title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1743 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.