with static images. However, natural vision requires us to extract visual information that constantly changes due to egocentric movements or dynamics of the world. It is unclear to what extent spatio-temporal regularity, an inherent regularity in dynamic vision, affects human gaze distribution and saliency computation in visual attention models. In this free-viewing eye-tracking study we manipulated the spatio-temporal regularity of traffic videos by presenting them in normal video sequence, reversed video sequence, normal frame sequence, and randomised frame sequence. The recorded human gaze allocation was then used as the ‘ground truth’ to examine the predictive ability of a number of state-of-the-art visual attention models. The analysis revealed high inter-observer agreement across individual human observers, but all the tested attention models performed significantly worse than humans. The inferior predictability of the models was evident from indistinguishable gaze prediction irrespective of stimuli presentation sequence, and weak central fixation bias. Our findings suggest that a realistic visual attention model for the processing of dynamic scenes should incorporate human visual sensitivity with spatio-temporal regularity and central fixation bias. creator: Jiawei Xu creator: Shigang Yue creator: Federica Menchinelli creator: Kun Guo uri: https://doi.org/10.7717/peerj.2946 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Xu et al. title: Epidermal cell death in frogs with chytridiomycosis link: https://peerj.com/articles/2925 last-modified: 2017-02-01 description: BackgroundAmphibians are declining at an alarming rate, and one of the major causes of decline is the infectious disease chytridiomycosis. Parasitic fungal sporangia occur within epidermal cells causing epidermal disruption, but these changes have not been well characterised. Apoptosis (planned cell death) can be a damaging response to the host but may alternatively be a mechanism of pathogen removal for some intracellular infections.MethodsIn this study we experimentally infected two endangered amphibian species Pseudophryne corroboree and Litoria verreauxii alpina with the causal agent of chytridiomycosis. We quantified cell death in the epidermis through two assays: terminal transferase-mediated dUTP nick end-labelling (TUNEL) and caspase 3/7.ResultsCell death was positively associated with infection load and morbidity of clinically infected animals. In infected amphibians, TUNEL positive cells were concentrated in epidermal layers, correlating to the localisation of infection within the skin. Caspase activity was stable and low in early infection, where pathogen loads were light but increasing. In animals that recovered from infection, caspase activity gradually returned to normal as the infection cleared. Whereas, in amphibians that did not recover, caspase activity increased dramatically when infection loads peaked.DiscussionIncreased cell death may be a pathology of the fungal parasite, likely contributing to loss of skin homeostatic functions, but it is also possible that apoptosis suppression may be used initially by the pathogen to help establish infection. Further research should explore the specific mechanisms of cell death and more specifically apoptosis regulation during fungal infection. creator: Laura A. Brannelly creator: Alexandra A. Roberts creator: Lee F. Skerratt creator: Lee Berger uri: https://doi.org/10.7717/peerj.2925 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Brannelly et al. title: Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata) link: https://peerj.com/articles/2920 last-modified: 2017-02-01 description: A metabolomic study has been performed to identify sensitive and robust biomarkers of malnutrition in farmed fish, using gilthead sea bream (Sparus aurata) as a model. The metabolomic fingerprinting of serum from fasted fish was assessed by means of ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. More than 15,000 different m/z ions were detected and Partial Least Squares–Discriminant analysis allowed a clear differentiation between the two experimental groups (fed and 10-day fasted fish) with more than 90% of total variance explained by the two first components. The most significant metabolites (up to 45) were elucidated on the basis of their tandem mass spectra with a broad representation of amino acids, oligopeptides, urea cycle metabolites, L-carnitine-related metabolites, glutathione-related metabolites, fatty acids, lysophosphatidic acids, phosphatidylcholines as well as biotin- and noradrenaline-related metabolites. This untargeted approach highlighted important adaptive responses in energy and oxidative metabolism, contributing to identify robust and nutritionally-regulated biomarkers of health and metabolic condition that will serve to assess the welfare status of farmed fish. creator: Ruben Gil-Solsona creator: Jaime Nácher-Mestre creator: Leticia Lacalle-Bergeron creator: Juan Vicente Sancho creator: Josep Alvar Calduch-Giner creator: Félix Hernández creator: Jaume Pérez-Sánchez uri: https://doi.org/10.7717/peerj.2920 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gil-Solsona et al. title: Successive DNA extractions improve characterization of soil microbial communities link: https://peerj.com/articles/2915 last-modified: 2017-02-01 description: Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. creator: Mauricio R. Dimitrov creator: Annelies J. Veraart creator: Mattias de Hollander creator: Hauke Smidt creator: Johannes A. van Veen creator: Eiko E. Kuramae uri: https://doi.org/10.7717/peerj.2915 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Dimitrov et al.