title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2018-05 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Assessing canalisation of intraspecific variation on a macroevolutionary scale: the case of crinoid arms through the Phanerozoic link: https://peerj.com/articles/4899 last-modified: 2018-05-31 description: Clades that represent a new ‘Bauplan’ have been hypothesised to exhibit more variability than more derived clades. Accordingly, there is an expectation of greater variation around the time of the origin of a clade than later in its evolutionary history. This ‘canalisation’ has been tested in terms of morphological disparity (interspecific variation), whereas intraspecific variation in macroevolution is rarely studied. We analysed extensive data of brachial counts in crinoid populations from the Ordovician to the Recent to test for canalisation in morphological intraspecific variation. Our results show no support for the canalisation hypothesis through the Phanerozoic. This lack of pattern is maintained even when considering crinoid subclades separately. Our study is an example of the lack of universality in such macroevolutionary patterns both in terms of organisms and in terms of modules within them. It is also an example on the challenges and limitations of palaeontological studies of macroevolutionary processes. creator: Catalina Pimiento creator: Kit Lam Tang creator: Samuel Zamora creator: Christian Klug creator: Marcelo R. Sánchez-Villagra uri: https://doi.org/10.7717/peerj.4899 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Pimiento et al. title: Factors influencing the willingness to participate in medical research: a nationwide survey in Taiwan link: https://peerj.com/articles/4874 last-modified: 2018-05-31 description: BackgroundParticipation rate is one of the main challenges medical researchers face. We examined how demographic background and trust in medical research affect the willingness of people to participate in medical research in Taiwan.MethodsData from the 2011 Taiwan Genomic Survey (a nationwide representative face-to-face survey) were analyzed. The survey included a vignette of a researcher conducting a clinical trial of an investigative medicinal product, and questions for interviewees regarding their willingness to participate in research after they were informed of the scenario description. A total of 3,159 people, aged 18 to 70 years, were sampled, and 1,538 of them completed the survey. With missing data excluded, a total of 1,389 respondents were included in the final analysis.ResultsAbout 12 percent of the respondents answered that they would be willing to participate in medical research. Respondents who had college degrees or above and were married or lived with significant others were less likely to participate in medical research. By contrast, male respondents, and respondents whose household family members had biomedicine-related degrees or had one themselves were more likely to participate in medical research. After adjustment for demographic factors, respondents were more likely to participate in medical research if: (1) they expressed trust in doctors conducting medical research; (2) they agreed that doctors would never ask them to join medical research studies that might harm them; (3) they thought that participating in a medical research study would be safe; and (4) they agreed that researchers had no selfish reasons for doing the medical research.DiscussionSome of our findings, such as the effects of education level and marital status on participation in medical research, are different from most findings of previous studies conducted in other countries. This study is useful for developing strategies to improve participant recruitment. Relevant discussions on research ethics and policies, such as the importance of public trust in medical researchers, could also be based on this study. creator: Hung-En Liu creator: Ming-Chieh Li uri: https://doi.org/10.7717/peerj.4874 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu and Li title: Some like it hot: factors impacting thermal preferences of two Ponto-Caspian amphipods Dikerogammarus villosus (Sovinsky, 1894) and Dikerogammarus haemobaphes (Eichwald, 1841) link: https://peerj.com/articles/4871 last-modified: 2018-05-31 description: Temperature is a crucial factor determining biology and ecology of poikilothermic animals. It often constitutes an important barrier for invasive species originating from different climate zones but, on the other hand, may facilitate the invasion process of animals with wide thermal preferences and high resistance to extreme temperatures. In our experimental study, we investigated the thermal behaviour of two Ponto-Caspian amphipod crustaceans—Dikerogammarus villosus and Dikerogammarus haemobaphes. Both species are known to live under a wide range of thermal conditions which may promote their invasion. Moreover, both these amphipods are hosts for microsporidian parasites which co-evolved with them within the Ponto-Caspian region and spread in European waters. As the presence of a parasite may influence the thermal preferences of its host, we expected to observe behavioural changes in infected individuals of the studied amphipods leading to (1) behavioural fever (selecting a warmer habitat) or (2) anapyrexia (selecting a colder habitat). The experiment (N = 20) was carried out for 30 min in a 100 cm. 20 cm from boths sides were not avaliable for amphipods long thermal gradient (0–40 °C), using 30 randomly selected adult amphipod individuals of one species. At the end of each trial, we checked the position of amphipods along the gradient and determined their sex and infection status (uninfected or infected by one of microsporidium species). D. villosus was infected with Cucumispora dikerogammari whereas D. haemobaphes was a host for C. dikerogammari, Dictyocoela muelleri or D. berillonum. Thermal preferences of amphipods depended on their species and sex. Females of D. villosus preferred warmer microhabitats (often much above 30 °C) than conspecific males and females of D. haemobaphes, whereas no significant differences were found among males of both species and both sexes of D. haemobaphes. Moreover, infected males of D. villosus stayed in warmer water more often than uninfected males of this species, selecting temperatures higher than 30 °C, which may be explained either as a behavioural fever constituting a defence mechanism of a host against the infection, or as a parasite manipulation of the host behaviour increasing the parasite fitness. On the other hand, none of the parasite species affected the thermal preferences of D. haemobaphes, including also C. dikerogammari, changing the behaviour of D. villosus. Our research presents the complexity of the thermal behaviour of studied amphipods and the evidence that microsporidia may trigger a change in temperature preferendum of their host species and those observations may be the result of different host-parasite coevolution time which may vary for the two host species (Poulin, 2010). creator: Michał Rachalewski creator: Jarosław Kobak creator: Eliza Szczerkowska-Majchrzak creator: Karolina Bącela-Spychalska uri: https://doi.org/10.7717/peerj.4871 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rachalewski et al. title: Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura) and description of Ocellated treefrog Itapotihyla langsdorffii vocalizations link: https://peerj.com/articles/4813 last-modified: 2018-05-31 description: BackgroundAnuran vocalizations, such as advertisement and release calls, are informative for taxonomy because species recognition can be based on those signals. Thus, a proper acoustic description of the calls may support taxonomic decisions and may contribute to knowledge about amphibian phylogeny.MethodsHere we present a perspective on advertisement call descriptions of the frog subfamily Lophyohylinae, through a literature review and a spatial analysis presenting bioacoustic coldspots (sites with high diversity of species lacking advertisement call descriptions) for this taxonomic group. Additionally, we describe the advertisement and release calls of the still poorly known treefrog, Itapotihyla langsdorffii. We analyzed recordings of six males using the software Raven Pro 1.4 and calculated the coefficient of variation for classifying static and dynamic acoustic properties.Results and DiscussionWe found that more than half of the species within the subfamily do not have their vocalizations described yet. Most of these species are distributed in the western and northern Amazon, where recording sampling effort should be strengthened in order to fill these gaps. The advertisement call of I. langsdorffii is composed of 3–18 short unpulsed notes (mean of 13 ms long), presents harmonic structure, and has a peak dominant frequency of about 1.4 kHz. This call usually presents amplitude modulation, with decreasing intensity along the sequence of notes. The release call is a simple unpulsed note with an average duration of 9 ms, and peak dominant frequency around 1.8 kHz. Temporal properties presented higher variations than spectral properties at both intra- and inter-individual levels. However, only peak dominant frequency was static at intra-individual level. High variability in temporal properties and lower variations related to spectral ones is usual for anurans; The first set of variables is determined by social environment or temperature, while the second is usually related to species-recognition process. Here we review and expand the acoustic knowledge of the subfamily Lophyohylinae, highlighting areas and species for future research. creator: Lucas Rodriguez Forti creator: Roseli Maria Foratto creator: Rafael Márquez creator: Vânia Rosa Pereira creator: Luís Felipe Toledo uri: https://doi.org/10.7717/peerj.4813 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Forti et al. title: The smallest biggest theropod dinosaur: a tiny pedal ungual of a juvenile Spinosaurus from the Cretaceous of Morocco link: https://peerj.com/articles/4785 last-modified: 2018-05-30 description: We describe a nearly complete pedal ungual phalanx, discovered in the Kem Kem Beds (Cenomanian) of Tafilalt region, south-eastern Morocco. The bone is symmetric, pointed, low, elongate, and almost flat ventrally in lateral aspect. This peculiar morphology allows to refer the specimen to the smallest known individual of the genus Spinosaurus. The bone belongs to an early juvenile individual and it is proportionally identical to the ungual of the third digit of a large partial skeleton recently found, suggesting an isometric growth for this part of the pes and the retention of peculiar locomotor adaptations—such as traversing soft substrates or paddling—during the entire lifespan. creator: Simone Maganuco creator: Cristiano Dal Sasso uri: https://doi.org/10.7717/peerj.4785 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Maganuco and Dal Sasso title: Assessment of the ecotoxicity of urban estuarine sediment using benthic and pelagic copepod bioassays link: https://peerj.com/articles/4936 last-modified: 2018-05-30 description: Urban estuarine sediments are sinks to a range of contaminants of anthropogenic origin, and a key challenge is to characterize the risk of these compounds to receiving environments. In this study, the toxicity of urban estuarine sediments was tested using acute and chronic bioassays in the benthic harpacticoid Quinquelaophonte sp., and in the planktonic calanoid Gladioferens pectinatus, two New Zealand copepod species. The sediment samples from the estuary tributary sites significantly impacted reproduction in Quinquelaophonte sp. However, results from one of the estuary sites were not significantly different to those from the tributaries sites, suggesting that chemicals other than trace metals, polycyclic aromatic hydrocarbons and ammonia may be the causative stressors. Sediment elutriate samples had significant effects on reproductive endpoints in G. pectinatus, and on the induction of DNA damage in cells, as shown by the comet assay. The results indicate that sediment contamination at the Ahuriri Estuary has the potential to impact biological processes of benthic and pelagic organisms. The approach used provides a standardized methodology to assess the toxicity of estuarine sediments. creator: Maria P. Charry creator: Vaughan Keesing creator: Mark Costello creator: Louis A. Tremblay uri: https://doi.org/10.7717/peerj.4936 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Charry et al. title: Urbanization alters small rodent community composition but not abundance link: https://peerj.com/articles/4885 last-modified: 2018-05-30 description: Desert ecosystems are one of the fastest urbanizing areas on the planet. This rapid shift has the potential to alter the abundances and species richness of herbivore and plant communities. Herbivores, for example, are expected to be more abundant within urban desert remnant parks located within cities due to anthropogenic activities that concentrate food resources and reduce native predator populations. Despite this assumption, previous research conducted around Phoenix, AZ, USA has shown that top-down herbivory led to equally reduced plant biomass in both urban and outlying locations. It is unclear if this insignificant difference in herbivory at urban and outlying sites is due to unaltered desert herbivore populations or altered activity levels that counteract abundance differences. Small rodent herbivore/granivore populations were surveyed at four sites inside and four sites outside of the core of Phoenix during fall 2014 and spring 2015 in order to determine whether abundances and richness differ significantly between urban and rural sites. In order to survey species composition and abundance at these sites, 100 Sherman traps and eight larger wire traps that are designed to attract and capture small vertebrates such as mice, rats, and squirrels were set at each site for two consecutive trap nights. Results suggest that the commonly assumed effect of urbanization on herbivore abundances does not apply to small rodent populations in a desert city, as overall small rodent abundances were statistically similar regardless of location. Though a significant difference was not found for species richness, a significant difference between small rodent genus richness at these sites was observed, with altered community composition. The compositional differences likely reflect the altered vegetative community and may impact ecological interactions at these sites. creator: Jessica N. Alvarez Guevara creator: Becky A. Ball uri: https://doi.org/10.7717/peerj.4885 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Alvarez Guevara and Ball title: A new species of spotted leaf frog, genus Phasmahyla (Amphibia, Phyllomedusidae) from Southeast Brazil link: https://peerj.com/articles/4900 last-modified: 2018-05-30 description: Based on concordant differences in male advertisement call, tadpole morphology, and absence of haplotype sharing in the barcoding 16S mitochondrial DNA, we describe here a new species of spotted leaf frog of the genus Phasmahyla from Atlantic Forest, State of Rio de Janeiro, Southeast Brazil. The new species is most similar to P. cochranae (type locality) and P. spectabilis (type locality). It differs from these species by the size of the calcar, moderate-sized body (snout-vent length 30.4–34.4 mm in adult eight males), and in the advertisement call. The tadpoles of Phasmahyla lisbella sp. nov. differ from P. exilis, P. spectabilis, P. timbo, P. guttata and P. jandaia because they do not have row of teeth in the anterior part; differ from P. cruzi by the shape of the anterior end of the oral disc. Through genetic data (phylogenetic distance and haplotype genealogy) we diagnosed the new species where the genetic divergences among its congeners is about 3–6% in a fragment of the 16S rRNA gene, which is above the threshold typically characterizing distinct species of anurans. However, the new species can be distinguished from other congeneric species based on an integrative approach (molecular, bioacoustics, larval, and adult morphology). creator: Elvis Almeida Pereira creator: Lucas Custódio Lomba Rocha creator: Henrique Folly creator: Hélio Ricardo da Silva creator: Diego José Santana uri: https://doi.org/10.7717/peerj.4900 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Pereira et al. title: Top-down and bottom-up controls on southern New England salt marsh crab populations link: https://peerj.com/articles/4876 last-modified: 2018-05-30 description: Southern New England salt marsh vegetation and habitats are changing rapidly in response to sea-level rise. At the same time, fiddler crab (Uca spp.) distributions have expanded and purple marsh crab (Sesarma reticulatum) grazing on creekbank vegetation has increased. Sea-level rise and reduced predation pressure drive these changing crab populations but most studies focus on one species; there is a need for community-level assessments of impacts from multiple crab species. There is also a need to identify additional factors that can affect crab populations. We sampled crabs and environmental parameters in four Rhode Island salt marshes in 2014 and compiled existing data to quantify trends in crab abundance and multiple factors that potentially affect crabs. Crab communities were dominated by fiddler and green crabs (Carcinus maenas); S. reticulatum was much less abundant. Burrow sizes suggest that Uca is responsible for most burrows. On the marsh platform, burrows and Carcinus abundance were negatively correlated with elevation, soil moisture, and soil percent organic matter and positively correlated with soil bulk density. Uca abundance was negatively correlated with Spartina patens cover and height and positively correlated with Spartina alterniflora cover and soil shear strength. Creekbank burrow density increased dramatically between 1998 and 2016. During the same time, fishing effort and the abundance of birds that prey on crabs decreased, and water levels increased. Unlike in other southern New England marshes where recreational overfishing is hypothesized to drive increasing marsh crab abundance, we propose that changes in crab abundance were likely unrelated to recreational finfish over-harvest; instead, they better track sea-level rise and changing abundances of alternate predators, such as birds. We predict that marsh crab abundance will continue to expand with ongoing sea-level rise, at least until inundation thresholds for crab survival are exceeded. creator: Kenneth B. Raposa creator: Richard A. McKinney creator: Cathleen Wigand creator: Jeffrey W. Hollister creator: Cassie Lovall creator: Katelyn Szura creator: John A. Gurak, Jr. creator: Jason McNamee creator: Christopher Raithel creator: Elizabeth B. Watson uri: https://doi.org/10.7717/peerj.4876 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Raposa et al. title: Multi-dimensional Precision Livestock Farming: a potential toolbox for sustainable rangeland management link: https://peerj.com/articles/4867 last-modified: 2018-05-30 description: BackgroundPrecision Livestock Farming (PLF) is a promising approach to minimize the conflicts between socio-economic activities and landscape conservation. However, its application on extensive systems of livestock production can be challenging. The main difficulties arise because animals graze on large natural pastures where they are exposed to competition with wild herbivores for heterogeneous and scarce resources, predation risk, adverse weather, and complex topography. Considering that the 91% of the world’s surface devoted to livestock production is composed of extensive systems (i.e., rangelands), our general aim was to develop a PLF methodology that quantifies: (i) detailed behavioural patterns, (ii) feeding rate, and (iii) costs associated with different behaviours and landscape traits.MethodsFor this, we used Merino sheep in Patagonian rangelands as a case study. We combined data from an animal-attached multi-sensor tag (tri-axial acceleration, tri-axial magnetometry, temperature sensor and Global Positioning System) with landscape layers from a Geographical Information System to acquire data. Then, we used high accuracy decision trees, dead reckoning methods and spatial data processing techniques to show how this combination of tools could be used to assess energy balance, predation risk and competition experienced by livestock through time and space.ResultsThe combination of methods proposed here are a useful tool to assess livestock behaviour and the different factors that influence extensive livestock production, such as topography, environmental temperature, predation risk and competition for heterogeneous resources. We were able to quantify feeding rate continuously through time and space with high accuracy and show how it could be used to estimate animal production and the intensity of grazing on the landscape. We also assessed the effects of resource heterogeneity (inferred through search times), and the potential costs associated with predation risk, competition, thermoregulation and movement on complex topography.DiscussionThe quantification of feeding rate and behavioural costs provided by our approach could be used to estimate energy balance and to predict individual growth, survival and reproduction. Finally, we discussed how the information provided by this combination of methods can be used to develop wildlife-friendly strategies that also maximize animal welfare, quality and environmental sustainability. creator: Agustina di Virgilio creator: Juan M. Morales creator: Sergio A. Lambertucci creator: Emily L.C. Shepard creator: Rory P. Wilson uri: https://doi.org/10.7717/peerj.4867 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 di Virgilio et al. title: Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach link: https://peerj.com/articles/4838 last-modified: 2018-05-30 description: Tumor samples obtained from a single cancer patient spatially or temporally often consist of varying cell populations, each harboring distinct mutations that uniquely characterize its genome. Thus, in any given samples of a tumor having more than two haplotypes, defined as a scaffold of single nucleotide variants (SNVs) on the same homologous genome, is evidence of heterogeneity because humans are diploid and we would therefore only observe up to two haplotypes if all cells in a tumor sample were genetically homogeneous. We characterize tumor heterogeneity by latent haplotypes and present state-space formulation of the feature allocation model for estimating the haplotypes and their proportions in the tumor samples. We develop an efficient sequential Monte Carlo (SMC) algorithm that estimates the states and the parameters of our proposed state-space model, which are equivalently the haplotypes and their proportions in the tumor samples. The sequential algorithm produces more accurate estimates of the model parameters when compared with existing methods. Also, because our algorithm processes the variant allele frequency (VAF) of a locus as the observation at a single time-step, VAF from newly sequenced candidate SNVs from next-generation sequencing (NGS) can be analyzed to improve existing estimates without re-analyzing the previous datasets, a feature that existing solutions do not possess. creator: Oyetunji E. Ogundijo creator: Xiaodong Wang uri: https://doi.org/10.7717/peerj.4838 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ogundijo and Wang title: Potent antibacterial, antioxidant and toxic activities of extracts from Passiflora suberosa L. leaves link: https://peerj.com/articles/4804 last-modified: 2018-05-30 description: Passiflora suberosa L. belonging to the family Passifloraceae is an important medicinal plant used in traditional medicinal system in Sri Lanka to treat diabetes, hypertension and skin diseases. We extracted P. suberosa leaves under reflux conditions using different solvents (hexane, chloroform, methanol and water), then subjected to phytochemical screening. Alkaloids, flavonoids and saponins and saponins and anthraquinones were present in hexane and chloroform extracts. Alkaloids, unsaturated sterols, triterpenes, saponins, flavonoids and tannins were observed in both methanol and aqueous extracts. Proanthocyanidins were observed only in the aqueous extract. Hence, aqueous and methanol extracts with most classes of phytochemicals present were subjected to antimicrobial, antioxidant, antihaemolytic activities and Brine shrimp lethality studies. Antibacterial activity and minimum inhibition concentrations were evaluated using three Gram-positive (Bacillus subtilis, Staphylococcus aureus and Enterococcus faecium) and three Gram-negative bacteria (Pseudumonas aeruginosa, Salmonella typhimuriam and Escherichia coli). The results indicated that only the methanol extract of P. suberosa exhibited antibacterial activities against all the strains of Gram-negative and Gram-positive bacterial with stronger activity against Gram-negative bacteria. DPHH (2,2-diphenyl-1-picrylhydrazy) scavenging assay was adopted to evaluate antioxidant properties while antihaemolytic and toxic activities were studied respectively using cow blood and Brine shrimp lethality assay. The IC50 values of the aqueous extract in both antioxidant and antihaemolytic assays were significantly lower than the standard ascorbic acid. Similar results were observed in the Brine shrimp lethality assay. In conclusion both aqueous and methanol extracts of P. suberosa leaves showed the presence of majority of phytochemicals including proanthocyanidins. Antibacterial activity was obtained only for methanol extract with better activity against Gram-negative bacteria. The aqueous extract showed better antioxidant, antihaemolytic and toxic activities than the methanol extract and their respective standards. Further investigations on the chemical composition and possible isolation of active ingredients is warranted. creator: Kumudu R.V. Bandara creator: Chayanika Padumadasa creator: Dinithi C. Peiris uri: https://doi.org/10.7717/peerj.4804 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bandara et al. title: Comparisons of weed community, soil health and economic performance between wheat-maize and garlic-soybean rotation systems under different weed managements link: https://peerj.com/articles/4799 last-modified: 2018-05-30 description: This study compared the impacts of different weed managements on weed community, soil health and economic performance between the wheat–maize (WM) and garlic–soybean (GS) rotations. A total of four treatments (H0T, tillage without herbicide; H0T0, without both herbicide and tillage; HT, both herbicide and tillage; HT0, herbicide without tillage) were designed for both rotations. A total of 16 weed species were recorded in the WM rotation, with life forms of 62% for annuals, 12% for annual + perennial and 20% for perennials. While in the GS rotation, there were 17 weed species, with 71% being annuals. When crop rotation changed from WM to GS, the topsoil layer seed bank (0–5 cm) decreased by 137%. GS rotation always had higher earthworm densities than that of WM under the same condition. Organic weed control (H0T, H0T0) from both WM and GS added more soil organic matters than the chemical methods (HT and HT0). Economically, up to 69% higher net profit had been achieved in the GS than WM for their organic products. This study provides an ecological basis to guide organic farming practices, especially for weed management in the future. creator: Mahmud A. Muminov creator: Liyue Guo creator: Yanjie Song creator: Xian Gu creator: Yu Cen creator: Jie Meng creator: Gaoming Jiang uri: https://doi.org/10.7717/peerj.4799 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Muminov et al. title: Variations in early life history traits of Japanese anchovy Engraulis japonicus in the Yangtze River Estuary link: https://peerj.com/articles/4789 last-modified: 2018-05-30 description: Resources of Japanese anchovy (Engraulis japonicus Temminck & Schlegel, 1846) are undergoing dramatic recessions in China as the consequence of intensifying anthropogenic activities. Elucidating the influences of local-scale environmental factors on early life history traits is of great importance to design strategies conserving and restoring the declining anchovy resources. In this research, we studied hatching date and early growth of anchovy in the Yangtze River Estuary (YRE) using information obtained from otolith microstructure. Onset of hatching season and growth rates of anchovy was compared to populations in Japan and Taiwan. In YRE, the hatching date of anchovy ranged from February 26th to April 6th and mean growth rate ranged from 0.27 to 0.77 mm/d. Anchovies hatching later had higher growth rates than individuals hatching earlier before the 25th day. Among populations, hatching onsets of anchovy from the higher latitude were later than populations in the lower latitude, and growth rates of anchovy in YRE were much lower than populations in Japan and Taiwan. Variations in hatching onsets and early growth patterns of anchovy thus provide important knowledge on understanding the adaptation of anchovy in YRE and designing management strategies on conserving China’s anchovy resources. creator: Chunlong Liu creator: Weiwei Xian creator: Shude Liu creator: Yifeng Chen uri: https://doi.org/10.7717/peerj.4789 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu et al. title: Treatment of collagenase-induced osteoarthritis with a viral vector encoding TSG-6 results in ectopic bone formation link: https://peerj.com/articles/4771 last-modified: 2018-05-30 description: ObjectiveTumor necrosis factor-inducible gene 6 (TSG-6) has anti-inflammatory and chondroprotective effects in mouse models of inflammatory arthritis. Because cartilage damage and inflammation are also observed in osteoarthritis (OA), we determined the effect of viral overexpression of TSG-6 in experimental osteoarthritis.MethodsBone marrow-derived cells were differentiated to multinucleated osteoclasts in the presence of recombinant TSG-6 or after transduction with a lentiviral TSG-6 expression vector. Multi-nucleated osteoclasts were analyzed after tartrate resistant acid phosphatase staining and resorption activity was determined on dentin slices. Collagenase-induced osteoarthritis (CIOA) was induced in C57BL/6 mice after intra-articular injection of an adenoviral TSG-6 or control luciferase expression vector. Inflammation-related protease activity was measured using bioluminescent Prosense probes. After a second adenovirus injection, cartilage damage was assessed in histological sections stained with Safranin-O. Ectopic bone formation was scored in X-ray images of the affected knees.ResultsTSG-6 did not inhibit the formation of multi-nucleated osteoclasts, but caused a significant reduction in the resorption activity on dentin slices. Adenoviral TSG-6 gene therapy in CIOA could not reduce the cartilage damage compared to the luciferase control virus and no significant difference in inflammation-related protease activity was noted between the TSG-6 and control treated group. Instead, X-ray analysis and histological analysis revealed the presence of ectopic bone formation in the TSG-6 treated group.ConclusionGene therapy based on the expression of TSG-6 could not provide cartilage protection in experimental osteoarthritis, but instead resulted in increased ectopic bone formation. creator: Mathijs G.A. Broeren creator: Irene Di Ceglie creator: Miranda B. Bennink creator: Peter L.E.M. van Lent creator: Wim B. van den Berg creator: Marije I. Koenders creator: Esmeralda N. Blaney Davidson creator: Peter M. van der Kraan creator: Fons A.J. van de Loo uri: https://doi.org/10.7717/peerj.4771 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Broeren et al. title: Applying fecal microbiota transplantation (FMT) to treat recurrent Clostridium difficile infections (rCDI) in children link: https://peerj.com/articles/4663 last-modified: 2018-05-30 description: BackgroundFecal Microbiota Transplantation (FMT) is an innovative means of treating recurrent Clostridium difficile infection (rCDI), through restoration of gut floral balance. However, there is a lack of data concerning the efficacy of FMT and its impact on the gut microbiome among pediatric patients. This study analyzes clinical outcomes and microbial community composition among 15 pediatric patients treated for rCDI via FMT.MethodsThis is a prospective, observational, pilot study of 15 children ≤18 years, who presented for rCDI and who met inclusion criteria for FMT at a pediatric hospital and pediatric gastroenterology clinic. Past medical history and demographics were recorded at enrollment and subsequent follow-up. Specimens of the donors’ and the patients’ pre-FMT and post-FMT fecal specimen were collected and used to assess microbiome composition via 16S rRNA gene sequencing.ResultsFMT successfully prevented rCDI episodes for minimum of 3 months post-FMT in all patients, with no major adverse effects. Three patients reported continued GI bleeding; however, all three also had underlying Inflammatory Bowel Disease (IBD). Our analyses confirm a significant difference between pre-and post-FMT gut microbiome profiles (Shannon diversity index), whereas no significant difference was observed between post-FMT and donor microbiome profiles. At the phyla level, post-FMT profiles showed significantly increased levels of Bacteroidetes and significantly decreased levels of Proteobacteria. Subjects with underlying IBD showed no difference in their pre-and post-FMT profiles.ConclusionThe low rate of recurrence or re-infection by C. difficile, coupled with minimal adverse effects post-FMT, suggests that FMT is a viable therapeutic means to treat pediatric rCDI. Post-FMT microbiomes are different from pre-FMT microbiomes, and similar to those of healthy donors, suggesting successful establishment of a healthier microbiome. creator: Shaaz Fareed creator: Neha Sarode creator: Frank J. Stewart creator: Aneeq Malik creator: Elham Laghaie creator: Saadia Khizer creator: Fengxia Yan creator: Zoe Pratte creator: Jeffery Lewis creator: Lilly Cheng Immergluck uri: https://doi.org/10.7717/peerj.4663 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Fareed et al. title: Resurrection and typification of Elatine campylosperma (Elatinaceae), a long-forgotten waterwort species link: https://peerj.com/articles/4913 last-modified: 2018-05-29 description: The name Elatine campylosperma Seub. is generally treated as one of the synonyms of E. macropoda Guss. However, recent morphological, phylogenetic and karyological studies indicate that this judgement should be revised. In the present paper we typify the name E. campylosperma, review its taxonomic history and provide a thorough description, with compilation of previously published data and our new measurements from in vitro cultures. Based on our herbarium survey, we outline its Atlantic-Mediterranean distribution area (Spain, France, Italy, Greece, Turkey and Algeria). Habitat preferences are summarized from our field observations, water quality measurements and the label information of the herbarium specimens examined. Intact E. campylosperma seeds were found in faecal samples of the Eurasian Coot (Fulica atra L.) in southern Spain and two of them were germinated, suggesting that E. campylosperma has a capacity for long distance dispersal via endozoochory. creator: Attila Takács creator: Attila Molnár V. creator: Balázs A. Lukács creator: Timea Nagy creator: Ádám Lovas-Kiss creator: Andy J. Green creator: Agnieszka Popiela creator: Lajos Somlyay uri: https://doi.org/10.7717/peerj.4913 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Takács et al. title: Unilateral application of an external pneumatic compression therapy improves skin blood flow and vascular reactivity bilaterally link: https://peerj.com/articles/4878 last-modified: 2018-05-29 description: BackgroundWe sought to determine the effects of unilateral lower-limb external pneumatic compression (EPC) on bilateral lower-limb vascular reactivity and skin blood flow.MethodsThirty-two participants completed this two-aim study. In AIM1 (n = 18, age: 25.5 ± 4.7 years; BMI: 25.6 ± 3.5 kg/m2), bilateral femoral artery blood flow and reactivity (flow mediated dilation [FMD]) measurements were performed via ultrasonography at baseline (PRE) and immediately following 30-min of unilateral EPC treatment (POST). AIM2 (n = 14, age: 25.9 ± 4.5; BMI: 27.2 ± 2.7 kg/m2) involved 30-min unilateral EPC (n = 7) or sham (n = 7) treatment with thermographic bilateral lower-limb mean skin temperature (MST) measurements at baseline, 15-min of treatment (T15) and 0, 30 and 60-min (R0, R30, R60) following treatment.ResultsComparative data herein are presented as mean ± 95% confidence interval. AIM1: No significant effects on total reactive hyperemia blood flow were observed for the treated (i.e., compressed) or untreated (i.e., non-compressed) leg. A significant effect of time, but no time*leg interaction, was observed for relative FMD indicating higher reactivity bilaterally with unilateral EPC treatment (FMD: +0.41 ± 0.09% across both legs; p < 0.05). AIM2: Unilateral EPC treatment was associated with significant increases in whole-leg MST from baseline during (T15: +0.63 ± 0.56 °C in the visible untreated/contralateral leg, p < 0.025) and immediately following treatment (i.e., R0) in both treated (+1.53 ± 0.59 °C) and untreated (+0.60 ± 0.45 °C) legs (p < 0.0125). Across both legs, MST remained elevated with EPC at 30-min post-treatment (+0.60 ± 0.45 °C; p < 0.0167) but not at 60-min post (+0.27 ± 0.46 °C; p = 0.165). Sham treatment was associated with a significant increase in the treated leg immediately post-treatment (+1.12 ± 0.31 °C; p < 0.0167), but not in the untreated leg (−0.27 ± 0.12 °C). MST in neither the treated or untreated leg were increased relative to baseline at R30 or R60 (p > 0.05). Finally, during treatment and at all post-treatment time points (i.e., R0, R30 and R60), independent of treatment group (EPC vs. sham), there was a significant effect of region. The maximum increase in MST was observed at the R0 time point and was significantly (p < 0.05) larger in the thigh region (+1.02 ± 0.31 °C) than the lower-leg (+0.47 ± 0.29 °C) region. However, similar rates of MST decline from R0 in the thigh and lower leg regions were observed at the R30 and R60 time points.DiscussionUnilateral EPC may be an effective intervention for increasing skin blood flow and/or peripheral conduit vascular reactivity in the contralateral limb. While EPC was effective in increasing whole-leg MST bilaterally, there appeared to be a more robust response in the thigh compared to the lower-leg. Thus, proximity along the leg may be an important consideration in prospective treatment strategies. creator: Jeffrey S. Martin creator: Allison M. Martin creator: Petey W. Mumford creator: Lorena P. Salom creator: Angelique N. Moore creator: David D. Pascoe uri: https://doi.org/10.7717/peerj.4878 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Martin et al. title: MIPhy: identify and quantify rapidly evolving members of large gene families link: https://peerj.com/articles/4873 last-modified: 2018-05-29 description: After transitioning to a new environment, species often exhibit rapid phenotypic innovation. One of the fastest mechanisms for this is duplication followed by specialization of existing genes. When this happens to a member of a gene family, it tends to leave a detectable phylogenetic signature of lineage-specific expansions and contractions. These can be identified by analyzing the gene family across several species and identifying patterns of gene duplication and loss that do not correlate with the known relationships between those species. This signature, termed phylogenetic instability, has been previously linked to adaptations that change the way an organism samples and responds to its environment; conversely, low phylogenetic instability has been previously linked to proteins with endogenous functions. With the increase in genome-level data, there is a need to identify and quantify phylogenetic instability. Here, we present Minimizing Instability in Phylogenetics (MIPhy), a tool that solves this problem by quantifying the incongruence of a gene’s evolutionary history. The motivation behind MIPhy was to produce a tool to aid in interpreting phylogenetic trees. It can predict which members of a gene family are under adaptive evolution, working only from a gene tree and the relationship between the species under consideration. While it does not conduct any estimation of positive selection—which is the typical indication of adaptive evolution—the results tend to agree. We demonstrate the usefulness of MIPhy by accurately predicting which members of the mammalian cytochrome P450 gene superfamily metabolize xenobiotics and which metabolize endogenous compounds. Our predictions correlate very well with known substrate specificities of the human enzymes. We also analyze the Caenorhabditis collagen gene family and use MIPhy to predict genes that produce an observable phenotype when knocked down in C. elegans, and show that our predictions correlate well with existing knowledge. The software can be downloaded and installed from https://github.com/dave-the-scientist/miphy and is also available as an online web tool at http://www.miphy.wasmuthlab.org. creator: David M. Curran creator: John S. Gilleard creator: James D. Wasmuth uri: https://doi.org/10.7717/peerj.4873 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Curran et al. title: Associations between psychometrically assessed life history strategy and daily behavior: data from the Electronically Activated Recorder (EAR) link: https://peerj.com/articles/4866 last-modified: 2018-05-29 description: Life history theory has generated cogent, well-supported hypotheses about individual differences in human biodemographic traits (e.g., age at sexual maturity) and psychometric traits (e.g., conscientiousness), but little is known about how variation in life history strategy (LHS) is manifest in quotidian human behavior. Here I test predicted associations between the self-report Arizona Life History Battery and frequencies of 12 behaviors observed over 72 h in 91 US college students using the Electronically Activated Recorder (EAR), a method of gathering periodic brief audio recordings as participants go about their daily lives. Bayesian multi-level aggregated binomial regression analysis found no strong associations between ALHB scores and behavior frequencies. One behavior, presence at amusement venues (bars, concerts, sports events) was weakly positively associated with ALHB-assessed slow LHS, contrary to prediction. These results may represent a challenge to the ALHB’s validity. However, it remains possible that situational influences on behavior, which were not measured in the present study, moderate the relationships between psychometrically-assessed LHS and quotidian behavior. creator: Joseph H. Manson uri: https://doi.org/10.7717/peerj.4866 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Manson title: Socio-economic factors and management regimes as drivers of tree cover change in Nepal link: https://peerj.com/articles/4855 last-modified: 2018-05-29 description: Despite the local and global importance of forests, deforestation is driven by various socio-economic and biophysical factors continues in many countries. In Nepal, in response to massive deforestation, the community forestry program has been implemented to reduce deforestation and support livelihoods. After four decades of its inception, the effectiveness of this program on forest cover change remains mostly unknown. This study analyses the spatial and temporal patterns of tree cover change along with a few socio-economic drivers of tree cover change to examine the effectiveness of the community forestry program for conserving forests or in reducing deforestation. We also investigate the socio-economic factors and policy responses as manifested through the community forestry program responsible for the tree cover change at the district level. The total tree cover area in the year 2000 in Nepal was ∼4,746,000 hectares, and our analysis reveals that between 2001 and 2016, Nepal has lost ∼46,000 ha and gained ∼12,200 ha of areas covered by trees with a substantial spatial and temporal variations. After accounting socio-economic drivers of forest cover change, our analysis showed that districts with the larger number of community forests had a minimum loss in tree cover, while districts with the higher proportion of vegetation covered by community forests had a maximum gain in tree cover. This indicates a positive contribution of the community forestry program to reducing deforestation and increasing tree cover. creator: Sujata Shrestha creator: Uttam B. Shrestha creator: Kamal Bawa uri: https://doi.org/10.7717/peerj.4855 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shrestha et al. title: Genomic analysis of red-tide water bloomed with Heterosigma akashiwo in Geoje link: https://peerj.com/articles/4854 last-modified: 2018-05-29 description: Microbial community structures of harmful algal bloom (HAB) caused by Heterosigma akashiwo in Geoje were analyzed using the MiSeq platform. To analyze phytoplankton communities without cross-reactivity with predominant bacteria, a new phytoplankton-specific 23S universal primer set was designed by modifying two previously used ones. The new universal primer set turned out to be a useful tool for the analysis of the phytoplankton community; it showed a high specificity for phytoplankton without cross-reactivity to bacterial sequences as well as the wide taxon coverage presenting from prokaryotic cyanobacteria to eukaryotic algae. Next Generation Sequencing (NGS) data generated by two universal primer sets (16S and 23S) provided useful information about the H. akashiwo bloom. According to the 23S universal primer set, proportions of H. akashiwo increased by more than 200-fold as the bloom occurred and its numbers were high enough to detect in control sites. Its operational taxonomic units (OTUs) were detected in the bloom sites at low proportions suggesting that the 16S universal primer set may not be as effective for monitoring harmful algal blooming (HAB) as the 23S universal primer set. In addition, several abundant OTUs in Chlorophyta were not presented by the 16S universal primer set in this study. However, the 16S primer set was useful for detecting decreases in Foraminifera as HAB occurred suggesting that genomic analyses using two universal primer sets would provide more reliable data for understanding microbial community changes by various environmental or ecological events, including HAB. Genomic analyses using two universal primer sets was also useful for determining a correlation between microbial components as HAB occurred. Heterosigma akashiwo was positively correlated with other bloom species, including Karenia mikimotoi, Teleaulax amphioxeia, and bacteria in Verrucomicrobia. creator: Hye-Eun Kang creator: Tae-Ho Yoon creator: Sunyoung Yoon creator: Hak Jun Kim creator: Hyun Park creator: Chang-Keun Kang creator: Hyun-Woo Kim uri: https://doi.org/10.7717/peerj.4854 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kang et al. title: Modeling transcriptional activation changes to Gal4 variants via structure-based computational mutagenesis link: https://peerj.com/articles/4844 last-modified: 2018-05-29 description: As a DNA binding transcriptional activator, Gal4 promotes the expression of genes responsible for galactose metabolism. The Gal4 protein from Saccharomyces cerevisiae (baker’s yeast) has become a model for studying eukaryotic transcriptional activation in general because its regulatory properties mirror those of several eukaryotic organisms, including mammals. Given the availability of a crystallographic structure for Gal4, here we implement an in silico mutagenesis technique that makes use of a four-body knowledge-based energy function, in order to empirically quantify the structural impacts associated with single residue substitutions on the Gal4 protein. These results were used to examine the structure-function relationship in Gal4 based on a recently published experimental mutagenesis study, whereby functional changes to a uniformly distributed set of 1,068 single residue Gal4 variants were obtained by measuring their transcriptional activation levels relative to wild-type. A significant correlation was observed between computed (scalar) structural effect data and measured activity values for this collection of single residue Gal4 variants. Additionally, attribute vectors quantifying position-specific environmental impacts were generated for each of the Gal4 variants via computational mutagenesis, and we implemented supervised classification and regression statistical machine learning algorithms to train predictive models of variant Gal4 activity based on these structural changes. All models performed well under cross-validation testing, with balanced accuracy reaching 91% among the classification models, and with the actual and predicted activity values displaying a correlation as high as r = 0.80 for the regression models. Reliable predictions of transcriptional activation levels for Gal4 variants that have yet to be studied can be instantly generated by submitting their respective structure-based feature vectors to the trained models for testing. Such a computational pre-screening of Gal4 variants may potentially reduce costs associated with running large-scale mutagenesis experiments. creator: Majid Masso creator: Nitin Rao creator: Purnima Pyarasani uri: https://doi.org/10.7717/peerj.4844 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Masso et al. title: Changes in species abundance after seven years of elevated atmospheric CO2 and warming in a Subarctic birch forest understorey, as modified by rodent and moth outbreaks link: https://peerj.com/articles/4843 last-modified: 2018-05-29 description: A seven-year long, two-factorial experiment using elevated temperatures (5 °C) and CO2 (concentration doubled compared to ambient conditions) designed to test the effects of global climate change on plant community composition was set up in a Subarctic ecosystem in northernmost Sweden. Using point-frequency analyses in permanent plots, an increased abundance of the deciduous Vaccinium myrtillus, the evergreens V. vitis-idaea and Empetrum nigrum ssp. hermaphroditum and the grass Avenella flexuosa was found in plots with elevated temperatures. We also observed a possibly transient community shift in the warmed plots, from the vegetation being dominated by the deciduous V. myrtillus to the evergreen V. vitis-idaea. This happened as a combined effect of V. myrtillus being heavily grazed during two events of herbivore attack—one vole outbreak (Clethrionomys rufocanus) followed by a more severe moth (Epirrita autumnata) outbreak that lasted for two growing seasons—producing a window of opportunity for V. vitis-idaea to utilize the extra light available as the abundance of V. myrtillus decreased, while at the same time benefitting from the increased growth in the warmed plots. Even though the effect of the herbivore attacks did not differ between treatments they may have obscured any additional treatment effects. This long-term study highlights that also the effects of stochastic herbivory events need to be accounted for when predicting future plant community changes. creator: Brita M. Svensson creator: Bengt Å. Carlsson creator: Jerry M. Melillo uri: https://doi.org/10.7717/peerj.4843 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Svensson et al. title: Sorting nexin-1 is a candidate tumor suppressor and potential prognostic marker in gastric cancer link: https://peerj.com/articles/4829 last-modified: 2018-05-29 description: Sorting nexin-1 (SNX1) is an important functional protein in cell endocytosis, efflux, protein sorting, cell signal transduction, etc; however, the expression, the role and clinical relevance of SNX1 have not been investigated in gastric cancer (GC). In this study, we first performed a bioinformatics investigation using the data obtained from The Cancer Genome Atlas (TCGA) database. The result showed that SNX1 mRNA levels were significantly lower in GC tissues than in paracancerous tissues. In a study of 150 cases of GC, including 60 cases with paired paracancerous and cancer tissues and 90 cases with detailed follow-up information, SNX1 expression was analyzed by immunohistochemistry. Our study on paired paracancerous and cancer tissues showed that SNX1 protein expression remarkably decreased in GC tissues (50/60, 83.33%). A study on 90 patients with detailed follow-up information showed that tumors with higher SNX1 protein level were correlated with better clinicopathologic stages (p = 0.0285), nodal status (p = 0.0286), smaller tumor sizes (p = 0.0294) and a better survival rate in patients with GC (p = 0.0245). Univariate analysis of the 90 patients with GC showed that low-level SNX1 was significantly correlated with decreased overall survival of GC patients (p = 0.008), and associated with a relatively higher cumulative hazard of death. Exogenous expression of SNX1 inhibited the growth, migration, invasion and promoted the apoptosis and enhanced the sensitivity of GC cells to the chemotherapeutic drug 5-Fluorouracil (5-Fu) in vitro, while knockdown of SNX1 by short hairpin RNA (shRNA) significantly promoted the growth, migration, invasion and reduced the apoptosis and the sensitivity of GC cells to 5-Fu. SNX1 also showed to influence the levels of epithelial-mesenchymal transition markers including Vimentin, Snail, and E-cadherin in GC cells in vitro. Taken together, we propose here that SNX1 serves as a tumor suppressor and prognostic marker that reduces tumor cell malignancy for GC. creator: Xiao-Yong Zhan creator: Yaqiong Zhang creator: Ertao Zhai creator: Qing-Yi Zhu creator: Yulong He uri: https://doi.org/10.7717/peerj.4829 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhan et al. title: Genome-wide characterization and expression analysis of GRAS gene family in pepper (Capsicum annuum L.) link: https://peerj.com/articles/4796 last-modified: 2018-05-29 description: Plant-specific GRAS transcription factors regulate various biological processes in plant growth, development and stress responses. However, this important gene family was not fully characterized in pepper (Capsicum annuum L.), an economically important vegetable crop. Here, a total of 50 CaGRAS members were identified in pepper genome and renamed by their respective chromosomal distribution. Genomic organization revealed that most CaGRAS genes (84%) have no intron. Phylogenetic analysis divided pepper CaGRAS members into 10 subfamilies, with each having distinct conserved domains and functions. For the expansion of the GRAS genes in pepper, segmental duplication contributed more than tandem duplication did. Gene expression analysis in various tissues demonstrated that most of CaGRAS genes exhibited a tissue- and development stage-specific expression pattern, uncovering their potential functions in pepper growth and development. Moreover, 21 CaGRAS genes were differentially expressed under cold, drought, salt and gibberellin acid (GA) treatments, indicating that they may implicated in plant response to abiotic stress. Notably, GA responsive cis-elements were detected in the promoter regions of the majority of CaGRAS genes, suggesting that CaGRAS may involve in signal cross-talking. The first comprehensive analysis of GRAS gene family in pepper genome by this study provide insights into understanding the GRAS-mediated regulation network, benefiting the genetic improvements in pepper and some other relative plants. creator: Baoling Liu creator: Yan Sun creator: Jinai Xue creator: Xiaoyun Jia creator: Runzhi Li uri: https://doi.org/10.7717/peerj.4796 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Liu et al. title: Exosomes in cancer: small vesicular transporters for cancer progression and metastasis, biomarkers in cancer therapeutics link: https://peerj.com/articles/4763 last-modified: 2018-05-29 description: Cancer progression is a polygenic procedure in which the exosomes can function as substantial roles. Exosomes are tiny, phospholipid bilayer membrane nanovesicles of endocytic derivation with a diameter of 40–100 nm. These nanovesicles can transport bioactive molecules containing mRNAs, proteins, DNA fragments, and non-coding RNAs from a donor cell to recipient cells, and cause the alteration in genetic and epigenetic factors and reprogramming of the target cells. Many diverse cell types such as mesenchymal cells, immune cells, and cancer cells can induce the release of exosomes. Increasing evidence illustrated that the exosomes derived from tumor cells might trigger the tumor initiation, tumor cell growth and progression, metastasis, and drug resistance. The secreted nanovesicles of exosomes can play significant roles in cells communicate via shuttling the nucleic acid molecules and proteins to target cells and tissues. In this review, we discussed multiple mechanisms related to biogenesis, load, and shuttle of the exosomes. Also, we illustrated the diverse roles of exosomes in several types of human cancer development, tumor immunology, angiogenesis, and metastasis. The exosomes may act as the promising biomarkers for the prognosis of various types of cancers which suggested a new pathway for anti-tumor therapeutic of these nanovesicles and promoted exosome-based cancer for clinical diagnostic and remedial procedures. creator: Atefe Abak creator: Alireza Abhari creator: Sevda Rahimzadeh uri: https://doi.org/10.7717/peerj.4763 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Abak et al. title: DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes link: https://peerj.com/articles/4742 last-modified: 2018-05-29 description: The reconstruction of genomes using mapping-based approaches with short reads experiences difficulties when resolving repetitive regions. These repetitive regions in genomes result in low mapping qualities of the respective reads, which in turn lead to many unresolved bases. Currently, the reconstruction of these regions is often based on modified references in which the repetitive regions are masked. However, for many references, such masked genomes are not available or are based on repetitive regions of other genomes. Our idea is to identify repetitive regions in the reference genome de novo. These regions can then be used to reconstruct them separately using short read sequencing data. Afterward, the reconstructed repetitive sequence can be inserted into the reconstructed genome. We present the program detection, characterization, and reconstruction of repetitive regions, which performs these steps automatically. Our results show an increased base pair resolution of the repetitive regions in the reconstruction of Treponema pallidum samples, resulting in fewer unresolved bases. creator: Alexander Seitz creator: Friederike Hanssen creator: Kay Nieselt uri: https://doi.org/10.7717/peerj.4742 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Seitz et al. title: Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data link: https://peerj.com/articles/4925 last-modified: 2018-05-28 description: High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal internal transcribed spacer (ITS) amplicons, we created two ITS spike-in control mock communities composed of cloned DNA in plasmids: a biological mock community, consisting of ITS sequences from fungal taxa, and a synthetic mock community (SynMock), consisting of non-biological ITS-like sequences. Using these spike-in controls we show that: (1) a non-biological synthetic control (e.g., SynMock) is the best solution for parameterizing bioinformatics pipelines, (2) pre-clustering steps for variable length amplicons are critically important, (3) a major source of bias is attributed to the initial polymerase chain reaction (PCR) and thus HTAS read abundances are typically not representative of starting values. We developed AMPtk, a versatile software solution equipped to deal with variable length amplicons and quality filter HTAS data based on spike-in controls. While we describe herein a non-biological SynMock community for ITS sequences, the concept and AMPtk software can be widely applied to any HTAS dataset to improve data quality. creator: Jonathan M. Palmer creator: Michelle A. Jusino creator: Mark T. Banik creator: Daniel L. Lindner uri: https://doi.org/10.7717/peerj.4925 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: The relationship between body mass index and pain, disease activity, depression and anxiety in women with fibromyalgia link: https://peerj.com/articles/4917 last-modified: 2018-05-28 description: BackgroundObesity is a possible factor which affects severity of symptoms and disease activity in fibromyalgia syndrome (FMS). The aim of our study was to determine the association between body mass index (BMI) and pain, tender point count (TPC), disease activity, anxiety and depression in patients with FMS.MethodsThis was a descriptive study. A total of 124 female FMS patients between 18 and 55 years of age were enrolled. FMS patients were evaluated with visual analog scale (VAS), fibromyalgia impact questionnaire (FIQ), Hamilton anxiety scale (HAM-A) and Hamilton depression scale (HAM-D). Patients were divided into three groups according to BMI levels: normal weight, overweight and obese. Normal weight was defined as BMI 18.5–24.9, overweight as BMI 25.0–29.9 and obesity as BMI ≥ 30. We assessed the BMI status and its association with symptom severity in patients with FMS.ResultsSignificant differences were detected in VAS, TPC, FIQ and HAM-D among the groups (p < 0.05). There were no significant differences between the groups in HAM-A (p = 0.328). The highest scores were found in the obese group. Significant positive correlations were determined between BMI levels and VAS, TPC, FIQ and HAM-D (r = 0.277, p = 0.002; r = 0.384, p < 0.001; r = 0.292, p = 0.001; r = 0.357, p < 0.001).DiscussionObese female FMS patients had higher levels of pain, TPC, disease activity and depression. BMI was significantly and positively correlated with clinical manifestations of FMS. Therefore, FMS treatment programs should include weight loss strategies. creator: Burhan Fatih Koçyiğit creator: Ramazan Azim Okyay uri: https://doi.org/10.7717/peerj.4917 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Koçyiğit and Okyay title: Change of niche in guanaco (Lama guanicoe): the effects of climate change on habitat suitability and lineage conservatism in Chile link: https://peerj.com/articles/4907 last-modified: 2018-05-28 description: BackgroundThe main goal of this contribution was to define the ecological niche of the guanaco (Lama guanicoe), to describe potential distributional changes, and to assess the relative importance of niche conservatism and divergence processes between the two lineages described for the species (L.g. cacsilensis and L.g. guanicoe).MethodsWe used maximum entropy to model lineage’s climate niche from 3,321 locations throughout continental Chile, and developed future niche models under climate change for two extreme greenhouse gas emission scenarios (RCP2.6 and RCP8.5). We evaluated changes of the environmental niche and future distribution of the largest mammal in the Southern Cone of South America. Evaluation of niche conservatism and divergence were based on identity and background similarity tests.ResultsWe show that: (a) the current geographic distribution of lineages is associated with different climatic requirements that are related to the geographic areas where these lineages are located; (b) future distribution models predict a decrease in the distribution surface under both scenarios; (c) a 3% decrease of areal protection is expected if the current distribution of protected areas is maintained, and this is expected to occur at the expense of a large reduction of high quality habitats under the best scenario; (d) current and future distribution ranges of guanaco mostly adhere to phylogenetic niche divergence hypotheses between lineages.DiscussionAssociating environmental variables with species ecological niche seems to be an important aspect of unveiling the particularities of, both evolutionary patterns and ecological features that species face in a changing environment. We report specific descriptions of how these patterns may play out under the most extreme climate change predictions and provide a grim outlook of the future potential distribution of guanaco in Chile. From an ecological perspective, while a slightly smaller distribution area is expected, this may come with an important reduction of available quality habitats. From the evolutionary perspective, we describe the limitations of this taxon as it experiences forces imposed by climate change dynamics. creator: Andrea G. Castillo creator: Dominique Alò creator: Benito A. González creator: Horacio Samaniego uri: https://doi.org/10.7717/peerj.4907 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Castillo et al. title: Transcranial direct current stimulation over the right DLPFC selectively modulates subprocesses in working memory link: https://peerj.com/articles/4906 last-modified: 2018-05-28 description: BackgroundWorking memory, as a complex system, consists of two independent components: manipulation and maintenance process, which are defined as executive control and storage process. Previous studies mainly focused on the overall effect of transcranial direct current stimulation (tDCS) on working memory. However, little has been known about the segregative effects of tDCS on the sub-processes within working memory.MethodTranscranial direct current stimulation, as one of the non-invasive brain stimulation techniques, is being widely used to modulate the cortical activation of local brain areas. This study modified a spatial n-back experiment with anodal and cathodal tDCS exertion on the right dorsolateral prefrontal cortex (DLPFC), aiming to investigate the effects of tDCS on the two sub-processes of working memory: manipulation (updating) and maintenance. Meanwhile, considering the separability of tDCS effects, we further reconfirmed the causal relationship between the right DLPFC and the sub-processes of working memory with different tDCS conditions.ResultsThe present study showed that cathodal tDCS on the right DLPFC selectively improved the performance of the modified 2-back task in the difficult condition, whereas anodal tDCS significantly reduced the performance of subjects and showed an speeding-up tendency of response time. More precisely, the results of discriminability index and criterion showed that only cathodal tDCS enhanced the performance of maintenance in the difficult condition. Neither of the two tDCS conditions affected the performance of manipulation (updating).ConclusionThese findings provide evidence that cathodal tDCS of the right DLPFC selectively affects maintenance capacity. Besides, cathodal tDCS also serves as an interference suppressor to reduce the irrelevant interference, thereby indirectly improving the working memory capacity. Moreover, the right DLPFC is not the unique brain regions for working memory manipulation (updating). creator: Jiarui Wang creator: Jinhua Tian creator: Renning Hao creator: Lili Tian creator: Qiang Liu uri: https://doi.org/10.7717/peerj.4906 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wang et al. title: Proteomics of Nasonia vitripennis and the effects of native Wolbachia infection on N. vitripennis link: https://peerj.com/articles/4905 last-modified: 2018-05-28 description: BackgroundNasonia vitripennis, a parasitic wasp, is a good model organism to study developmental and evolutionary genetics and to evaluate the interactions between insect hosts and their symbionts. Wolbachia may be the most prevalent endosymbiont among insect species due to their special ability to improve the fitness of the infected hosts. Transinfection of bacteria or fungi could substantially alter the expression of host immune system components. However, few studies have focused on the effects of native Wolbachia infection. Accordingly, in this study, we evaluated the proteomics of N. vitripennis following Wolbachia infection.MethodsWe studied the proteomics of N. vitripennis following native Wolbachia infection and in antibiotic-treated Wolbachia-free samples using isobaric tags for relative and absolute quantification-liquid chromatography tandem mass spectrometry, accompanying with some ecological experiments.ResultsIn total, 3,096 proteins were found to be associated with a wide range of biological processes, molecular functions, and cellular components. Interestingly, there were few significant changes in immune or reproductive proteins between samples with and without Wolbachia infection. Differentially expressed proteins were involved in the binding process, catalytic activity, and the metabolic process, as confirmed by quantitative reverse transcription polymerase chain reaction.DiscussionInvasion of any pathogen or bacterium within a short time can cause an immunoreaction in the host. Our results implied that during the long process of coexistence, the immune system of the host was not as sensitive as when the symbiont initially infected the host, implying that the organisms had gradually adjusted to cohabitation. creator: Jie Li creator: Ningxin Wang creator: Yong Liu creator: Shiqi Qiu uri: https://doi.org/10.7717/peerj.4905 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: Clinicopathologic characteristics, laboratory parameters, treatment protocols, and outcomes of pancreatic cancer: a retrospective cohort study of 1433 patients in China link: https://peerj.com/articles/4893 last-modified: 2018-05-28 description: ObjectivesThe prognosis of people with pancreatic cancer is extremely unfavorable. However, the prognostic factors remain largely undefined. We aimed to perform comprehensive analyses of clinicopathologic characteristics, laboratory parameters, and treatment protocols for exploring their role as prognostic factors of pancreatic cancer.MethodsPatients diagnosed with pancreatic cancer and hospitalized at the China National Cancer Center between April 2006 and May 2016 were enrolled in this retrospective cohort study. Clinicopathologic characteristics, laboratory parameters, and treatment protocols were compared among patients at different stages of the disease. The association between these factors and overall survival (OS) was analyzed using the Kaplan–Meier method and Cox proportional hazards model.ResultsThe present study included 1,433 consecutive patients with pancreatic cancer. Median OS was 10.6 months (95% confidence interval [CI] 9.8–11.3 months), with 1-, 3-, and 5-year survival rates of 43.7%, 14.8%, and 8.8%, respectively. Cox multivariate analysis findings identified the following factors as independent predictors of OS: gender (female vs male, hazard ratio 0.72, 95% CI [0.54–0.95]); elevated total bilirubin (TBil; 1.82, 1.34–2.47); elevated carbohydrate antigen 19-9 (CA19-9; 1.72, 1.17–2.54); tumor being located in pancreatic body and tail (1.52, 1.10–2.10); advanced T stage (T3-4 vs T1-2, 1.62, 1.15–2.27); lymph node metastasis (1.57, 1.20–2.07); distant metastasis (1.59, 1.12–2.27); the presence of surgical resection (0.53, 0.34–0.81); and the presence of systemic chemotherapy (0.62, 0.45–0.82).ConclusionsBeing male, elevated TBil and carcinoembryonic antigen, tumor being located in pancreatic body and tail, advanced T stage, lymph node and distant metastasis, the absence of surgical resection, and the absence of systematic chemotherapy were associated with worse OS in patients with pancreatic cancer. creator: Shuisheng Zhang creator: Xiaozhun Huang creator: Yuan Tian creator: Saderbieke Aimaiti creator: Jianwei Zhang creator: Jiuda Zhao creator: Yingtai Chen creator: Chengfeng Wang uri: https://doi.org/10.7717/peerj.4893 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Zhang et al. title: BLAST-based validation of metagenomic sequence assignments link: https://peerj.com/articles/4892 last-modified: 2018-05-28 description: When performing bioforensic casework, it is important to be able to reliably detect the presence of a particular organism in a metagenomic sample, even if the organism is only present in a trace amount. For this task, it is common to use a sequence classification program that determines the taxonomic affiliation of individual sequence reads by comparing them to reference database sequences. As metagenomic data sets often consist of millions or billions of reads that need to be compared to reference databases containing millions of sequences, such sequence classification programs typically use search heuristics and databases with reduced sequence diversity to speed up the analysis, which can lead to incorrect assignments. Thus, in a bioforensic setting where correct assignments are paramount, assignments of interest made by “first-pass” classifiers should be confirmed using the most precise methods and comprehensive databases available. In this study we present a BLAST-based method for validating the assignments made by less precise sequence classification programs, with optimal parameters for filtering of BLAST results determined via simulation of sequence reads from genomes of interest, and we apply the method to the detection of four pathogenic organisms. The software implementing the method is open source and freely available. creator: Adam L. Bazinet creator: Brian D. Ondov creator: Daniel D. Sommer creator: Shashikala Ratnayake uri: https://doi.org/10.7717/peerj.4892 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bazinet et al. title: Predicting New Zealand riverine fish reference assemblages link: https://peerj.com/articles/4890 last-modified: 2018-05-28 description: Biomonitoring is a common method to monitor environmental change in river ecosystems, a key advantage of biomonitoring over snap-shot physicochemical monitoring is that it provides a more stable, long-term insight into change that is also effects-based. In New Zealand, the main biomonitoring method is a macroinvertebrate sensitivity scoring index, with little established methods available for biomonitoring of fish. This study models the contemporary distribution of common freshwater fish and then uses those models to predict freshwater fish assemblages for each river reach under reference conditions. Comparison of current fish assemblages with those predicted in reference conditions (as observed/expected (O/E) ratios) may provide a suitable option for freshwater fish biomonitoring. Most of the fish communities throughout the central North Island and lower reaches show substantial deviation from the modelled reference community. Most of this deviation is explained by nutrient enrichment, followed by downstream barriers (i.e. dams) and loss of riparian vegetation. The presence of modelled introduced species had relatively little impact on the presence of the modelled native fish. The maps of O/E fish assemblage may provide a rapid way to identify potential restoration sites. creator: Adam D. Canning uri: https://doi.org/10.7717/peerj.4890 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Canning title: Expression analysis of vitellogenins in the workers of the red imported fire ant (Solenopsis invicta) link: https://peerj.com/articles/4875 last-modified: 2018-05-28 description: Vitellogenin has been proposed to regulate division of labor and social organization in social insects. The red imported fire ant (Solenopsis invicta) harbors four distinct, adjacent vitellogenin genes (Vg1, Vg2, Vg3, and Vg4). Contrary to honey bees that have a single Vg ortholog as well as potentially fertile nurses, and to other ant species that lay trophic eggs, S. invicta workers completely lack ovaries or the ability to lay eggs. This provides a unique model to investigate whether Vg duplication in S. invicta was followed by subfunctionalization to acquire non-reproductive functions and whether Vg was co-opted to regulate behavior within the worker caste. To investigate these questions, we compared the expression patterns of S. invicta Vg genes among workers from different morphological subcastes or performing different tasks. RT-qPCRs revealed higher relative expression of Vg1 in major workers compared to both medium and minor workers, and of Vg2 in major workers when compared to minor workers. Relative expression of Vg1 was also higher in carbohydrate foragers when compared to nurses and protein foragers. By contrast, the level of expression of Vg2, Vg3, and Vg4 were not significantly different among the workers performing the specific tasks. Additionally, we analyzed the relationship between the expression of the Vg genes and S-hydroprene, a juvenile hormone analog. No changes in Vg expression were recorded in workers 12 h after application of the analog. Our results suggest that in S. invicta the Vg gene underwent subfunctionalization after duplication to new functions based on the expression bias observed in these data. This may suggest an alternative and still unknown function for Vg in the workers that needs to be investigated further. creator: Chloe Hawkings creator: Cecilia Tamborindeguy uri: https://doi.org/10.7717/peerj.4875 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hawkings and Tamborindeguy title: Redescription and affinities of Hulsanpes perlei (Dinosauria, Theropoda) from the Upper Cretaceous of Mongolia link: https://peerj.com/articles/4868 last-modified: 2018-05-28 description: Hulsanpes perlei is an enigmatic theropod dinosaur from the Baruungoyot Formation (?mid- to upper Campanian, Upper Cretaceous) of Mongolia. It was discovered in 1970, during the third Polish-Mongolian paleontological expedition to the Nemegt Basin. The taxon is known based on a partial braincase and an incomplete right hindlimb. However, the braincase fragment has never been described nor illustrated. We redescribe all elements that form the holotype of Hulsanpes and discuss the affinities of this taxon. The braincase fragment is interpreted as belonging to the inner ear region, and includes the floccular recess and part of the labyrinth. Hulsanpes perlei is confirmed as a valid taxon, diagnosed by a unique combination of metatarsal characters, including two autapomorphies. Historically, it represents the oldest record of the recently-established clade Halszkaraptorinae. Our findings identify subcursorial adaptations for Hulsanpes, shared with Mahakala, and differentiating them from Halszkaraptor. As such, appendicular disparity in the potentially sympatric halszkaraptorines suggest a reduced ecological overlap among these taxa, which may explain the co-occurrence of multiple species of this clade during the latest Cretaceous in what is now the Nemegt Basin. creator: Andrea Cau creator: Daniel Madzia uri: https://doi.org/10.7717/peerj.4868 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cau and Madzia title: Antioxidant status of rats’ blood and liver affected by sodium selenite and selenium nanoparticles link: https://peerj.com/articles/4862 last-modified: 2018-05-28 description: BackgroundSelenium is an essential element; however, at higher doses, it can be toxic. Therefore, alternative nanotechnological solutions are required to overcome toxicological issues, rather than conventional alternatives. Nanoparticles show new and promising properties that may be able to suppress toxicity while maintaining the positive effects of selenium on an organism. The aim of the experiment was to determine the influence of sodium selenite and selenium nanoparticles (SeNPs) on the antioxidant status of rats.MethodsThe males of the outbreed rat strain Wistar albino were selected as a model organism. Animals were fed different forms of selenium. The control group was given a mixture without selenium addition, whereas other groups were fed a mixture containing sodium selenite, Se-49, and Se-100 SeNPs respectively. The duration of the trial was 30 days.ResultsAnalysis of blood and liver was performed where the concentration of reduced (GSH) and oxidised (GSSG) glutathione, and total selenium content were measured. In the liver, a significant reduction in GSSG was found for all experiment groups. Blood samples showed a significant reduction in GSH and an increase in GSSG.DiscussionThese results show that SeNPs may be an alternative to dietary selenium for animal organisms. creator: Lenka Urbankova creator: Pavel Horky creator: Jiri Skladanka creator: Magdalena Pribilova creator: Vendula Smolikova creator: Pavel Nevrkla creator: Natalia Cernei creator: Zuzana Lackova creator: Josef Hedbavny creator: Andrea Ridoskova creator: Vojtech Adam creator: Pavel Kopel uri: https://doi.org/10.7717/peerj.4862 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Urbankova et al. title: Linear Lepidopteran ambidensovirus 1 sequences drive random integration of a reporter gene in transfected Spodoptera frugiperda cells link: https://peerj.com/articles/4860 last-modified: 2018-05-28 description: BackgroundThe Lepidopteran ambidensovirus 1 isolated from Junonia coenia (hereafter JcDV) is an invertebrate parvovirus considered as a viral transduction vector as well as a potential tool for the biological control of insect pests. Previous works showed that JcDV-based circular plasmids experimentally integrate into insect cells genomic DNA.MethodsIn order to approach the natural conditions of infection and possible integration, we generated linear JcDV-gfp based molecules which were transfected into non permissive Spodoptera frugiperda (Sf9) cultured cells. Cells were monitored for the expression of green fluorescent protein (GFP) and DNA was analyzed for integration of transduced viral sequences. Non-structural protein modulation of the VP-gene cassette promoter activity was additionally assayed.ResultsWe show that linear JcDV-derived molecules are capable of long term genomic integration and sustained transgene expression in Sf9 cells. As expected, only the deletion of both inverted terminal repeats (ITR) or the polyadenylation signals of NS and VP genes dramatically impairs the global transduction/expression efficiency. However, all the integrated viral sequences we characterized appear “scrambled” whatever the viral content of the transfected vector. Despite a strong GFP expression, we were unable to recover any full sequence of the original constructs and found rearranged viral and non-viral sequences as well. Cellular flanking sequences were identified as non-coding ones. On the other hand, the kinetics of GFP expression over time led us to investigate the apparent down-regulation by non-structural proteins of the VP-gene cassette promoter.ConclusionAltogether, our results show that JcDV-derived sequences included in linear DNA molecules are able to drive efficiently the integration and expression of a foreign gene into the genome of insect cells, whatever their composition, provided that at least one ITR is present. However, the transfected sequences were extensively rearranged with cellular DNA during or after random integration in the host cell genome. Lastly, the non-structural proteins seem to participate in the regulation of p9 promoter activity rather than to the integration of viral sequences. creator: Francine Rizk creator: Sylvain Laverdure creator: Emmanuelle d’Alençon creator: Hervé Bossin creator: Thierry Dupressoir uri: https://doi.org/10.7717/peerj.4860 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rizk et al. title: Tea cultivar classification and biochemical parameter estimation from hyperspectral imagery obtained by UAV link: https://peerj.com/articles/4858 last-modified: 2018-05-28 description: It is generally feasible to classify different species of vegetation based on remotely sensed images, but identification of different sub-species or even cultivars is uncommon. Tea trees (Camellia sinensis L.) have been proven to show great differences in taste and quality between cultivars. We hypothesize that hyperspectral remote sensing would make it possibly to classify cultivars of plants and even to estimate their taste-related biochemical components. In this study, hyperspectral data of the canopies of tea trees were collected by hyperspectral camera mounted on an unmanned aerial vehicle (UAV). Tea cultivars were classified according to the spectral characteristics of the tea canopies. Furthermore, two major components influencing the taste of tea, tea polyphenols (TP) and amino acids (AA), were predicted. The results showed that the overall accuracy of tea cultivar classification achieved by support vector machine is higher than 95% with proper spectral pre-processing method. The best results to predict the TP and AA were achieved by partial least squares regression with standard normal variant normalized spectra, and the ratio of TP to AA—which is one proven index for tea taste—achieved the highest accuracy (RCV = 0.66, RMSECV = 13.27) followed by AA (RCV = 0.62, RMSECV = 1.16) and TP (RCV = 0.58, RMSECV = 10.01). The results indicated that classification of tea cultivars using the hyperspectral remote sensing from UAV was successful, and there is a potential to map the taste-related chemical components in tea plantations from UAV platform; however, further exploration is needed to increase the accuracy. creator: Yexin Tu creator: Meng Bian creator: Yinkang Wan creator: Teng Fei uri: https://doi.org/10.7717/peerj.4858 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tu et al. title: Estimation of different data compositions for early-season crop type classification link: https://peerj.com/articles/4834 last-modified: 2018-05-28 description: Timely and accurate crop type distribution maps are an important inputs for crop yield estimation and production forecasting as multi-temporal images can observe phenological differences among crops. Therefore, time series remote sensing data are essential for crop type mapping, and image composition has commonly been used to improve the quality of the image time series. However, the optimal composition period is unclear as long composition periods (such as compositions lasting half a year) are less informative and short composition periods lead to information redundancy and missing pixels. In this study, we initially acquired daily 30 m Normalized Difference Vegetation Index (NDVI) time series by fusing MODIS, Landsat, Gaofen and Huanjing (HJ) NDVI, and then composited the NDVI time series using four strategies (daily, 8-day, 16-day, and 32-day). We used Random Forest to identify crop types and evaluated the classification performances of the NDVI time series generated from four composition strategies in two studies regions from Xinjiang, China. Results indicated that crop classification performance improved as crop separabilities and classification accuracies increased, and classification uncertainties dropped in the green-up stage of the crops. When using daily NDVI time series, overall accuracies saturated at 113-day and 116-day in Bole and Luntai, and the saturated overall accuracies (OAs) were 86.13% and 91.89%, respectively. Cotton could be identified 40∼60 days and 35∼45 days earlier than the harvest in Bole and Luntai when using daily, 8-day and 16-day composition NDVI time series since both producer’s accuracies (PAs) and user’s accuracies (UAs) were higher than 85%. Among the four compositions, the daily NDVI time series generated the highest classification accuracies. Although the 8-day, 16-day and 32-day compositions had similar saturated overall accuracies (around 85% in Bole and 83% in Luntai), the 8-day and 16-day compositions achieved these accuracies around 155-day in Bole and 133-day in Luntai, which were earlier than the 32-day composition (170-day in both Bole and Luntai). Therefore, when the daily NDVI time series cannot be acquired, the 16-day composition is recommended in this study. creator: Pengyu Hao creator: Mingquan Wu creator: Zheng Niu creator: Li Wang creator: Yulin Zhan uri: https://doi.org/10.7717/peerj.4834 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hao et al. title: Agronomical, biochemical and histological response of resistant and susceptible wheat and barley under BYDV stress link: https://peerj.com/articles/4833 last-modified: 2018-05-28 description: Barley yellow dwarf virus-PAV (BYDV-PAV) is one of the major viruses causing a widespread and serious viral disease affecting cereal crops. To gain a better understanding of plant defence mechanisms of BYDV resistance genes (Bdv2 and RYd2) against BYDV-PAV infection, the differences in agronomical, biochemical and histological changes between susceptible and resistant wheat and barley cultivars were investigated. We found that root growth and total dry matter of susceptible cultivars showed greater reduction than that of resistant ones after infection. BYDV infected leaves in susceptible wheat and barley cultivars showed a significant reduction in photosynthetic pigments, an increase in the concentration of reducing sugar. The protein levels were also low in infected leaves. There was a significant increase in total phenol contents in resistant cultivars, which might reflect a protective mechanism of plants against virus infection. In phloem tissue, sieve elements (SE) and companion cells (CC) were severely damaged in susceptible cultivars after infection. It is suggested that restriction of viral movement in the phloem tissue and increased production of phenolic compounds may play a role in the resistance and defensive mechanisms of both Bdv2 and RYd2 against virus infection. creator: Shormin Choudhury creator: Hongliang Hu creator: Philip Larkin creator: Holger Meinke creator: Sergey Shabala creator: Ibrahim Ahmed creator: Meixue Zhou uri: https://doi.org/10.7717/peerj.4833 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Choudhury et al. title: Early and long-term results of minimally invasive mitral valve surgery through a right mini-thoracotomy approach: a retrospective propensity-score matched analysis link: https://peerj.com/articles/4810 last-modified: 2018-05-28 description: BackgroundMinimally invasive mitral valve surgery (MVS) via right mini-thoracotomy has recently attracted a lot of attention. Minimally invasive MVS shows postoperative results that are comparable to those of conventional MVS through the median sternotomy as per various earlier studies.MethodsBetween 2000 and 2016, a total of 669 isolated mitral valve procedures for isolated mitral valve regurgitation were performed. A propensity score-matched analysis was generated for the elimination of the differences in relevant preoperative risk factors between the cohorts and included 227 patient pairs. Only degenerative mitral valve regurgitation was included. The aim of our study was to examine if the minimally MVS is superior to the conventional approach through sternotomy based on a retrospective propensity-matched analysis. The primary endpoints were early mortality and long-term survival. The secondary endpoints included postoperative complications.ResultsThe in-hospital mortality rate was significantly higher within the conventional sternotomy cohort (3.1%, n = 7 vs 0.4%, n = 1 for the minimally invasive cohort; p = 0.032). The incidence of stroke and exploration for bleeding was comparable. In contrast, the necessity for dialysis was significantly lower in the minimally invasive cohort (p = 0.044). Postoperative pain was not significantly lower in the minimally invasive MVS cohort (p = 0.862). While patients who underwent minimally invasive MVS experienced longer bypass and cross-clamp times, their lengths of stay in the intensive care unit and in the hospital, did not differ from the conventionally operated collective (p = 0.779 and p = 0.516), respectively. The mitral valve repair rate of 81.1% in the minimally invasive cohort was significantly superior to that of the conventional approach, which was 46.3% (p < 0.0001). The one-, five-, and 10-year survival rates were significantly higher in the minimally invasive cohort compared to the conventional approach (96%, 90%, and 84% vs. 89%, 85%, and 70%; log rank p = 0.004).ConclusionDespite prolonged cardiopulmonary bypass and cross-clamping times, the minimally invasive MVS may be considered a safe approach that is equivalent to standard median sternotomy with lower early mortality and superior long-term survival. creator: Sabreen Mkalaluh creator: Marcin Szczechowicz creator: Bashar Dib creator: Anton Sabashnikov creator: Gabor Szabo creator: Matthias Karck creator: Alexander Weymann uri: https://doi.org/10.7717/peerj.4810 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Mkalaluh et al. title: Redescription of Phymolepis  cuifengshanensis (Antiarcha: Yunnanolepididae) using high-resolution computed tomography and new insights into anatomical details of the endocranium in antiarchs link: https://peerj.com/articles/4808 last-modified: 2018-05-28 description: BackgroundYunnanolepidoids constitute either the most basal consecutive segments or the most primitive clade of antiarchs, a highly diversified jawed vertebrate group from the Silurian and Early Devonian periods. Although the general morphology of yunnanolepidoids is well established, their endocranial features remain largely unclear, thus hindering our further understanding of antiarch evolution, and early gnathostome evolution. Phymolepis cuifengshanensis, a yunnanolepidoid from the Early Devonian of southwestern China, is re-described in detail to reveal the information on endocranial anatomy and additional morphological data of head and trunk shields.MethodsWe scanned the material of P. cuifengshanensis using high-resolution computed tomography and generated virtual restorations to show the internal morphology of its dermal shield. The dorsal aspect of endocranium in P. cuifengshanensis was therefore inferred. The phylogenetic analysis of antiarchs was conducted based on a revised and expanded dataset that incorporates 10 new cranial characters.ResultsThe lateroventral fossa of trunk shield and Chang’s apparatus are three-dimensionally restored in P. cuifengshanensis. The canal that is positioned just anterior to the internal cavity of Chang’s apparatus probably corresponds to the rostrocaudal canal of euantiarchs. The endocranial morphology of P. cuifengshanensis corroborates a general pattern for yunnanolepidoids with additional characters distinguishing them from sinolepids and euantiarchs, such as a developed cranio-spinal process, an elongated endolymphatic duct, and a long occipital portion.DiscussionIn light of new data from Phymolepis and Yunnanolepis, we summarized the morphology on the visceral surface of head shield in antiarchs, and formulated an additional 10 characters for the phylogenetic analysis. These cranial characters exhibit a high degree of morphological disparity between major subgroups of antiarchs, and highlight the endocranial character evolution in antiarchs. creator: Yajing Wang creator: Min Zhu uri: https://doi.org/10.7717/peerj.4808 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang and Zhu title: A guideline for reporting experimental protocols in life sciences link: https://peerj.com/articles/4795 last-modified: 2018-05-28 description: Experimental protocols are key when planning, performing and publishing research in many disciplines, especially in relation to the reporting of materials and methods. However, they vary in their content, structure and associated data elements. This article presents a guideline for describing key content for reporting experimental protocols in the domain of life sciences, together with the methodology followed in order to develop such guideline. As part of our work, we propose a checklist that contains 17 data elements that we consider fundamental to facilitate the execution of the protocol. These data elements are formally described in the SMART Protocols ontology. By providing guidance for the key content to be reported, we aim (1) to make it easier for authors to report experimental protocols with necessary and sufficient information that allow others to reproduce an experiment, (2) to promote consistency across laboratories by delivering an adaptable set of data elements, and (3) to make it easier for reviewers and editors to measure the quality of submitted manuscripts against an established criteria. Our checklist focuses on the content, what should be included. Rather than advocating a specific format for protocols in life sciences, the checklist includes a full description of the key data elements that facilitate the execution of the protocol. creator: Olga Giraldo creator: Alexander Garcia creator: Oscar Corcho uri: https://doi.org/10.7717/peerj.4795 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Giraldo et al. title: Do latitudinal gradients exist in New Zealand stream invertebrate metacommunities? link: https://peerj.com/articles/4898 last-modified: 2018-05-25 description: That biodiversity declines with latitude is well known, but whether a metacommunity process is behind this gradient has received limited attention. We tested the hypothesis that dispersal limitation is progressively replaced by mass effects with increasing latitude, along with a series of related hypotheses. We explored these hypotheses by examining metacommunity structure in stream invertebrate metacommunities spanning the length of New Zealand’s two largest islands (∼1,300 km), further disentangling the role of dispersal by deconstructing assemblages into strong and weak dispersers. Given the highly dynamic nature of New Zealand streams, our alternative hypothesis was that these systems are so unpredictable (at different stages of post-flood succession) that metacommunity structure is highly context dependent from region to region. We rejected our primary hypotheses, pinning this lack of fit on the strong unpredictability of New Zealand’s dynamic stream ecosystems and fauna that has evolved to cope with these conditions. While local community structure turned over along this latitudinal gradient, metacommunity structure was highly context dependent and dispersal traits did not elucidate patterns. Moreover, the emergent metacommunity types exhibited no trends, nor did the important environmental variables. These results provide a cautionary tale for examining singular metacommunities. The considerable level of unexplained contingency suggests that any inferences drawn from one-off snapshot sampling may be misleading and further points to the need for more studies on temporal dynamics of metacommunity processes. creator: Jonathan D. Tonkin creator: Russell G. Death creator: Timo Muotka creator: Anna Astorga creator: David A. Lytle uri: https://doi.org/10.7717/peerj.4898 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tonkin et al. title: Allocation pattern and accumulation potential of carbon stock in natural spruce forests in northwest China link: https://peerj.com/articles/4859 last-modified: 2018-05-25 description: BackgroundThe spruce forests are dominant communities in northwest China, and play a key role in national carbon budgets. However, the patterns of carbon stock distribution and accumulation potential across stand ages are poorly documented.MethodsWe investigated the carbon stocks in biomass and soil in the natural spruce forests in the region by surveys on 39 plots. Biomass of tree components were estimated using allometric equations previously established based on tree height and diameter at breast height, while biomass in understory (shrub and herb) and forest floor were determined by total harvesting method. Fine root biomass was estimated by soil coring technique. Carbon stocks in various biomass components and soil (0–100 cm) were estimated by analyzing the carbon content of each component.ResultsThe results showed that carbon stock in these forest ecosystems can be as high as 510.1 t ha−1, with an average of 449.4 t ha−1. Carbon stock ranged from 28.1 to 93.9 t ha−1 and from 0.6 to 8.7 t ha−1 with stand ages in trees and deadwoods, respectively. The proportion of shrubs, herbs, fine roots, litter and deadwoods ranged from 0.1% to 1% of the total ecosystem carbon, and was age-independent. Fine roots and deadwood which contribute to about 2% of the biomass carbon should be attached considerable weight in the investigation of natural forests. Soil carbon stock did not show a changing trend with stand age, ranging from 254.2 to 420.0 t ha−1 with an average of 358.7 t ha−1. The average value of carbon sequestration potential for these forests was estimated as 29.4 t ha−1, with the lower aged ones being the dominant contributor. The maximum carbon sequestration rate was 2.47 t ha−1 year−1 appearing in the growth stage of 37–56 years.ConclusionThe carbon stock in biomass was the major contributor to the increment of carbon stock in ecosystems. Stand age is not a good predictor of soil carbon stocks and accurate evaluation of the soil carbon dynamics thus requires long-term monitoring in situ. The results not only revealed carbon stock status and dynamics in these natural forests but were helpful to understand the role of Natural Forest Protection project in forest carbon sequestration as well. creator: Jun-Wei Yue creator: Jin-Hong Guan creator: Lei Deng creator: Jian-Guo Zhang creator: Guoqing Li creator: Sheng Du uri: https://doi.org/10.7717/peerj.4859 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yue et al. title: Effect of Sofosbuvir plus Ribavirin therapy on hepatitis C patients in Pakistan: a retrospective study link: https://peerj.com/articles/4853 last-modified: 2018-05-25 description: BackgroundThe annual global deaths from viral hepatitis is 1.4 million. Pakistan has the second highest burden of hepatitis C in the world. There is dire need to evaluate the response of new direct acting antivirals for the treatment of hepatitis C patients in Pakistan. World Health Organization has developed a strategy to treat 80% of HCV patients by 2030. In Pakistan, HCV treatment rate is 1%. The aim of the study was to analyze the effect of Sofosbuvir plus Ribavirin therapy on HCV patients in Pakistan.MethodsAn observational study was conducted at Fauji Foundation Hospital Rawalpindi from November-2016 to July-2017. All the drugs were administered according to the guidelines of Asia Pacific Association for the Study of Liver (APASL) for the treatment of HCV patients. A total 327 chronic HCV patients were enrolled in the study and 304 completed the treatment. Patients belonged to three different groups including treatment: Naïve patients (n = 107), Non-Responder patients (n = 126) and patients who relapsed to Interferon therapy (n = 71). All the patients were given Sofosbuvir plus Ribavirin therapy for 24 weeks and the early virological response (EVR) and end treatment response (ETR) was calculated. Different parameters including patient age, viral load, viral genotype, blood picture, ultrasound findings and liver function tests were also studied.ResultsOut of 304 patients, 301 (99%) achieved EVR and 300 achieved ETR (98.7%). End treatment response was 95.6% in HCV genotype 1 and 98.9% in HCV genotype 3 patients. ETR was 99.06% in treatment Naïve, 99.20% in non-responders and 97.18% in previously relapsed patients. We did not find the association of any host and viral factor in the determination of EVR and ETR.ConclusionThe Sofosbuvir plus Ribavirin treatment is highly effective, safe and cost-effective for the treatment of hepatitis C patients in Pakistan. creator: Zubia Jamil creator: Yasir Waheed creator: Maryam Malik creator: Asghar A. Durrani uri: https://doi.org/10.7717/peerj.4853 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Jamil et al. title: Physical fitness predicts technical-tactical and time-motion profile in simulated Judo and Brazilian Jiu-Jitsu matches link: https://peerj.com/articles/4851 last-modified: 2018-05-25 description: BackgroundAmong combat sports, Judo and Brazilian Jiu-Jitsu (BJJ) present elevated physical fitness demands from the high-intensity intermittent efforts. However, information regarding how metabolic and neuromuscular physical fitness is associated with technical-tactical performance in Judo and BJJ fights is not available. This study aimed to relate indicators of physical fitness with combat performance variables in Judo and BJJ.MethodsThe sample consisted of Judo (n = 16) and BJJ (n = 24) male athletes. At the first meeting, the physical tests were applied and, in the second, simulated fights were performed for later notational analysis.ResultsThe main findings indicate: (i) high reproducibility of the proposed instrument and protocol used for notational analysis in a mobile device; (ii) differences in the technical-tactical and time-motion patterns between modalities; (iii) performance-related variables are different in Judo and BJJ; and (iv) regression models based on metabolic fitness variables may account for up to 53% of the variances in technical-tactical and/or time-motion variables in Judo and up to 31% in BJJ, whereas neuromuscular fitness models can reach values up to 44 and 73% of prediction in Judo and BJJ, respectively. When all components are combined, they can explain up to 90% of high intensity actions in Judo.DiscussionIn conclusion, performance prediction models in simulated combat indicate that anaerobic, aerobic and neuromuscular fitness variables contribute to explain time-motion variables associated with high intensity and technical-tactical variables in Judo and BJJ fights. creator: Victor S. Coswig creator: Paulo Gentil creator: João C.A. Bueno creator: Bruno Follmer creator: Vitor A. Marques creator: Fabrício B. Del Vecchio uri: https://doi.org/10.7717/peerj.4851 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Coswig et al. title: A survey on sleep assessment methods link: https://peerj.com/articles/4849 last-modified: 2018-05-25 description: PurposeA literature review is presented that aims to summarize and compare current methods to evaluate sleep.MethodsCurrent sleep assessment methods have been classified according to different criteria; e.g., objective (polysomnography, actigraphy…) vs. subjective (sleep questionnaires, diaries…), contact vs. contactless devices, and need for medical assistance vs. self-assessment. A comparison of validation studies is carried out for each method, identifying their sensitivity and specificity reported in the literature. Finally, the state of the market has also been reviewed with respect to customers’ opinions about current sleep apps.ResultsA taxonomy that classifies the sleep detection methods. A description of each method that includes the tendencies of their underlying technologies analyzed in accordance with the literature. A comparison in terms of precision of existing validation studies and reports.DiscussionIn order of accuracy, sleep detection methods may be arranged as follows: Questionnaire < Sleep diary < Contactless devices < Contact devices < PolysomnographyA literature review suggests that current subjective methods present a sensitivity between 73% and 97.7%, while their specificity ranges in the interval 50%–96%. Objective methods such as actigraphy present a sensibility higher than 90%. However, their specificity is low compared to their sensitivity, being one of the limitations of such technology. Moreover, there are other factors, such as the patient’s perception of her or his sleep, that can be provided only by subjective methods. Therefore, sleep detection methods should be combined to produce a synergy between objective and subjective methods. The review of the market indicates the most valued sleep apps, but it also identifies problems and gaps, e.g., many hardware devices have not been validated and (especially software apps) should be studied before their clinical use. creator: Vanessa Ibáñez creator: Josep Silva creator: Omar Cauli uri: https://doi.org/10.7717/peerj.4849 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ibáñez et al. title: The global burden of HIV-1 drug resistance in the past 20 years link: https://peerj.com/articles/4848 last-modified: 2018-05-25 description: Genotypic drug resistance testing has been an integral part of the clinical management of HIV patients for almost 20 years, not only assisting treatment choices but also informing drug development. Accurate estimations on the worldwide circulation of drug resistance are difficult to obtain, particularly in low/middle-income countries. In this work, we queried two of the largest public HIV sequence repositories in the world—Los Alamos and Stanford HIVdb—to derive global prevalence, time trends and geodemographic predictors of HIV drug resistance. Different genotypic interpretation systems were used to ascertain resistance to reverse transcriptase and protease inhibitors. Continental, subtype-specific (including circulating recombinant forms) stratification as well as analysis on drug-naïve isolates were performed. Geographic information system analysis correlated country-specific drug resistance to sociodemographic and health indicators obtained from the World Bank. By looking at over 33,000 sequences worldwide between 1996 and 2016, increasing drug resistance trends with non-B subtypes and recombinants were found; transmitted drug resistance appeared to remain stable in the last decade. While an increase in drug resistance is expected with antiretroviral therapy rollout in resource-constrained areas, the plateau effect in areas covered by the most modern drug regimens warns against the downgrading of the resistance issue. creator: Maurizio Zazzi creator: Hui Hu creator: Mattia Prosperi uri: https://doi.org/10.7717/peerj.4848 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zazzi et al. title: Rapid evolution of the Helicobacter pylori AlpA adhesin in a high gastric cancer risk region from Colombia link: https://peerj.com/articles/4846 last-modified: 2018-05-25 description: To be able to survive, Helicobacter pylori must adhere to the gastric epithelial cells of its human host. For this purpose, the bacterium employs an array of adhesins, for example, AlpA. The adhesin AlpA has been proposed as a major adhesin because of its critical role in human stomach colonization. Therefore, understanding how AlpA evolved could be important for the development of new diagnostic strategies. However, the genetic variation and microevolutionary patterns of alpA have not been described in Colombia. The study aim was to describe the variation patterns and microevolutionary process of alpA in Colombian clinical isolates of H. pylori. The existing polymorphisms, which are deviations from the neutral model of molecular evolution, and the genetic differentiation of the alpA gene from Colombian clinical isolates of H. pylori were determined. The analysis shows that gene conversion and purifying selection have shaped the evolution of three different variants of alpA in Colombia. creator: Andrés Julián Gutiérrez-Escobar creator: Gina Méndez-Callejas creator: Orlando Acevedo creator: Maria Mercedes Bravo uri: https://doi.org/10.7717/peerj.4846 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gutiérrez-Escobar et al. title: Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs link: https://peerj.com/articles/4842 last-modified: 2018-05-25 description: Toll-like receptors (TLRs) are an important component of innate immunity, the first line of pathogen defence. One of the major roles of TLRs includes recognition of pathogen-associated molecular patterns. Amphibians are currently facing population declines and even extinction due to chytridiomycosis caused by the Batrachochytrium dendrobatidis (Bd) fungus. Evidence from other vertebrates shows that TLR2 and TLR4 are involved in innate immunity against various fungi. Such genes therefore may play a functional role in amphibian-chytridiomycosis dynamics. Frogs from East Asia appear to be tolerant to Bd, so we examined the genetic diversity that underlies TLR2 and TLR4 from three Japanese Ranidae frog species, Rana japonica, R. ornativentris and R. tagoi tagoi (n = 5 per species). We isolated 27 TLR2 and 20 TLR4 alleles and found that these genes are evolutionarily conserved, with overall evidence supporting purifying selection. In contrast, site-by-site analysis of selection identified several specific codon sites under positive selection, some of which were located in the variable leucine rich repeat domains. In addition, preliminary expression levels of TLR2 and TLR4 from transcriptome data showed overall low expression. Although it remains unclear whether infectious pathogens are a selective force acting on TLRs of Japanese frogs, our results support that certain sites in TLRs of these species may have experienced pathogen-mediated selection. creator: Quintin Lau creator: Takeshi Igawa creator: Tiffany A. Kosch creator: Yoko Satta uri: https://doi.org/10.7717/peerj.4842 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lau et al. title: Shelters can negatively affect growth and welfare in lumpfish if feed is delivered continuously link: https://peerj.com/articles/4837 last-modified: 2018-05-25 description: Due to the socioeconomic importance of salmon farming in the North Atlantic and the economic impact of sea lice in this industry, there is high demand for novel pest control methods. One such method is the use of cleaner fish to remove the lice from the salmon. A cleaner fish that has recently gained in popularity due to its ability to work in cold water, is the lumpfish (Cyclopterus lumpus). This fish varies in efficiency, but when mortality is low and cleaning optimal, the fish are successful in keeping parasite burdens low. However, there is some concern for the welfare of lumpfish in the industry, because mortality is often high. This is sometimes attributed to inadequate feeding and shelter. Here we compare growth, body condition, and fin health of fish reared for four weeks in a crossed treatment design crossing shelter availability (shelter vs none) and feed delivery method (manual meal time feeds and continuous automated feeding). In terms of weight gain, shelter availability interacted with feeding method, with fish that had access to shelters and were fed using automated feeders gaining less weight than other fish. Fin health was not affected, but body condition was lowered both by access to shelter and being fed continuously. The results indicate a need to carefully consider how feeding method and shelter use is combined, both in cages and during rearing on land. creator: Asa Johannesen creator: Nakita E. Joensen creator: Eyðfinn Magnussen uri: https://doi.org/10.7717/peerj.4837 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Johannesen et al. title: Fingerprinting snakes: paleontological and paleoecological implications of zygantral growth rings in Serpentes link: https://peerj.com/articles/4819 last-modified: 2018-05-25 description: We introduce a new non-destructive source of skeletochronological data with applications to species identification, associating disarticulated remains, assessing minimum number of individuals (MNI), and collection management of fossil snakes, but with potential implications for all bony vertebrates, extinct or extant. Study of a diverse sample of Recent henophidian snakes confirms that annual growth cycles (AGCs) visible on the surface of the vertebral zygantrum correspond to lines of arrested growth in osteohistological thin sections and accordingly reflect chronological age. None of the specimens considered here showed signs of remodelling of the zygantrum, suggesting that a complete, unaltered age record is preserved. We tested potential influences on AGCs with a single experimental organism, a male Bogertophis subocularis, that was raised at a controlled temperature and with constant access to mice and water. The conditions in which this individual was maintained, including that it had yet to live through a full reproductive cycle, enabled us to determine that its AGCs reflect only the annual solar cycle, and neither temperature, nor resource availability, nor energy diversion to gametogenesis could explain that it still exhibited lines of arrested growth. Moreover, growth lines in this specimen are deposited toward the end of the growth season in the fall, and not in the winter, during which this individual continued to feed and grow, even though this mid-latitude species would normally be hibernating and not growing. This suggests that growth lines are not caused by hibernation, but reflect the onset of a physiological cycle preparing Bogertophis subocularis for winter rest. That being said, hibernation and reproductive cycle could still influence the amount of time represented by an individual growth line. Growth-line number and AGC spacing-pattern, plus centrum length, are used to estimate MNI of the Early Eocene fossil snake Boavus occidentalis collected from the Willwood Formation over two field seasons during the late 19th century. We identified eight or nine individuals among specimens previously parcelled among two specimen lots collected during those expeditions. creator: Holger Petermann creator: Jacques A. Gauthier uri: https://doi.org/10.7717/peerj.4819 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Petermann and Gauthier title: Feeding behavior and trophic interaction of three shark species in the Galapagos Marine Reserve link: https://peerj.com/articles/4818 last-modified: 2018-05-25 description: There is great concern about the future of sharks in Ecuador because of the lack of biological knowledge of most species that inhabit the region. This paper analyzes the feeding behavior of the pelagic thresher shark (Alopias pelagicus), the blue shark (Prionace glauca) and the silky shark (Carcharhinus falciformis) through the use of stable isotopes of carbon and nitrogen (δ13C and δ15N), with the aim of determining the degree of interaction between these species in the Galapagos Marine Reserve. No interspecific differences were found in use of oceanic vs. inshore feeding areas (δ13C: Kruskal–Wallis test, p = 0.09). The position in the hierarchy of the food web where A. pelagicus feeds differed from that of the other species (δ15N: Kruskal–Wallis test, p = 0.01). There were no significant differences in δ13C and δ15N values between males and females of the three species (Student’s t-test, p > 0.05), which suggests that both sexes have a similar feeding behavior. A specialist strategy was observed in P. glauca (trophic niche breadth TNB = 0.69), while the other species were found to be generalist (A. pelagicus TNB = 1.50 and C. falciformis TNB = 1.09). The estimated trophic level (TL) varied between the three species. C. falciformis occupied the highest trophic level (TL = 4.4), making it a quaternary predator in the region. The results of this study coincide with the identified behavior in these predators in other areas of the tropical Pacific (Colombia and Mexico), and suggest a pelagic foraging strategy with differential consumption of prey between the three species. These ecological aspects can provide timely information when implementing in conservation measures for these shark species in the Tropical Pacific and Galapagos Marine Reserve. creator: Diego Páez-Rosas creator: Paul Insuasti-Zarate creator: Marjorie Riofrío-Lazo creator: Felipe Galván-Magaña uri: https://doi.org/10.7717/peerj.4818 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Páez-Rosas et al. title: The influence of temperature and photoperiod on the timing of brood onset in hibernating honey bee colonies link: https://peerj.com/articles/4801 last-modified: 2018-05-25 description: In order to save resources, honey bee (Apis mellifera) colonies in the temperate zones stop brood rearing during winter. Brood rearing is resumed in late winter to build up a sufficient worker force that allows to exploit floral resources in upcoming spring. The timing of brood onset in hibernating colonies is crucial and a premature brood onset could lead to an early depletion of energy reservoirs. However, the mechanisms underlying the timing of brood onset and potential risks of mistiming in the course of ongoing climate change are not well understood. To assess the relative importance of ambient temperature and photoperiod as potential regulating factors for brood rearing activity in hibernating colonies, we overwintered 24 honey bee colonies within environmental chambers. The colonies were assigned to two different temperature treatments and three different photoperiod treatments to disentangle the individual and interacting effects of temperature and photoperiod. Tracking in-hive temperature as indicator for brood rearing activity revealed that increasing ambient temperature triggered brood onset. Under cold conditions, photoperiod alone did not affect brood onset, but the light regime altered the impact of higher ambient temperature on brood rearing activity. Further the number of brood rearing colonies increased with elapsed time which suggests the involvement of an internal clock. We conclude that timing of brood onset in late winter is mainly driven by temperature but modulated by photoperiod. Climate warming might change the interplay of these factors and result in mismatches of brood phenology and environmental conditions. creator: Fabian Nürnberger creator: Stephan Härtel creator: Ingolf Steffan-Dewenter uri: https://doi.org/10.7717/peerj.4801 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Nürnberger et al. title: Reef fish communities are spooked by scuba surveys and may take hours to recover link: https://peerj.com/articles/4886 last-modified: 2018-05-24 description: Ecological monitoring programs typically aim to detect changes in the abundance of species of conservation concern or which reflect system status. Coral reef fish assemblages are functionally important for reef health and these are most commonly monitored using underwater visual surveys (UVS) by divers. In addition to estimating numbers, most programs also collect estimates of fish lengths to allow calculation of biomass, an important determinant of a fish’s functional impact. However, diver surveys may be biased because fishes may either avoid or are attracted to divers and the process of estimating fish length could result in fish counts that differ from those made without length estimations. Here we investigated whether (1) general diver disturbance and (2) the additional task of estimating fish lengths affected estimates of reef fish abundance and species richness during UVS, and for how long. Initial estimates of abundance and species richness were significantly higher than those made on the same section of reef after diver disturbance. However, there was no evidence that estimating fish lengths at the same time as abundance resulted in counts different from those made when estimating abundance alone. Similarly, there was little consistent bias among observers. Estimates of the time for fish taxa that avoided divers after initial contact to return to initial levels of abundance varied from three to 17 h, with one group of exploited fishes showing initial attraction to divers that declined over the study period. Our finding that many reef fishes may disperse for such long periods after initial contact with divers suggests that monitoring programs should take great care to minimise diver disturbance prior to surveys. creator: Michael J. Emslie creator: Alistair J. Cheal creator: M. Aaron MacNeil creator: Ian R. Miller creator: Hugh P.A. Sweatman uri: https://doi.org/10.7717/peerj.4886 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Emslie et al. title: Identification of stem rust resistance genes in wheat cultivars in China using molecular markers link: https://peerj.com/articles/4882 last-modified: 2018-05-24 description: Wheat stem rust caused by Puccinia graminis f. sp. tritici Eriks. & E. Henn. (Pgt), is a major disease that has been effectively controlled using resistance genes. The appearance and spread of Pgt races such as Ug99, TKTTF, and TTTTF, which are virulent to most stem rust-resistant genes currently deployed in wheat breeding programs, renewed the interest in breeding cultivars resistant to wheat stem rust. It is therefore important to investigate the levels of resistance or vulnerability of wheat cultivars to Pgt races. Resistance to Pgt races 21C3CTHQM, 34MKGQM, and 34C3RTGQM was evaluated in 136 Chinese wheat cultivars at the seedling stage. A total of 124 cultivars (91.2%) were resistant to the three races. Resistance genes Sr2, Sr24, Sr25, Sr26, Sr31, and Sr38 were analyzed using molecular markers closely linked to them, and 63 of the 136 wheat cultivars carried at least one of these genes: 21, 25, and 28 wheat cultivars likely carried Sr2, Sr31, and Sr38, respectively. Cultivars “Kehan 3” and “Jimai 22” likely carried Sr25. None of the cultivars carried Sr24 or Sr26. These cultivars with known stem rust resistance genes provide valuable genetic material for breeding resistant wheat cultivars. creator: Xiaofeng Xu creator: Depeng Yuan creator: Dandan Li creator: Yue Gao creator: Ziyuan Wang creator: Yang Liu creator: Siting Wang creator: Yuanhu Xuan creator: Hui Zhao creator: Tianya Li creator: Yuanhua Wu uri: https://doi.org/10.7717/peerj.4882 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Xu et al. title: Why is nonword reading so variable in adult skilled readers? link: https://peerj.com/articles/4879 last-modified: 2018-05-24 description: When the task is reading nonwords aloud, skilled adult readers are very variable in the responses they produce: a nonword can evoke as many as 24 different responses in a group of such readers. Why is nonword reading so variable? We analysed a large database of reading responses to nonwords, which documented that two factors contribute to this variability. The first factor is variability in graphemic parsing (the parsing of a letter string into its constituent graphemes): the same nonword can be graphemically parsed in different ways by different readers. The second factor is phoneme assignment: even when all subjects produce the same graphemic parsing of a nonword, they vary in what phonemes they assign to the resulting set of graphemes. We consider the implications of these results for the computational modelling of reading, for the assessment of impairments of nonword reading, and for the study of reading aloud in other alphabetically written languages and in nonalphabetic writing systems. creator: Max Coltheart creator: Anastasia Ulicheva uri: https://doi.org/10.7717/peerj.4879 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Coltheart and Ulicheva title: On the taxonomic status and distribution of African species of Otomops (Chiroptera: Molossidae) link: https://peerj.com/articles/4864 last-modified: 2018-05-24 description: BackgroundFree-tailed bats of the genus Otomops are poorly known, and most species are documented from a handful of widely scattered localities. Recently, two allopatric species of Otomops were recognized in continental Africa: Otomops martiensseni (Matschie, 1897) in southern, central and western Africa, and the new species O. harrisoniRalph et al., 2015 in the northeast and in Yemen.MethodsWe collected additional samples of Otomops in Kenya and Rwanda where the ranges of these taxa approach one another to clarify their geographic ranges and taxonomic status. Mitochondrial and nuclear intron sequences served to identify and delimit species; we also documented their echolocation call variation and ectoparasite complements.ResultsOtomops martiensseni, the southern African species, was documented in northern Kenya in Marsabit National Park. O. harrisoni, the northeastern African–Arabian species, was documented in southern Kenya and in a cave in Musanze District, Rwanda. Moreover, individuals of both species were found together at the Musanze cave, establishing them in precise spatial and temporal sympatry. Analyses of mitochondrial and nuclear loci identify no evidence of admixture between these forms, although available samples limit the power of this analysis. Echolocation call differences are also apparent among the three localities we analyzed. Three orders of insects and two families of mites are newly reported as ectoparasites of O. harrisoni.DiscussionOur results corroborate species rank for O. harrisoni and establish a zone of potential geographic overlap with O. martiensseni spanning at least 800 km of latitude. The new records establish the species in sympatry in northern Rwanda and add an additional species to the bat faunas of both Kenya and Rwanda. Future studies are needed to understand Otomops roosting requirements and movements, thereby explaining the paucity of known colonies and yielding better estimates of their conservation status. The discovery of mixed roosting associations in Rwanda invites further investigation. creator: Bruce D. Patterson creator: Paul W. Webala creator: Michael Bartonjo creator: Julius Nziza creator: Carl W. Dick creator: Terrence C. Demos uri: https://doi.org/10.7717/peerj.4864 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Patterson et al. title: Divergent and convergent evolution of housekeeping genes in human–pig lineage link: https://peerj.com/articles/4840 last-modified: 2018-05-24 description: Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes. creator: Kai Wei creator: Tingting Zhang creator: Lei Ma uri: https://doi.org/10.7717/peerj.4840 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wei et al. title: The variable monoaminergic outcomes of cleaner fish brains when facing different social and mutualistic contexts link: https://peerj.com/articles/4830 last-modified: 2018-05-24 description: The monoamines serotonin and dopamine are important neuromodulators present in the central nervous system, known to be active regulators of social behaviour in fish as in other vertebrates. Our aim was to investigate the region-specific brain monoaminergic differences arising when individual cleaners face a client (mutualistic context) compared to when they are introduced to another conspecific (conspecific context), and to understand the relevance of visual assessment compared to the impact of physical contact with any partner. We demonstrated that serotoninergic activity at the diencephalon responds mostly to the absence of physical contact with clients whereas cerebellar dopaminergic activity responds to actual cleaning engagement. We provide first insights on the brain’s monoaminergic (region-specific) response variations, involved in the expression of cleaner fishes’ mutualistic and conspecific behaviour. These results contribute to a better understanding of the monoaminergic activity in accordance to different socio-behavioural contexts. creator: Murilo S. de Abreu creator: João P.M. Messias creator: Per-Ove Thörnqvist creator: Svante Winberg creator: Marta C. Soares uri: https://doi.org/10.7717/peerj.4830 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 De Abreu et al. title: High correlation between skin color based on CIELAB color space, epidermal melanocyte ratio, and melanocyte melanin content link: https://peerj.com/articles/4815 last-modified: 2018-05-24 description: BackgroundTo treat skin color disorders, such as vitiligo or burns, melanocytes are transplanted for tissue regeneration. However, melanocyte distribution in the human body varies with age and location, making it difficult to select the optimal donor skin to achieve a desired color match. Determining the correlations with the desired skin color measurement based on CIELAB color, epidermal melanocyte numbers, and melanin content of individual melanocytes is critical for clinical application.MethodFifteen foreskin samples from Asian young adults were analyzed for skin color, melanocyte ratio (melanocyte proportion in the epidermis), and melanin concentration. Furthermore, an equation was developed based on CIELAB color with melanocyte ratio, melanin concentration, and the product of melanocyte ratio and melanin concentration. The equation was validated by seeding different ratios of keratinocytes and melanocytes in tissue-engineered skin substitutes, and the degree of fitness in expected skin color was confirmed.ResultsLinear regression analysis revealed a significant strong negative correlation (r =  − 0.847, R2 = 0.717) between CIELAB L* value and the product of the epidermal melanocyte ratio and cell-based melanin concentration. Furthermore, the results showed that an optimal skin color match was achieved by the formula.DiscussionWe found that L* value was correlated with the value obtained from multiplying the epidermal melanocyte ratio (R) and melanin content (M) and that this correlation was more significant than either L* vs M or L* vs R. This suggests that more accurate prediction of skin color can be achieved by considering both R and M. Therefore, precise skin color match in treating vitiligo or burn patients would be potentially achievable based on extensive collection of skin data from people of Asian descent. creator: Wen-Shyan Huang creator: Yi-Wen Wang creator: Kun-Che Hung creator: Pai-Shan Hsieh creator: Keng-Yen Fu creator: Lien-Guo Dai creator: Nien-Hsien Liou creator: Kuo-Hsing Ma creator: Jiang-Chuan Liu creator: Niann-Tzyy Dai uri: https://doi.org/10.7717/peerj.4815 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Huang et al. title: Water mites (Acari, Hydrachnidia) of riparian springs in a small lowland river valley: what are the key factors for species distribution? link: https://peerj.com/articles/4797 last-modified: 2018-05-24 description: This paper examines the impact of disturbance factors—flooding and intermittency—on the distribution of water mites in the riparian springs situated in the valley of a small lowland river, the Krąpiel. The landscape factors and physicochemical parameters of the water were analysed in order to gain an understanding of the pattern of water mite assemblages in the riparian springs. Three limnological types of springs were examined (helocrenes, limnocrenes and rheocrenes) along the whole course of the river and a total of 35 water mite species were found. Our study shows that flooding influences spring assemblages, causing a decrease in crenobiontic water mites in flooded springs. The impact of intermittency resulted in a high percentage of species typical of temporary water bodies. Surprisingly, the study revealed the positive impact of the anthropogenic transformation of the river valley: preventing the riparian springs from flooding enhances the diversity of crenobiontic species in non-flooded springs. In the conclusion, our study revealed that further conservation strategies for the protection of the riparian springs along large rivers would take into account ongoing climatic changes and possible the positive impact of the anthropogenic transformation of river valleys. creator: Andrzej Zawal creator: Robert Stryjecki creator: Edyta Buczyńska creator: Paweł Buczyński creator: Joanna Pakulnicka creator: Aleksandra Bańkowska creator: Tomasz Czernicki creator: Katarzyna Janusz creator: Agnieszka Szlauer-Łukaszewska creator: Vladimir Pešić uri: https://doi.org/10.7717/peerj.4797 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zawal et al. title: The role of gut microbiota in the regulation of standard metabolic rate in female Periplaneta americana link: https://peerj.com/articles/4717 last-modified: 2018-05-24 description: Insect gut microbiota contribute significantly to host nutritional ecology. Disrupting insect gut microbial assemblages impacts nutrient provisioning functions, and can potentially affect host standard metabolic rate (SMR), a measure of host energy balance. In this study, we evaluated the effect of disrupting gut microbial assemblages on the SMR of female Periplaneta americana cockroaches fed dog food (DF, high protein/carbohydrate (p/c) ratio), and cellulose-amended dog food (CADF, 30% dog food, 70% cellulose, low p/c ratio) diets, supplemented with none, low, or high antibiotic doses. Bacterial loads decreased significantly between diet types (P = 0.04) and across antibiotic doses (P = 0.04). There was a significant diet type x antibiotic dose interaction on SMR of females on both diets (P = 0.05) by the end of the seven-day experimental period. In CADF-fed females, SMR decreased linearly with decreasing bacterial load. However, SMR of DF-fed females on the low dose was significantly higher than those in the control and high dose groups. This is interpreted as a diet-dependent response by low dose DF-fed females to the loss of nutritional services provided by gut bacteria. Severe reductions in bacterial load at high doses reduced SMR of females on both diet types. This study provides insights into the potential role of gut bacteria as modulators of host energy expenditure under varying dietary conditions. creator: Paul A. Ayayee creator: Andrew Ondrejech creator: George Keeney creator: Agustí Muñoz-Garcia uri: https://doi.org/10.7717/peerj.4717 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ayayee et al. title: Planning protected areas network that are relevant today and under future climate change is possible: the case of Atlantic Forest endemic birds link: https://peerj.com/articles/4689 last-modified: 2018-05-24 description: BackgroundA key strategy in biodiversity conservation is the establishment of protected areas. In the future, however, the redistribution of species in response to ongoing climate change is likely to affect species’ representativeness in those areas. Here we quantify the effectiveness of planning protected areas network to represent 151 birds endemic to the Brazilian Atlantic Forest hotspot, under current and future climate change conditions for 2050.MethodsWe combined environmental niche modeling and systematic conservation planning using both a county and a regional level planning strategy. We recognized the conflict between biodiversity conservation and economic development, including socio-economic targets (as opposed to biological only) and using planning units that are meaningful for policy-makers.ResultsWe estimated an average contraction of 29,500 km2 in environmentally suitable areas for birds, representing 52% of currently suitable areas. Still, the most cost-effective solution represented almost all target species, requiring only ca. 10% of the Atlantic Forest counties to achieve that representativeness, independent of strategy. More than 50% of these counties were selected both in the current and future planned networks, representing >83% of the species.DiscussionOur results indicate that: (i) planning protected areas network currently can be useful to represent species under climate change; (ii) the overlapped planning units in the best solution for both current and future conditions can be considered as “no regret” areas; (iii) priority counties are spread throughout the biome, providing specific guidance wherever the possibility of creating protected area arises; and (iv) decisions can occur at different administrative spheres (Federal, State or County) as we found quite similar numerical solutions using either county or regional level strategies. creator: Mariana M. Vale creator: Thiago V. Souza creator: Maria Alice S. Alves creator: Renato Crouzeilles uri: https://doi.org/10.7717/peerj.4689 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Vale et al. title: Altitudinal patterns in breeding bird species richness and density in relation to climate, habitat heterogeneity, and migration influence in a temperate montane forest (South Korea) link: https://peerj.com/articles/4857 last-modified: 2018-05-23 description: Altitudinal patterns in the population ecology of mountain bird species are useful for predicting species occurrence and behavior. Numerous hypotheses about the complex interactions among environmental factors have been proposed; however, these still remain controversial. This study aimed to identify the altitudinal patterns in breeding bird species richness or density and to test the hypotheses that climate, habitat heterogeneity (horizontal and vertical), and heterospecific attraction in a temperate forest, South Korea. We conducted a field survey of 142 plots at altitudes between 200 and 1,400 m a.s.l in the breeding season. A total of 2,771 individuals from 53 breeding bird species were recorded. Altitudinal patterns of species richness and density showed a hump-shaped pattern, indicating that the highest richness and density could be observed at moderate altitudes. Models constructed with 13 combinations of six variables demonstrated that species richness was positively correlated with vertical and horizontal habitat heterogeneity. Density was positively correlated with vertical, but not horizontal habitat heterogeneity, and negatively correlated with migratory bird ratio. No significant relationships were found between spring temperature and species richness or density. Therefore, the observed patterns in species richness support the hypothesis that habitat heterogeneity, rather than climate, is the main driver of species richness. Also, neither habitat heterogeneity nor climate hypotheses fully explains the observed patterns in density. However, vertical habitat heterogeneity does likely help explain observed patterns in density. The heterospecific attraction hypothesis did not apply to the distribution of birds along the altitudinal gradient. Appropriate management of vertical habitat heterogeneity, such as vegetation cover, should be maintained for the conservation of bird diversity in this area. creator: Jin-Yong Kim creator: Sanghun Lee creator: Man-Seok Shin creator: Chang-Hoon Lee creator: Changwan Seo creator: Soo Hyung Eo uri: https://doi.org/10.7717/peerj.4857 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kim et al. title: Primate occurrence across a human-impacted landscape in Guinea-Bissau and neighbouring regions in West Africa: using a systematic literature review to highlight the next conservation steps link: https://peerj.com/articles/4847 last-modified: 2018-05-23 description: BackgroundWest African landscapes are largely characterised by complex agroforest mosaics. Although the West African forests are considered a nonhuman primate hotspot, knowledge on the distribution of many species is often lacking and out-of-date. Considering the fast-changing nature of the landscapes in this region, up-to-date information on primate occurrence is urgently needed, particularly of taxa such as colobines, which may be more sensitive to habitat modification than others. Understanding wildlife occurrence and mechanisms of persistence in these human-dominated landscapes is fundamental for developing effective conservation strategies.MethodsIn this paper, we aim to review current knowledge on the distribution of three threatened primates in Guinea-Bissau and neighbouring regions, highlighting research gaps and identifying priority research and conservation action. We conducted a systematic literature review of primate studies from 1976 to 2016 in Guinea-Bissau, southern Senegal and western Guinea (Boké Region). We mapped historical observation records of chimpanzee (Pan troglodytes verus), Temminck’s red colobus (Pilicolobus badius temminckii) and king colobus (Colobus polykomos), including our preliminary survey data from Dulombi, a newly established National Park (NP) in Guinea-Bissau.ResultsWe found 151 documents, including 87 journal articles, that contained field data on primates in this region. In Guinea-Bissau, nearly all studies focussed south of the Corubal River, including mainly Cantanhez, Cufada, and Boé NP’s. In Senegal, most of the data came from Fongoli and Niokolo-Koba NP. In Boké (Guinea) studies are few, with the most recent data coming from Sangarédi. In Dulombi NP we recorded eight primate species, including chimpanzees, red colobus and king colobus. Across the selected region, chimpanzees, red colobus and king colobus were reported in eleven, twelve and seven protected areas, respectively.DiscussionOur study demonstrates large geographical research gaps particularly for the two colobines. For the first time after more than two decades, we confirm the presence of red colobus and king colobus north of the Corubal River in Guinea-Bissau. The little information available from large parts of the red colobus range raises questions regarding levels of population fragmentation in this species, particularly in Casamance and across northern Guinea-Bissau. There are still no records demonstrating the occurrence of king colobus in Senegal, and the presence of a viable population in north-eastern Guinea-Bissau remains uncertain. While the occurrence of chimpanzees in Guinea-Bissau and Senegal is well documented, data from Boké (Guinea) are sparse and out-of-date. Our approach—the mapping of data gathered from a systematic literature review—allows us to provide recommendations for selecting future geographical survey locations and planning further research and conservation strategies in this region. creator: Elena Bersacola creator: Joana Bessa creator: Amélia Frazão-Moreira creator: Dora Biro creator: Cláudia Sousa creator: Kimberley Jane Hockings uri: https://doi.org/10.7717/peerj.4847 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bersacola et al. title: Impact of crop residue management on crop production and soil chemistry after seven years of crop rotation in temperate climate, loamy soils link: https://peerj.com/articles/4836 last-modified: 2018-05-23 description: Society is increasingly demanding a more sustainable management of agro-ecosystems in a context of climate change and an ever growing global population. The fate of crop residues is one of the important management aspects under debate, since it represents an unneglectable quantity of organic matter which can be kept in or removed from the agro-ecosystem. The topic of residue management is not new, but the need for global conclusion on the impact of crop residue management on the agro-ecosystem linked to local pedo-climatic conditions has become apparent with an increasing amount of studies showing a diversity of conclusions. This study specifically focusses on temperate climate and loamy soil using a seven-year data set. Between 2008 and 2016, we compared four contrasting residue management strategies differing in the amount of crop residues returned to the soil (incorporation vs. exportation of residues) and in the type of tillage (reduced tillage (10 cm depth) vs. conventional tillage (ploughing at 25 cm depth)) in a field experiment. We assessed the impact of the crop residue management on crop production (three crops—winter wheat, faba bean and maize—cultivated over six cropping seasons), soil organic carbon content, nitrate (${\mathrm{NO}}_{3}^{-}$NO3−), phosphorus (P) and potassium (K) soil content and uptake by the crops. The main differences came primarily from the tillage practice and less from the restitution or removal of residues. All years and crops combined, conventional tillage resulted in a yield advantage of 3.4% as compared to reduced tillage, which can be partly explained by a lower germination rate observed under reduced tillage, especially during drier years. On average, only small differences were observed for total organic carbon (TOC) content of the soil, but reduced tillage resulted in a very clear stratification of TOC and also of P and K content as compared to conventional tillage. We observed no effect of residue management on the ${\mathrm{NO}}_{3}^{-}$NO3− content, since the effect of fertilization dominated the effect of residue management. To confirm the results and enhance early tendencies, we believe that the experiment should be followed up in the future to observe whether more consistent changes in the whole agro-ecosystem functioning are present on the long term when managing residues with contrasted strategies. creator: Marie-Pierre Hiel creator: Sophie Barbieux creator: Jérôme Pierreux creator: Claire Olivier creator: Guillaume Lobet creator: Christian Roisin creator: Sarah Garré creator: Gilles Colinet creator: Bernard Bodson creator: Benjamin Dumont uri: https://doi.org/10.7717/peerj.4836 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hiel et al. title: Predicting the potential distributions of the invasive cycad scale Aulacaspis yasumatsui (Hemiptera: Diaspididae) under different climate change scenarios and the implications for management link: https://peerj.com/articles/4832 last-modified: 2018-05-23 description: Cycads are an ancient group of gymnosperms that are popular as landscaping plants, though nearly all of them are threatened or endangered in the wild. The cycad aulacaspis scale (CAS), Aulacaspis yasumatsui Takagi (Hemiptera: Diaspididae), has become one of the most serious pests of cycads in recent years; however, the potential distribution range and the management approach for this pest are unclear. A potential risk map of cycad aulacaspis scale was created based on occurrence data under different climatic conditions and topology factors in this study. Furthermore, the future potential distributions of CAS were projected for the periods 2050s and 2070s under three different climate change scenarios (GFDL-CM3, HADGEM2-AO and MIROC5) described in the Special Report on Emissions Scenarios of the IPCC (Intergovernmental Panel on Climate Change). The model suggested high environmental suitability for the continents of Asia and North America, where the species has already been recorded. The potential distribution expansions or reductions were also predicted under different climate change conditions. Temperature of Driest Quarter (Bio9) was the most important factor, explaining 48.1% of the distribution of the species. The results also suggested that highly suitable habitat for CAS would exist in the study area if the mean temperature of 15–20 °C in the driest quarter and a mean temperature of 25–28 °C the wettest quarter. This research provides a theoretical reference framework for developing policy to manage and control this invasive pest. creator: Jiufeng Wei creator: Qing Zhao creator: Wanqing Zhao creator: Hufang Zhang uri: https://doi.org/10.7717/peerj.4832 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wei et al. title: Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution link: https://peerj.com/articles/4828 last-modified: 2018-05-23 description: Oxygyne Schltr. (Thismiaceae) is a rare and little-known genus of achlorophyllous mycoheterotrophic perennial herbs with one of the most remarkable distributions of all angiosperm plant genera globally, being disjunct between Japan and West–Central Africa. Each species is known only from a single location, and in most cases from a single specimen. This monographic study names, describes and maps two new species, Oxygyne duncanii Cheek from cloud forest in SW Region Cameroon and O. frankei Cheek from gallery forest in the Central African Republic, representing the first new Oxygyne species described from Africa in 112 years, and raising the number of described Oxygyne species from four to six. Oxygyne duncanii is remarkable for sharing more morphological characters with two of the three Japanese species (O. hyodoi C.Abe & Akasawa, O. shinzatoi (H. Ohashi) Tsukaya) than with the geographically much closer type species of the genus, O. triandra from Mt Cameroon. Based mainly on herbarium specimens and field observations made in Cameroon and Japan during a series of botanical surveys, we provide descriptions, synonymy, mapping and extinction risk assessments for each species of Oxygyne, together with keys to the genera of Thismiaceae and the species of Oxygyne. The subterranean structures of African Oxygyne are described for the first time, and found to be consistent with those of the Japanese species. We review and reject an earlier proposal that the Japanese species should be segregated from the African species as a separate genus, Saionia Hatus. The only character that separates the two disjunct species groups is now flower colour: blue or partly-blue in the Japanese species compared with orange-brown in the African species. Studies of the pollination biology and mycorrhizal partners of Oxygyne are still lacking. Two of the six species, O. triandra Schltr. and O. hyodoi, appear to be extinct, and the remaining four are assessed as Critically Endangered using the IUCN 2012 criteria. To avoid further extinction, an urgent requirement is for conservation management of the surviving species in the wild. Since few achlorophyllous mycoheterotrophs have been successfully cultivated from seed to maturity, ex situ conservation will not be viable for these species and protection in the wild is the only viable option. While natural habitat survives, further botanical surveys could yet reveal additional new species between Central Africa and Japan. creator: Martin Cheek creator: Hirokazu Tsukaya creator: Paula J. Rudall creator: Kenji Suetsugu uri: https://doi.org/10.7717/peerj.4828 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cheek et al. title: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota link: https://peerj.com/articles/4827 last-modified: 2018-05-23 description: Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research. creator: Katti R. Horng creator: Holly H. Ganz creator: Jonathan A. Eisen creator: Stanley L. Marks uri: https://doi.org/10.7717/peerj.4827 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Horng et al. title: Evidence-based economic analysis demonstrates that ecosystem service benefits of water hyacinth management greatly exceed research and control costs link: https://peerj.com/articles/4824 last-modified: 2018-05-23 description: Invasive species management can be a victim of its own success when decades of effective control cause memories of past harm to fade and raise questions of whether programs should continue. Economic analysis can be used to assess the efficiency of investing in invasive species control by comparing ecosystem service benefits to program costs, but only if appropriate data exist. We used a case study of water hyacinth (Eichhornia crassipes (Mart.) Solms), a nuisance floating aquatic plant, in Louisiana to demonstrate how comprehensive record-keeping supports economic analysis. Using long-term data sets, we developed empirical and spatio-temporal simulation models of intermediate complexity to project invasive species growth for control and no-control scenarios. For Louisiana, we estimated that peak plant cover would be 76% higher without the substantial growth rate suppression (84% reduction) that appeared due primarily to biological control agents. Our economic analysis revealed that combined biological and herbicide control programs, monitored over an unusually long time period (1975–2013), generated a benefit-cost ratio of about 34:1 derived from the relatively modest costs of $124 million ($2013) compared to the $4.2 billion ($2013) in benefits to anglers, waterfowl hunters, boating-dependent businesses, and water treatment facilities over the 38-year analysis period. This work adds to the literature by: (1) providing evidence of the effectiveness of water hyacinth biological control; (2) demonstrating use of parsimonious spatio-temporal models to estimate benefits of invasive species control; and (3) incorporating activity substitution into economic benefit transfer to avoid overstating benefits. Our study suggests that robust and cost-effective economic analysis is enabled by good record keeping and generalizable models that can demonstrate management effectiveness and promote social efficiency of invasive species control. creator: Lisa A. Wainger creator: Nathan E. Harms creator: Cedric Magen creator: Dong Liang creator: Genevieve M. Nesslage creator: Anna M. McMurray creator: Al F. Cofrancesco uri: https://doi.org/10.7717/peerj.4824 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Immunogenicity evaluation of MS2 phage-mediated chimeric nanoparticle displaying an immunodominant B cell epitope of foot-and-mouth disease virus link: https://peerj.com/articles/4823 last-modified: 2018-05-23 description: Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals that has caused tremendous economic losses worldwide. In this study, we designed a chimeric nanoparticles (CNPs) vaccine that displays the predominant epitope of the serotype O foot-and-mouth disease virus (FMDV) VP1 131-160 on the surface of MS2 phage. The recombinant protein was expressed in Escherichia Coli and can self-assemble into CNPs with diameter at 25–30 nm in vitro. A tandem repeat peptide epitopes (TRE) was prepared as control. Mice were immunized with CNPs, TRE and commercialized synthetic peptide vaccines (PepVac), respectively. The ELISA results showed that CNPs stimulated a little higher specific antibody levels to PepVac, but was significantly higher than the TRE groups. Moreover, the results from specific IFN-γ responses and lymphocyte proliferation test indicated that CNP immunized mice exhibited significantly enhanced cellular immune response compared to TRE. These results suggested that the CNPs constructed in current study could be a potential alternative vaccine in future FMDV control. creator: Guoqiang Wang creator: Yunchao Liu creator: Hua Feng creator: Yumei Chen creator: Suzhen Yang creator: Qiang Wei creator: Juan Wang creator: Dongmin Liu creator: Gaiping Zhang uri: https://doi.org/10.7717/peerj.4823 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Sample entropy analysis for the estimating depth of anaesthesia through human EEG signal at different levels of unconsciousness during surgeries link: https://peerj.com/articles/4817 last-modified: 2018-05-23 description: Estimating the depth of anaesthesia (DoA) in operations has always been a challenging issue due to the underlying complexity of the brain mechanisms. Electroencephalogram (EEG) signals are undoubtedly the most widely used signals for measuring DoA. In this paper, a novel EEG-based index is proposed to evaluate DoA for 24 patients receiving general anaesthesia with different levels of unconsciousness. Sample Entropy (SampEn) algorithm was utilised in order to acquire the chaotic features of the signals. After calculating the SampEn from the EEG signals, Random Forest was utilised for developing learning regression models with Bispectral index (BIS) as the target. Correlation coefficient, mean absolute error, and area under the curve (AUC) were used to verify the perioperative performance of the proposed method. Validation comparisons with typical nonstationary signal analysis methods (i.e., recurrence analysis and permutation entropy) and regression methods (i.e., neural network and support vector machine) were conducted. To further verify the accuracy and validity of the proposed methodology, the data is divided into four unconsciousness-level groups on the basis of BIS levels. Subsequently, analysis of variance (ANOVA) was applied to the corresponding index (i.e., regression output). Results indicate that the correlation coefficient improved to 0.72 ± 0.09 after filtering and to 0.90 ± 0.05 after regression from the initial values of 0.51 ± 0.17. Similarly, the final mean absolute error dramatically declined to 5.22 ± 2.12. In addition, the ultimate AUC increased to 0.98 ± 0.02, and the ANOVA analysis indicates that each of the four groups of different anaesthetic levels demonstrated significant difference from the nearest levels. Furthermore, the Random Forest output was extensively linear in relation to BIS, thus with better DoA prediction accuracy. In conclusion, the proposed method provides a concrete basis for monitoring patients’ anaesthetic level during surgeries. creator: Quan Liu creator: Li Ma creator: Shou-Zen Fan creator: Maysam F. Abbod creator: Jiann-Shing Shieh uri: https://doi.org/10.7717/peerj.4817 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu et al. title: An improved primer set and amplification protocol with increased specificity and sensitivity targeting the Symbiodinium ITS2 region link: https://peerj.com/articles/4816 last-modified: 2018-05-23 description: The Internal Transcribed Spacer 2 (ITS2) rRNA gene is a commonly targeted genetic marker to assess diversity of Symbiodinium, a dinoflagellate genus of algal endosymbionts that is pervasively associated with marine invertebrates, and notably reef-building corals. Here we tested three commonly used ITS2 primer pairs (SYM_VAR_5.8S2/SYM_VAR_REV, ITSintfor2/ITSReverse, and ITS-DINO/ITS2Rev2) with regard to amplification specificity and sensitivity towards Symbiodinium, as well as sub-genera taxonomic bias. We tested these primers over a range of sample types including three coral species, coral surrounding water, reef surface water, and open ocean water to assess their suitability for use in large-scale next generation sequencing projects and to develop a standardised PCR protocol. We found the SYM_VAR_5.8S2/SYM_VAR_REV primers to perform superior to the other tested ITS2 primers. We therefore used this primer pair to develop a standardised PCR protocol. To do this, we tested the effect of PCR-to-PCR variation, annealing temperature, cycle number, and different polymerase systems on the PCR efficacy. The Symbiodinium ITS2 PCR protocol developed here delivers improved specificity and sensitivity towards Symbiodinium with apparent minimal sub-genera taxonomic bias across all sample types. In particular, the protocol’s ability to amplify Symbiodinium from a range of environmental sources will facilitate the study of Symbiodinium populations across biomes. creator: Benjamin C.C. Hume creator: Maren Ziegler creator: Julie Poulain creator: Xavier Pochon creator: Sarah Romac creator: Emilie Boissin creator: Colomban de Vargas creator: Serge Planes creator: Patrick Wincker creator: Christian R. Voolstra uri: https://doi.org/10.7717/peerj.4816 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hume et al. title: Endozoochory by mallard in New Zealand: what seeds are dispersed and how far? link: https://peerj.com/articles/4811 last-modified: 2018-05-23 description: In Europe and North America waterfowl are major dispersers of aquatic and terrestrial plants, but in New Zealand their role has yet to be investigated. Mallards were introduced to New Zealand in the late 1800s, and today they are the most abundant and widespread waterfowl in the country. To assess seed dispersal, we radiomarked 284 female mallards from two study sites during the pre-breeding (June–August) and breeding (August–December) periods in 2014–2015, and examined movements that occurred within 24, 48 or 72 h when seed dispersal by endozoochory is considered likely. During June and July 2015, we collected 29 faecal samples from individual female mallards during radiomarking and 24 samples from mallard flocks. We recovered 69 intact seeds from the faecal samples and identified 12 plant taxa. Of the plant seeds identified and dispersed by mallards in this study, 40% were members of the Asteraceae family, nine plant species were alien to New Zealand, and the indigenous-status of three unidentified taxa could not be determined. Two taxa (and 9% of seeds) were germinated following gut passage: an unidentified Asteraceae and Solanum nigrum. During the pre-breeding and breeding periods, movement of females within 24 h averaged 394 m (SD = 706 m) and 222 m (SD = 605 m) respectively, with maximum distances of 3,970 m and 8,028 m. Maxima extended to 19,230 m within 48 h. Most plant species recorded are generally assumed to be self-dispersed or dispersed by water; mechanisms that provide a much lower maximum dispersal distance than mallards. The ability of mallards to disperse viable seeds up to 19 km within 48 h suggests they have an important and previously overlooked role as vectors for a variety of wetland or grassland plant species in New Zealand. creator: Riley D. Bartel creator: Jennifer L. Sheppard creator: Ádám Lovas-Kiss creator: Andy J. Green uri: https://doi.org/10.7717/peerj.4811 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bartel et al. title: Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining link: https://peerj.com/articles/4806 last-modified: 2018-05-23 description: The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from ‘reading the literature’. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm (filter) was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already ‘known’, and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and filter to (i) discover novel candidate associations between different genes or proteins in the network, and (ii) rapidly evaluate the potential role of any one particular gene or protein. The full network is provided as an open-source resource. creator: Sanna M. Kreula creator: Suwisa Kaewphan creator: Filip Ginter creator: Patrik R. Jones uri: https://doi.org/10.7717/peerj.4806 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kreula et al. title: A brief introduction to mixed effects modelling and multi-model inference in ecology link: https://peerj.com/articles/4794 last-modified: 2018-05-23 description: The use of linear mixed effects models (LMMs) is increasingly common in the analysis of biological data. Whilst LMMs offer a flexible approach to modelling a broad range of data types, ecological data are often complex and require complex model structures, and the fitting and interpretation of such models is not always straightforward. The ability to achieve robust biological inference requires that practitioners know how and when to apply these tools. Here, we provide a general overview of current methods for the application of LMMs to biological data, and highlight the typical pitfalls that can be encountered in the statistical modelling process. We tackle several issues regarding methods of model selection, with particular reference to the use of information theory and multi-model inference in ecology. We offer practical solutions and direct the reader to key references that provide further technical detail for those seeking a deeper understanding. This overview should serve as a widely accessible code of best practice for applying LMMs to complex biological problems and model structures, and in doing so improve the robustness of conclusions drawn from studies investigating ecological and evolutionary questions. creator: Xavier A. Harrison creator: Lynda Donaldson creator: Maria Eugenia Correa-Cano creator: Julian Evans creator: David N. Fisher creator: Cecily E.D. Goodwin creator: Beth S. Robinson creator: David J. Hodgson creator: Richard Inger uri: https://doi.org/10.7717/peerj.4794 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Harrison et al. title: Evaluation of the glycemic effect of Ceratonia siliqua pods (Carob) on a streptozotocin-nicotinamide induced diabetic rat model link: https://peerj.com/articles/4788 last-modified: 2018-05-23 description: BackgroundCeratonia siliqua pods (carob) have been nominated to control the high blood glucose of diabetics. In Yemen, however, its antihyperglycemic activity has not been yet assessed. Thus, this study evaluated the in vitro inhibitory effect of the methanolic extract of carob pods against α-amylase and α-glucosidase and the in vivo glycemic effect of such extract in streptozotocin-nicotinamide induced diabetic rats.Methods2,2-diphenyl-1-picrylhydrazyl (DPPH) and Ferric reducing antioxidant power assay (FRAP) were applied to evaluate the antioxidant activity of carob. In vitro cytotoxicity of carob was conducted on human hepatocytes (WRL68) and rat pancreatic β-cells (RIN-5F). Acute oral toxicity of carob was conducted on a total of 18 male and 18 female Sprague-Dawley (SD) rats, which were subdivided into three groups (n = 6), namely: high and low dose carob-treated (CS5000 and CS2000, respectively) as well as the normal control (NC) receiving a single oral dose of 5,000 mg kg−1 carob, 2,000 mg kg−1 carob and 5 mL kg−1 distilled water for 14 days, respectively. Alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, total bilirubin, creatinine and urea were assessed. Livers and kidneys were harvested for histopathology. In vitro inhibitory effect against α-amylase and α-glucosidase was evaluated. In vivo glycemic activity was conducted on 24 male SD rats which were previously intraperitoneally injected with 55 mg kg−1 streptozotocin (STZ) followed by 210 mg kg−1nicotinamide to induce type 2 diabetes mellitus. An extra non-injected group (n = 6) was added as a normal control (NC). The injected-rats were divided into four groups (n = 6), namely: diabetic control (D0), 5 mg kg−1glibenclamide-treated diabetic (GD), 500 mg kg−1 carob-treated diabetic (CS500) and 1,000 mg kg−1 carob-treated diabetic (CS1000). All groups received a single oral daily dose of their treatment for 4 weeks. Body weight, fasting blood glucose (FBG), oral glucose tolerance test, biochemistry, insulin and hemostatic model assessment were assessed. Pancreases was harvested for histopathology.ResultsCarob demonstrated a FRAP value of 3191.67 ± 54.34 µmoL Fe++ and IC50 of DPPH of 11.23 ± 0.47 µg mL−1. In vitro, carob was non-toxic on hepatocytes and pancreatic β-cells. In acute oral toxicity, liver and kidney functions and their histological sections showed no abnormalities. Carob exerted an in vitro inhibitory effect against α-amylase and α-glucosidase with IC50 of 92.99 ± 0.22 and 97.13 ± 4.11 µg mL−1, respectively. In diabetic induced rats, FBG of CS1000 was significantly less than diabetic control. Histological pancreatic sections of CS1000 showed less destruction of β-cells than CS500 and diabetic control.ConclusionCarob pod did not cause acute systemic toxicity and showed in vitro antioxidant effects. On the other hand, inhibiting α-amylase and α-glucosidase was evident. Interestingly, a high dose of carob exhibits an in vivo antihyperglycemic activity and warrants further in-depth study to identify the potential carob extract composition. creator: Mousa A. Qasem creator: Mohamed Ibrahim Noordin creator: Aditya Arya creator: Abdulsamad Alsalahi creator: Soher Nagi Jayash uri: https://doi.org/10.7717/peerj.4788 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Qasem et al. title: The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species link: https://peerj.com/articles/4723 last-modified: 2018-05-23 description: Colobanthus apetalus is a member of the genus Colobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genus Colobanthus consists of 25 species, including Colobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome of C. apetalus. The complete cp genome of C. apetalus has the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison of C. apetalus and C. quitensis cp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae and C. apetalus, and it revealed that C. apetalus and C. quitensis form a clade that is closely related to Silene species and Agrostemma githago. Moreover, the genus Silene appeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae. creator: Piotr Androsiuk creator: Jan Paweł Jastrzębski creator: Łukasz Paukszto creator: Adam Okorski creator: Agnieszka Pszczółkowska creator: Katarzyna Joanna Chwedorzewska creator: Justyna Koc creator: Ryszard Górecki creator: Irena Giełwanowska uri: https://doi.org/10.7717/peerj.4723 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Androsiuk et al. title: Giant worms chez moi! Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipalium spp., Diversibipalium spp.) in metropolitan France and overseas French territories link: https://peerj.com/articles/4672 last-modified: 2018-05-22 description: BackgroundSpecies of the genera Bipalium and Diversibipalium, or bipaliines, are giants among land planarians (family Geoplanidae), reaching length of 1 m; they are also easily distinguished from other land flatworms by the characteristic hammer shape of their head. Bipaliines, which have their origin in warm parts of Asia, are invasive species, now widespread worldwide. However, the scientific literature is very scarce about the widespread repartition of these species, and their invasion in European countries has not been studied.MethodsIn this paper, on the basis of a four year survey based on citizen science, which yielded observations from 1999 to 2017 and a total of 111 records, we provide information about the five species present in Metropolitan France and French overseas territories. We also investigated the molecular variability of cytochrome-oxidase 1 (COI) sequences of specimens.ResultsThree species are reported from Metropolitan France: Bipalium kewense, Diversibipalium multilineatum, and an unnamed Diversibipalium ‘black’ species. We also report the presence of B. kewense from overseas territories, such as French Polynesia (Oceania), French Guiana (South America), the Caribbean French islands of Martinique, Guadeloupe, Saint Martin and Saint Barthélemy, and Montserrat (Central America), and La Réunion island (off South-East Africa). For B. vagum, observations include French Guiana, Guadeloupe, Martinique, Saint Barthélemy, Saint Martin, Montserrat, La Réunion, and Florida (USA). A probable new species, Diversibipalium sp. ‘blue,’ is reported from Mayotte Island (off South–East Africa). B. kewense, B. vagum and D. multilineatum each showed 0% variability in their COI sequences, whatever their origin, suggesting that the specimens are clonal, and that sexual reproduction is probably absent. COI barcoding was efficient in identifying species, with differences over 10% between species; this suggests that barcoding can be used in the future for identifying these invasive species. In Metropolitan south–west France, a small area located in the Department of Pyrénées-Atlantiques was found to be a hot-spot of bipaliine biodiversity and abundance for more than 20 years, probably because of the local mild weather.DiscussionThe present findings strongly suggest that the species present in Metropolitan France and overseas territories should be considered invasive alien species. Our numerous records in the open in Metropolitan France raise questions: as scientists, we were amazed that these long and brightly coloured worms could escape the attention of scientists and authorities in a European developed country for such a long time; improved awareness about land planarians is certainly necessary. creator: Jean-Lou Justine creator: Leigh Winsor creator: Delphine Gey creator: Pierre Gros creator: Jessica Thévenot uri: https://doi.org/10.7717/peerj.4672 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Justine et al. title: Molecular response of canola to salt stress: insights on tolerance mechanisms link: https://peerj.com/articles/4822 last-modified: 2018-05-22 description: Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies. creator: Reza Shokri-Gharelo creator: Pouya Motie Noparvar uri: https://doi.org/10.7717/peerj.4822 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shokri-Gharelo and Noparvar title: Identifying potentially marker symptoms of attention-deficit/hyperactivity disorder link: https://peerj.com/articles/4820 last-modified: 2018-05-22 description: BackgroundFor the diagnosis of attention-deficit/hyperactivity disorder (ADHD), the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) proposes that adherence to six symptoms in either group (inattention and hyperactivity/impulsivity) will lead to the diagnosis of one of three presentations of the disorder. Underlying this diagnostic algorithm is the assumption that the 18 symptoms have equal relevance for the diagnosis of ADHD, all are equally severe, and all have the same power to detect the presence of the disorder in all its degrees of severity, without considering the possibility of using marker symptoms. However, several studies have suggested that ADHD symptoms differ in both their power to discriminate the presence of the disorder and the degree of severity they represent. The aim of the present study was to replicate the results of previous research by evaluating the discriminative capacity and relative severity of ADHD symptoms, as well as to extend the investigation of this topic to Spanish-speaking Latin American samples.MethodsThe properties of ADHD symptoms rated by the parents of 474 Chilean children were analyzed. Symptom parameters were estimated using the graded response model.ResultsThe results suggest that symptoms of ADHD differ substantially in both the accuracy with which they reflect the presence of the disorder, and their relative severity. Symptoms “easily distracted by extraneous stimuli” and “have difficulty sustaining attention in tasks” (inattention) and “is on the go, acting as if driven by motor” (hyperactivity/impulsivity) were the most informative, and those with relatively lower severity thresholds.DiscussionThe fact that symptoms differ substantially in the probability of being observed conditionally to the trait level suggests the need to refine the diagnostic process by weighting the severity of the symptom, and even to assess the possibility of defining ADHD marker symptoms, as has been done in other disorders. creator: Víctor B. Arias creator: Igor Esnaola creator: Jairo Rodríguez-Medina uri: https://doi.org/10.7717/peerj.4820 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Arias et al. title: Effect of Reactive Black 5 azo dye on soil processes related to C and N cycling link: https://peerj.com/articles/4802 last-modified: 2018-05-22 description: Azo dyes are one of the largest classes of synthetic dyes being used in textile industries. It has been reported that 15–50% of these dyes find their way into wastewater that is often used for irrigation purpose in developing countries. The effect of azo dyes contamination on soil nitrogen (N) has been studied previously. However, how does the azo dye contamination affect soil carbon (C) cycling is unknown. Therefore, we assessed the effect of azo dye contamination (Reactive Black 5, 30 mg kg−1 dry soil), bacteria that decolorize this dye and dye + bacteria in the presence or absence of maize leaf litter on soil respiration, soil inorganic N and microbial biomass. We found that dye contamination did not induce any change in soil respiration, soil microbial biomass or soil inorganic N availability (P > 0.05). Litter evidently increased soil respiration. Our study concludes that the Reactive Black 5 azo dye (applied in low amount, i.e., 30 mg kg−1 dry soil) contamination did not modify organic matter decomposition, N mineralization and microbial biomass in a silty loam soil. creator: Khadeeja Rehman creator: Tanvir Shahzad creator: Amna Sahar creator: Sabir Hussain creator: Faisal Mahmood creator: Muhammad H. Siddique creator: Muhammad A. Siddique creator: Muhammad I. Rashid uri: https://doi.org/10.7717/peerj.4802 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rehman et al. title: Influence of aprepitant on the pharmacodynamics and pharmacokinetics of gliclazide in rats and rabbits link: https://peerj.com/articles/4798 last-modified: 2018-05-22 description: BackgroundConcomitant drug administration is a general phenomenon in patients with chronic diseases such as diabetes mellitus. Among the currently available oral antidiabetic drugs, gliclazide is a commonly prescribed drug considering its multiple benefits in diabetic patients. Aprepitant is a commonly prescribed antiemetic drug which is mainly metabolized by CYP3A4, reported to have modest inductive and inhibitory effects on CYP2C9 and CYP3A4, respectively. Since gliclazide is metabolized by CYP2C9 (major) and CYP3A4 (minor), it is very difficult to predict the influence of aprepitant and its metabolic interaction with gliclazide. Considering the complexity associated with the combination of aprepitant and gliclazide, this study was designed to evaluate the influence of aprepitant on the pharmacodynamics (PD) and pharmacokinetics (PK) of gliclazide in animal models.MethodsThe PD interaction studies were conducted in both rodent (normal and alloxan-induced diabetic rats) and non-rodent (rabbits) animal models (n = 6) while the PK interaction study was conducted in normal rabbits (n = 6). An extrapolated human therapeutic oral dose of gliclazide, aprepitant and their combination were administered to rats and rabbits with 7 days washout between each treatment. For the multiple-dose interaction study, the same groups were administered with an interacting drug (aprepitant) for 7 days and then the combination of aprepitant and gliclazide on the 8th day. From the collected animal blood samples, blood glucose (by Glucose-Oxidase/Peroxidase method), insulin (by ELISA method) and gliclazide concentration levels (by HPLC method) were determined. Non-compartmental PK analysis was conducted by Phoenix WinNonlin software to determine the PK parameters of gliclazide. Statistical analysis was performed by student’s paired t-test.ResultsThe pharmacodynamic activity (blood glucose reduction and insulin levels) of gliclazide was significantly (p < 0.05) influenced by aprepitant in normal and diabetic condition without any convulsions in animals. There was a significant (p < 0.05) increase in concentration levels and Area Under the Curve of gliclazide while significant (p < 0.05) decrease in clearance levels of gliclazide in rabbits. The PK interaction with gliclazide is relatively more with the multiple dose treatment of aprepitant over single dose treatment.ConclusionIn combination, aprepitant significantly influenced the pharmacodynamic activity of gliclazide in animal models. Considering this, care should be taken when this combination is prescribed for the clinical benefit in diabetic patients. creator: Raghunandan Reddy Kura creator: Eswar Kumar Kilari creator: Mastan Shaik uri: https://doi.org/10.7717/peerj.4798 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Kura et al. title: Large mammal burrows in late Miocene calcic paleosols from central Argentina: paleoenvironment, taphonomy and producers link: https://peerj.com/articles/4787 last-modified: 2018-05-22 description: Large cylindrical sediment-filled structures interpreted as mammal burrows occur within the loess-paleosol sequence of the late Miocene Cerro Azul Formation of central Argentina. A total of 115 burrow fills from three localities were measured. They are typically shallowly dipping, subcylindrical, unbranched structures with rounded ends and lacking enlargements. The horizontal diameter of the burrows range between 0.15 and 1.50 m, with most of the burrows in the interval of 0.39 to 0.98 m. Geometric morphometric analysis of transverse cross-sections support their distinct subcircular and elliptical (horizontally flattened) shapes. Burrow fills are typically laminated in the lower part and massive in the upper part. The laminated intervals reflect pulses of flowing water entering the abandoned burrow during moderate rains, whereas massive intervals reflect mass flow input of dense sediment-water mixtures during heavy rains that produced sheet floods. Approximately 1% of the burrows contained fragmentary, disarticulated and weathered mammal bones that were introduced in the open burrow by currents along with other sedimentary particles. Analysis of the tetrapod burrow fossil record suggests that Miocene burrows, including those studied herein, reflect a remarkable increase in the average size of the fossorial fauna. We conclude that large late Miocene mammals dug burrows essentially as a shelter against environmental extremes and to escape predation. The simple architecture of the burrows suggests that the producers essentially foraged aboveground. Several mammal groups acquired fossorial habits in response to cold and seasonally dry climatic conditions that prevailed during the late Miocene in southern South America. The considerable range of horizontal diameters of the studied burrows can be attributed to a variety of producers, including dasypodids, the notoungulate Paedotherium minor, Glyptodontidae and Proscelidodon sp. creator: María Cristina Cardonatto creator: Ricardo Néstor Melchor uri: https://doi.org/10.7717/peerj.4787 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cardonatto and Melchor title: Potentially inappropriate use of benzodiazepines and z-drugs in the older population—analysis of associations between long-term use and patient-related factors link: https://peerj.com/articles/4614 last-modified: 2018-05-22 description: IntroductionThe long-term use of benzodiazepines (BZD) and z-drugs in older populations is associated with a variety of sociodemographic and health-related factors. Recent studies reported that long-term BZD and z-drugs use is associated with increased age, female sex, and severe negative psychological (e.g., depression) and somatic (e.g., chronic disease) factors. The current study explores the sociodemographic and health-related factors associated with long-term BZD and z-drugs use in the elderly.MethodsWe conducted a cross-sectional survey among randomly selected patients of one health insurance plan (“AOK North-West”) with BZD and z-drugs prescriptions in the past 12 months. The sample was stratified by appropriate German prescription guidelines (yes vs. no) and age (50–65 vs. >65 years). To examine the association of selected sociodemographic and psychological variables (e.g., sex, employment status, quality of life, depression) with long-term use, a binary logistic regression analysis was conducted.ResultsIn total, data from 340 patients were analyzed. The mean age was 72.1 (SD = 14.5) years, and the most commonly used substances were zopiclon (38.1%), oxazepam (18.1%), and lorazepam (13.8%). The mean defined daily dose (DDD) was 0.73 (SD = 0.47). Insomnia was the main reason for prescribing BZD and z-drugs. The long-term use of BZD and z-drugs was significantly associated with unemployment (OR = 2.9, 95% CI [1.2–7.1]) and generally problematic medication use (OR = 0.5, 95% CI [0.2–1.0]).DiscussionUnemployment status and problematic medication use had a significant association with the patient-reported, long-term use of BZD and z-drugs. Divergent prescription patterns might suggest problematic patterns of BZD and z-drugs use. The causal connection between the identified factors and problematic BZD and z-drugs prescription is not discussed in this paper. Nevertheless, employment status and possible evidence of general problematic drug use may be a warning signal to the prescribers of BZD and z-drugs. creator: Aliaksandra Mokhar creator: Niklas Tillenburg creator: Jörg Dirmaier creator: Silke Kuhn creator: Martin Härter creator: Uwe Verthein uri: https://doi.org/10.7717/peerj.4614 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mokhar et al. title: Impact of input data (in)accuracy on overestimation of visible area in digital viewshed models link: https://peerj.com/articles/4835 last-modified: 2018-05-21 description: Viewshed analysis is a GIS tool in standard use for more than two decades to perform numerous scientific and practical tasks. The reliability of the resulting viewshed model depends on the computational algorithm and the quality of the input digital surface model (DSM). Although many studies have dealt with improving viewshed algorithms, only a few studies have focused on the effect of the spatial accuracy of input data. Here, we compare simple binary viewshed models based on DSMs having varying levels of detail with viewshed models created using LiDAR DSM. The compared DSMs were calculated as the sums of digital terrain models (DTMs) and layers of forests and buildings with expertly assigned heights. Both elevation data and the visibility obstacle layers were prepared using digital vector maps differing in scale (1:5,000, 1:25,000, and 1:500,000) as well as using a combination of a LiDAR DTM with objects vectorized on an orthophotomap. All analyses were performed for 104 sample locations of 5 km2, covering areas from lowlands to mountains and including farmlands as well as afforested landscapes. We worked with two observer point heights, the first (1.8 m) simulating observation by a person standing on the ground and the second (80 m) as observation from high structures such as wind turbines, and with five estimates of forest heights (15, 20, 25, 30, and 35 m). At all height estimations, all of the vector-based DSMs used resulted in overestimations of visible areas considerably greater than those from the LiDAR DSM. In comparison to the effect from input data scale, the effect from object height estimation was shown to be secondary. creator: Ondřej Lagner creator: Tomáš Klouček creator: Petra Šímová uri: https://doi.org/10.7717/peerj.4835 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lagner et al. title: On the efficiency of the genetic code after frameshift mutations link: https://peerj.com/articles/4825 last-modified: 2018-05-21 description: Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”. creator: Regine Geyer creator: Amir Madany Mamlouk uri: https://doi.org/10.7717/peerj.4825 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Geyer and Madany Mamlouk title: Understanding mitochondrial myopathies: a review link: https://peerj.com/articles/4790 last-modified: 2018-05-21 description: Mitochondria are small, energy-producing structures vital to the energy needs of the body. Genetic mutations cause mitochondria to fail to produce the energy needed by cells and organs which can cause severe disease and death. These genetic mutations are likely to be in the mitochondrial DNA (mtDNA), or possibly in the nuclear DNA (nDNA). The goal of this review is to assess the current understanding of mitochondrial diseases. This review focuses on the pathology, causes, risk factors, symptoms, prevalence data, symptomatic treatments, and new research aimed at possible preventions and/or treatments of mitochondrial diseases. Mitochondrial myopathies are mitochondrial diseases that cause prominent muscular symptoms such as muscle weakness and usually present with a multitude of symptoms and can affect virtually all organ systems. There is no cure for these diseases as of today. Treatment is generally supportive and emphasizes symptom management. Mitochondrial diseases occur infrequently and hence research funding levels tend to be low in comparison with more common diseases. On the positive side, quite a few genetic defects responsible for mitochondrial diseases have been identified, which are in turn being used to investigate potential treatments. Speech therapy, physical therapy, and respiratory therapy have been used in mitochondrial diseases with variable results. These therapies are not curative and at best help with maintaining a patient’s current abilities to move and function. creator: Abhimanyu S. Ahuja uri: https://doi.org/10.7717/peerj.4790 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ahuja title: Multilocus phylogeny of the parasitic wasps in the tribe Euphorini (Hymenoptera: Braconidae) with revised generic classifications link: https://peerj.com/articles/4783 last-modified: 2018-05-21 description: BackgroundParasitic wasps in the family Braconidae are important regulators of insect pests, particularly in forest and agroecosystems. Within Braconidae, wasps in the tribe Euphorini (Euphorinae) attack economically damaging plant bugs (Miridae) that are major pests of field and vegetable crops. However, the evolutionary relationships of this tribe have been historically problematic. Most generic concepts have been based on ambiguous morphological characters which often leads to misidentification, complicating their use in biological control.MethodsUsing a combination of three genes (COI, 28S, and CAD) and 80 taxa collected worldwide, we conducted Bayesian inference using MrBayes, and maximum likelihood analyses using RAxML and IQ-Tree on individual gene trees as well as the concatenated dataset.ResultsThe monophyly of the tribe Euphorini and the two genera Peristenus and Leiophron were confirmed using maximum likelihood and Bayesian inference. The subgeneric classifications of Leiophron sensu lato were not supported, and the monotypic genus Mama was also not supported.DiscussionEuphoriella, Euphoriana, Euphorus, and Mama syn. n, have been synonymized under Leiophron. Mama mariaesyn. n was placed as a junior synonym of Leiophron reclinator. The generic concepts of Peristenus and Leiophron were refined to reflect the updated phylogeny. Further we discuss the need for revising Euphorini given the number of undescribed species within the tribe. creator: Yuanmeng Miles Zhang creator: Julia Stigenberg creator: Jacqueline Hope Meyer creator: Barbara Jo-Anne Sharanowski uri: https://doi.org/10.7717/peerj.4783 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Intolerance of uncertainty and conditioned place preference in opioid addiction link: https://peerj.com/articles/4775 last-modified: 2018-05-21 description: Several personality factors have been implicated in vulnerability to addiction by impacting learning and decision making. One such factor is intolerance of uncertainty (IU), the tendency to perceive uncertain situations negatively and avoid them. Conditioned place preference (CPP), which compares preference for contexts paired with reward, has been used to examine the motivation for both drug and non-drug rewards. However, preference for locations associated with non-drug reward, as well as the potential influence of IU, has not been thoroughly studied in individuals with addiction. In the current study, we examined CPP using a computer-based task in a sample of addicted individuals undergoing opioid maintenance treatment and never-addicted controls. Patients were confirmed to have higher IU than controls. In the CPP task, the two groups did not differ in overall time spent in the previously-rewarded context. However, controls were more likely than patients to immediately return to this context. Contrary to our predictions, IU was not a significant predictor of preference for the previously-rewarded context, although higher IU in controls was associated with a higher number of rewards obtained in the task. No such relationship was found in patients. creator: Milen L. Radell creator: Michael Todd Allen creator: Belinda Favaloro creator: Catherine E. Myers creator: Paul Haber creator: Kirsten Morley creator: Ahmed A. Moustafa uri: https://doi.org/10.7717/peerj.4775 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Radell et al. title: Effects of long-term fertilisation on aggregates and dynamics of soil organic carbon in a semi-arid agro-ecosystem in China link: https://peerj.com/articles/4758 last-modified: 2018-05-21 description: BackgroundLong-term fertilisation has a large influence on soil physical and chemical properties in agro-ecosystems. The effects on the distribution of aggregates, however, are not fully understood. We determined the dynamic change of the distribution of aggregates and soil organic carbon (SOC) content over time in a long-term field experiment established in 1998 on the Loess Plateau of China and illustrated the relationship between them.MethodsWe determined SOC content and the distribution of aggregates in nine fertiliser treatments: manure (M); nitrogen (N); phosphorus (P); M and N; M, N, and P; M and P; N and P; bare land; and an unfertilised control. These parameters were then used for a path analysis and to analyse the fractal dimension (Dv).ResultsThe organic fertiliser increased SOC content. The proportions of 0.1–0.25 mm microaggregates and 0.25–0.5 mm macroaggregates were higher and the proportion of the 0.01–0.05 mm size class of the silt + clay fraction was lower in the treatments receiving organic fertiliser (M, MN, MNP, and MP) than that in the control, indicating that the addition of organic fertiliser promoted aggregation. The distribution of aggregates characterised by their fractal dimension (Dv), however, did not differ among the treatments.DiscussionDv was strongly correlated with the proportion of the <0.002 mm size class of the silt + clay fraction that did not differ significantly among the treatments. The change in the distribution of aggregates was strongly correlated with SOC content, which could produce organic polymer binding agents to increase the proportion of larger particles. Long-term application of organic fertiliser is thus necessary for the improvement and maintenance of soil quality in semi-arid agricultural land when residues are removed. creator: Jiaoyang Zhang creator: Caili Sun creator: Guobin Liu creator: Sha Xue uri: https://doi.org/10.7717/peerj.4758 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Living upside down: patterns of red coral settlement in a cave link: https://peerj.com/articles/4649 last-modified: 2018-05-21 description: BackgroundLarval settlement and intra-specific interactions during the recruitment phase are crucial in determining the distribution and density of sessile marine populations. Marine caves are confined and stable habitats. As such, they provide a natural laboratory to study the settlement and recruitment processes in sessile invertebrates, including the valuable Mediterranean red coral Corallium rubrum. In the present study, the spatial and temporal variability of red coral settlers in an underwater cave was investigated by demographic and genetic approaches.MethodsSixteen PVC tiles were positioned on the walls and ceiling of the Colombara Cave, Ligurian Sea, and recovered after twenty months. A total of 372 individuals of red coral belonging to two different reproductive events were recorded. Basal diameter, height, and number of polyps were measured, and seven microsatellites loci were used to evaluate the genetic relationships among individuals and the genetic structure.ResultsSignificant differences in the colonization rate were observed both between the two temporal cohorts and between ceiling and walls. No genetic structuring was observed between cohorts. Overall, high levels of relatedness among individuals were found.ConclusionThe results show that C. rubrumindividuals on tiles are highly related at very small spatial scales, suggesting that nearby recruits are likely to be sibs. Self-recruitment and the synchronous settlement of clouds of larvae could be possible explanations for the observed pattern. creator: Federica Costantini creator: Luca Rugiu creator: Carlo Cerrano creator: Marco Abbiati uri: https://doi.org/10.7717/peerj.4649 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Costantini et al. title: I understand you feel that way, but I feel this way: the benefits of I-language and communicating perspective during conflict link: https://peerj.com/articles/4831 last-modified: 2018-05-18 description: Using hypothetical scenarios, we provided participants with potential opening statements to a conflict discussion that varied on I/you language and communicated perspective. Participants rated the likelihood that the recipient of the statement would react in a defensive manner. Using I-language and communicating perspective were both found to reduce perceptions of hostility. Statements that communicated both self- and other-perspective using I-language (e.g. ‘I understand why you might feel that way, but I feel this way, so I think the situation is unfair’) were rated as the best strategy to open a conflict discussion. Simple acts of initial language use can reduce the chances that conflict discussion will descend into a downward spiral of hostility. creator: Shane L. Rogers creator: Jill Howieson creator: Casey Neame uri: https://doi.org/10.7717/peerj.4831 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rogers et al. title: Fitness consequences of fish circadian behavioural variation in exploited marine environments link: https://peerj.com/articles/4814 last-modified: 2018-05-18 description: The selective properties of fishing that influence behavioural traits have recently gained interest. Recent acoustic tracking experiments have revealed between-individual differences in the circadian behavioural traits of marine free-living fish; these differences are consistent across time and ecological contexts and generate different chronotypes. Here, we hypothesised that the directional selection resulting from fishing influences the wild circadian behavioural variation and affects differently to individuals in the same population differing in certain traits such as awakening time or rest onset time. We developed a spatially explicit social-ecological individual-based model (IBM) to test this hypothesis. The parametrisation of our IBM was fully based on empirical data; which represent a fishery formed by patchily distributed diurnal resident fish that are exploited by a fleet of mobile boats (mostly bottom fisheries). We ran our IBM with and without the observed circadian behavioural variation and estimated selection gradients as a quantitative measure of trait change. Our simulations revealed significant and strong selection gradients against early-riser chronotypes when compared with other behavioural and life-history traits. Significant selection gradients were consistent across a wide range of fishing effort scenarios. Our theoretical findings enhance our understanding of the selective properties of fishing by bridging the gaps among three traditionally separated fields: fisheries science, behavioural ecology and chronobiology. We derive some general predictions from our theoretical findings and outline a list of empirical research needs that are required to further understand the causes and consequences of circadian behavioural variation in marine fish. creator: Martina Martorell-Barceló creator: Andrea Campos-Candela creator: Josep Alós uri: https://doi.org/10.7717/peerj.4814 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Martorell-Barceló et al. title: A quantitative approach to determine the taxonomic identity and ontogeny of the pycnodontiform fish Pycnodus (Neopterygii, Actinopterygii) from the Eocene of Bolca Lagerstätte, Italy link: https://peerj.com/articles/4809 last-modified: 2018-05-18 description: BackgroundThe pycnodontiform fish Pycnodus is one of the representatives of the highly diverse actinopterygian fish fauna from the early Eocene Bolca Lagerstätte, representing one of the youngest and thus last occurrences of this extinct neopterygian clade. This genus has historically been used as a wastebasket taxon in regards to poorly known pycnodontiform fossils. Authors have argued over the specific status of the Bolca Lagerstätte Pycnodus in terms of how many species are contained within the genus with some arguing for multiple species and others suggesting lumping all Bolca specimens together into one species.MethodsHere, we use a quantitative approach performing biometric and geometric morphometric analyses on 52 specimens of Pycnodus in order to determine if the morphological variability within the sample might be related to inter- or intraspecific variation.ResultsThe analyses revealed that the variations of body shape, morphometric and meristic characters cannot be used to distinguish different morphotypes. On the contrary, our results show a remarkable link between shape and size, related to ontogeny.DiscussionDifferences in body shape of small (juvenile) and large (adult) individuals is probably related to different microhabitats occupation on the Bolca reef with juveniles sheltering within crevices on the reef and adults being more powerful swimmers that swim above the coral. Taxonomically, we suggest that the Bolca Pycnodus should be referred to strictly as Pycnodus apodus as this was the name given to the holotype. Additionally, an overview of species assigned to Pycnodus is given. creator: John Joseph Cawley creator: Giuseppe Marramà creator: Giorgio Carnevale creator: Jürgen Kriwet uri: https://doi.org/10.7717/peerj.4809 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cawley et al. title: Helicobacter pylori genetic diversification in the Mongolian gerbil model link: https://peerj.com/articles/4803 last-modified: 2018-05-18 description: Helicobacter pylori requires genetic agility to infect new hosts and establish long-term colonization of changing gastric environments. In this study, we analyzed H. pylori genetic adaptation in the Mongolian gerbil model. This model is of particular interest because H. pylori-infected gerbils develop a high level of gastric inflammation and often develop gastric adenocarcinoma or gastric ulceration. We analyzed the whole genome sequences of H. pylori strains cultured from experimentally infected gerbils, in comparison to the genome sequence of the input strain. The mean annualized single nucleotide polymorphism (SNP) rate per site was 1.5e−5, which is similar to the rates detected previously in H. pylori-infected humans. Many of the mutations occurred within or upstream of genes associated with iron-related functions (fur, tonB1, fecA2, fecA3, and frpB3) or encoding outer membrane proteins (alpA, oipA, fecA2, fecA3, frpB3 and cagY). Most of the SNPs within coding regions (86%) were non-synonymous mutations. Several deletion or insertion mutations led to disruption of open reading frames, suggesting that the corresponding gene products are not required or are deleterious during chronic H. pylori colonization of the gerbil stomach. Five variants (three SNPs and two deletions) were detected in isolates from multiple animals, which suggests that these mutations conferred a selective advantage. One of the mutations (FurR88H) detected in isolates from multiple animals was previously shown to confer increased resistance to oxidative stress, and we now show that this SNP also confers a survival advantage when H. pylori is co-cultured with neutrophils. Collectively, these analyses allow the identification of mutations that are positively selected during H. pylori colonization of the gerbil model. creator: Amber C. Beckett creator: John T. Loh creator: Abha Chopra creator: Shay Leary creator: Aung Soe Lin creator: Wyatt J. McDonnell creator: Beverly R.E.A. Dixon creator: Jennifer M. Noto creator: Dawn A. Israel creator: Richard M. Peek Jr creator: Simon Mallal creator: Holly M. Scott Algood creator: Timothy L. Cover uri: https://doi.org/10.7717/peerj.4803 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Beckett et al. title: Association of epilepsy and asthma: a population-based retrospective cohort study link: https://peerj.com/articles/4792 last-modified: 2018-05-18 description: BackgroundEpidemiologic data supporting the epilepsy–asthma association are insufficient. Therefore, we examined this association in this study.MethodsBy using claims data from the National Health Insurance Research Database (Taiwan), we executed a retrospective cohort analysis. Analysis 1 entailed comparing 150,827 patients diagnosed as having incident asthma during 1996–2013 with disease-free controls who were selected randomly during the same period, frequency matched in terms of age and sex. Similarly, analysis 2 entailed comparing 25,274 patients newly diagnosed as having epilepsy with sex- and age-matched controls who were selected randomly. At the end of 2013, we evaluated in analysis 1 the epilepsy incidence and risk and evaluated in analysis 2 the asthma incidence and risk. We applied Kaplan–Meier analysis to derive plots of the proportion of asthma-free seizures.ResultsIn analysis 1, the asthma group exhibited a higher epilepsy incidence than did the control group (3.05 versus 2.26 per 1,000 person-years; adjusted hazard ratio: 1.39, 95% CI [1.33–1.45]). We also noted a greater risk of subsequent epilepsy in women and girls. In analysis 2, we determined that the asthma incidence between the control and epilepsy groups did not differ significantly; however, some age subgroups including children and individuals in their 30s had an increased risk. A negative association was found in adolescents. The Kaplan–Meier analysis revealed epilepsy to be positively associated with subsequent onset of asthma within seven years of epilepsy diagnosis.DiscussionAsthma may be associated with high epilepsy risk, and epilepsy may be associated with high asthma risk among children and individuals in their 30s. Nevertheless, people with epilepsy in other age subgroups should be aware of the possibility of developing asthma within seven years of epilepsy diagnosis. creator: Kuo-Liang Chiang creator: Fang-Chuan Kuo creator: Jen-Yu Lee creator: Chin-Yin Huang uri: https://doi.org/10.7717/peerj.4792 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chiang et al. title: Diagnostic accuracy of Onen’s Alternative Grading System combined with Doppler evaluation of ureteral jets as an alternative in the diagnosis of obstructive hydronephrosis in children link: https://peerj.com/articles/4791 last-modified: 2018-05-18 description: IntroductionUreteropelvic junction obstruction (UPJO) is a common congenital anomaly leading to varying degrees of hydronephrosis (HN), ranging from no apparent effect on the renal function to atrophy. Evaluation of these children is based on Diuretic Renal Scintigraphy (DRS) and Ultrasonography (US). Recent studies have suggested that new parameters of conventional and color Doppler ultrasonography (CDUS) may be useful in discriminating which kidneys are obstructed. The present study aims to assess the diagnostic accuracy of such parameters in the diagnosis of obstruction in children with UPJO.MethodsWe evaluated 44 patients (33 boys) with a mean age of 6.53 ± 4.39 years diagnosed with unilateral high-grade hydronephrosis (SFU grades 3 and 4). All underwent DRS and index tests (conventional US and CDUS to evaluate ureteral jets frequency) within a maximum interval of two weeks. Hydronephrotic units were reclassified according to the alternative grading system (AGS) proposed by Onen et al. Obstruction in the DRS was defined as a differential renal function <40% on the affected side and/or features indicating poor drainage function like T1/2 >20 minutes after the administration of furosemide, and a plateau or ascending pattern of the excretion curve.ResultsNineteen hydronephrotic units (43.1%) were obstructed. Some degree of cortical atrophy—grades 3 (segmental) or 4 (diffuse)—was present in those obstructed units. AGS grades had 100% sensitivity, 76% of specificity and 86.4% of accuracy. The absence of ureteral jets had a sensitivity of 73.68%, a specificity of 100% with an accuracy of 88.6%. When we analyzed the two aspects together and considered obstructed the renal units classified as AGS grade 3 or 4 with no jets, sensitivity increased to 78.9%, accuracy to 92%, remaining with a maximum specificity of 100%. These features combined would allow us to avoid performing DRS in 61% of our patients, leaving more invasive tests to inconclusive cases.ConclusionsAlthough DRS remains the mainstay to distinguishing obstructive from non-obstructive kidneys, grade of hydronephrosis and frequency of ureteral jets, independently or in combination may be a reliable alternative in the mostly cases.This alternative approach has high accuracy, it is less invasive, easily reproducible and may play a role in the diagnosis of obstruction in pediatric population. creator: Jose de Bessa Jr creator: Cicilia M. Rodrigues creator: Maria Cristina Chammas creator: Eduardo P. Miranda creator: Cristiano M. Gomes creator: Paulo R. Moscardi creator: Marcia C. Bessa creator: Carlos A. Molina creator: Ricardo B. Tiraboschi creator: Jose M. Netto creator: Francisco T. Denes uri: https://doi.org/10.7717/peerj.4791 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 De Bessa Jr et al. title: Effects of sandfish (Holothuria scabra) removal on shallow-water sediments in Fiji link: https://peerj.com/articles/4773 last-modified: 2018-05-18 description: Sea cucumbers play an important role in the recycling and remineralization of organic matter (OM) in reef sands through feeding, excretion, and bioturbation processes. Growing demand from Asian markets has driven the overexploitation of these animals globally. The implications of sea cucumber fisheries for shallow coastal ecosystems and their management remain poorly understood. To address this knowledge gap, the current study manipulated densities of Holothuria scabra within enclosures on a reef flat in Fiji, between August 2015 and February 2016, to study the effects of sea cucumber removal on sedimentary function as a biocatalytic filter system. Three treatments were investigated: (i) high density (350 g m−2 wet weight; ca. 15 individuals); (ii) natural density (60 g m−2; ca. 3 individuals); and (iii) exclusion (0 g m−2). Quantity of sediment reworked through ingestion by H. scabra, grain size distribution, O2 penetration depth, and sedimentary oxygen consumption (SOC) were quantified within each treatment. Findings revealed that the natural population of H. scabra at the study site can rework ca. 10,590 kg dry sediment 1,000 m−2 year−1; more than twice the turnover rate recorded for H. atra and Stichopus chloronotus. There was a shift towards finer fraction grains in the high treatment. In the exclusion treatment, the O2 penetration depth decreased by 63% following a 6 °C increase in water temperature over the course of two months, while in the high treatment no such change was observed. SOC rates increased ca. two-fold in the exclusion treatment within the first month, and were consistently higher than in the high treatment. These results suggest that the removal of sea cucumbers can reduce the capacity of sediments to buffer OM pulses, impeding the function and productivity of shallow coastal ecosystems. creator: Steven Lee creator: Amanda K. Ford creator: Sangeeta Mangubhai creator: Christian Wild creator: Sebastian C.A. Ferse uri: https://doi.org/10.7717/peerj.4773 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lee et al. title: Larval exposure to the neonicotinoid imidacloprid impacts adult size in the farmland butterfly Pieris brassicae link: https://peerj.com/articles/4772 last-modified: 2018-05-18 description: Populations of farmland butterflies have been suffering from substantial population declines in recent decades. These declines have been correlated with neonicotinoid usage both in Europe and North America but experimental evidence linking these correlations is lacking. The potential for non-target butterflies to be exposed to trace levels of neonicotinoids is high, due to the widespread contamination of agricultural soils and wild plants in field margins. Here we provide experimental evidence that field realistic, sub-lethal exposure to the neonicotinoid imidacloprid negatively impacts the development of the common farmland butterfly Pieris brassicae. Cabbage plants were watered with either 0, 1, 10, 100 or 200 parts per billion imidacloprid, to represent field margin plants growing in contaminated agricultural soils and these were fed to P. brassicae larvae. The approximate digestibility (AD) of the cabbage as well as behavioural responses by the larvae to simulated predator attacks were measured but neither were affected by neonicotinoid treatment. However, the duration of pupation and the size of the adult butterflies were both significantly reduced in the exposed butterflies compared to the controls, suggesting that adult fitness is compromised through exposure to this neonicotinoid. creator: Penelope R. Whitehorn creator: George Norville creator: Andre Gilburn creator: Dave Goulson uri: https://doi.org/10.7717/peerj.4772 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Whitehorn et al. title: Effect of elevated temperature on membrane lipid saturation in Antarctic notothenioid fish link: https://peerj.com/articles/4765 last-modified: 2018-05-18 description: Homeoviscous adaptation (HVA) is a key cellular response by which fish protect their membranes against thermal stress. We investigated evolutionary HVA (long time scale) in Antarctic and non-Antarctic fish. Membrane lipid composition was determined for four Perciformes fish: two closely related Antarctic notothenioid species (Trematomus bernacchii and Pagothenia borchgrevinki); a diversified related notothenioid Antarctic icefish (Chionodraco hamatus); and a New Zealand species (Notolabrus celidotus). The membrane lipid compositions were consistent across the three Antarctic species and these were significantly different from that of the New Zealand species. Furthermore, acclimatory HVA (short time periods with seasonal changes) was investigated to determine whether stenothermal Antarctic fish, which evolved in the cold, stable environment of the Southern Ocean, have lost the acclimatory capacity to modulate their membrane saturation states, making them vulnerable to anthropogenic global warming. We compared liver membrane lipid composition in two closely related Antarctic fish species acclimated at 0 °C (control temperature), 4 °C for a period of 14 days in T. bernacchii and 28 days for P. borchgrevinki, and 6 °C for 7 days in both species. Thermal acclimation at 4 °C did not result in changed membrane saturation states in either Antarctic species. Despite this, membrane functions were not compromised, as indicated by declining serum osmolality, implying positive compensation by enhanced hypo-osmoregulation. Increasing the temperature to 6 °C did not change the membrane lipids of P. borchgrevinki. However, in T. bernacchii, thermal acclimation at 6 °C resulted in an increase of membrane saturated fatty acids and a decline in unsaturated fatty acids. This is the first study to show a homeoviscous response to higher temperatures in an Antarctic fish, although for only one of the two species examined. creator: Vanita C. Malekar creator: James D. Morton creator: Richard N. Hider creator: Robert H. Cruickshank creator: Simon Hodge creator: Victoria J. Metcalf uri: https://doi.org/10.7717/peerj.4765 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Malekar et al. title: Tetrapod tracks in Permo–Triassic eolian beds of southern Brazil (Paraná Basin) link: https://peerj.com/articles/4764 last-modified: 2018-05-18 description: Tetrapod tracks in eolianites are widespread in the fossil record since the late Paleozoic. Among these ichnofaunas, the ichnogenus Chelichnus is the most representative of the Permian tetrapod ichnological record of eolian deposits of Europe, North America and South America, where the Chelichnus Ichnofacies often occurs. In this contribution, we describe five sets of tracks (one of which is preserved in cross-section), representing the first occurrence of Dicynodontipus and Chelichnus in the “Pirambóia Formation” of southern Brazil. This unit represents a humid desert in southwestern Pangea and its lower and upper contacts lead us to consider its age as Lopingian–Induan. The five sets of tracks studied were compared with several ichnotaxa and body fossils with appendicular elements preserved, allowing us to attribute these tracks to dicynodonts and other indeterminate therapsids. Even though the “Pirambóia Formation” track record is sparse and sub-optimally preserved, it is an important key to better understand the occupation of arid environments by tetrapods across the Permo–Triassic boundary. creator: Heitor Francischini creator: Paula Dentzien-Dias creator: Spencer G. Lucas creator: Cesar L. Schultz uri: https://doi.org/10.7717/peerj.4764 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Francischini et al. title: Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles link: https://peerj.com/articles/4793 last-modified: 2018-05-17 description: The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only eight bacterial groups, including members of the Acinetobacter, Enterobacteriacea, Pseudomonas, Lactococcus, and Comamonas. The Acinetobacter and Enterobacteriacea together accounted for 35% of the total average 16S rRNA ribotypes recovered from all specimens. Further, microbiome diversity and community structure was significantly linked to beetle diet breadth, between those foraging on less than two plant types (specialists) versus over nine plant types (generalists). Moraxellaceae, Enterobacteriaceae, and Pseudomonadaceae were highly prevalent in specialist species, and also present in eggs, while Rickettsiaceae associated exclusively with generalist beetles. Bacteria isolated from Cephaloleia digestive systems had distinct capabilities and suggested a possible beneficial role in both digestion of plant-based compounds, including xylose, mannitol, and pectin, and possible detoxification, via lipases. Cephaloleia species are currently expanding their diets to include exotic invasive plants, yet it is unknown whether their microbial community plays a role in this transition. In this study, colonization of invasive plants was correlated with a dysbiosis of the microbiome, suggesting a possible relationship between gut bacteria and niche adaptation. creator: Chelsea L. Blankenchip creator: Dana E. Michels creator: H. Elizabeth Braker creator: Shana K. Goffredi uri: https://doi.org/10.7717/peerj.4793 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Blankenchip et al. title: The effect of climate change on the distribution of a tropical zoanthid (Palythoa caribaeorum) and its ecological implications link: https://peerj.com/articles/4777 last-modified: 2018-05-17 description: Palythoa caribaeorum is a zoanthid often dominant in shallow rocky environments along the west coast of the Atlantic Ocean, from the tropics to the subtropics. This species has high environmental tolerance and is a good space competitor in reef environments. Considering current and future scenarios in the global climate regime, this study aimed to model and analyze the distribution of P. caribaeorum, generating maps of potential distribution for the present and the year 2100. The distribution was modeled using maximum entropy (Maxent) based on 327 occurrence sites retrieved from the literature. Calcite concentration, maximum chlorophyll-a concentration, salinity, pH, and temperature range yielded a model with the smallest Akaike information criterion (2649.8), and were used in the present and future distribution model. Data from the HadGEM2-ES climate model were used to generate the projections for the year 2100. The present distribution of P. caribaeorum shows that parts of the Brazilian coast, Caribbean Sea, and Florida are suitable regions for the species, as they are characterized by high salinity and pH and small temperature variation. An expansion of the species’ distribution was forecast northward under mild climate scenarios, while a decrease of suitable areas was forecast in the south. In the climate scenario with the most intense changes, P. caribaeorum would lose one-half of its suitable habitats, including the northernmost and southernmost areas of its distribution. The Caribbean Sea and northeastern Brazil, as well as other places under the influence of coastal upwellings, may serve as potential havens for this species. creator: Leonardo M. Durante creator: Igor C.S. Cruz creator: Tito M.C. Lotufo uri: https://doi.org/10.7717/peerj.4777 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Durante et al. title: Greenland shark (Somniosus microcephalus) feeding behavior on static fishing gear, effect of SMART (Selective Magnetic and Repellent-Treated) hook deterrent technology, and factors influencing entanglement in bottom longlines link: https://peerj.com/articles/4751 last-modified: 2018-05-17 description: The Greenland Shark (Somniosus microcephalus) is the most common bycatch in the Greenland halibut (Reinhardtius hippoglossoides) bottom longline fishery in Cumberland Sound, Canada. Historically, this inshore fishery has been prosecuted through the ice during winter but winter storms and unpredictable landfast ice conditions since the mid-1990s have led to interest in developing a summer fishery during the ice-free season. However, bycatch of Greenland shark was found to increase substantially with 570 sharks captured during an experimental Greenland halibut summer fishery (i.e., mean of 6.3 sharks per 1,000 hooks set) and mortality was reported to be about 50% due in part to fishers killing sharks that were severely entangled in longline gear. This study investigated whether the SMART (Selective Magnetic and Repellent-Treated) hook technology is a practical deterrent to Greenland shark predation and subsequent bycatch on bottom longlines. Greenland shark feeding behavior, feeding kinematics, and variables affecting entanglement/disentanglement and release are also described. The SMART hook failed to deter Greenland shark predation, i.e., all sharks were captured on SMART hooks, some with more than one SMART hook in their jaw. Moreover, recently captured Greenland sharks did not exhibit a behavioral response to SMART hooks. In situ observations of Greenland shark feeding show that this species uses a powerful inertial suction mode of feeding and was able to draw bait into the mouth from a distance of 25–35 cm. This method of feeding is suggested to negate the potential deterrent effects of electropositive metal and magnetic alloy substitutions to the SMART hook technology. The number of hooks entangled by a Greenland shark and time to disentangle and live-release a shark was found to increase with body length. creator: Scott M. Grant creator: Rennie Sullivan creator: Kevin J. Hedges uri: https://doi.org/10.7717/peerj.4751 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Grant et al. title: Citizen science data suggest that a novel rig improves landing rate and reduces injury and handling time in recreational angling with artificial lures in Baltic pike (Esox lucius) link: https://peerj.com/articles/4744 last-modified: 2018-05-17 description: The optimal terminal gear in hook-and-line recreational fishing maximizes landing rates and minimizes injury to the fish because some fish will be released after capture. We designed a novel rig configuration in artificial lure fishing for top predators and examined its effectiveness in angling for Baltic northern pike (Esox lucius) using a citizen science approach based on observational data collected from volunteer anglers in the field. The novel rig included two changes to traditional rig designs common to artificial lure angling. First, hooks were mounted in a way giving better hook exposure and eliminating lever-arm effects from the lure to the hooks once a fish is hooked. This construction allowed the second change, being a shift to hooks 4–5 sizes smaller than those used on traditional hook mounts. We analysed observational data collected by volunteer anglers using either the novel rig or a standard rig mount in two types of artificial lures (softbait and hardbait) of the same size (about 17 cm). Using N = 768 pike contacts as input data, we showed the landing rates of pike targeted with artificial lures significantly and substantially increased from 45% with normal-rigs to 85% when the same lure types were fished with the novel rig configuration. Lure type and water temperature had no effects on landing rates. Moreover, hardbaits on normal-rigs produced significantly more injury, bleeding and elevated unhooking time compared to fish captured on hardbaits with release-rigs. We conclude that simple changes to traditional hook sizes and mounts in lure fishing may benefit both anglers and the fishes that are to be released and that citizen science projects with volunteer anglers are able to provide good data in proof-of-concept studies. Further experimental studies are needed to differentiate hook size from hook mount effects because both variables were confounded in the results of the observational data presented here. creator: Jens Jakob Bursell creator: Robert Arlinghaus uri: https://doi.org/10.7717/peerj.4744 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bursell and Arlinghaus title: Perinatal specimens of Maiasaura from the Upper Cretaceous of Montana (USA): insights into the early ontogeny of saurolophine hadrosaurid dinosaurs link: https://peerj.com/articles/4734 last-modified: 2018-05-17 description: Perinatal specimens of hadrosaurids discovered in the late 1970’s by field crews from Princeton University were significant in providing evidence of the early ontogenetic stages in North American dinosaurs. These specimens from the Campanian (Upper Cretaceous) Two Medicine Formation of Montana consist of over a dozen skeletons referable to the saurolophine hadrosaurid Maiasaura peeblesorum, but never fully figured or described. Here, we provide a more complete documentation of the morphology of these specimens, along with an examination of variation during a large span of the development of saurolophine hadrosaurids. Many ontogenetic changes in the available facial and mandibular elements are associated with the progressive elongation of the preorbital region of the skull and mandible. In the postcranium, limb bones change nearly isometrically, with exception of certain elements of the forelimb. Some cranial and postcranial characters commonly used for inferring hadrosaurid phylogenetic relationships remain invariable during the ontogeny of M. peeblesorum. This indicates that early ontogenetic stages may still provide a limited amount of character information useful for systematics and phylogenetic inference. creator: Albert Prieto-Marquez creator: Merrilee F. Guenther uri: https://doi.org/10.7717/peerj.4734 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Prieto-Marquez and Guenther title: Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in a Mediterranean fishery link: https://peerj.com/articles/4707 last-modified: 2018-05-17 description: In the Balearic Islands, different trammel net designs have been adopted to promote fisheries sustainability and reduce discards. Here, we compare the catch performance of three trammel net designs targeting the spiny lobster Palinurus elephas in terms of biomass, species composition and revenue from commercial catches and discards. Designs differ in the netting fiber type (standard polyfilament, PMF, or a new polyethylene multi-monofilament, MMF) and the use of a guarding net or greca, a mesh piece intended to reduce discards. Catches were surveyed by an on-board observer from 1,550 netting walls corresponding to 70 nets. The number of marketable species captured indicated that the lobster trammel net fishery has multiple targets, which contribute significantly to the total revenue. The discarded species ranged from habitat-forming species to elasmobranches, but the magnitude of gear-habitat interactions on the long term dynamics of benthos remains unclear. No relevant differences in revenue and weight of discards were detected after Bayesian analyses. However, the species composition of discards was different when using greca. Interestingly, high immediate survival was found for discarded undersized lobsters, while a seven day survival assessment, using captive observation, gave an asymptotic estimate of survival probability as 0.64 (95% CI [0.54–0.76]). Therefore, it is recommended that it would be beneficial for this stock if an exemption from the EU landing obligation regulation was sought for undersized lobsters in the Balearic trammel net fishery. creator: Gaetano Catanese creator: Hilmar Hinz creator: Maria del Mar Gil creator: Miquel Palmer creator: Michael Breen creator: Antoni Mira creator: Elena Pastor creator: Amalia Grau creator: Andrea Campos-Candela creator: Elka Koleva creator: Antoni Maria Grau creator: Beatriz Morales-Nin uri: https://doi.org/10.7717/peerj.4707 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Catanese et al. title: Identification and expression analysis of cytokinin metabolic genes IPTs, CYP735A and CKXs in the biofuel plant Jatropha curcas link: https://peerj.com/articles/4812 last-modified: 2018-05-16 description: The seed oil of Jatropha curcas is considered a potential bioenergy source that could replace fossil fuels. However, the seed yield of Jatropha is low and has yet to be improved. We previously reported that exogenous cytokinin treatment increased the seed yield of Jatropha. Cytokinin levels are directly regulated by isopentenyl transferase (IPT), cytochrome P450 monooxygenase, family 735, subfamily A (CYP735A), and cytokinin oxidase/dehydrogenase (CKX). In this study, we cloned six IPT genes, one JcCYP735A gene, and seven JcCKX genes. The expression patterns of these 14 genes in various organs were determined using real-time quantitative PCR. JcIPT1 was primarily expressed in roots and seeds, JcIPT2 was expressed in roots, apical meristems, and mature leaves, JcIPT3 was expressed in stems and mature leaves, JcIPT5 was expressed in roots and mature leaves, JcIPT6 was expressed in seeds at 10 days after pollination, and JcIPT9 was expressed in mature leaves. JcCYP735A was mainly expressed in roots, flower buds, and seeds. The seven JcCKX genes also showed different expression patterns in different organs of Jatropha. In addition, CK levels were detected in flower buds and seeds at different stages of development. The concentration of N6-(Δ2-isopentenyl)-adenine (iP), iP-riboside, and trans-zeatin (tZ) increased with flower development, and the concentration of iP decreased with seed development, while that of tZ increased. We further analyzed the function of JcCYP735A using the CRISPR-Cas9 system, and found that the concentrations of tZ and tZ-riboside decreased significantly in the Jccyp735a mutants, which showed severely retarded growth. These findings will be helpful for further studies of the functions of cytokinin metabolic genes and understanding the roles of cytokinins in Jatropha growth and development. creator: Li Cai creator: Lu Zhang creator: Qiantang Fu creator: Zeng-Fu Xu uri: https://doi.org/10.7717/peerj.4812 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Cai et al. title: Geographical variation in colour of female threespine stickleback (Gasterosteus aculeatus) link: https://peerj.com/articles/4807 last-modified: 2018-05-16 description: The ecological multifunctionality of colour often results in multiple selective pressures operating on a single trait. Most research on colour evolution focuses on males because they are the most conspicuous sex in most species. This bias can limit inferences about the ecological drivers of colour evolution. For example, little is known about population divergence in colour of female threespine stickleback (Gasterosteus aculeatus), which is among the most intensively-studied model vertebrates in evolution, ecology, and behaviour. In contrast, the evolution and ecology of colour in male stickleback has received considerable attention. One aspect of female colouration that is lacking previous research is non-ornamental body colour. Non-ornamental colour can play defensive and social roles, and indicate other aspects of female stickleback ecology. To remedy this knowledge gap, we measured the colour and brightness of one dorsal and one ventral lateral area on female stickleback from nine lake populations on Vancouver Island. We found that lake populations varied in overall colour brightness and dorso-ventral contrast. In addition, we found that female brightness increased with lake size, indicating potential ecological drivers of these colour differences. Our results demonstrate that there is substantial scope for future research on female colour diversification, which has been overlooked because past researchers focused on dramatic male nuptial colours. creator: Connor M. French creator: Travis Ingram creator: Daniel I. Bolnick uri: https://doi.org/10.7717/peerj.4807 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 French et al. title: Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines link: https://peerj.com/articles/4781 last-modified: 2018-05-16 description: Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region. creator: Andrian P. Gajigan creator: Aletta T. Yñiguez creator: Cesar L. Villanoy creator: Maria Lourdes San Diego-McGlone creator: Gil S. Jacinto creator: Cecilia Conaco uri: https://doi.org/10.7717/peerj.4781 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gajigan et al. title: Genetic inactivation of alpha-synuclein affects embryonic development of dopaminergic neurons of the substantia nigra, but not the ventral tegmental area, in mouse brain link: https://peerj.com/articles/4779 last-modified: 2018-05-16 description: Lesion of the dopaminergic neurons of the nigrostriatal system is a key feature of Parkinson’s disease (PD). Alpha-synuclein is a protein that is a major component of Lewy bodies, histopathological hallmarks of PD, and is involved in regulation of dopamine (DA) neurotransmission. Previous studies of knockout mice have shown that inactivation of alpha-synuclein gene can lead to the reduction in number of DA neurons in the substantia nigra (SN). DA neurons of the SN are known to be the most affected in PD patients whereas DA neurons of neighboring ventral tegmental area (VTA) are much less susceptible to degeneration. Here we have studied the dynamics of changes in TH-positive cell numbers in the SN and VTA during a critical period of their embryonic development in alpha-synuclein knockout mice. This precise study of DA neurons during development of the SN revealed that not only is the number of DA neurons reduced by the end of the period of ontogenic selection, but that the way these neurons are formed is altered in alpha-synuclein knockout mice. At the same time, DA neurons in the VTA are not affected. Alpha-synuclein exerts a modulating effect on the formation of DA neurons in the SN and has no effect on the formation of DA neurons in VTA, the structure that is much less susceptible to degeneration in a brain with PD, suggesting a potential role of alpha-synuclein in the development of the population of DA neurons in substantia nigra. creator: Tatiana V. Tarasova creator: Olga A. Lytkina creator: Valeria V. Goloborshcheva creator: Larisa N. Skuratovskaya creator: Alexandr I. Antohin creator: Ruslan K. Ovchinnikov creator: Michail S. Kukharsky uri: https://doi.org/10.7717/peerj.4779 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tarasova et al. title: Novel, non-symbiotic isolates of Neorhizobium from a dryland agricultural soil link: https://peerj.com/articles/4776 last-modified: 2018-05-16 description: Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium, as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium, closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium. All the isolates lacked nod and nif symbiotic genes but contained a repABC replication/maintenance region, characteristic of rhizobial plasmids, within large contigs from their draft genome sequences. These repABC sequences were related, but not identical, to repABC sequences found in symbiotic plasmids from N. galegae, suggesting that the non-symbiotic isolates have the potential to harbor symbiotic plasmids. This is the first report of non-symbiotic members of Neorhizobium from soil. creator: Amalia Soenens creator: Juan Imperial uri: https://doi.org/10.7717/peerj.4776 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Soenens and Imperial title: Pollution of the sediments of the coastal zone of the Sambia Peninsula and the Curonian Spit (Southeastern Baltic Sea) link: https://peerj.com/articles/4770 last-modified: 2018-05-16 description: The detailed environmental survey of the coastal zone of the Kaliningrad Region northern coast was carried out. The pollutants distribution in the silty clay fraction and calculation of ecological indexes allowed the evaluation of distribution of potentially harmful elements (PHEs). The sources of pollution in the most intensively used areas were identified, and transit and accumulation zones were allocated. A large area of anomalous content of PHEs was revealed on the underwater coastal slope of the Curonian Spit National Park, which is situated far from the sources of pollution. The alongshore bed load transport provides the contamination of the underwater slope whereas the beaches are less exposed to pollution. creator: Alexander Krek creator: Viktor Krechik creator: Aleksandr Danchenkov creator: Elena Krek uri: https://doi.org/10.7717/peerj.4770 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Krek et al. title: A new species of Pseudopaludicola (Anura, Leiuperinae) from Espírito Santo, Brazil link: https://peerj.com/articles/4766 last-modified: 2018-05-16 description: We describe a new anuran species of the genus Pseudopaludicola that inhabits sandy areas in resting as associated to the Atlantic Forest biome in the state of Espírito Santo, Brazil. The new species is characterized by: SVL 11.7–14.6 mm in males, 14.0–16.7 mm in females; body slender; fingertips knobbed, with a central groove; hindlimbs short; abdominal fold complete; arytenoid cartilages wide; prepollex with base and two segments; prehallux with base and one segment; frontoparietal fontanelle partially exposed; advertisement call with one note composed of two isolated pulses per call; call dominant frequency ranging 4,380–4,884 Hz; diploid chromosome number 22; and Ag-NORs on 8q subterminal. In addition, its 16S rDNA sequence shows high genetic distances when compared to sequences of related species, which provides strong evidence that the new species is an independent lineage. creator: Dario E. Cardozo creator: Diego Baldo creator: Nadya Pupin creator: João Luiz Gasparini creator: Célio F. Baptista Haddad uri: https://doi.org/10.7717/peerj.4766 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cardozo et al. title: Integrated bioinformatic changes and analysis of retina with time in diabetic rats link: https://peerj.com/articles/4762 last-modified: 2018-05-16 description: Diabetic retinopathy (DR) is the most common chronic complication of diabetes. It can cause impaired vision and even blindness. However, the pathological mechanism of DR is still unknown. In the present study, we use bioinformatic analysis to reveal the pathological changes of early DR in a streptozotocin (STZ) induced diabetes rat model. The dataset GSE28831 was downloaded from the Gene Expression Omnibus (GEO) database. To clarify the pathological mechanism of early DR, genes which were up-regulated (UP group) or down-regulated (DOWN group) over time were identified. One hundred eighty six genes in the UP group and 85 genes in the DOWN group were defined. There were in total 28 Gene ontology (GO) terms with a P value lower than 0.05 in UP group, including astrocyte development, neutrophil chemotaxis, neutrophil aggregation, mesenchymal cell proliferation and so on. In the DOWN group, there were totally 14 GO terms with a P value lower than 0.05, including visual perception, lens development in camera-type eye, camera-type eye development, bicellular tight junction and so on. Signaling pathways were analyzed with all genes in the UP and DOWN groups, and leukocyte transendothelial migration and tight junction were selected. Protein–protein interaction (PPI) network was constructed and six hub genes Diras3, Actn1, Tssk6, Cnot6l, Tek and Fgf4 were selected with connection degree ≥5. S100a8, S100a9 and Tek may be potential targets for DR diagnosis and treatment. This study provides the basis for the diagnosis and treatment of DR in the future. creator: Zekai Cui creator: Qiaolang Zeng creator: Yonglong Guo creator: Shiwei Liu creator: Jiansu Chen uri: https://doi.org/10.7717/peerj.4762 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cui et al. title: Occurrence of termites (Isoptera) on living and standing dead trees in a tropical dry forest in Mexico link: https://peerj.com/articles/4731 last-modified: 2018-05-16 description: Termites play a key role as ecosystem engineers in numerous ecological processes though their role in the dynamics of wood degradation in tropical dry forests, particularly at the level of the crown canopy, has been little studied. In this study, we analysed the occurrence of termites in the forest canopy by evaluating the density and proportion of living and standing dead trees associated with termites in deciduous and riparian habitats of the tropical dry forest in Chamela, Mexico. The results indicated that 60–98% of standing dead trees and 23–59% of living trees in Chamela were associated with termites. In particular, we found that the density of standing dead trees was higher in deciduous forests (0.057–0.066 trees/m2) than in riparian forests (0.022 and 0.027 trees/m2), even though the proportion of trees was not significantly different among habitats. Additionally, we found a higher density of trees associated with termites in trees of smaller size classes (0.01–0.09 trees/m2) than in larger class sizes (0–0.02 trees/m2). Interestingly, 72% of variation in the density of trees associated with termites is explained by the density of standing dead trees. Overall, these results indicate that standing dead tree availability might be the main factor regulating termite populations in Chamela forest and suggest that termites could play a key role in the decomposition of above-ground dead wood, mediating the incorporation of suspended and standing dead wood into the soil. creator: Nancy Calderón-Cortés creator: Luis H. Escalera-Vázquez creator: Ken Oyama uri: https://doi.org/10.7717/peerj.4731 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Calderón-Cortés et al. title: Overwintering temperature and body condition shift emergence dates of spring-emerging solitary bees link: https://peerj.com/articles/4721 last-modified: 2018-05-16 description: Solitary bees in seasonal environments must align their life-cycles with favorable environmental conditions and resources; the timing of their emergence is highly fitness relevant. In several bee species, overwintering temperature influences both emergence date and body weight at emergence. High variability in emergence dates among specimens overwintering at the same temperatures suggests that the timing of emergence also depends on individual body conditions. However, possible causes for this variability, such as individual differences in body size or weight, have been rarely studied. In a climate chamber experiment using two spring-emerging mason bees (Osmia cornuta and O. bicornis), we investigated the relationship between temperature, emergence date, body weight, and body size, the last of which is not affected by overwintering temperature. Our study showed that body weight declined during hibernation more strongly in warm than in cold overwintering temperatures. Although bees emerged earlier in warm than in cold overwintering temperatures, at the time of emergence, bees in warm overwintering temperatures had lower body weights than bees in cold overwintering temperatures (exception of male O. cornuta). Among specimens that experienced the same overwintering temperatures, small and light bees emerged later than their larger and heavier conspecifics. Using a simple mechanistic model we demonstrated that spring-emerging solitary bees use a strategic approach and emerge at a date that is most promising for their individual fitness expectations. Our results suggest that warmer overwintering temperatures reduce bee fitness by causing a decrease in body weight at emergence. We showed furthermore that in order to adjust their emergence dates, bees use not only temperature but also their individual body condition as triggers. This may explain differing responses to climate warming within and among bee populations and may have consequences for bee-plant interactions as well as for the persistence of bee populations under climate change. creator: Mariela Schenk creator: Oliver Mitesser creator: Thomas Hovestadt creator: Andrea Holzschuh uri: https://doi.org/10.7717/peerj.4721 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Schenk et al. title: Identification of potential crucial genes and pathways associated with vein graft restenosis based on gene expression analysis in experimental rabbits link: https://peerj.com/articles/4704 last-modified: 2018-05-16 description: Occlusive artery disease (CAD) is the leading cause of death worldwide. Bypass graft surgery remains the most prevalently performed treatment for occlusive arterial disease, and veins are the most frequently used conduits for surgical revascularization. However, the clinical efficacy of bypass graft surgery is highly affected by the long-term potency rates of vein grafts, and no optimal treatments are available for the prevention of vein graft restenosis (VGR) at present. Hence, there is an urgent need to improve our understanding of the molecular mechanisms involved in mediating VGR. The past decade has seen the rapid development of genomic technologies, such as genome sequencing and microarray technologies, which will provide novel insights into potential molecular mechanisms involved in the VGR program. Ironically, high throughput data associated with VGR are extremely scarce. The main goal of the current study was to explore potential crucial genes and pathways associated with VGR and to provide valid biological information for further investigation of VGR. A comprehensive bioinformatics analysis was performed using high throughput gene expression data. Differentially expressed genes (DEGs) were identified using the R and Bioconductor packages. After functional enrichment analysis of the DEGs, protein–protein interaction (PPI) network and sub-PPI network analyses were performed. Finally, nine potential hub genes and fourteen pathways were identified. These hub genes may interact with each other and regulate the VGR program by modulating the cell cycle pathway. Future studies focusing on revealing the specific cellular and molecular mechanisms of these key genes and pathways involved in regulating the VGR program may provide novel therapeutic targets for VGR inhibition. creator: Qiang Liu creator: Xiujie Yin creator: Mingzhu Li creator: Li Wan creator: Liqiao Liu creator: Xiang Zhong creator: Zhuoqi Liu creator: Qun Wang uri: https://doi.org/10.7717/peerj.4704 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu et al. title: Coarse- and fine-scale patterns of distribution and habitat selection places an Amazonian floodplain curassow in double jeopardy link: https://peerj.com/articles/4617 last-modified: 2018-05-16 description: Patterns of habitat selection are influenced by local productivity, resource availability, and predation risk. Species have taken millions of years to hone the macro- and micro-habitats they occupy, but these may now overlap with contemporary human threats within natural species ranges. Wattled Curassow (Crax globulosa), an endemic galliform species of the western Amazon, is threatened by both hunting and habitat loss, and is restricted to white-water floodplain forests of major Amazonian rivers. In this study conducted along the Juruá River, Amazonas, Brazil, we quantified the ranging ecology and fine-scale patterns of habitat selection of the species. We estimated the home range size of C. globulosa using conventional VHF telemetry. To estimate patterns of habitat selection, we used geo-locations of day ranges to examine the extent and intensity of use across the floodplain, which were then compared to a high-resolution flood map of the study area. We captured two females and one male, which we monitored for 13 months between September 2014 and September 2015. Average home range size was 283 ha, based on the 95% aLoCoH estimator. Wattled Curassows selected areas of prolonged flood pulses (six to eight months/year) and had a consistent tendency to be near open water, usually in close proximity to river banks and lakes, especially during the dry season. Amazonian floodplains are densely settled, and the small portions of floodplain habitat used by Wattled Curassows are both the most accessible to hunters and most vulnerable to deforestation. As a result, the geographic and ecological distribution of Wattled Curassows places them at much higher extinction risk at multiple spatial scales, highlighting the need to consider habitat preferences within their conservation strategy. creator: Gabriel A. Leite creator: Izeni P. Farias creator: André L. S. Gonçalves creator: Joseph E. Hawes creator: Carlos A. Peres uri: https://doi.org/10.7717/peerj.4617 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Leite et al. title: Modelling the growth of the brown frog (Rana dybowskii) link: https://peerj.com/articles/4587 last-modified: 2018-05-16 description: Well-controlled development leads to uniform body size and a better growth rate; therefore, the ability to determine the growth rate of frogs and their period of sexual maturity is essential for producing healthy, high-quality descendant frogs. To establish a working model that can best predict the growth performance of frogs, the present study examined the growth of one-year-old and two-year-old brown frogs (Rana dybowskii) from metamorphosis to hibernation (18 weeks) and out-hibernation to hibernation (20 weeks) under the same environmental conditions. Brown frog growth was studied and mathematically modelled using various nonlinear, linear, and polynomial functions. The model input values were statistically evaluated using parameters such as the Akaike’s information criterion. The body weight/size ratio (Kwl) and Fulton’s condition factor (K) were used to compare the weight and size of groups of frogs during the growth period. The results showed that the third- and fourth-order polynomial models provided the most consistent predictions of body weight for age 1 and age 2 brown frogs, respectively. Both the Gompertz and third-order polynomial models yielded similarly adequate results for the body size of age 1 brown frogs, while the Janoschek model produced a similarly adequate result for the body size of age 2 brown frogs. The Brody and Janoschek models yielded the highest and lowest estimates of asymptotic weight, respectively, for the body weights of all frogs. The Kwl value of all frogs increased from 0.40 to 3.18. The K value of age 1 frogs decreased from 23.81 to 9.45 in the first four weeks. The K value of age 2 frogs remained close to 10. Graphically, a sigmoidal trend was observed for body weight and body size with increasing age. The results of this study will be useful not only for amphibian research but also for frog farming management strategies and decisions. creator: Qing Tong creator: Xiao-peng Du creator: Zong-fu Hu creator: Li-yong Cui creator: Hong-bin Wang uri: https://doi.org/10.7717/peerj.4587 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tong et al. title: Breast fibroblasts in both cancer and normal tissues induce phenotypic transformation of breast cancer stem cells: a preliminary study link: https://peerj.com/articles/4805 last-modified: 2018-05-15 description: BackgroundBreast cancer stem cells (BCSCs) are associated with the invasion of breast cancer. In recent years, studies have demonstrated different phenotypes among BCSCs. Furthermore, BCSCs of diverse phenotypes are present at different tumour sites and different histological stages. Fibroblasts are involved in the phenotypic transformation of BCSCs. Cancer-associated fibroblasts (CAFs) participate in the induction of epithelial–mesenchymal transition, thereby promoting the acquisition of stem cell characteristics, but little is known about the role of normal fibroblasts (NFs) in the phenotypic transformation of BCSCs or about the effect of CAFs and NFs on BCSC phenotypes.MethodsA total of six pairs of primary CAFs and NFs were isolated from surgical samples of breast cancer patients and subjected to morphological, immunohistochemical, cell invasion and proteomics analyses. After establishing a cell culture system with conditioned medium from CAFs and NFs, we used the mammosphere formation assay to explore the effect of CAFs and NFs on the self-renewal ability of BCSCs. The effect of CAFs and NFs on the phenotypic differentiation of BCSCs was further analysed by flow cytometry and immunofluorescence.ResultsThe isolated CAFs and NFs did not show significant differences in cell morphology or alpha-smooth muscle actin (α-SMA) expression, but cell invasion and proteomics analyses demonstrated heterogeneity among these fibroblasts. Both CAFs and NFs could promote the generation of BCSCs, but CAFs displayed a greater ability than NFs in promoting mammosphere formation. Conditioned medium from CAFs increased the proportion of aldehyde dehydrogenase-1 positive (ALDH1+) BCSCs, but conditioned medium from NFs was more likely to promote the generation of CD44+CD24− BCSCs from MCF-7 cells.DiscussionThis study validated the heterogeneity among CAFs and NFs and expanded on the conclusion that fibroblasts promote the generation of cancer stem cells. Our results particularly emphasized the effect of NFs on the phenotypic transformation of BCSCs. In addition, this study further highlighted the roles of CAFs and NFs in the induction of different phenotypes in BCSCs. creator: Bixiao Wang creator: Chunfang Xi creator: Mingwei Liu creator: Haichen Sun creator: Shuang Liu creator: Lei Song creator: Hua Kang uri: https://doi.org/10.7717/peerj.4805 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Wang et al. title: Latent profiles of elite Malaysian athletes’ use of psychological skills and techniques and relations with mental toughness link: https://peerj.com/articles/4778 last-modified: 2018-05-15 description: BackgroundThe majority of past work on athletes’ use of psychological skills and techniques (PSTs) has adopted a variable-centered approach in which the statistical relations among study variables are averaged across a sample. However, variable-centered-analyses exclude the possibility that PSTs may be used in tandem or combined in different ways across practice and competition settings. With this empirical gap in mind, the purposes of this study were to identify the number and type of profiles of elite athletes’ use of PSTs, and examine differences between these clusters in terms of their self-reported mental toughness.MethodsIn this cross-sectional survey study, 285 Malaysian elite athletes (170 males, 115 females) aged 15–44 years (M = 18.89, SD = 4.49) completed measures of various PSTs and mental toughness. Latent profile analysis was employed to determine the type and number of profiles that best represent athletes’ reports of their use of PSTs in practice and competition settings, and examine differences between these classes in terms of self-reported mental toughness.ResultsOur results revealed three profiles (low, moderate, high use) in both practice and competition settings that were distinguished primarily according to quantitative differences in the absolute levels of reported use across most of the PSTs assessed in practice and competition settings, which in turn, were differentially related with mental toughness. Specifically, higher use of PSTs was associated with higher levels of mental toughness.ConclusionThis study provides one of the first analyses of the different configurations of athletes’ use of PSTs that typify unique subgroups of performers. An important next step is to examine the longitudinal (in) stability of such classes and therefore provide insight into the temporal dynamics of different configurations of athletes’ use of PSTs. creator: Vellapandian Ponnusamy creator: Robin L.J. Lines creator: Chun-Qing Zhang creator: Daniel F. Gucciardi uri: https://doi.org/10.7717/peerj.4778 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ponnusamy et al. title: Protection of cultured brain endothelial cells from cytokine-induced damage by α-melanocyte stimulating hormone link: https://peerj.com/articles/4774 last-modified: 2018-05-15 description: The blood–brain barrier (BBB), an interface between the systemic circulation and the nervous system, can be a target of cytokines in inflammatory conditions. Pro-inflammatory cytokines tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β) induce damage in brain endothelial cells and BBB dysfunction which contribute to neuronal injury. The neuroprotective effects of α-melanocyte stimulating hormone (α-MSH) were investigated in experimental models, but there are no data related to the BBB. Based on our recent study, in which α-MSH reduced barrier dysfunction in human intestinal epithelial cells induced by TNF-α and IL-1β, we hypothesized a protective effect of α-MSH on brain endothelial cells. We examined the effect of these two pro-inflammatory cytokines, and the neuropeptide α-MSH on a culture model of the BBB, primary rat brain endothelial cells co-cultured with rat brain pericytes and glial cells. We demonstrated the expression of melanocortin-1 receptor in isolated rat brain microvessels and cultured brain endothelial cells by RT-PCR and immunohistochemistry. TNF-α and IL-1β induced cell damage, measured by impedance and MTT assay, which was attenuated by α-MSH (1 and 10 pM). The peptide inhibited the cytokine-induced increase in brain endothelial permeability, and restored the morphological changes in cellular junctions visualized by immunostaining for claudin-5 and β-catenin. Elevated production of reactive oxygen species and the nuclear translocation of NF-κB were also reduced by α-MSH in brain endothelial cells stimulated by cytokines. We demonstrated for the first time the direct beneficial effect of α-MSH on cultured brain endothelial cells, indicating that this neurohormone may be protective at the BBB. creator: András Harazin creator: Alexandra Bocsik creator: Lilla Barna creator: András Kincses creator: Judit Váradi creator: Ferenc Fenyvesi creator: Vilmos Tubak creator: Maria A. Deli creator: Miklós Vecsernyés uri: https://doi.org/10.7717/peerj.4774 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Harazin et al. title: Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations link: https://peerj.com/articles/4769 last-modified: 2018-05-15 description: Elucidating the molecular mechanism of helix–coil transitions of short peptides is a long-standing conundrum in physical chemistry. Although the helix–coil transitions of poly-glutamic acid (PGA) have been extensively studied, the molecular details of its unfolding process still remain unclear. We performed all-atom canonical molecular dynamics simulations for a 20-residue PGA, over a total of 19 μs, in order to investigate its helix-unfolding processes in atomic resolution. Among the 28 simulations, starting with the α-helical conformation, all showed an unfolding process triggered by the unwinding of terminal residues, rather than by kinking and unwinding of the middle region of the chain. The helix–coil–helix conformation which is speculated by the previous experiments was not observed. Upon comparison between the N- and C-termini, the latter tended to be unstable and easily unfolded. While the probabilities of helix elongation were almost the same among the N-terminal, middle, and C-terminal regions of the chain, unwinding of the helix was enriched at the C-terminal region. The turn and 310-helix conformations were kinetic intermediates in the formation and deformation of α-helix, consistent with the previous computational studies for Ala-based peptides. creator: Naoki Ogasawara creator: Kota Kasahara creator: Ryosuke Iwai creator: Takuya Takahashi uri: https://doi.org/10.7717/peerj.4769 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ogasawara et al. title: An examination of the impact of Olson’s extinction on tetrapods from Texas link: https://peerj.com/articles/4767 last-modified: 2018-05-15 description: It has been suggested that a transition between a pelycosaurian-grade synapsid dominated fauna of the Cisuralian (early Permian) and the therapsid dominated fauna of the Guadalupian (middle Permian) was accompanied by, and possibly driven by, a mass extinction dubbed Olson’s Extinction. However, this interpretation of the record has recently been criticised as being a result of inappropriate time-binning strategies: calculating species richness within international stages or substages combines extinctions occurring throughout the late Kungurian stage into a single event. To address this criticism, I examine the best record available for the time of the extinction, the tetrapod-bearing formations of Texas, at a finer stratigraphic scale than those previously employed. Species richness is calculated using four different time-binning schemes: the traditional Land Vertebrate Faunachrons (LVFs); a re-definition of the LVFs using constrained cluster analysis; individual formations treated as time bins; and a stochastic approach assigning specimens to half-million-year bins. Diversity is calculated at the genus and species level, both with and without subsampling, and extinction rates are also inferred. Under all time-binning schemes, both at the genus and species level, a substantial drop in diversity occurs during the Redtankian LVF. Extinction rates are raised above background rates throughout this time, but the biggest peak occurs in the Choza Formation (uppermost Redtankian), coinciding with the disappearance from the fossil record of several of amphibian clades. This study, carried out at a finer stratigraphic scale than previous examinations, indicates that Olson’s Extinction is not an artefact of the method used to bin data by time in previous analyses. creator: Neil Brocklehurst uri: https://doi.org/10.7717/peerj.4767 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brocklehurst title: Impact of Front Range sources on reactive nitrogen concentrations and deposition in Rocky Mountain National Park link: https://peerj.com/articles/4759 last-modified: 2018-05-15 description: Human influenced atmospheric reactive nitrogen (RN) is impacting ecosystems in Rocky Mountain National Park (ROMO). Due to ROMO’s protected status as a Class 1 area, these changes are concerning, and improving our understanding of the contributions of different types of RN and their sources is important for reducing impacts in ROMO. In July–August 2014 the most comprehensive measurements (to date) of RN were made in ROMO during the Front Range Air Pollution and Photochemistry Éxperiment (FRAPPÉ). Measurements included peroxyacetyl nitrate (PAN), C1–C5 alkyl nitrates, and high-time resolution NOx, NOy, and ammonia. A limited set of measurements was extended through October. Co-located measurements of a suite of volatile organic compounds provide information on source types impacting ROMO. Specifically, we use ethane as a tracer of oil and gas operations and tetrachloroethylene (C2Cl4) as an urban tracer to investigate their relationship with RN species and transport patterns. Results of this analysis suggest elevated RN concentrations are associated with emissions from oil and gas operations, which are frequently co-located with agricultural production and livestock feeding areas in the region, and from urban areas. There also are periods where RN at ROMO is impacted by long-range transport. We present an atmospheric RN budget and a nitrogen deposition budget with dry and wet components. Total deposition for the period (7/1–9/30) was estimated at 1.58 kg N/ha, with 87% from wet deposition during this period of above average precipitation. Ammonium wet deposition was the dominant contributor to total nitrogen deposition followed by nitrate wet deposition and total dry deposition. Ammonia was estimated to be the largest contributor to dry deposition followed by nitric acid and PAN (other species included alkyl nitrates, ammonium and nitrate). All three species are challenging to measure routinely, especially at high time resolution. creator: Katherine B. Benedict creator: Anthony J. Prenni creator: Amy P. Sullivan creator: Ashley R. Evanoski-Cole creator: Emily V. Fischer creator: Sara Callahan creator: Barkley C. Sive creator: Yong Zhou creator: Bret A. Schichtel creator: Jeffrey L. Collett Jr uri: https://doi.org/10.7717/peerj.4759 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Knowing your neighbourhood—the effects of Epichloë endophytes on foliar fungal assemblages in perennial ryegrass in dependence of season and land-use intensity link: https://peerj.com/articles/4660 last-modified: 2018-05-15 description: Epichloë endophytes associated with cool-season grass species can protect their hosts from herbivory and can suppress mycorrhizal colonization of the hosts’ roots. However, little is known about whether or not Epichloë endophyte infection can also change the foliar fungal assemblages of the host. We tested 52 grassland study sites along a land-use intensity gradient in three study regions over two seasons (spring vs. summer) to determine whether Epichloë infection of the host grass Lolium perenne changes the fungal community structure in leaves. Foliar fungal communities were assessed by Next Generation Sequencing of the ITS rRNA gene region. Fungal community structure was strongly affected by study region and season in our study, while land-use intensity and infection with Epichloë endophytes had no significant effects. We conclude that effects on non-systemic endophytes resulting from land use practices and Epichloë infection reported in other studies were masked by local and seasonal variability in this study’s grassland sites. creator: Julia König creator: Marco Alexandre Guerreiro creator: Derek Peršoh creator: Dominik Begerow creator: Jochen Krauss uri: https://doi.org/10.7717/peerj.4660 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 König et al. title: Modulation of transcriptional activity in brain lower grade glioma by alternative splicing link: https://peerj.com/articles/4686 last-modified: 2018-05-14 description: Proteins that modify the activity of transcription factors (TFs) are often called modulators and play a vital role in gene transcriptional regulation. Alternative splicing is a critical step of gene processing, and differentially spliced isoforms may have different functions. Alternative splicing can modulate gene function by adding or removing certain protein domains and thereby influence the activity of a protein. The objective of this study is to investigate the role of alternative splicing in modulating the transcriptional regulation in brain lower grade glioma (LGG), especially transcription factor ELK1, which is closely related to various disorders, including Alzheimer’s disease and Down syndrome. The results showed that changes in the exon inclusion ratio of proteins APP and STK16 are associated with changes in the expression correlation between ELK1 and its targets. In addition, the structural features of the two modulators are strongly associated with the pathological impact of exon inclusion. The results of our analysis suggest that alternatively spliced proteins have different functions in modifying transcription factors and can thereby induce the dysregulation of multiple genes. creator: Jin Li creator: Yang Wang creator: Xianglian Meng creator: Hong Liang uri: https://doi.org/10.7717/peerj.4686 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Chitin distribution in the Oithona digestive and reproductive systems revealed by fluorescence microscopy link: https://peerj.com/articles/4685 last-modified: 2018-05-14 description: Among copepods, which are the most abundant animals on Earth, the genus Oithona is described as one of the most numerous and plays a major role in the marine food chain and biogeochemical cycles, particularly through the excretion of chitin-coated fecal pellets. Despite the morphology of several Oithona species is well known, knowledge of its internal anatomy and chitin distribution is still limited. To answer this problem, Oithona nana and O. similis individuals were stained by Wheat Germ Agglutinin-Fluorescein IsoThioCyanate (WGA-FITC) and DiAmidino-2-PhenylIndole (DAPI) for fluorescence microscopy observations. The image analyses allowed a new description of the organization and chitin content of the digestive and reproductive systems of Oithona male and female. Chitin microfibrils were found all along the digestive system from the stomach to the hindgut with a higher concentration at the peritrophic membrane of the anterior midgut. Several midgut shrinkages were observed and proposed to be involved in faecal pellet shaping and motion. Amorphous chitin structures were also found to be a major component of the ducts and seminal vesicles and receptacles. The rapid staining protocol we proposed allowed a new insight into the Oithona internal anatomy and highlighted the role of chitin in the digestion and reproduction. This method could be applied to a wide range of copepods in order to perform comparative anatomy analyses. creator: Kevin Sugier creator: Benoit Vacherie creator: Astrid Cornils creator: Patrick Wincker creator: Jean-Louis Jamet creator: Mohammed-Amin Madoui uri: https://doi.org/10.7717/peerj.4685 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Sugier et al. title: Testing methods to mitigate Caribbean yellow-band disease on Orbicella faveolata link: https://peerj.com/articles/4800 last-modified: 2018-05-11 description: Outbreaks of coral diseases continue to reduce global coral populations. In the Caribbean, yellow band is a severe and wide-spread disease that commonly affects corals of the Orbicella spp. complex, significantly impeding coral reproduction, and hindering the natural recovery of Orbicella spp. populations. Caribbean yellow-band disease (CYBD) lesions may be severe, and often result in the complete loss of coral tissue. The slow spread of CYBD, however, provides an opportunity to test methods to mitigate the disease. Here we report the results of in situ experiments, conducted within Buck Island Reef National Monument in St. Croix, USVI, to test the effectiveness of three techniques to minimize disease impact on Orbicella faveolata: (1) shading, (2) aspirating, and (3) chiseling a “firebreak” to isolate the lesion. Neither shading nor aspirating the diseased tissue significantly reduced CYBD tissue loss. However, chiseling reduced the rate and amount of tissue lost by 31%. While 30–40% of the chiseled lesions appeared to be free of disease signs 12–16 months after treatment, success significantly and steadily declined over 23 months, indicating a possible lack of long-term viability of the technique. The results of this study demonstrate that creating a “firebreak” between diseased and healthy-appearing tissue slows the spread of the disease and may prolong the life of O. faveolata colonies. The firebreak method yielded the best results of all the techniques tested, and also required the least amount of effort and resources. However, we do not recommend that this treatment alone be used for long-term disease mitigation. Rather, we propose that modifications of this and other treatment options be sought. The results also highlight the need for extended monitoring of CYBD after any treatment, due to the slow but variable rate and pattern of tissue loss in this disease. creator: Carly J. Randall creator: Elizabeth M. Whitcher creator: Tessa Code creator: Clayton Pollock creator: Ian Lundgren creator: Zandy Hillis-Starr creator: Erinn M. Muller uri: https://doi.org/10.7717/peerj.4800 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Randall et al. title: ‘2TM proteins’: an antigenically diverse superfamily with variable functions and export pathways link: https://peerj.com/articles/4757 last-modified: 2018-05-11 description: Malaria is a disease that affects millions of people annually. An intracellular habitat and lack of protein synthesizing machinery in erythrocytes pose numerous difficulties for survival of the human pathogen Plasmodium falciparum. The parasite refurbishes the infected red blood cell (iRBC) by synthesis and export of several proteins in an attempt to suffice its metabolic needs and evade the host immune response. Immune evasion is largely mediated by surface display of highly polymorphic protein families known as variable surface antigens. These include the two trans-membrane (2TM) superfamily constituted by multicopy repetitive interspersed family (RIFINs), subtelomeric variable open reading frame (STEVORs) and Plasmodium falciparum Maurer’s cleft two trans-membrane proteins present only in P. falciparum and some simian infecting Plasmodium species. Their hypervariable region flanked by 2TM domains exposed on the iRBC surface is believed to generate antigenic diversity. Though historically named “2TM superfamily,” several A-type RIFINs and some STEVORs assume one trans-membrane topology. RIFINs and STEVORs share varied functions in different parasite life cycle stages like rosetting, alteration of iRBC rigidity and immune evasion. Additionally, a member of the STEVOR family has been implicated in merozoite invasion. Differential expression of these families in laboratory strains and clinical isolates propose them to be important for host cell survival and defense. The role of RIFINs in modulation of host immune response and presence of protective antibodies against these surface exposed molecules in patient sera highlights them as attractive targets of antimalarial therapies and vaccines. 2TM proteins are Plasmodium export elements positive, and several of these are exported to the infected erythrocyte surface after exiting through the classical secretory pathway within parasites. Cleaved and modified proteins are trafficked after packaging in vesicles to reach Maurer’s clefts, while information regarding delivery to the iRBC surface is sparse. Expression and export timing of the RIFIN and Plasmodium falciparum erythrocyte membrane protein1 families correspond to each other. Here, we have compiled and comprehended detailed information regarding orthologues, domain architecture, surface topology, functions and trafficking of members of the “2TM superfamily.” Considering the large repertoire of proteins included in the 2TM superfamily and recent advances defining their function in malaria biology, a surge in research carried out on this important protein superfamily is likely. creator: Jasweer Kaur creator: Rachna Hora uri: https://doi.org/10.7717/peerj.4757 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kaur and Hora title: A strategy to find novel candidate anti-Alzheimer’s disease drugs by constructing interaction networks between drug targets and natural compounds in medical plants link: https://peerj.com/articles/4756 last-modified: 2018-05-11 description: BackgroundAlzheimer’ disease (AD) is an ultimately fatal degenerative brain disorder that has an increasingly large burden on health and social care systems. There are only five drugs for AD on the market, and no new effective medicines have been discovered for many years. Chinese medicinal plants have been used to treat diseases for thousands of years, and screening herbal remedies is a way to develop new drugs.MethodsWe used molecular docking to screen 30,438 compounds from Traditional Chinese Medicine (TCM) against a comprehensive list of AD target proteins. TCM compounds in the top 0.5% of binding affinity scores for each target protein were selected as our research objects. Structural similarities between existing drugs from DrugBank database and selected TCM compounds as well as the druggability of our candidate compounds were studied. Finally, we searched the CNKI database to obtain studies on anti-AD Chinese plants from 2007 to 2017, and only clinical studies were included.ResultsA total of 1,476 compounds (top 0.5%) were selected as drug candidates. Most of these compounds are abundantly found in plants used for treating AD in China, especially the plants from two genera Panax and Morus. We classified the compounds by single target and multiple targets and analyzed the interactions between target proteins and compounds. Analysis of structural similarity revealed that 17 candidate anti-AD compounds were structurally identical to 14 existing approved drugs. Most of them have been reported to have a positive effect in AD. After filtering for compound druggability, we identified 11 anti-AD compounds with favorable properties, seven of which are found in anti-AD Chinese plants. Of 11 anti-AD compounds, four compounds 5,862, 5,863, 5,868, 5,869 have anti-inflammatory activity. The compound 28,814 mainly has immunoregulatory activity. The other six compounds have not yet been reported for any biology activity at present.DiscussionNatural compounds from TCM provide a broad prospect for the screening of anti-AD drugs. In this work, we established networks to systematically study the connections among natural compounds, approved drugs, TCM plants and AD target proteins with the goal of identifying promising drug candidates. We hope that our study will facilitate in-depth research for the treatment of AD in Chinese medicine. creator: Bi-Wen Chen creator: Wen-Xing Li creator: Guang-Hui Wang creator: Gong-Hua Li creator: Jia-Qian Liu creator: Jun-Juan Zheng creator: Qian Wang creator: Hui-Juan Li creator: Shao-Xing Dai creator: Jing-Fei Huang uri: https://doi.org/10.7717/peerj.4756 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chen et al. title: The evaluation of anoxia responsive E2F DNA binding activity in the red eared slider turtle, Trachemys scripta elegans link: https://peerj.com/articles/4755 last-modified: 2018-05-11 description: In many cases, the DNA-binding activity of a transcription factor does not change, while its transcriptional activity is greatly influenced by the make-up of bound proteins. In this study, we assessed the protein composition and DNA-binding ability of the E2F transcription factor complex to provide insight into cell cycle control in an anoxia tolerant turtle through the use of a modified ELISA protocol. This modification also permits the use of custom DNA probes that are tailored to a specific DNA binding region, introducing the ability to design capture probes for non-model organisms. Through the use of EMSA and ELISA DNA binding assays, we have successfully determined the in vitro DNA binding activity and complex dynamics of the Rb/E2F cell cycle regulatory mechanisms in an anoxic turtle, Trachemys scripta elegans. Repressive cell cycle proteins (E2F4, Rb, HDAC4 and Suv39H1) were found to significantly increase at E2F DNA-binding sites upon anoxic exposure in anoxic turtle liver. The lack of p130 involvement in the E2F DNA-bound complex indicates that anoxic turtle liver may maintain G1 arrest for the duration of stress survival. creator: Kyle K. Biggar creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4755 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Biggar and Storey title: Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest link: https://peerj.com/articles/4754 last-modified: 2018-05-11 description: Plant–microbial interactions in the litter layer represent one of the most relevant interactions for biogeochemical cycling as litter decomposition is a key first step in carbon and nitrogen turnover. However, our understanding of these interactions in the litter layer remains elusive. In an old-growth mixed Nothofagus forest in Patagonia, we studied the effects of single tree species identity and the mixture of three tree species on the fungal and bacterial composition in the litter layer. We also evaluated the effects of nitrogen (N) addition on these plant–microbial interactions. In addition, we compared the magnitude of stimulation of litter decomposition due to home field advantage (HFA, decomposition occurs more rapidly when litter is placed beneath the plant species from which it had been derived than beneath a different plant species) and N addition that we previously demonstrated in this same forest, and used microbial information to interpret these results. Tree species identity had a strong and significant effect on the composition of fungal communities but not on the bacterial community of the litter layer. The microbial composition of the litter layer under the tree species mixture show an averaged contribution of each single tree species. N addition did not erase the plant species footprint on the fungal community, and neither altered the bacterial community. N addition stimulated litter decomposition as much as HFA for certain tree species, but the mechanisms behind N and HFA stimulation may have differed. Our results suggest that stimulation of decomposition from N addition might have occurred due to increased microbial activity without large changes in microbial community composition, while HFA may have resulted principally from plant species’ effects on the litter fungal community. Together, our results suggest that plant–microbial interactions can be an unconsidered driver of litter decomposition in temperate forests. creator: Lucía Vivanco creator: Nicolás Rascovan creator: Amy T. Austin uri: https://doi.org/10.7717/peerj.4754 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Vivanco et al. title: Do running speed and shoe cushioning influence impact loading and tibial shock in basketball players? link: https://peerj.com/articles/4753 last-modified: 2018-05-11 description: BackgroundTibial stress fracture (TSF) is a common injury in basketball players. This condition has been associated with high tibial shock and impact loading, which can be affected by running speed, footwear condition, and footstrike pattern. However, these relationships were established in runners but not in basketball players, with very little research done on impact loading and speed. Hence, this study compared tibial shock, impact loading, and foot strike pattern in basketball players running at different speeds with different shoe cushioning properties/performances.MethodsEighteen male collegiate basketball players performed straight running trials with different shoe cushioning (regular-, better-, and best-cushioning) and running speed conditions (3.0 m/s vs. 6.0 m/s) on a flat instrumented runway. Tri-axial accelerometer, force plate and motion capture system were used to determine tibial accelerations, vertical ground reaction forces and footstrike patterns in each condition, respectively. Comfort perception was indicated on a 150 mm Visual Analogue Scale. A 2 (speed) × 3 (footwear) repeated measures ANOVA was used to examine the main effects of shoe cushioning and running speeds.ResultsGreater tibial shock (P < 0.001; η2 = 0.80) and impact loading (P < 0.001; η2 = 0.73–0.87) were experienced at faster running speeds. Interestingly, shoes with regular-cushioning or best-cushioning resulted in greater tibial shock (P = 0.03; η2 = 0.39) and impact loading (P = 0.03; η2 = 0.38–0.68) than shoes with better-cushioning. Basketball players continued using a rearfoot strike during running, regardless of running speed and footwear cushioning conditions (P > 0.14; η2 = 0.13).DiscussionThere may be an optimal band of shoe cushioning for better protection against TSF. These findings may provide insights to formulate rehabilitation protocols for basketball players who are recovering from TSF. creator: Wing-Kai Lam creator: Jacobus Liebenberg creator: Jeonghyun Woo creator: Sang-Kyoon Park creator: Suk-Hoon Yoon creator: Roy Tsz-Hei Cheung creator: Jiseon Ryu uri: https://doi.org/10.7717/peerj.4753 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lam et al. title: Westwards and northwards dispersal of Triosteum himalayanum (Caprifoliaceae) from the Hengduan Mountains region based on chloroplast DNA phylogeography link: https://peerj.com/articles/4748 last-modified: 2018-05-11 description: The varying topography and environment that resulted from paleoorogeny and climate fluctuations of the Himalaya–Hengduan Mountains (HHM) areas had a considerable impact on the evolution of biota during the Quaternary. To understand the phylogeographic pattern and historical dynamics of Triosteum himalayanum (Caprifoliaceae), we sequenced three chloroplast DNA fragments (rbcL-accD, rps15-ycf1, and trnH-psbA) from 238 individuals representing 20 populations. Nineteen haplotypes (H1–H19) were identified based on 23 single-site mutations and eight indels. Most haplotypes were restricted to a single population or neighboring populations. Analysis of molecular variance revealed that variations among populations were much higher than that within populations for the overall gene pool, as well as for the East Himalayan group (EH group) and the North Hengduan group (NHM group), but not for the Hengduan Mountains group (HM group). Ecoregions representing relatively high genetic diversity or high frequencies of private haplotypes were discovered, suggesting that this alpine herbaceous plant underwent enhanced allopatric divergence in isolated and fragmented locations during the Quaternary glaciations. The current phylogeographic structure of T. himalayanum might be due to heterogeneous habitats and Quaternary climatic oscillations. Based on the phylogeographic structure of T. himalayanum populations, the phylogenetic relationship of identified haplotypes and palaeodistributional reconstruction, we postulated both westwards and northwards expansion from the HM group for this species. The westwards dispersal corridor could be long, narrow mountain areas and/or the Yarlung Zangbo Valley, while the northwards movement path could be south–north oriented mountains and low-elevation valleys. creator: Hai-rui Liu creator: Qing-bo Gao creator: Fa-qi Zhang creator: Gulzar Khan creator: Shi-long Chen uri: https://doi.org/10.7717/peerj.4748 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Liu et al. title: From the Guiana Highlands to the Brazilian Atlantic Rain Forest: four new species of Selaginella (Selaginellaceae – Lycopodiophyta: S. agioneuma, S. magnafornensis, S. ventricosa, and S. zartmanii) link: https://peerj.com/articles/4708 last-modified: 2018-05-11 description: We describe four new species in the genus Selaginella (i.e., S. agioneuma, S. magnafornensis, S. ventricosa, and S. zartmanii) from Brazil, all presently classified in subg. Stachygynandrum. For each of the new taxa we discuss taxonomic affinities and provide information on habitat, distribution, and conservation status. In addition, line drawings and scanning electron microscope (SEM) images of stems sections, leaves, and spores (when present) are included. Selaginella agioneuma and S. magnafornensis are from the State of Espíritu Santo where they inhabit premontane to montane Atlantic rain forests in the Reserva Biológica Augusto Ruschi and Parque Estadual Forno Grande, respectively. Selaginella ventricosa was collected in upper montane forests at Parque Nacional Serra da Mocidade, State of Roraima and S. zartmanii in premontane Amazon rain forests on upper Rio Negro at Mpio. São Gabriel da Cachoeira, Amazonas State in both Serra Curicuriari and the Morro dos Seis Lagos Biological Reserve. creator: Iván A. Valdespino creator: Christian A. López creator: Adriel M. Sierra creator: Jorge Ceballos uri: https://doi.org/10.7717/peerj.4708 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Valdespino et al. title: Comparison of hoop-net trapping and visual surveys to monitor abundance of the Rio Grande cooter (Pseudemys gorzugi) link: https://peerj.com/articles/4677 last-modified: 2018-05-11 description: Abundance estimates play an important part in the regulatory and conservation decision-making process. It is important to correct monitoring data for imperfect detection when using these data to track spatial and temporal variation in abundance, especially in the case of rare and elusive species. This paper presents the first attempt to estimate abundance of the Rio Grande cooter (Pseudemys gorzugi) while explicitly considering the detection process. Specifically, in 2016 we monitored this rare species at two sites along the Black River, New Mexico via traditional baited hoop-net traps and less invasive visual surveys to evaluate the efficacy of these two sampling designs. We fitted the Huggins closed-capture estimator to estimate capture probabilities using the trap data and distance sampling models to estimate detection probabilities using the visual survey data. We found that only the visual survey with the highest number of observed turtles resulted in similar abundance estimates to those estimated using the trap data. However, the estimates of abundance from the remaining visual survey data were highly variable and often underestimated abundance relative to the estimates from the trap data. We suspect this pattern is related to changes in the basking behavior of the species and, thus, the availability of turtles to be detected even though all visual surveys were conducted when environmental conditions were similar. Regardless, we found that riverine habitat conditions limited our ability to properly conduct visual surveys at one site. Collectively, this suggests visual surveys may not be an effective sample design for this species in this river system. When analyzing the trap data, we found capture probabilities to be highly variable across sites and between age classes and that recapture probabilities were much lower than initial capture probabilities, highlighting the importance of accounting for detectability when monitoring this species. Although baited hoop-net traps seem to be an effective sampling design, it is important to note that this method required a relatively high trap effort to reliably estimate abundance. This information will be useful when developing a larger-scale, long-term monitoring program for this species of concern. creator: Ivana Mali creator: Adam Duarte creator: Michael R.J. Forstner uri: https://doi.org/10.7717/peerj.4677 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Mali et al. title: Lighten up the dark: metazoan parasites as indicators for the ecology of Antarctic crocodile icefish (Channichthyidae) from the north-west Antarctic Peninsula link: https://peerj.com/articles/4638 last-modified: 2018-05-11 description: Due to its remote and isolated location, Antarctica is home to a unique diversity of species. The harsh conditions have shaped a primarily highly adapted endemic fauna. This includes the notothenioid family Channichthyidae. Their exceptional physiological adaptations have made this family of icefish the focus of many studies. However, studies on their ecology, especially on their parasite fauna, are comparatively rare. Parasites, directly linked to the food chain, can function as biological indicators and provide valuable information on host ecology (e.g., trophic interactions) even in remote habitats with limited accessibility, such as the Southern Ocean. In the present study, channichthyid fish (Champsocephalus gunnari: n = 25, Chaenodraco wilsoni: n = 33, Neopagetopsis ionah: n = 3, Pagetopsis macropterus: n = 4, Pseudochaenichthys georgianus: n = 15) were collected off South Shetland Island, Elephant Island, and the tip of the Antarctic Peninsula (CCAML statistical subarea 48.1). The parasite fauna consisted of 14 genera and 15 species, belonging to the six taxonomic groups including Digenea (four species), Nematoda (four), Cestoda (two), Acanthocephala (one), Hirudinea (three), and Copepoda (one). The stomach contents were less diverse with only Crustacea (Euphausiacea, Amphipoda) recovered from all examined fishes. Overall, 15 new parasite-host records could be established, and possibly a undescribed genotype or even species might exist among the nematodes. creator: Thomas Kuhn creator: Vera M.A. Zizka creator: Julian Münster creator: Regina Klapper creator: Simonetta Mattiucci creator: Judith Kochmann creator: Sven Klimpel uri: https://doi.org/10.7717/peerj.4638 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kuhn et al. title: Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications link: https://peerj.com/articles/4370 last-modified: 2018-05-11 description: The discovery of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka in 2006 was heralded as a major breakthrough of the decade in stem cell research. The ability to reprogram human somatic cells to a pluripotent embryonic stem cell-like state through the ectopic expression of a combination of embryonic transcription factors was greeted with great excitement by scientists and bioethicists. The reprogramming technology offers the opportunity to generate patient-specific stem cells for modeling human diseases, drug development and screening, and individualized regenerative cell therapy. However, fundamental questions have been raised regarding the molecular mechanism of iPSCs generation, a process still poorly understood by scientists. The efficiency of reprogramming of iPSCs remains low due to the effect of various barriers to reprogramming. There is also the risk of chromosomal instability and oncogenic transformation associated with the use of viral vectors, such as retrovirus and lentivirus, which deliver the reprogramming transcription factors by integration in the host cell genome. These challenges can hinder the therapeutic prospects and promise of iPSCs and their clinical applications. Consequently, extensive studies have been done to elucidate the molecular mechanism of reprogramming and novel strategies have been identified which help to improve the efficiency of reprogramming methods and overcome the safety concerns linked with iPSC generation. Distinct barriers and enhancers of reprogramming have been elucidated, and non-integrating reprogramming methods have been reported. Here, we summarize the progress and the recent advances that have been made over the last 10 years in the iPSC field, with emphasis on the molecular mechanism of reprogramming, strategies to improve the efficiency of reprogramming, characteristics and limitations of iPSCs, and the progress made in the applications of iPSCs in the field of disease modelling, drug discovery and regenerative medicine. Additionally, this study appraises the role of genomic editing technology in the generation of healthy iPSCs. creator: Adekunle Ebenezer Omole creator: Adegbenro Omotuyi John Fakoya uri: https://doi.org/10.7717/peerj.4370 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Omole and Fakoya title: Glycosylceramide modifies the flavor and metabolic characteristics of sake yeast link: https://peerj.com/articles/4768 last-modified: 2018-05-10 description: In the manufacture of sake, Japanese traditional rice wine, sake yeast is fermented with koji, which is steamed rice fermented with the non-pathogenic fungus Aspergillus oryzae. During fermentation, sake yeast requires lipids, such as unsaturated fatty acids and sterols, in addition to substances provided by koji enzymes for fermentation. However, the role of sphingolipids on the brewing characteristics of sake yeast has not been studied. In this study, we revealed that glycosylceramide, one of the sphingolipids abundant in koji, affects yeast fermentation. The addition of soy, A. oryzae, and Grifola frondosa glycosylceramide conferred a similar effect on the flavor profiles of sake yeast. In particular, the addition of A. oryzae and G. frondosa glycosylceramide were very similar in terms of the decreases in ethyl caprylate and ethyl 9-decenoate. The addition of soy glycosylceramide induced metabolic changes to sake yeast such as a decrease in glucose, increases in ethanol and glycerol and changes in several amino acids and organic acids concentrations. Tricarboxylic acid (TCA) cycle, pyruvate metabolism, starch and sucrose metabolism, and glycerolipid metabolism were overrepresented in the cultures incubated with sake yeast and soy glycosylceramide. This is the first study of the effect of glycosylceramide on the flavor and metabolic profile of sake yeast. creator: Jannatul Ferdouse creator: Yuki Yamamoto creator: Seiga Taguchi creator: Yumiko Yoshizaki creator: Kazunori Takamine creator: Hiroshi Kitagaki uri: https://doi.org/10.7717/peerj.4768 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ferdouse et al. title: Loss anticipation and outcome during the Monetary Incentive Delay Task: a neuroimaging systematic review and meta-analysis link: https://peerj.com/articles/4749 last-modified: 2018-05-10 description: BackgroundReward seeking and avoidance of punishment are key motivational processes. Brain-imaging studies often use the Monetary Incentive Delay Task (MIDT) to evaluate motivational processes involved in maladaptive behavior. Although the bulk of research has been done on the MIDT reward events, little is known about the neural basis of avoidance of punishment. Therefore, we conducted a meta-analysis of brain activations during anticipation and receipt of monetary losses in healthy controls.MethodsAll functional neuro-imaging studies using the MIDT in healthy controls were retrieved using PubMed, Google Scholar & EMBASE databases. Functional neuro-imaging data was analyzed using the Seed-based d Mapping Software.ResultsThirty-five studies met the inclusion criteria, comprising 699 healthy adults. In both anticipation and loss outcome phases, participants showed large and robust activations in the bilateral striatum, (anterior) insula, and anterior cingulate gyrus relatively to Loss > Neutral contrast. Although relatively similar activation patterns were observed during the two event types, they differed in the pattern of prefrontal activations: ventro-lateral prefrontal activations were observed during loss anticipation, while medial prefrontal activations were observed during loss receipt.DiscussionConsidering that previous meta-analyses highlighted activations in the medial prefrontal cortex/anterior cingulate cortex, the anterior insula and the ventral striatum, the current meta-analysis highlighted the potential specificity of the ventro-lateral prefrontal regions, the median cingulate cortex and the amygdala in the loss events. Future studies can rely on these latter results to examine the neural correlates of loss processing in psychiatric populations characterized by harm avoidance or insensitivity to punishment. creator: Jules R. Dugré creator: Alexandre Dumais creator: Nathalie Bitar creator: Stéphane Potvin uri: https://doi.org/10.7717/peerj.4749 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dugré et al. title: Exotic lagomorph may influence eagle abundances and breeding spatial aggregations: a field study and meta-analysis on the nearest neighbor distance link: https://peerj.com/articles/4746 last-modified: 2018-05-10 description: The introduction of alien species could be changing food source composition, ultimately restructuring demography and spatial distribution of native communities. In Argentine Patagonia, the exotic European hare has one of the highest numbers recorded worldwide and is now a widely consumed prey for many predators. We examine the potential relationship between abundance of this relatively new prey and the abundance and breeding spacing of one of its main consumers, the Black-chested Buzzard-Eagle (Geranoaetus melanoleucus). First we analyze the abundance of individuals of a raptor guild in relation to hare abundance through a correspondence analysis. We then estimated the Nearest Neighbor Distance (NND) of the Black-chested Buzzard-eagle abundances in the two areas with high hare abundances. Finally, we performed a meta-regression between the NND and the body masses of Accipitridae raptors, to evaluate if Black-chested Buzzard-eagle NND deviates from the expected according to their mass. We found that eagle abundance was highly associated with hare abundance, more than with any other raptor species in the study area. Their NND deviates from the value expected, which was significantly lower than expected for a raptor species of this size in two areas with high hare abundance. Our results support the hypothesis that high local abundance of prey leads to a reduction of the breeding spacing of its main predator, which could potentially alter other interspecific interactions, and thus the entire community. creator: Facundo Barbar creator: Gonzalo O. Ignazi creator: Fernando Hiraldo creator: Sergio A. Lambertucci uri: https://doi.org/10.7717/peerj.4746 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Barbar et al. title: A new large-bodied thalattosuchian crocodyliform from the Lower Jurassic (Toarcian) of Hungary, with further evidence of the mosaic acquisition of marine adaptations in Metriorhynchoidea link: https://peerj.com/articles/4668 last-modified: 2018-05-10 description: Based on associated and three-dimensionally preserved cranial and postcranial remains, a new thalattosuchian crocodyliform, Magyarosuchus fitosi gen. et sp. nov. from the Lower Jurassic (Upper Toarcian) Kisgerecse Marl Formation, Gerecse Mountains, Hungary is described here. Phylogenetic analyses using three different datasets indicate that M. fitosi is the sister taxon of Pelagosaurus typus forming together the basal-most sub-clade of Metriorhynchoidea. With an estimated body length of 4.67–4.83 m M. fitosi is the largest known non-metriorhynchid metriorhynchoid. Besides expanding Early Jurassic thalattosuchian diversity, the new specimen is of great importance since, unlike most contemporaneous estuarine, lagoonal or coastal thalattosuchians, it comes from an ‘ammonitico rosso’ type pelagic deposit of the Mediterranean region of the Tethys. A distal caudal vertebra having an unusually elongate and dorsally projected neural spine implies the presence of at least a rudimentary hypocercal tail fin and a slight ventral displacement of the distal caudal vertebral column in this basal metriorhynchoid. The combination of retaining heavy dorsal and ventral armors and having a slight hypocercal tail is unique, further highlighting the mosaic manner of marine adaptations in Metriorhynchoidea. creator: Attila Ősi creator: Mark T. Young creator: András Galácz creator: Márton Rabi uri: https://doi.org/10.7717/peerj.4668 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ősi et al. title: Development of a site fidelity index based on population capture-recapture data link: https://peerj.com/articles/4782 last-modified: 2018-05-09 description: BackgroundSite fidelity is considered as an animal’s tendency to return to a previously occupied place; this is a component of animal behaviour that allows us to understand movement patterns and aspects related to the animal’s life history. Although there are many site fidelity metrics, the lack of standardisation presents a considerable challenge in terms of comparability among studies.MethodsThis investigation focused on the theoretical development of a standardised composite site fidelity index and its statistical distribution in order to obtain reliable population-level site fidelity comparisons. The arithmetic and harmonic means were used as mathematical structures in order to create different indexes by combining the most commonly used indicators for site fidelity such as Occurrence, Permanence and Periodicity. The index performance was then evaluated in simulated populations and one real population of Commerson’s dolphins (Cephalorhynchus commersonii (Lacépède 1804)). In the first case, the indexes were evaluated based on how they were affected by different probability values such as the occurrence of the individual within the study area (φ) and capture probability (p). As a precision measure for the comparison of the indexes, the Wald confidence interval (CI) and the mean square error were applied. Given that there was no previous data concerning the distribution parameters of this population, bootstrap CIs were applied for the study case.ResultsEight alternative indexes were developed. The indexes with an arithmetic mean structure, in general, had a consistently inferior performance than those with a harmonic mean structure. The index IH4, in particular, achieved the best results in all of the scenarios and in the study case. Additionally, this index presented a normal distribution. As such, it was proposed as a standardised measure for site fidelity (Standardised Site Fidelity Index—SSFI).DiscussionThe SSFI is the first standardised metric that quantifies site fidelity at a populational level. It is an estimator that varies between zero and one and works in situations where detection is not perfect and effort can be constant or not. Moreover, it has an associated CI that allows users to make comparisons. creator: Ayelen Tschopp creator: Mariano A. Ferrari creator: Enrique A. Crespo creator: Mariano A. Coscarella uri: https://doi.org/10.7717/peerj.4782 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tschopp et al. title: The performance of cleaner wrasse, Labroides dimidiatus, in a reversal learning task varies across experimental paradigms link: https://peerj.com/articles/4745 last-modified: 2018-05-09 description: Testing performance in controlled laboratory experiments is a powerful tool for understanding the extent and evolution of cognitive abilities in non-human animals. However, cognitive testing is prone to a number of potential biases, which, if unnoticed or unaccounted for, may affect the conclusions drawn. We examined whether slight modifications to the experimental procedure and apparatus used in a spatial task and reversal learning task affected performance outcomes in the bluestreak cleaner wrasse, Labroides dimidiatus (hereafter “cleaners”). Using two-alternative forced-choice tests, fish had to learn to associate a food reward with a side (left or right) in their holding aquarium. Individuals were tested in one of four experimental treatments that differed slightly in procedure and/or physical set-up. Cleaners from all four treatment groups were equally able to solve the initial spatial task. However, groups differed in their ability to solve the reversal learning task: no individuals solved the reversal task when tested in small tanks with a transparent partition separating the two options, whereas over 50% of individuals solved the task when performed in a larger tank, or with an opaque partition. These results clearly show that seemingly insignificant details to the experimental set-up matter when testing performance in a spatial task and might significantly influence the outcome of experiments. These results echo previous calls for researchers to exercise caution when designing methodologies for cognition tasks to avoid misinterpretations. creator: Simon Gingins creator: Fanny Marcadier creator: Sharon Wismer creator: Océane Krattinger creator: Fausto Quattrini creator: Redouan Bshary creator: Sandra A. Binning uri: https://doi.org/10.7717/peerj.4745 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Gingins et al. title: Pelagic larval duration, growth rate, and population genetic structure of the tidepool snake moray Uropterygius micropterus around the southern Ryukyu Islands, Taiwan, and the central Philippines link: https://peerj.com/articles/4741 last-modified: 2018-05-09 description: The relationships between pelagic larval duration (PLD) and geographic distribution patterns or population genetic structures of fishes remain obscure and highly variable among species. To further understand the early life history of the tidepool snake moray Uropterygius micropterus and the potential relationship between PLD and population genetic structure of this species, otolith microstructure and population genetics based on concatenated mtDNA sequence (cytochrome b and cytochrome oxidase subunit I, 1,336 bp) were analyzed for 195 specimens collected from eight locations around the southern Ryukyu Islands, Taiwan, and the central Philippines. Eels with longer PLD and lower otolith growth rates were observed at relatively higher latitudes with lower water temperatures (54.6 ± 7.7 days and 1.28 ± 0.16 µm day−1 on Ishigaki Island, Japan, vs. 43.9 ± 4.9 days and 1.60 ± 0.19 µm day−1 on Badian, the Philippines), suggesting that leptocephali grew faster and had shortened pelagic periods in warmer waters. Meanwhile, the eels along the southwest coast of Taiwan had relatively longer PLD (57.9 ± 10.5 days), which might be associated with the more complex ocean current systems compared to their counterparts collected along the east coast of Taiwan (52.6 ± 8.0 days). However, the southwestern and eastern Taiwan groups had similar otolith growth rates (1.33 ± 0.19 µm day−1 vs. 1.36 ± 0.16 µm day−1). Despite the intergroup variation in PLD, genetic analysis revealed fluent gene flow among the tidepool snake morays in the study regions, implying that intraspecies PLD variation had a weak effect on genetic structure. The leptocephalus stage might have ensured the widespread gene flow among the study areas and leptocephalus growth was likely influenced by regional water temperature. creator: Wen-Chien Huang creator: Jui-Tsung Chang creator: Chun Liao creator: Atsushi Tawa creator: Yoshiyuki Iizuka creator: Te-Yu Liao creator: Jen-Chieh Shiao uri: https://doi.org/10.7717/peerj.4741 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Huang et al. title: Primary producers may ameliorate impacts of daytime CO2 addition in a coastal marine ecosystem link: https://peerj.com/articles/4739 last-modified: 2018-05-09 description: Predicting the impacts of ocean acidification in coastal habitats is complicated by bio-physical feedbacks between organisms and carbonate chemistry. Daily changes in pH and other carbonate parameters in coastal ecosystems, associated with processes such as photosynthesis and respiration, often greatly exceed global mean predicted changes over the next century. We assessed the strength of these feedbacks under projected elevated CO2 levels by conducting a field experiment in 10 macrophyte-dominated tide pools on the coast of California, USA. We evaluated changes in carbonate parameters over time and found that under ambient conditions, daytime changes in pH, pCO2, net ecosystem calcification (NEC), and O2 concentrations were strongly related to rates of net community production (NCP). CO2 was added to pools during daytime low tides, which should have reduced pH and enhanced pCO2. However, photosynthesis rapidly reduced pCO2 and increased pH, so effects of CO2 addition were not apparent unless we accounted for seaweed and surfgrass abundances. In the absence of macrophytes, CO2 addition caused pH to decline by ∼0.6 units and pCO2 to increase by ∼487 µatm over 6 hr during the daytime low tide. As macrophyte abundances increased, the impacts of CO2 addition declined because more CO2 was absorbed due to photosynthesis. Effects of CO2addition were, therefore, modified by feedbacks between NCP, pH, pCO2, and NEC. Our results underscore the potential importance of coastal macrophytes in ameliorating impacts of ocean acidification. creator: Matthew E.S. Bracken creator: Nyssa J. Silbiger creator: Genevieve Bernatchez creator: Cascade J.B. Sorte uri: https://doi.org/10.7717/peerj.4739 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bracken et al. title: Is high-intensity interval cycling feasible and more beneficial than continuous cycling for knee osteoarthritic patients? Results of a randomised control feasibility trial link: https://peerj.com/articles/4738 last-modified: 2018-05-09 description: BackgroundKnee osteoarthritis (OA) patients often suffer joint pain and stiffness, which contributes to negative changes in body composition, strength, physical performance (function), physical activity and health-related quality of life. To reduce these symptoms and side effects of knee OA, moderate-intensity continuous training (MICT) cycling is often recommended. While resistance training is considered the optimal form of training to improve sarcopenic outcomes, it imposes higher joint loads and requires supervision, either initially or continuously by trained exercise professionals. Therefore, this pilot study sought to gain some insight into the feasibility and potential benefits of high-intensity interval training (HIIT) cycling as an alternative exercise option to MICT cycling for individuals with knee OA.MethodsTwenty-seven middle-aged and older adults with knee OA were randomly allocated to either MICT or HIIT, with both programs involving four unsupervised home-based cycling sessions (∼25 min per session) each week for eight weeks. Feasibility was assessed by enrolment rate, withdrawal rate, exercise adherence and number of adverse effects. Efficacy was assessed by health-related quality of life (Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) and Lequesne index), physical function (Timed Up and Go (TUG), Sit to Stand (STS) and preferred gait speed) and body composition (body mass, BMI, body fat percentage and muscle mass).ResultsTwenty-seven of the interested 50 potential participants (54%) enrolled in the study, with 17 of the 27 participants completing the trial (withdrawal rate of 37%); with the primary withdrawal reasons being unrelated injuries or illness or family related issues. Of the 17 participants who completed the trial, exercise adherence was very high (HIIT 94%; MICT 88%). While only three individuals (one in the MICT and two in the HIIT group) reported adverse events, a total of 28 adverse events were reported, with 24 of these attributed to one HIIT participant. Pre–post-test analyses indicated both groups significantly improved their WOMAC scores, with the HIIT group also significantly improving in the TUG and STS. The only significant between-group difference was observed in the TUG, whereby the HIIT group improved significantly more than the MICT group. No significant changes were observed in the Lequesne index, gait speed or body composition for either group.DiscussionAn unsupervised home-based HIIT cycle program appears somewhat feasible for middle-aged and older adults with knee OA and may produce similar improvements in health-related quality of life but greater improvements in physical function than MICT. These results need to be confirmed in larger randomised controlled trials to better elucidate the potential for HIIT to improve outcomes for those with knee OA. Additional research needs to identify and modify the potential barriers affecting the initiation and adherence to home-based HIIT cycling exercise programs by individuals with knee OA. creator: Justin W. Keogh creator: Josephine Grigg creator: Christopher J. Vertullo uri: https://doi.org/10.7717/peerj.4738 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Keogh et al. title: Global opportunities for mariculture development to promote human nutrition link: https://peerj.com/articles/4733 last-modified: 2018-05-09 description: An estimated two billion people worldwide currently suffer from micronutrient malnutrition, and almost one billion are calorie deficient. Providing adequate nutrition is a growing global challenge. Seafood is one of the most important sources of both protein and micronutrients for many, yet production from wild capture fisheries has stagnated. In contrast, aquaculture is the world’s fastest-growing food production sector and now supplies over half of all seafood consumed globally. Mariculture, or the farming of brackish and marine species, accounts for roughly one-third of all aquaculture production and has received increasing attention as a potential supplement for wild-caught marine fisheries. By analyzing global patterns in seafood reliance, malnutrition levels, and economic opportunity, this study identifies where mariculture has the greatest potential to improve human nutrition. We calculate a mariculture opportunity index for 117 coastal nations by drawing on a diverse set of seafood production, trade, consumption, and nutrition data. Seventeen primary variables are combined into country-level scores for reliance on seafood, opportunity for nutritional improvement, and opportunity for economic development of mariculture. The final mariculture opportunity score identifies countries with high seafood reliance combined with high nutritional and economic opportunity scores. We find that island nations in Southeast Asia and the Caribbean are consistently identified as countries with high mariculture opportunity. In other regions, nutritional and economic opportunity scores are not significantly correlated, and we discuss the implications of this finding for crafting appropriate development policy. Finally, we identify key challenges to ameliorating malnutrition through mariculture development, including insufficient policy infrastructure, government instability, and ensuring local consumption of farmed fish. Our analysis is an important step towards prioritizing nations where the economic and nutritional benefits of expanding mariculture may be jointly captured. creator: Owen R. Liu creator: Renato Molina creator: Margaret Wilson creator: Benjamin S. Halpern uri: https://doi.org/10.7717/peerj.4733 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu et al. title: Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer link: https://peerj.com/articles/4719 last-modified: 2018-05-09 description: BackgroundUsing DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these “housekeeping genes” (HKGs) could separate one normal human tissue type from another. Current focus on identifying “specific disease markers” is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers.MethodsMicroarray and RNA-seq data for normal lungs, lung adenocarcinomas (AD), squamous cell carcinomas of the lung (SQCLC), and small cell carcinomas of the lung (SCLC) were collected from online databases. Using 374 of 451 HKGs, differentially expressed genes between pairs of sample types were determined via two-sided, homoscedastic t-test. Principal component analysis and hierarchical clustering classified normal lung and lung cancers subtypes according to relative gene expression variations. We used uni- and multi-variate cox-regressions to identify significant predictors of overall survival in AD patients. Classifying genes were selected using a set of training samples and then validated using an independent test set. Gene Ontology was examined by PANTHER.ResultsThis study showed that the differential expression patterns of 242, 245, and 99 HKGs were able to distinguish normal lung from AD, SCLC, and SQCLC, respectively. From these, 70 HKGs were common across the three lung cancer subtypes. These HKGs have low expression variation compared to current lung cancer markers (e.g., EGFR, KRAS) and were involved in the most common biological processes (e.g., metabolism, stress response). In addition, the expression pattern of 106 HKGs alone was a significant classifier of AD versus SQCLC. We further highlighted that a panel of 13 HKGs was an independent predictor of overall survival and cumulative risk in AD patients.DiscussionHere we report HKG expression patterns may be an effective tool for evaluation of lung cancer states. For example, the differential expression pattern of 70 HKGs alone can separate normal lung tissue from various lung cancers while a panel of 106 HKGs was a capable class predictor of subtypes of non-small cell carcinomas. We also reported that HKGs have significantly lower variance compared to traditional cancer markers across samples, highlighting the robustness of a panel of genes over any one specific biomarker. Using RNA-seq data, we showed that the expression pattern of 13 HKGs is a significant, independent predictor of overall survival for AD patients. This reinforces the predictive power of a HKG panel across different gene expression measurement platforms. Thus, we propose the expression patterns of HKGs alone may be sufficient for the diagnosis and prognosis of individuals with lung cancer. creator: Yu-Chun Chang creator: Yan Ding creator: Lingsheng Dong creator: Lang-Jing Zhu creator: Roderick V. Jensen creator: Li-Li Hsiao uri: https://doi.org/10.7717/peerj.4719 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chang et al. title: The rice XA21 ectodomain fused to the Arabidopsis EFR cytoplasmic domain confers resistance to Xanthomonas oryzae pv. oryzae link: https://peerj.com/articles/4456 last-modified: 2018-05-09 description: Rice (Oryza sativa) plants expressing the XA21 cell-surface receptor kinase are resistant to Xanthomonas oryzae pv. oryzae (Xoo) infection. We previously demonstrated that expressing a chimeric protein containing the ELONGATION FACTOR Tu RECEPTOR (EFR) ectodomain and the XA21 endodomain (EFR:XA21) in rice does not confer robust resistance to Xoo. To test if the XA21 ectodomain is required for Xoo resistance, we produced transgenic rice lines expressing a chimeric protein consisting of the XA21 ectodomain and EFR endodomain (XA21:EFR) and inoculated these lines with Xoo. We also tested if the XA21:EFR rice plants respond to a synthetic sulfated 21 amino acid derivative (RaxX21-sY) of the activator of XA21-mediated immunity, RaxX. We found that five independently transformed XA21:EFR rice lines displayed resistance to Xoo as measured by lesion length analysis, and showed that five lines share characteristic markers of the XA21 defense response (generation of reactive oxygen species and defense response gene expression) after treatment with RaxX21-sY. Our results indicate that expression of the XA21:EFR chimeric receptor in rice confers resistance to Xoo. These results suggest that the endodomain of the EFR and XA21 immune receptors are interchangeable and the XA21 ectodomain is the key determinant conferring robust resistance to Xoo. creator: Nicholas C. Thomas creator: Nir Oksenberg creator: Furong Liu creator: Daniel Caddell creator: Alina Nalyvayko creator: Yen Nguyen creator: Benjamin Schwessinger creator: Pamela C. Ronald uri: https://doi.org/10.7717/peerj.4456 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Thomas et al. title: Transcriptomic studies reveal a key metabolic pathway contributing to a well-maintained photosynthetic system under drought stress in foxtail millet (Setaria italica L.) link: https://peerj.com/articles/4752 last-modified: 2018-05-08 description: Drought stress is one of the most important abiotic factors limiting crop productivity. A better understanding of the effects of drought on millet (Setaria italica L.) production, a model crop for studying drought tolerance, and the underlying molecular mechanisms responsible for drought stress responses is vital to improvement of agricultural production. In this study, we exposed the drought resistant F1 hybrid, M79, and its parental lines E1 and H1 to drought stress. Subsequent physiological analysis demonstrated that M79 showed higher photosynthetic energy conversion efficiency and drought tolerance than its parents. A transcriptomic study using leaves collected six days after drought treatment, when the soil water content was about ∼20%, identified 3066, 1895, and 2148 differentially expressed genes (DEGs) in M79, E1 and H1 compared to the respective untreated controls, respectively. Further analysis revealed 17 Gene Ontology (GO) enrichments and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in M79, including photosystem II (PSII) oxygen-evolving complex, peroxidase (POD) activity, plant hormone signal transduction, and chlorophyll biosynthesis. Co-regulation analysis suggested that these DEGs in M79 contributed to the formation of a regulatory network involving multiple biological processes and pathways including photosynthesis, signal transduction, transcriptional regulation, redox regulation, hormonal signaling, and osmotic regulation. RNA-seq analysis also showed that some photosynthesis-related DEGs were highly expressed in M79 compared to its parental lines under drought stress. These results indicate that various molecular pathways, including photosynthesis, respond to drought stress in M79, and provide abundant molecular information for further analysis of the underlying mechanism responding to this stress. creator: Weiping Shi creator: Jingye Cheng creator: Xiaojie Wen creator: Jixiang Wang creator: Guanyan Shi creator: Jiayan Yao creator: Liyuan Hou creator: Qian Sun creator: Peng Xiang creator: Xiangyang Yuan creator: Shuqi Dong creator: Pingyi Guo creator: Jie Guo uri: https://doi.org/10.7717/peerj.4752 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Shi et al. title: Biodiversity of the Great Barrier Reef—how adequately is it protected? link: https://peerj.com/articles/4747 last-modified: 2018-05-08 description: BackgroundThe Great Barrier Reef (GBR) is the world’s most iconic coral reef ecosystem, recognised internationally as a World Heritage Area of outstanding significance. Safeguarding the biodiversity of this universally important reef is a core legislative objective; however, ongoing cumulative impacts including widespread coral bleaching and other detrimental impacts have heightened conservation concerns for the future of the GBR.MethodsHere we review the literature to report on processes threatening species on the GBR, the status of marine biodiversity, and evaluate the extent of species-level monitoring and reporting. We assess how many species are listed as threatened at a global scale and explore whether these same species are protected under national threatened species legislation. We conclude this review by providing future directions for protecting potentially endangered elements of biodiversity within the GBR.ResultsMost of the threats identified to be harming the diversity of marine life on the GBR over the last two–three decades remain to be effectively addressed and many are worsening. The inherent resilience of this globally significant coral reef ecosystem has been seriously compromised and various elements of the biological diversity for which it is renowned may be at risk of silent extinction. We show at least 136 of the 12,000+ animal species known to occur on the GBR (approximately 20% of the 700 species assessed by the IUCN) occur in elevated categories of threat (Critically Endangered, Endangered or Vulnerable) at a global scale. Despite the wider background level of threat for these 136 species, only 23 of them are listed as threatened under regional or national legislation.DiscussionTo adequately protect the biodiversity values of the GBR, it may be necessary to conduct further targeted species-level monitoring and reporting to complement ecosystem management approaches. Conducting a vigorous value of information analysis would provide the opportunity to evaluate what new and targeted information is necessary to support dynamic management and to safeguard both species and the ecosystem as a whole. Such an analysis would help decision-makers determine if further comprehensive biodiversity surveys are needed, especially for those species recognised to be facing elevated background levels of threat. If further monitoring is undertaken, it will be important to ensure it aligns with and informs the GBRMPA Outlook five-year reporting schedule. The potential also exists to incorporate new environmental DNA technologies into routine monitoring to deliver high-resolution species data and identify indicator species that are cursors of specific disturbances. Unless more targeted action is taken to safeguard biodiversity, we may fail to pass onto future generations many of the values that comprise what is universally regarded as the world’s most iconic coral reef ecosystem. creator: Zoe T. Richards creator: Jon C. Day uri: https://doi.org/10.7717/peerj.4747 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Richards and Day title: Nature-derived lignan compound VB-1 exerts hair growth-promoting effects by augmenting Wnt/β-catenin signaling in human dermal papilla cells link: https://peerj.com/articles/4737 last-modified: 2018-05-08 description: BackgroundVitexin is a kind of lignan compound which has been shown to possess a variety of pharmacological effects, such as anti-inflammatory, anti-oxidative and anti-cancer activities. However the effect of vitexin on hair regeneration has not been elaborated.MethodsThe proliferation of human dermal papilla cells (hDPCs) was examined by cell counting and continuous cell culture after vitexin compound 1 (VB-1) was treated. The expression of lef1, wnt5a, bmp2, bmp4, alpl and vcan was examined by RT-PCR. The expression of dkk1, tgf-β1, active-β-Catenin, and AXIN2 was examined by RT-PCR or immunoblotting. Hair shaft growth was measured in the absence or presence of VB-1.ResultsWe demonstrated that VB-1 significantly promotes the proliferation of hDPCs in a concentration-dependent manner within a certain concentration range. Among the hair growth-related genes investigated, dkk1 was clearly down-regulated in hDPCs treated with VB-1. The increased active β-Catenin and decreased AXIN2 protein levels suggest that VB-1 facilitates Wnt/β-catenin signaling in hDPCs in vitro. The expression of DP signature genes was also upregulated after VB-1 treatment. Our study further indicated that VB-1 promotes human hair follicle (HF) growth by HF organ culture assay.DiscussionVB-1 may exert hair growth-promoting effects via augmenting Wnt/β-catenin signaling in hDPCs. creator: Jieshu Luo creator: Mengting Chen creator: Yingzi Liu creator: Hongfu Xie creator: Jian Yuan creator: Yingjun Zhou creator: Jinsong Ding creator: Zhili Deng creator: Ji Li uri: https://doi.org/10.7717/peerj.4737 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Luo et al. title: Asymmetries in mother-infant behaviour in Barbary macaques (Macaca sylvanus) link: https://peerj.com/articles/4736 last-modified: 2018-05-08 description: Asymmetries in the maternal behaviour and anatomy might play an important role in the development of primate manual lateralization. In particular, early life asymmetries in mother’s and infant’s behaviour have been suggested to be associated with the development of the hand preference of the offspring. The aim of this study was to investigate the presence of behavioural asymmetries in different behavioural categories of mother-infant dyads of zoo-living Barbary macaques (Macaca sylvanus). The study subjects were 14 Barbary macaques involved in seven mother-infant dyads housed in Parco Natura Viva, Italy. For the mothers, bouts of hand preference for maternal cradling and infant retrieval were collected. For the infants, we focused on nipple preference and hand preference for clinging on mother ventrum. Moreover, we collected bouts of hand preference for food reaching in both groups. No significant group-level bias was found for any of the behavioural categories in either mothers or infants. However, at the individual level, six out of seven mothers showed a significant cradling bias, three toward the right hand and three toward the left hand. Moreover, all infants showed a significant nipple preference, six toward the mother’s right nipple, one toward the left nipple. Furthermore, a significant correlation was found between the infant nipple preference and their hand preference for food reaching, suggesting that maternal environment rather than behaviour might affect the development of hand preference in Old World monkeys. Our findings seem partially to add to previous literature on perceptual lateralization in different species of non-primate mammals, reporting a lateral bias in mother-infant interactions. Given the incongruences between our study and previous research in great apes and humans, our results seem to suggest possible phylogenetic differences in the lateralization of mothers and infants within the Primates order. creator: Barbara Regaiolli creator: Caterina Spiezio creator: William Donald Hopkins uri: https://doi.org/10.7717/peerj.4736 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Regaiolli et al. title: Plasma proteomic analysis of systemic lupus erythematosus patients using liquid chromatography/tandem mass spectrometry with label-free quantification link: https://peerj.com/articles/4730 last-modified: 2018-05-08 description: ContextSystemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease with unknown etiology.ObjectiveHuman plasma is comprised of over 10 orders of magnitude concentration of proteins and tissue leakages. The changes in the abundance of these proteins have played an important role in various human diseases. Therefore, the research objective of this study is to identify the significantly altered expression levels of plasma proteins from SLE patients compared with healthy controls using proteomic analysis. The plasma proteome profiles of both SLE patients and controls were compared.MethodsA total of 19 active SLE patients and 12 healthy controls plasma samples were analyzed using high-resolution electrospray ionization liquid chromatography-tandem mass spectrometry (LC-ESI-MS/MS) followed by label-free quantification.ResultsA total of 19 proteins showed a significant level of expression in the comparative LC-ESI-MS/MS triplicate analysis; among these, 14 proteins had >1.5- to three-fold up-regulation and five had <0.2- to 0.6-fold down-regulation. Gene ontology and DAVID (Database Annotation Visualization, and Integrated Discovery) functional enrichment analysis revealed that these proteins are involved in several important biological processes including acute phase inflammatory responses, complement activation, hemostasis, and immune system regulation.ConclusionOur study identified a group of differentially expressed proteins in the plasma of SLE patients that are involved in the imbalance of the immune system and inflammatory responses. Therefore, these findings may have the potential to be used as prognostic/diagnostic markers for SLE disease assessment or disease monitoring. creator: Rashmi Madda creator: Shih-Chang Lin creator: Wei-Hsin Sun creator: Shir-Ly Huang uri: https://doi.org/10.7717/peerj.4730 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Madda et al. title: Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011–2016 link: https://peerj.com/articles/4724 last-modified: 2018-05-08 description: Swine are economically important food animals, but highly contagious porcine epidemic diarrhea virus (PEDV) and rotavirus can afflict pig herds and contribute significantly to piglet morbidity and mortality. While there have been studies on rotavirus group A (RVA) in Thailand, reports of rotavirus group C (RVC) are limited. Here, we aimed to identify the prevalence of RVC circulating on Thai commercial swine farms. We analyzed 769 feces and intestine mucosal contents of pigs affected with diarrhea between 2011 and 2016 using RT-PCR specific for the PEDV spike (S), rotavirus glycoprotein (G) VP7, and protease-sensitive protein (P) VP4 genes. We found that 6.6% (51/769) of samples tested positive for RVC, of which 11 samples were co-infected with RVA and four samples were co-infected with PEDV. Three samples tested positive for all three viruses. Phylogenetic analysis of the VP7 gene showed that the most frequent RVC genotype was G1, which grouped with the prototypic RVC Cowden strain. While G6 and G9 were also common, G3 was relatively rare. Analysis of the VP4 gene revealed that the most common P type was P[5], followed by P[4], P[7], and P[1]. In all, there were six G/P combinations (G6P[5], G1P[1], G1P[4], G1P[5], G9P[4], and G9P[7]), of which G6P[5] was the most predominant. creator: Supansa Tuanthap creator: Cherdpong Phupolphan creator: Supol Luengyosluechakul creator: Ausanee Duang-in creator: Apiradee Theamboonlers creator: Suphot Wattanaphansak creator: Sompong Vongpunsawad creator: Alongkorn Amonsin creator: Yong Poovorawan uri: https://doi.org/10.7717/peerj.4724 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tuanthap et al. title: The brown anole dewlap revisited: do predation pressure, sexual selection, and species recognition shape among-population signal diversity? link: https://peerj.com/articles/4722 last-modified: 2018-05-08 description: Animal signalling structures are amongst the most variable characteristics, as they are subjected to a diversity of selection pressures. A well-known example of a diverse signalling system in the animal kingdom is the dewlap of Anolis lizards. Dewlap characteristics can vary remarkably among and within species, and also between sexes. Although a considerable amount of studies have attempted to disentangle the functional significance of the staggering dewlap diversity in Anolis, the underlying evolutionary processes remain elusive. In this study, we focus on the contribution of biotic selective pressures in shaping geographic variation in dewlap design (size, colour, and pattern) and dewlap display behaviour at the intraspecific level. Notably, we have tried to replicate and extend previously reported results hereof in both sexes of the brown anole lizard (Anolis sagrei). To do this, we assembled a dataset consisting of 17 A. sagrei heterogeneous island populations from the Caribbean and specifically tested whether predation pressure, sexual selection, or species recognition could explain interpopulational variation in an array of dewlap characteristics. Our findings show that in neither males nor females estimates of predation pressure (island size, tail break frequency, model attack rate, presence of predatory Leiocephalus lizards) or sexual selection (sexual size dimorphism) could explain variation in dewlap design. We did find that A. sagrei males from larger islands showed higher dewlap display intensities than males from smaller islands, but the direct connection with predation pressure remains ambiguous and demands further investigation. Last, we could show indirect support for species recognition only in males, as they are more likely to have a ‘spotted’ dewlap pattern when co-occurring with a higher number of syntopic Anolis species. In conclusion, we found overall limited support for the idea that the extensive interpopulational variability in dewlap design and use in A. sagrei is mediated by variation in their biotic environment. We propose a variety of conceptual and methodological explanations for this unexpected finding. creator: Simon Baeckens creator: Tess Driessens creator: Raoul Van Damme uri: https://doi.org/10.7717/peerj.4722 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Baeckens et al. title: Seasonal migrations, body temperature fluctuations, and infection dynamics in adult amphibians link: https://peerj.com/articles/4698 last-modified: 2018-05-08 description: Risks of parasitism vary over time, with infection prevalence often fluctuating with seasonal changes in the annual cycle. Identifying the biological mechanisms underlying seasonality in infection can enable better prediction and prevention of future infection peaks. Obtaining longitudinal data on individual infections and traits across seasons throughout the annual cycle is perhaps the most effective means of achieving this aim, yet few studies have obtained such information for wildlife. Here, we tracked spiny common toads (Bufo spinosus) within and across annual cycles to assess seasonal variation in movement, body temperatures and infection from the fungal parasite, Batrachochytrium dendrobatidis (Bd). Across annual cycles, toads did not consistently sustain infections but instead gained and lost infections from year to year. Radio-tracking showed that infected toads lose infections during post-breeding migrations, and no toads contracted infection following migration, which may be one explanation for the inter-annual variability in Bd infections. We also found pronounced seasonal variation in toad body temperatures. Body temperatures approached 0 °C during winter hibernation but remained largely within the thermal tolerance range of Bd. These findings provide direct documentation of migratory recovery (i.e., loss of infection during migration) and escape in a wild population. The body temperature reductions that we observed during hibernation warrant further consideration into the role that this period plays in seasonal Bd dynamics. creator: David R. Daversa creator: Camino Monsalve-Carcaño creator: Luis M. Carrascal creator: Jaime Bosch uri: https://doi.org/10.7717/peerj.4698 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Daversa et al. title: Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing link: https://peerj.com/articles/4671 last-modified: 2018-05-08 description: BackgroundSimilar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities (“microbiomes”) in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis.Methods & ResultsSurface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus. However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons.DiscussionSignificant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month, season, water temperature, and salinity. The 2013–2014 dry season (October–April), was warmer and wetter than historical averages. This may have driven significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were observed in these dry season months, possibly creating favorable bacterial growth conditions. Potentially pathogenic genera were present in the PEI. However their relatively low, non-significant abundance levels highlight their relatively low risk for public health concerns. This study represents the first to sample a large port at this sampling scale and sequencing depth. These data can help establish the inlet microbial community baseline and supplement the vital monitoring of local marine and recreational environments, all the more poignant in context of local reef disease outbreaks and worldwide coral reef collapse in wake of a harsh 2014–16 El Niño event. creator: Lauren O’Connell creator: Song Gao creator: Donald McCorquodale creator: Jay Fleisher creator: Jose V. Lopez uri: https://doi.org/10.7717/peerj.4671 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 O’Connell et al. title: Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts link: https://peerj.com/articles/4629 last-modified: 2018-05-08 description: The Lepidoptera is one of the most widespread and recognisable insect orders. Due to their remarkable diversity, economic and ecological importance, moths and butterflies have been studied extensively over the last 200 years. More recently, the relationship between Lepidoptera and their heritable microbial endosymbionts has received increasing attention. Heritable endosymbionts reside within the host’s body and are often, but not exclusively, inherited through the female line. Advancements in molecular genetics have revealed that host-associated microbes are both extremely prevalent among arthropods and highly diverse. Furthermore, heritable endosymbionts have been repeatedly demonstrated to play an integral role in many aspects of host biology, particularly host reproduction. Here, we review the major findings of research of heritable microbial endosymbionts of butterflies and moths. We promote the Lepidoptera as important models in the study of reproductive manipulations employed by heritable endosymbionts, with the mechanisms underlying male-killing and feminisation currently being elucidated in moths and butterflies. We also reveal that the vast majority of research undertaken of Lepidopteran endosymbionts concerns Wolbachia. While this highly prevalent bacterium is undoubtedly important, studies should move towards investigating the presence of other, and interacting endosymbionts, and we discuss the merits of examining the microbiome of Lepidoptera to this end. We finally consider the importance of understanding the influence of endosymbionts under global environmental change and when planning conservation management of endangered Lepidoptera species. creator: Anne Duplouy creator: Emily A. Hornett uri: https://doi.org/10.7717/peerj.4629 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Duplouy and Hornett title: Sponge community of the western Black Sea shallow water caves: diversity and spatial distribution link: https://peerj.com/articles/4596 last-modified: 2018-05-08 description: Marine caves possess unique biocoenotic and ecological characteristics. Sessile benthic species such as sponges associated with cave habitats typically show a marked zonation from the cave entrance towards the end of the cave. We describe three semi-submerged karstic caves of 50 to 83 m length and 936 to 2,291 m3 volume from the poorly explored cavernicolous fauna of North-East Bulgaria. We surveyed sponge diversity and spatial variability. Eight demosponge species were identified based on morphological and molecular data, of which six are known from the adjacent open sea waters of the Black Sea. Two species, Protosuberites denhartogi van Soest & de Kluijver, 2003 and Halichondria bowerbanki Burton, 1930, are reported from the Black Sea for the first time. The spatial sponge distribution inside the caves is in general similar, but shows some differences in species composition and distribution depending on cave relief and hydrodynamics. The species composition of sponges of Bulgarian caves is found to be different from Crimean caves. An updated checklist of the Black Sea sponges is provided. creator: Alexander Ereskovsky creator: Oleg A. Kovtun creator: Konstantin K. Pronin creator: Apostol Apostolov creator: Dirk Erpenbeck creator: Viatcheslav Ivanenko uri: https://doi.org/10.7717/peerj.4596 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ereskovsky et al. title: Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico link: https://peerj.com/articles/4780 last-modified: 2018-05-07 description: Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers. creator: Carolina A. Martínez-Gutiérrez creator: Hever Latisnere-Barragán creator: José Q. García-Maldonado creator: Alejandro López-Cortés uri: https://doi.org/10.7717/peerj.4780 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Martínez-Gutiérrez et al. title: Effects of nettle slurry (Urtica dioica L.) used as foliar fertilizer on potato (Solanum tuberosum L.) yield and plant growth link: https://peerj.com/articles/4729 last-modified: 2018-05-07 description: Organic agriculture is becoming increasingly important, and many natural products are now available for organic farmers to manage and improve their crops. Several ethnobotanical studies have indicated that the use of nettle slurry as fertilizer in organic farming for horticultural crops is spreading. Sometimes, however, the consequences of using these natural products have been poorly evaluated, and there is very little scientific evidence for the effects of using these slurries. In this study, we aimed to analyze the possible effect of nettle slurry on potato yields produced by organic farming. To achieve this main objective, we assessed the effect of nettle slurry on potato yields, plant size and growth parameters, chlorophyll content, and the presence of pests and diseases. Different slurry doses were assessed in 36 plots and nine variables were measured during the crop cycle. Under these field experimental conditions, nettle slurry (including one treatment with Urtica in combination with Equisetum) had no significant effects on yield, chlorophyll content, or the presence of pests and diseases in organic potato crops. The highest chlorophyll content was found in the double dose treatment, but the difference was not significant. This result, together with a small improvement in plant height with the double dose treatment, might indicate very slight crop enhancement which, under our experimental conditions, was not enough to improve yield. The Urtica and Equisetum slurry chemical analyses showed very low levels of nitrogen, phosphorus, and potassium. creator: Alfonso Garmendia creator: María Dolores Raigón creator: Olmo Marques creator: María Ferriol creator: Jorge Royo creator: Hugo Merle uri: https://doi.org/10.7717/peerj.4729 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Garmendia et al. title: Crystallization and structure analysis of the core motif of the Pks13 acyltransferase domain from Mycobacterium tuberculosis link: https://peerj.com/articles/4728 last-modified: 2018-05-07 description: Type I polyketide synthase 13 (Pks13) is involved in the final step of the biosynthesis of mycolic acid in Mycobacterium tuberculosis. Recent articles have reported that Pks13 is an essential enzyme in the mycolic acid biosynthesis pathway, and it has been deeply studied as a drug target in Tuberculosis. We report a high-resolution structure of the acyltransferase (AT) domain of Pks13 at 2.59 Å resolution. Structural comparison with the full-length AT domain (PDB code, 3TZW, and 3TZZ) reveals a different orientation of the C-terminal helix and rearrangement of some conserved residues. creator: Mingjing Yu creator: Chao Dou creator: Yijun Gu creator: Wei Cheng uri: https://doi.org/10.7717/peerj.4728 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Yu et al. title: A survey of the views and capabilities of community pharmacists in Western Australia regarding the rescheduling of selected oral antibiotics in a framework of pharmacist prescribing link: https://peerj.com/articles/4726 last-modified: 2018-05-07 description: BackgroundAntibiotic misuse in the community contributes to antimicrobial resistance. One way to address this may be by better utilizing community pharmacists’ skills in antibiotic prescribing. The aims of this study were to examine the level of support for “down-scheduling” selected antibiotics and to evaluate factors determining the appropriateness of community pharmacist prescribing for a limited range of infections, including their decision to refer to a doctor.MethodsSelf-administered questionnaires, including graded case vignette scenarios simulating real practice, were sent to Western Australian community pharmacists. In addition to descriptive statistics and chi-square testing, a General Estimating Equation (GEE) was used to identify factors associated with appropriateness of therapy and the decision to refer, for each of the seven vignettes.ResultsOf the 240 pharmacists surveyed, 90 (37.5%) responded, yielding 630 responses to seven different case vignettes. There was more than 60% respondent support for expanded prescribing (rescheduling) of commonly prescribed antibiotics. Overall 426/630 (67.6%) chose to treat the patient while the remaining 204/630 (32.4%) referred the patient to a doctor. Of those electing to treat, 380/426 (89.2%) opted to use oral antibiotics, with 293/380 (77.2%) treating with an appropriate selection and regimen. The GEE model indicated that pharmacists were more likely to prescribe inappropriately for conditions such as otitis media (p = 0.0060) and urinary tract infection in pregnancy (p < 0.0001) compared to more complex conditions. Over 80% of all pharmacists would refer the patient to a doctor following no improvement within 3 days, or within 24 h in the case of community acquired pneumonia. It was more common for younger pharmacists to refer the patient to a doctor (p = 0.0165).DiscussionThis study adds further insight into community pharmacy/pharmacist characteristics associated with appropriateness of oral antibiotic selection and the decision to refer to doctors. These findings require consideration in designing pharmacist over-the-counter prescribing models for oral antibiotics. creator: Fatima Sinkala creator: Richard Parsons creator: Bruce Sunderland creator: Kreshnik Hoti creator: Petra Czarniak uri: https://doi.org/10.7717/peerj.4726 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Sinkala et al. title: Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing link: https://peerj.com/articles/4725 last-modified: 2018-05-07 description: Bacterial endosymbionts that produce important phenotypic effects on their hosts are common among plant sap-sucking insects. Aphids have become a model system of insect-symbiont interactions. However, endosymbiont research has focused on a few aphid species, making it necessary to make greater efforts to other aphid species through different regions, in order to have a better understanding of the role of endosymbionts in aphids as a group. Aphid endosymbionts have frequently been studied by PCR-based techniques, using species-specific primers, nevertheless this approach may omit other non-target bacteria cohabiting a particular host species. Advances in high-throughput sequencing technologies are complementing our knowledge of microbial communities by allowing us the study of whole microbiome of different organisms. We used a 16S rRNA amplicon sequencing approach to study the microbiome of aphids in order to describe the bacterial community diversity in introduced populations of the cereal aphids, Sitobion avenae and Rhopalosiphum padi in Chile (South America). An absence of secondary endosymbionts and two common secondary endosymbionts of aphids were found in the aphids R. padi and S. avenae, respectively. Of those endosymbionts, Regiella insecticola was the dominant secondary endosymbiont among the aphid samples. In addition, the presence of a previously unidentified bacterial species closely related to a phytopathogenic Pseudomonad species was detected. We discuss these results in relation to the bacterial endosymbiont diversity found in other regions of the native and introduced range of S. avenae and R. padi. A similar endosymbiont diversity has been reported for both aphid species in their native range. However, variation in the secondary endosymbiont infection could be observed among the introduced and native populations of the aphid S. avenae, indicating that aphid-endosymbiont associations can vary across the geographic range of an aphid species. In addition, we discuss the potential role of aphids as vectors and/or alternative hosts of phytopathogenic bacteria. creator: Francisca Zepeda-Paulo creator: Sebastían Ortiz-Martínez creator: Andrea X. Silva creator: Blas Lavandero uri: https://doi.org/10.7717/peerj.4725 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zepeda-Paulo et al. title: Ultrasound-promoted synthesis of 2-organoselanyl-naphthalenes using Oxone® in aqueous medium as an oxidizing agent link: https://peerj.com/articles/4706 last-modified: 2018-05-07 description: A green methodology to synthesize 2-organoselanyl-naphthalenes based on the reaction of alkynols with diaryl diselenides is described. The electrophilic species of selenium were generated in situ, by the oxidative cleavage of the Se–Se bond of diaryl diselenides by Oxone® using water as the solvent. The reactions proceeded efficiently under ultrasonic irradiation as an alternative energy source, using a range of alkynols and diorganyl diselenides as starting materials. Through this methodology, the corresponding 2-organoselanyl-naphthalenes were obtained in moderate to good yields (56–94%) and in short reaction times (0.25–2.3 h). creator: Gelson Perin creator: Daniela Rodrigues Araujo creator: Patrick Carvalho Nobre creator: Eder João Lenardao creator: Raquel Guimarães Jacob creator: Marcio Santos Silva creator: Juliano Alex Roehrs uri: https://doi.org/10.7717/peerj.4706 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Perin et al. title: Viromes of one year old infants reveal the impact of birth mode on microbiome diversity link: https://peerj.com/articles/4694 last-modified: 2018-05-07 description: Establishing a diverse gut microbiota after birth is being increasingly recognised as important for preventing illnesses later in life. It is well established that bacterial diversity rapidly increases post-partum; however, few studies have examined the infant gut virome/phageome during this developmental period. We performed a metagenomic analysis of 20 infant faecal viromes at one year of age to determine whether spontaneous vaginal delivery (SVD) or caesarean section (CS) influenced viral composition. We find that birth mode results in distinctly different viral communities, with SVD infants having greater viral and bacteriophage diversity. We demonstrate that CrAssphage is acquired early in life, both in this cohort and two others, although no difference in birth mode is detected. A previous study has shown that bacterial OTU’s (operational taxonomic units) identified in the same infants could not discriminate between birth mode at 12 months of age. Therefore, our results indicate that vertical transmission of viral communities from mother to child may play a role in shaping the early life microbiome, and that birth mode should be considered when studying the early life gut virome. creator: Angela McCann creator: Feargal J. Ryan creator: Stephen R. Stockdale creator: Marion Dalmasso creator: Tony Blake creator: C. Anthony Ryan creator: Catherine Stanton creator: Susan Mills creator: Paul R. Ross creator: Colin Hill uri: https://doi.org/10.7717/peerj.4694 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 McCann et al. title: Small tropical islands with dense human population: differences in water quality of near-shore waters are associated with distinct bacterial communities link: https://peerj.com/articles/4555 last-modified: 2018-05-07 description: Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. However, even though bacteria are important mediators in coral reef ecosystems, little is known about the response of individual taxa and whole bacterial communities to these anthropogenic inputs. The present study is the first to investigate how bacterial community composition responds to small-scale changes in water quality in several coral reef habitats of the Spermonde Archipelago including the water column, particles, and back-reef sediments, on a densely populated and an uninhabited island. The main aims were to elucidate if (a) water quality indicators and organic matter concentrations differ between the uninhabited and the densely populated island of the archipelago, and (b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which are associated with differences in water quality. Several key water quality parameters, such as inorganic nitrate and phosphate, chlorophyll a, and transparent exopolymer particles (TEP) were significantly higher at the inhabited than at the uninhabited island. Bacterial communities in sediments and particle-attached communities were significantly different between the two islands with bacterial taxa commonly associated with nutrient and organic matter-rich conditions occurring in higher proportions at the inhabited island. Within the individual reef habitats, variations in bacterial community composition between the islands were associated with differences in water quality. We also observed that copiotrophic, opportunistic bacterial taxa were enriched at the inhabited island with its higher chlorophyll a, dissolved organic carbon and TEP concentrations. Given the increasing strain on tropical coastal ecosystems, this study suggests that effluents from densely populated islands lacking sewage treatment can alter bacterial communities that may be important for coral reef ecosystem function. creator: Hauke F. Kegler creator: Christiane Hassenrück creator: Pia Kegler creator: Tim C. Jennerjahn creator: Muhammad Lukman creator: Jamaluddin Jompa creator: Astrid Gärdes uri: https://doi.org/10.7717/peerj.4555 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kegler et al. title: The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia link: https://peerj.com/articles/4784 last-modified: 2018-05-04 description: Plasmid vectors based on bacteriophage integrases are important tools in molecular microbiology for the introduction of foreign DNA, especially into bacterial species where other systems for genetic manipulation are limited. Site specific integrases catalyze recombination between phage and bacterial attachment sites (attP and attB, respectively) and the best studied integrases in the actinomycetes are the serine integrases from the Streptomyces bacteriophages ΦC31 and ΦBT1. As this reaction is unidirectional and highly stable, vectors containing phage integrase systems have been used in a number of genetic engineering applications. Plasmids bearing the ΦBT1 integrase have been used to introduce DNA into Streptomyces and Amycolatopsis strains; however, they have not been widely studied in other actinobacterial genera. Here, we show that vectors based on ΦBT1 integrase can stably integrate into the chromosomes of a range of Nocardia species, and that this integration occurs despite the absence of canonical attB sites in these genomes. Furthermore, we show that a ΦBT1 integrase-based vector can insert at multiple pseudo-attB sites within a single strain and we determine the sequence of a pseudo-attB motif. These data suggest that ΦBT1 integrase-based vectors can be used to readily and semi-randomly introduce foreign DNA into the genomes of a range of Nocardia species. However, the precise site of insertion will likely require empirical determination in each species to avoid unexpected off-target effects. creator: Marion Herisse creator: Jessica L. Porter creator: Romain Guerillot creator: Takehiro Tomita creator: Anders Goncalves Da Silva creator: Torsten Seemann creator: Benjamin P. Howden creator: Timothy P. Stinear creator: Sacha J. Pidot uri: https://doi.org/10.7717/peerj.4784 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Herisse et al. title: Repurposing drugs to fast-track therapeutic agents for the treatment of cryptococcosis link: https://peerj.com/articles/4761 last-modified: 2018-05-04 description: Many infectious diseases disproportionately affect people in the developing world. Cryptococcal meningitis is one of the most common mycoses in HIV-AIDS patients, with the highest burden of disease in sub-Saharan Africa. Current best treatment regimens still result in unacceptably high mortality rates, and more effective antifungal agents are needed urgently. Drug development is hampered by the difficulty of developing effective antifungal agents that are not also toxic to human cells, and by a reluctance among pharmaceutical companies to invest in drugs that cannot guarantee a high financial return. Drug repurposing, where existing drugs are screened for alternative activities, is becoming an attractive approach in antimicrobial discovery programs, and various compound libraries are now commercially available. As these drugs have already undergone extensive optimisation and passed regulatory hurdles this can fast-track their progress to market for new uses. This study screened the Screen-Well Enzo library of 640 compounds for candidates that phenotypically inhibited the growth of Cryptococcus deuterogattii. The anthelminthic agent flubendazole, and L-type calcium channel blockers nifedipine, nisoldipine and felodipine, appeared particularly promising and were tested in additional strains and species. Flubendazole was very active against all pathogenic Cryptococcus species, with minimum inhibitory concentrations of 0.039–0.156 μg/mL, and was equally effective against isolates that were resistant to fluconazole. While nifedipine, nisoldipine and felodipine all inhibited Cryptococcus, nisoldipine was also effective against Candida, Saccharomyces and Aspergillus. This study validates repurposing as a rapid approach for finding new agents to treat neglected infectious diseases. creator: Megan Truong creator: Leigh G. Monahan creator: Dee A. Carter creator: Ian G. Charles uri: https://doi.org/10.7717/peerj.4761 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Truong et al. title: EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation link: https://peerj.com/articles/4750 last-modified: 2018-05-04 description: During the past decade, with the significant progress of computational power as well as ever-rising data availability, deep learning techniques became increasingly popular due to their excellent performance on computer vision problems. The size of the Protein Data Bank (PDB) has increased more than 15-fold since 1999, which enabled the expansion of models that aim at predicting enzymatic function via their amino acid composition. Amino acid sequence, however, is less conserved in nature than protein structure and therefore considered a less reliable predictor of protein function. This paper presents EnzyNet, a novel 3D convolutional neural networks classifier that predicts the Enzyme Commission number of enzymes based only on their voxel-based spatial structure. The spatial distribution of biochemical properties was also examined as complementary information. The two-layer architecture was investigated on a large dataset of 63,558 enzymes from the PDB and achieved an accuracy of 78.4% by exploiting only the binary representation of the protein shape. Code and datasets are available at https://github.com/shervinea/enzynet. creator: Afshine Amidi creator: Shervine Amidi creator: Dimitrios Vlachakis creator: Vasileios Megalooikonomou creator: Nikos Paragios creator: Evangelia I. Zacharaki uri: https://doi.org/10.7717/peerj.4750 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Amidi et al. title: Temporally-aware algorithms for the classification of anuran sounds link: https://peerj.com/articles/4732 last-modified: 2018-05-04 description: Several authors have shown that the sounds of anurans can be used as an indicator of climate change. Hence, the recording, storage and further processing of a huge number of anuran sounds, distributed over time and space, are required in order to obtain this indicator. Furthermore, it is desirable to have algorithms and tools for the automatic classification of the different classes of sounds. In this paper, six classification methods are proposed, all based on the data-mining domain, which strive to take advantage of the temporal character of the sounds. The definition and comparison of these classification methods is undertaken using several approaches. The main conclusions of this paper are that: (i) the sliding window method attained the best results in the experiments presented, and even outperformed the hidden Markov models usually employed in similar applications; (ii) noteworthy overall classification performance has been obtained, which is an especially striking result considering that the sounds analysed were affected by a highly noisy background; (iii) the instance selection for the determination of the sounds in the training dataset offers better results than cross-validation techniques; and (iv) the temporally-aware classifiers have revealed that they can obtain better performance than their non-temporally-aware counterparts. creator: Amalia Luque creator: Javier Romero-Lemos creator: Alejandro Carrasco creator: Luis Gonzalez-Abril uri: https://doi.org/10.7717/peerj.4732 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Luque et al. title: The pitfalls of short-range endemism: high vulnerability to ecological and landscape traps link: https://peerj.com/articles/4715 last-modified: 2018-05-04 description: Ecological traps attract biota to low-quality habitats. Landscape traps are zones caught in a vortex of spiralling degradation. Here, we demonstrate how short-range endemic (SRE) traits may make such taxa vulnerable to ecological and landscape traps. Three SRE species of mygalomorph spider were used in this study: Idiommata blackwalli, Idiosoma sigillatum and an undescribed Aganippe sp. Mygalomorphs can be long-lived (>43 years) and select sites for permanent burrows in their early dispersal phase. Spiderlings from two species, I. blackwalli (n = 20) and Aganippe sp. (n = 50), demonstrated choice for microhabitats under experimental conditions, that correspond to where adults typically occur in situ. An invasive veldt grass microhabitat was selected almost exclusively by spiderlings of I. sigillatum. At present, habitat dominated by veldt grass in Perth, Western Australia, has lower prey diversity and abundance than undisturbed habitats and therefore may act as an ecological trap for this species. Furthermore, as a homogenising force, veldt grass can spread to form a landscape trap in naturally heterogeneous ecosystems. Selection of specialised microhabitats of SREs may explain high extinction rates in old, stable landscapes undergoing (human-induced) rapid change. creator: Leanda D. Mason creator: Philip W. Bateman creator: Grant W. Wardell-Johnson uri: https://doi.org/10.7717/peerj.4715 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Mason et al. title: IL-6 and TNF-α salivary levels according to the periodontal status in Portuguese pregnant women link: https://peerj.com/articles/4710 last-modified: 2018-05-04 description: BackgroundPeriodontitis is associated with increased concentration of inflammatory markers and saliva has been proposed as a non-invasive diagnostic fluid in oral and systemic diseases. The levels of salivary biomarkers, such as cytokines, could potentially be used to distinguish periodontal healthy individuals from subjects with periodontal disease. The purpose of this study was to characterize the salivary levels of two inflammatory biomarkers associated with periodontitis, interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α), in order to assess whether these cytokines salivary levels could potentially be used to complement periodontitis pregnant women diagnose.MethodsForty-four pregnant women were distributed into three groups, according to their periodontal status: healthy, mild/moderate periodontitis and severe periodontitis. Unstimulated saliva was collected and analysis of TNF-α and IL-6 salivary levels were performed with Immulite®.ResultsWomen with periodontitis exhibited significantly higher levels (p = 0.001) of salivary IL-6 and TNF-α compared with the healthy group: 25.1 (±11.2) pg/mL vs. 16.3 (±5.0) pg/mL and 29.7 (±17.2) pg/mL vs. 16.2 (±7.6) pg/mL, approximately 1.5 and 1.8 times more, respectively. Additionally, cytokines were significantly increased (p < 0.05) in severe periodontitis compared to periodontal healthy pregnant women.ConclusionsThese results revealed that IL-6 and TNF-α salivary biomarkers provide high discriminatory capacity for distinguishing periodontal disease from periodontal health in pregnant women. creator: Vanessa Machado creator: Maria Fernanda Mesquita creator: Maria Alexandra Bernardo creator: Ester Casal creator: Luís Proença creator: José João Mendes uri: https://doi.org/10.7717/peerj.4710 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Machado et al. title: DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers link: https://peerj.com/articles/4705 last-modified: 2018-05-04 description: Biodiversity assessment of marine hard-bottom communities is hindered by the high diversity and size-ranges of the organisms present. We developed a DNA metabarcoding protocol for biodiversity characterization of structurally complex natural marine hard-bottom communities. We used two molecular markers: the “Leray fragment” of mitochondrial cytochrome c oxidase (COI), for which a novel primer set was developed, and the V7 region of the nuclear small subunit ribosomal RNA (18S). Eight different shallow marine littoral communities from two National Parks in Spain (one in the Atlantic Ocean and another in the Mediterranean Sea) were studied. Samples were sieved into three size fractions from where DNA was extracted separately. Bayesian clustering was used for delimiting molecular operational taxonomic units (MOTUs) and custom reference databases were constructed for taxonomic assignment. Despite applying stringent filters, we found high values for MOTU richness (2,510 and 9,679 MOTUs with 18S and COI, respectively), suggesting that these communities host a large amount of yet undescribed eukaryotic biodiversity. Significant gaps are still found in sequence reference databases, which currently prevent the complete taxonomic assignment of the detected sequences. In our dataset, 85% of 18S MOTUs and 64% of COI MOTUs could be identified to phylum or lower taxonomic level. Nevertheless, those unassigned were mostly rare MOTUs with low numbers of reads, and assigned MOTUs comprised over 90% of the total sequence reads. The identification rate might be significantly improved in the future, as reference databases are further completed. Our results show that marine metabarcoding, currently applied mostly to plankton or sediments, can be adapted to structurally complex hard bottom samples. Thus, eukaryotic metabarcoding emerges as a robust, fast, objective and affordable method to comprehensively characterize the diversity of marine benthic communities dominated by macroscopic seaweeds and colonial or modular sessile metazoans. The 18S marker lacks species-level resolution and thus cannot be recommended to assess the detailed taxonomic composition of these communities. Our new universal primers for COI can potentially be used for biodiversity assessment with high taxonomic resolution in a wide array of marine, terrestrial or freshwater eukaryotic communities. creator: Owen S. Wangensteen creator: Creu Palacín creator: Magdalena Guardiola creator: Xavier Turon uri: https://doi.org/10.7717/peerj.4705 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wangensteen et al. title: Candidate genes in gastric cancer identified by constructing a weighted gene co-expression network link: https://peerj.com/articles/4692 last-modified: 2018-05-04 description: BackgroundGastric cancer (GC) is one of the most common cancers with high mortality globally. However, the molecular mechanisms of GC are unclear, and the prognosis of GC is poor. Therefore, it is important to explore the underlying mechanisms and screen for novel prognostic markers and treatment targets.MethodsThe genetic and clinical data of GC patients in The Cancer Genome Atlas (TCGA) was analyzed by weighted gene co-expression network analysis (WGCNA). Modules with clinical significance and preservation were distinguished, and gene ontology and pathway enrichment analysis were performed. Hub genes of these modules were validated in the TCGA dataset and another independent dataset from the Gene Expression Omnibus (GEO) database by t-test. Furthermore, the significance of these genes was confirmed via survival analysis.ResultsWe found a preserved module consisting of 506 genes was associated with clinical traits including pathologic T stage and histologic grade. PDGFRB, COL8A1, EFEMP2, FBN1, EMILIN1, FSTL1 and KIRREL were identified as candidate genes in the module. Their expression levels were correlated with pathologic T stage and histologic grade, also affected overall survival of GC patients.ConclusionThese candidate genes may be involved in proliferation and differentiation of GC cells. They may serve as novel prognostic markers and treatment targets. Moreover, most of them were first reported in GC and deserved further research. creator: Jian Chen creator: Xiuwen Wang creator: Bing Hu creator: Yifu He creator: Xiaojun Qian creator: Wei Wang uri: https://doi.org/10.7717/peerj.4692 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chen et al. title: Bioinformatic analysis and identification of potential prognostic microRNAs and mRNAs in thyroid cancer link: https://peerj.com/articles/4674 last-modified: 2018-05-04 description: Thyroid cancer is one of the most common endocrine malignancies. Multiple evidences revealed that a large number of microRNAs and mRNAs were abnormally expressed in thyroid cancer tissues. These microRNAs and mRNAs play important roles in tumorigenesis. In the present study, we identified 72 microRNAs and 1,766 mRNAs differentially expressed between thyroid cancer tissues and normal thyroid tissues and evaluated their prognostic values using Kaplan-Meier survival curves by log-rank test. Seven microRNAs (miR-146b, miR-184, miR-767, miR-6730, miR-6860, miR-196a-2 and miR-509-3) were associated with the overall survival. Among them, three microRNAs were linked with six differentially expressed mRNAs (miR-767 was predicted to target COL10A1, PLAG1 and PPP1R1C; miR-146b was predicted to target MMP16; miR-196a-2 was predicted to target SYT9). To identify the key genes in the protein-protein interaction network , we screened out the top 10 hub genes (NPY, NMU, KNG1, LPAR5, CCR3, SST, PPY, GABBR2, ADCY8 and SAA1) with higher degrees. Only LPAR5 was associated with the overall survival. Multivariate analysis demonstrated that miR-184, miR-146b, miR-509-3 and LPAR5 were an independent risk factors for prognosis. Our results of the present study identified a series of prognostic microRNAs and mRNAs that have the potential to be the targets for treatment of thyroid cancer. creator: Jianing Tang creator: Deguang Kong creator: Qiuxia Cui creator: Kun Wang creator: Dan Zhang creator: Qianqian Yuan creator: Xing Liao creator: Yan Gong creator: Gaosong Wu uri: https://doi.org/10.7717/peerj.4674 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tang et al. title: Candidate genes associated with red colour formation revealed by comparative genomic variant analysis of red- and green-skinned fruits of Japanese apricot (Prunus mume) link: https://peerj.com/articles/4625 last-modified: 2018-05-04 description: The red-skinned fruit of Japanese apricot (Prunus mume Sieb. et Zucc) appeals to customers due to its eye-catching pigmentation, while the mechanism related to its colour formation is still unclear. In this study, genome re-sequencing of six Japanese apricot cultivars was carried out with approximately 92.2 Gb of clean bases using next-generation sequencing. A total of 32,004 unigenes were assembled with an average of 83.1% coverage rate relative to reference genome. A wide range of genetic variation was detected, including 7,387,057 single nucleotide polymorphisms, 456,222 insertions or deletions and 129,061 structural variations in all genomes. Comparative sequencing data revealed that 13 candidate genes were involved in biosynthesis of anthocyanin. Significantly higher expression patterns were observed in genes encoding three anthocyanin synthesis structural genes (4CL, F3H and UFGT), five transcription factors (MYB–bHLH–WD40 complexes and NAC) and five anthocyanin accumulation related genes (GST1, RT1, UGT85A2, ABC and MATE transporters) in red-skinned than in green-skinned Japanese apricots using reverse transcription-quantitative polymerase chain reaction. Eight main kinds of anthocyanin s were detected by UPLC/MS, and cyanidin 3-glucoside was identified as the major anthocyanin (124.2 mg/kg) in red-skinned cultivars. The activity of UDP-glucose flavonoid-3-O-glycosyltransferase enzyme determined by UPLC was significantly higher in all red-skinned cultivars, suggesting that it is the potential vital regulatory gene for biosynthesis of anthocyanin in Japanese apricot. creator: Xiaopeng Ni creator: Song Xue creator: Shahid Iqbal creator: Wanxu Wang creator: Zhaojun Ni creator: Muhammad Khalil-ur-Rehman creator: Zhihong Gao uri: https://doi.org/10.7717/peerj.4625 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Ni et al. title: Quantitative estimation of soil salinity by means of different modeling methods and visible-near infrared (VIS–NIR) spectroscopy, Ebinur Lake Wetland, Northwest China link: https://peerj.com/articles/4703 last-modified: 2018-05-03 description: Soil salinization is one of the most common forms of land degradation. The detection and assessment of soil salinity is critical for the prevention of environmental deterioration especially in arid and semi-arid areas. This study introduced the fractional derivative in the pretreatment of visible and near infrared (VIS–NIR) spectroscopy. The soil samples (n = 400) collected from the Ebinur Lake Wetland, Xinjiang Uyghur Autonomous Region (XUAR), China, were used as the dataset. After measuring the spectral reflectance and salinity in the laboratory, the raw spectral reflectance was preprocessed by means of the absorbance and the fractional derivative order in the range of 0.0–2.0 order with an interval of 0.1. Two different modeling methods, namely, partial least squares regression (PLSR) and random forest (RF) with preprocessed reflectance were used for quantifying soil salinity. The results showed that more spectral characteristics were refined for the spectrum reflectance treated via fractional derivative. The validation accuracies showed that RF models performed better than those of PLSR. The most effective model was established based on RF with the 1.5 order derivative of absorbance with the optimal values of R2 (0.93), RMSE (4.57 dS m−1), and RPD (2.78 ≥ 2.50). The developed RF model was stable and accurate in the application of spectral reflectance for determining the soil salinity of the Ebinur Lake wetland. The pretreatment of fractional derivative could be useful for monitoring multiple soil parameters with higher accuracy, which could effectively help to analyze the soil salinity. creator: Jingzhe Wang creator: Jianli Ding creator: Aerzuna Abulimiti creator: Lianghong Cai uri: https://doi.org/10.7717/peerj.4703 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Post-traumatic stress symptoms are associated with better performance on a delayed match-to-position task link: https://peerj.com/articles/4701 last-modified: 2018-05-03 description: Many individuals with posttraumatic stress disorder (PTSD) report experiencing frequent intrusive memories of the original traumatic event (e.g., flashbacks). These memories can be triggered by situations or stimuli that reflect aspects of the trauma and may reflect basic processes in learning and memory, such as generalization. It is possible that, through increased generalization, non-threatening stimuli that once evoked normal memories become associated with traumatic memories. Previous research has reported increased generalization in PTSD, but the role of visual discrimination processes has not been examined. To investigate visual discrimination in PTSD, 143 participants (Veterans and civilians) self-assessed for symptom severity were grouped according to the presence of severe PTSD symptoms (PTSS) vs. few/no symptoms (noPTSS). Participants were given a visual match-to-sample pattern separation task that varied trials by spatial separation (Low, Medium, High) and temporal delays (5, 10, 20, 30 s). Unexpectedly, the PTSS group demonstrated better discrimination performance than the noPTSS group at the most difficult spatial trials (Low spatial separation). Further assessment of accuracy and reaction time using diffusion drift modeling indicated that the better performance by the PTSS group on the hardest trials was not explained by slower reaction times, but rather a faster accumulation of evidence during decision making in conjunction with a reduced threshold, indicating a tendency in the PTSS group to decide quickly rather than waiting for additional evidence to support the decision. This result supports the need for future studies examining the precise role of discrimination and generalization in PTSD, and how these cognitive processes might contribute to expression and maintenance of PTSD symptoms. creator: Meghan D. Caulfield creator: Catherine E. Myers uri: https://doi.org/10.7717/peerj.4701 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Caulfield and Myers title: Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex link: https://peerj.com/articles/4654 last-modified: 2018-05-03 description: Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S FST = 0.13; SEQ-N FST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentially susceptible to future conservation threats, and we define eight genetically distinct management units along south east Queensland to guide future conservation management. The present findings at least can assist managers to plan for effective conservation and management of different fish species along coastal drainages of south east Queensland, Australia. creator: Md Rakeb-Ul Islam creator: Daniel J. Schmidt creator: David A. Crook creator: Jane M. Hughes uri: https://doi.org/10.7717/peerj.4654 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Islam et al. title: Relationships between parents’ academic backgrounds and incomes and building students’ healthy eating habits link: https://peerj.com/articles/4563 last-modified: 2018-05-03 description: BackgroundBuilding healthy eating habit is essential for all people. School and family are the prime institutions to instill this habit during early age. This study is aimed at understanding the impact of family such as parents’ educations and incomes on building students’ healthy eating habits.MethodsA survey on building students’ eating habits was conducted among primary school students of grade 4 (11 years) and 5 (12 years) from Kulim district, Malaysia. Data from 318 respondents were analysed. Descriptive statistics were used to find the present scenario of their knowledge, attitude and practices towards their eating habits while one-way ANOVA and independent sample t-test were used to find the differences between their practices based on students’ gender, parents’ educations and incomes.ResultsThe study finds that the students have a good knowledge of types of healthy food but yet their preferences are towards the unhealthy food. Though the students’ gender and parents’ educations are not found significantly related to students’ knowledge, attitude and practices towards healthy eating habits, parents’ incomes have significant influence on promoting the healthy eating habit.DiscussionFindings of this study can be useful to guide parents in healthy food choices and suggest them to be models to their children in building healthy eating habits. creator: Kazi Enamul Hoque creator: Kazi Fardinul Hoque creator: Revethy A/P Thanabalan uri: https://doi.org/10.7717/peerj.4563 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hoque et al. title: Stinging wasps (Hymenoptera: Aculeata), which species have the longest sting? link: https://peerj.com/articles/4743 last-modified: 2018-05-02 description: The stings of bees, wasps, and ants are something that catches the attention of anyone that experiences them. While many recent studies have focused on the pain inflicted by the stings of various stinging wasps, bees, or ants (Hymenoptera: Aculeata), little is known about how the length of the sting itself varies between species. Here, we investigate the sting length of a variety of aculeate wasps, and compare that to reported pain and toxicity values. We find that velvet ants (Hymenoptera: Mutillidae) have the longest sting compared to their body size out of any bee, wasp, or ant species. We also find that there is no link between relative sting length and pain; however, we did find an inverse relationship between relative sting length and toxicity with taxa having shorter relative stings being more toxic. While we found a significant relationship between host use and relative sting length, we suggest that the long sting length of the velvet ants is also related to their suite of defenses to avoid predation. creator: Emily A. Sadler creator: James P. Pitts creator: Joseph S. Wilson uri: https://doi.org/10.7717/peerj.4743 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Sadler et al. title: Influence and reliability of lower-limb arterial occlusion pressure at different body positions link: https://peerj.com/articles/4697 last-modified: 2018-05-02 description: BackgroundTotal arterial occlusive pressure (AOP) is used to prescribe pressures for surgery, blood flow restriction exercise (BFRE) and ischemic preconditioning (IPC). AOP is often measured in a supine position; however, the influence of body position on AOP measurement is unknown and may influence level of occlusion in different positions during BFR and IPC. The aim of this study was therefore to investigate the influence of body position on AOP.MethodsFifty healthy individuals (age = 29 ± 6 y) underwent AOP measurements on the dominant lower-limb in supine, seated and standing positions in a randomised order. AOP was measured automatically using the Delfi Personalised Tourniquet System device, with each measurement separated by 5 min of rest.ResultsArterial occlusive pressure was significantly lower in the supine position compared to the seated position (187.00 ± 32.5 vs 204.00 ± 28.5 mmHg, p < 0.001) and standing position (187.00 ± 32.5 vs 241.50 ± 49.3 mmHg, p < 0.001). AOP was significantly higher in the standing position compared to the seated position (241.50 ± 49.3 vs 204.00 ± 28.5 mmHg, p < 0.001).DiscussionArterial occlusive pressure measurement is body position dependent, thus for accurate prescription of occlusion pressure during surgery, BFR and IPC, AOP should be measured in the position intended for subsequent application of occlusion. creator: Luke Hughes creator: Owen Jeffries creator: Mark Waldron creator: Ben Rosenblatt creator: Conor Gissane creator: Bruce Paton creator: Stephen D. Patterson uri: https://doi.org/10.7717/peerj.4697 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Hughes et al. title: From in silico to in vitro: a trip to reveal flavonoid binding on the Rattus norvegicus Kir6.1 ATP-sensitive inward rectifier potassium channel link: https://peerj.com/articles/4680 last-modified: 2018-05-02 description: BackgroundATP-sensitive inward rectifier potassium channels (Kir), are a potassium channel family involved in many physiological processes. KATP dysfunctions are observed in several diseases such as hypoglycaemia, hyperinsulinemia, Prinzmetal angina–like symptoms, cardiovascular diseases.MethodsA broader view of the KATP mechanism is needed in order to operate on their regulation, and in this work we clarify the structure of the Rattus norvegicus ATP-sensitive inward rectifier potassium channel 8 (Kir6.1), which has been obtained through a homology modelling procedure. Due to the medical use of flavonoids, a considerable increase in studies on their influence on human health has recently been observed, therefore our aim is to study, through computational methods, the three-dimensional (3D) conformation together with mechanism of action of Kir6.1 with three flavonoids.ResultsComputational analysis by performing molecular dynamics (MD) and docking simulation on rat 3D modelled structure have been completed, in its closed and open conformation state and in complex with Quercetin, 5-Hydroxyflavone and Rutin flavonoids. Our study showed that only Quercetin and 5-Hydroxyflavone were responsible for a significant down-regulation of the Kir6.1 activity, stabilising it in a closed conformation. This hypothesis was supported by in vitro experiments demonstrating that Quercetin and 5-Hydroxyflavone were capable to inhibit KATP currents of rat tail main artery myocytes recorded by the patch-clamp technique.ConclusionCombined methodological approaches, such as molecular modelling, docking and MD simulations of Kir6.1 channel, used to elucidate flavonoids intrinsic mechanism of action, are introduced, revealing a new potential druggable protein site. creator: Alfonso Trezza creator: Vittoria Cicaloni creator: Piera Porciatti creator: Andrea Langella creator: Fabio Fusi creator: Simona Saponara creator: Ottavia Spiga uri: https://doi.org/10.7717/peerj.4680 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Trezza et al. title: From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes link: https://peerj.com/articles/4577 last-modified: 2018-05-02 description: With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data. creator: Nadine Havemann creator: Martin M. Gossner creator: Lars Hendrich creator: Jèrôme Morinière creator: Rolf Niedringhaus creator: Peter Schäfer creator: Michael J. Raupach uri: https://doi.org/10.7717/peerj.4577 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Havemann et al. title: Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient link: https://peerj.com/articles/4735 last-modified: 2018-05-01 description: Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex interplay between dispersal and environmental selection for microbial communities in nature. creator: Angus Angermeyer creator: Sarah C. Crosby creator: Julie A. Huber uri: https://doi.org/10.7717/peerj.4735 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Angermeyer et al. title: Is the future already here? The impact of climate change on the distribution of the eastern coral snake (Micrurus fulvius) link: https://peerj.com/articles/4647 last-modified: 2018-05-01 description: Anthropogenic climate change is a significant global driver of species distribution change. Although many species have undergone range expansion at their poleward limits, data on several taxonomic groups are still lacking. A common method for studying range shifts is using species distribution models to evaluate current, and predict future, distributions. Notably, many sources of ‘current’ climate data used in species distribution modeling use the years 1950–2000 to calculate climatic averages. However, this does not account for recent (post 2000) climate change. This study examines the influence of climate change on the eastern coral snake (Micrurus fulvius). Specifically, we: (1) identified the current range and suitable environment of M. fulvius in the Southeastern United States, (2) investigated the potential impacts of climate change on the distribution of M. fulvius, and (3) evaluated the utility of future models in predicting recent (2001–2015) records. We used the species distribution modeling program Maxent and compared both current (1950–2000) and future (2050) climate conditions. Future climate models showed a shift in the distribution of suitable habitat across a significant portion of the range; however, results also suggest that much of the Southeastern United States will be outside the range of current conditions, suggesting that there may be no-analog environments in the future. Most strikingly, future models were more effective than the current models at predicting recent records, suggesting that range shifts may already be occurring. These results have implications for both M. fulvius and its Batesian mimics. More broadly, we recommend future Maxent studies consider using future climate data along with current data to better estimate the current distribution. creator: Jennifer N. Archis creator: Christopher Akcali creator: Bryan L. Stuart creator: David Kikuchi creator: Amanda J. Chunco uri: https://doi.org/10.7717/peerj.4647 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Archis et al.