title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2017-09 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Growth of hybrid open access, 2009–2016 link: https://peerj.com/articles/3878 last-modified: 2017-09-29 description: Hybrid Open Access is an intermediate form of OA, where authors pay scholarly publishers to make articles freely accessible within journals, in which reading the content otherwise requires a subscription or pay-per-view. Major scholarly publishers have in recent years started providing the hybrid option for the vast majority of their journals. Since the uptake usually has been low per journal and scattered over thousands of journals, it has been very difficult to obtain an overview of how common hybrid articles are. This study, using the results of earlier studies as well as a variety of methods, measures the evolution of hybrid OA over time. The number of journals offering the hybrid option has increased from around 2,000 in 2009 to almost 10,000 in 2016. The number of individual articles has in the same period grown from an estimated 8,000 in 2009 to 45,000 in 2016. The growth in article numbers has clearly increased since 2014, after some major research funders in Europe started to introduce new centralized payment schemes for the article processing charges (APCs). creator: Bo-Christer Björk uri: https://doi.org/10.7717/peerj.3878 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Björk title: Effect of the environment on horizontal gene transfer between bacteria and archaea link: https://peerj.com/articles/3865 last-modified: 2017-09-29 description: BackgroundHorizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).ResultsWe investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.ConclusionsAnaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters. creator: Clara A. Fuchsman creator: Roy Eric Collins creator: Gabrielle Rocap creator: William J. Brazelton uri: https://doi.org/10.7717/peerj.3865 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Fuchsman et al. title: Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus? link: https://peerj.com/articles/3842 last-modified: 2017-09-29 description: BackgroundFragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus.MethodsWe sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk.ResultsWe found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands.DiscussionIn this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between full growth native forest remnants is mediated by the presence of dense shrublands and native forest corridors. In this sense, our results are important because they show how native forest patches and associated routes act as source of vector species in silvoagropecuary landscape, increasing the infection risk on human population. This study is the first approach to understand the epidemiological spatial context of silvoagropecuary risk of Hantavirus emergence. Further studies are needed to elucidate the effects of landscape fragmentation in order to generate new predictive models based on vector intrinsic attributes and landscape features. creator: Daniela Lazo-Cancino creator: Selim S. Musleh creator: Cristian E. Hernandez creator: Eduardo Palma creator: Enrique Rodriguez-Serrano uri: https://doi.org/10.7717/peerj.3842 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lazo-Cancino et al. title: A prospective study of the motivational and health dynamics of Internet Gaming Disorder link: https://peerj.com/articles/3838 last-modified: 2017-09-29 description: The American Psychiatric Association has identified Internet Gaming Disorder (IGD) as a potential psychiatric condition and called for research to investigate its etiology, stability, and impacts on health and behavior. The present study recruited 5,777 American adults and applied self-determination theory to examine how motivational factors influence, and are influenced by, IGD and health across a six month period. Following a preregistered analysis plan, results confirmed our hypotheses that IGD criteria are moderately stable and that they and basic psychological need satisfaction have a reciprocal relationship over time. Results also showed need satisfaction promoted health and served as a protective factor against IGD. Contrary to what was hypothesized, results provided no evidence directly linking IGD to health over time. Exploratory analyses suggested that IGD may have indirect effects on health by way of its impact on basic needs. Implications are discussed in terms of existing gaming addiction and motivational frameworks. creator: Netta Weinstein creator: Andrew K. Przybylski creator: Kou Murayama uri: https://doi.org/10.7717/peerj.3838 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Weinstein et al. title: Unraveling the diversification history of grasshoppers belonging to the “Trimerotropis pallidipennis” (Oedipodinae: Acrididae) species group: a hotspot of biodiversity in the Central Andes link: https://peerj.com/articles/3835 last-modified: 2017-09-29 description: The Andean Mountain range has been recognized as one of the biodiversity hotspots of the world. The proposed mechanisms for such species diversification, among others, are due to the elevation processes occurring during the Miocene and the intensive glacial action during the Pleistocene. In this study we investigated the diversification history of the grasshopper Trimerotropis pallidipennis species complex which shows a particularly wide latitudinal and altitudinal distribution range across the northern, central and southern Andes in South America. Many genetic lineages of this complex have been so far discovered, making it an excellent model to investigate the role of the central Andes Mountains together with climatic fluctuations as drivers of speciation. Phylogenetics, biogeographic and molecular clock analyses using a multi-locus dataset revealed that in Peru there are at least two, and possibly four genetic lineages. Two different stocks originated from a common ancestor from North/Central America—would have dispersed toward southern latitudes favored by the closure of the Panama Isthmus giving rise to two lineages, the coastal and mountain lineages, which still coexist in Peru (i.e., T. pallidipennis and T. andeana). Subsequent vicariant and dispersal events continued the differentiation process, giving rise to three to six genetic lineages (i.e., clades) detected in this study, which were geographically restricted to locations dispersed over the central Andes Mountains in South America. Our results provide another interesting example of “island diversification” motored by the topography plus unstable climatic conditions during the Pleistocene, pointing out the presence of a hotspot of diversification in the Andean region of Peru. creator: Noelia Verónica Guzmán creator: Silvia Mónica Pietrokovsky creator: Maria Marta Cigliano creator: Viviana Andrea Confalonieri uri: https://doi.org/10.7717/peerj.3835 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Guzmán et al. title: The relationship between sustained attention and aerobic fitness in a group of young adults link: https://peerj.com/articles/3831 last-modified: 2017-09-29 description: BackgroundA growing set of studies has shown a positive relationship between aerobic fitness and a broad array of cognitive functions. However, few studies have focused on sustained attention, which has been considered a fundamental cognitive process that underlies most everyday activities. The purpose of this study was to investigate the role of aerobic fitness as a key factor in sustained attention capacities in young adults.MethodsForty-four young adults (18–23 years) were divided into two groups as a function of the level of aerobic fitness (high-fit and low-fit). Participants completed the Psychomotor Vigilance Task (PVT) and an oddball task where they had to detect infrequent targets presented among frequent non-targets.ResultsThe analysis of variance (ANOVA) showed faster responses for the high-fit group than for the low-fit group in the PVT, replicating previous accounts. In the oddball task, the high-fit group maintained their accuracy (ACC) rate of target detection over time, while the low-fit group suffered a significant decline of response ACC throughout the task.DiscussionImportantly, the results show that the greater sustained attention capacity of high-fit young adults is not specific to a reaction time (RT) sustained attention task like the PVT, but it is also evident in an ACC oddball task. In sum, the present findings point to the important role of aerobic fitness on sustained attention capacities in young adults. creator: Luis F. Ciria creator: Pandelis Perakakis creator: Antonio Luque-Casado creator: Cristina Morato creator: Daniel Sanabria uri: https://doi.org/10.7717/peerj.3831 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ciria et al. title: Extracorporeal life support with left ventricular decompression—improved survival in severe cardiogenic shock: results from a retrospective study link: https://peerj.com/articles/3813 last-modified: 2017-09-29 description: ObjectiveExtracorporeal life support (ECLS) is a life-saving procedure used in the treatment of severe cardiogenic shock. Within this retrospective single centre study, we examined our experience in this critically ill patient cohort to assess outcomes and clinical parameters by comparison of ECLS with or without selective left ventricular decompression.MethodsBetween 2004 and 2014 we evaluated 48 adult patients with INTERMACS level 1 heart failure (age 49.7 ± 19.5 years), who received either central ECLS with (n = 20, 41.7%) or ECLS without (n = 28, 58.3%, including 10 peripheral ECLS) integrated left ventricular vent in our retrospective single centre trial.ResultsFollow up was 100% with a mean of 0.83 ± 1.85 years. Bridge to ventricular assist device was feasible in 29.2% (n = 14), bridge to transplant in 10.4% (n = 5) and bridge to recovery in 8.3% (n = 4). Overall 30-day survival was 37.5%, 6-month survival 27.1% and 1-year survival 25.0%. ECLS support with left ventricular decompression showed favourable 30-day survival compared to ECLS without left ventricular decompression (p = 0.034). Thirty-day as well as long-term survival did not differ between the subgroups (central ECLS with vent, ECLS without vent and peripheral ECLS without vent). Multivariate logistic regression adjusted for age and gender revealed ECLS without vent as independent factor influencing 30-day survival.ConclusionECLS is an established therapy for patients in severe cardiogenic shock. Independent of the ECLS approach, 30-day mortality is still high but with superior 30-day survival for patients with ECLS and left ventricular venting. Moreover, by unloading the ventricle, left ventricular decompression may provide an important time window for recovery or further treatment, such as bridge to bridge or bridge to transplant. creator: Bastian Schmack creator: Philipp Seppelt creator: Alexander Weymann creator: Christina Alt creator: Mina Farag creator: Rawa Arif creator: Andreas O. Doesch creator: Philip W. Raake creator: Klaus Kallenbach creator: Ashham Mansur creator: Aron-Frederik Popov creator: Matthias Karck creator: Arjang Ruhparwar uri: https://doi.org/10.7717/peerj.3813 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Schmack et al. title: Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9-cis-retinoic acid at the base of metazoan evolution link: https://peerj.com/articles/3789 last-modified: 2017-09-29 description: Trichoplax adhaerens, the only known species of Placozoa is likely to be closely related to an early metazoan that preceded branching of Cnidaria and Bilateria. This animal species is surprisingly well adapted to free life in the World Ocean inhabiting tidal costal zones of oceans and seas with warm to moderate temperatures and shallow waters. The genome of T. adhaerens (sp. Grell) includes four nuclear receptors, namely orthologue of RXR (NR2B), HNF4 (NR2A), COUP-TF (NR2F) and ERR (NR3B) that show a high degree of similarity with human orthologues. In the case of RXR, the sequence identity to human RXR alpha reaches 81% in the DNA binding domain and 70% in the ligand binding domain. We show that T. adhaerens RXR (TaRXR) binds 9-cis retinoic acid (9-cis-RA) with high affinity, as well as high specificity and that exposure of T. adhaerens to 9-cis-RA regulates the expression of the putative T. adhaerens orthologue of vertebrate L-malate-NADP+ oxidoreductase (EC 1.1.1.40) which in vertebrates is regulated by a heterodimer of RXR and thyroid hormone receptor. Treatment by 9-cis-RA alters the relative expression profile of T. adhaerens nuclear receptors, suggesting the existence of natural ligands. Keeping with this, algal food composition has a profound effect on T. adhaerens growth and appearance. We show that nanomolar concentrations of 9-cis-RA interfere with T. adhaerens growth response to specific algal food and causes growth arrest. Our results uncover an endocrine-like network of nuclear receptors sensitive to 9-cis-RA in T. adhaerens and support the existence of a ligand-sensitive network of nuclear receptors at the base of metazoan evolution. creator: Jan Philipp Novotný creator: Ahmed Ali Chughtai creator: Markéta Kostrouchová creator: Veronika Kostrouchová creator: David Kostrouch creator: Filip Kaššák creator: Radek Kaňa creator: Bernd Schierwater creator: Marta Kostrouchová creator: Zdenek Kostrouch uri: https://doi.org/10.7717/peerj.3789 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Novotný et al. title: The World (of Warcraft) through the eyes of an expert link: https://peerj.com/articles/3783 last-modified: 2017-09-29 description: Negative correlations between pupil size and the tendency to look at salient locations were found in recent studies (e.g., Mathôt et al., 2015). It is hypothesized that this negative correlation might be explained by the mental effort put by participants in the task that leads in return to pupil dilation. Here we present an exploratory study on the effect of expertise on eye-movement behavior. Because there is no available standard tool to evaluate WoW players’ expertise, we built an off-game questionnaire testing players’ knowledge about WoW and acquired skills through completed raids, highest rated battlegrounds, Skill Points, etc. Experts (N = 4) and novices (N = 4) in the massively multiplayer online role-playing game World of Warcraft (WoW) viewed 24 designed video segments from the game that differ in regards with their content (i.e, informative locations) and visual complexity (i.e, salient locations). Consistent with previous studies, we found a negative correlation between pupil size and the tendency to look at salient locations (experts, r =  − .17, p < .0001, and novices, r =  − .09, p < .0001). This correlation has been interpreted in terms of mental effort: People are inherently biased to look at salient locations (sharp corners, bright lights, etc.), but are able (i.e., experts) to overcome this bias if they invest sufficient mental effort. Crucially, we observed that this correlation was stronger for expert WoW players than novice players (Z =  − 3.3, p = .0011). This suggests that experts learned to improve control over eye-movement behavior by guiding their eyes towards informative, but potentially low-salient areas of the screen. These findings may contribute to our understanding of what makes an expert an expert. creator: Yousri Marzouki creator: Valériane Dusaucy creator: Myriam Chanceaux creator: Sebastiaan Mathôt uri: https://doi.org/10.7717/peerj.3783 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Marzouki et al. title: Multi-scale immunoepidemiological modeling of within-host and between-host HIV dynamics: systematic review of mathematical models link: https://peerj.com/articles/3877 last-modified: 2017-09-28 description: ObjectiveThe objective of this study is to conduct a systematic review of multi-scale HIV immunoepidemiological models to improve our understanding of the synergistic impact between the HIV viral-immune dynamics at the individual level and HIV transmission dynamics at the population level.BackgroundWhile within-host and between-host models of HIV dynamics have been well studied at a single scale, connecting the immunological and epidemiological scales through multi-scale models is an emerging method to infer the synergistic dynamics of HIV at the individual and population levels.MethodsWe reviewed nine articles using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) framework that focused on the synergistic dynamics of HIV immunoepidemiological models at the individual and population levels.ResultsHIV immunoepidemiological models simulate viral immune dynamics at the within-host scale and the epidemiological transmission dynamics at the between-host scale. They account for longitudinal changes in the immune viral dynamics of HIV+ individuals, and their corresponding impact on the transmission dynamics in the population. They are useful to analyze the dynamics of HIV super-infection, co-infection, drug resistance, evolution, and treatment in HIV+ individuals, and their impact on the epidemic pathways in the population. We illustrate the coupling mechanisms of the within-host and between-host scales, their mathematical implementation, and the clinical and public health problems that are appropriate for analysis using HIV immunoepidemiological models.ConclusionHIV immunoepidemiological models connect the within-host immune dynamics at the individual level and the epidemiological transmission dynamics at the population level. While multi-scale models add complexity over a single-scale model, they account for the time varying immune viral response of HIV+ individuals, and the corresponding impact on the time-varying risk of transmission of HIV+ individuals to other susceptibles in the population. creator: Nargesalsadat Dorratoltaj creator: Ryan Nikin-Beers creator: Stanca M. Ciupe creator: Stephen G. Eubank creator: Kaja M. Abbas uri: https://doi.org/10.7717/peerj.3877 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dorratoltaj et al. title: An exploration of strategies used by dressage horses to control moments around the center of mass when performing passage link: https://peerj.com/articles/3866 last-modified: 2017-09-28 description: BackgroundLocomotion results from the generation of ground reaction forces (GRF) that cause translations of the center of mass (COM) and generate moments that rotate the body around the COM. The trot is a diagonally-synchronized gait performed by horses at intermediate locomotor speeds. Passage is a variant of the trot performed by highly-trained dressage horses. It is distinguished from trot by having a slow speed of progression combined with great animation of the limbs in the swing phase. The slow speed of passage challenges the horse’s ability to control the sagittal-plane moments around the COM. Footfall patterns and peak GRF are known to differ between passage and trot, but their effects on balance management, which we define here as the ability to control nose-up/nose-down pitching moments around the horse’s COM to maintain a state of equilibrium, are not known. The objective was to investigate which biomechanical variables influence pitching moments around the COM in passage.MethodsThree highly-trained dressage horses were captured by a 10-camera motion analysis system (120 Hz) as they were ridden in passage over four force platforms (960 Hz). A full-body marker set was used to track the horse’s COM and measure balance variables including total body center of pressure (COP), pitching moments, diagonal dissociation timing, peak force production, limb protraction–retraction, and trunk posture. A total of twenty passage steps were extracted and partial correlation (accounting for horse) was used to investigate significant (P < 0.05) relationships between variables.ResultsHindlimb mean protraction–retraction correlated significantly with peak hindlimb propulsive forces (R = 0.821; P < 0.01), mean pitching moments (R = 0.546, P = 0.016), trunk range of motion, COM craniocaudal location and diagonal dissociation time (P < 0.05).DiscussionPitching moments around the COM were controlled by a combination of kinematic and kinetic adjustments that involve coordinated changes in GRF magnitudes, GRF distribution between the diagonal limb pairs, and the moment arms of the vertical GRFs. The moment arms depend on hoof placements relative to the COM, which were adjusted by changing limb protraction–retraction angles. Nose-up pitching moments could also be increased by providing a larger hindlimb propulsive GRF. creator: Hilary M. Clayton creator: Sarah Jane Hobbs uri: https://doi.org/10.7717/peerj.3866 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Clayton and Hobbs title: Slower EEG alpha generation, synchronization and “flow”—possible biomarkers of cognitive impairment and neuropathology of minor stroke link: https://peerj.com/articles/3839 last-modified: 2017-09-28 description: BackgroundWe investigated EEG rhythms, particularly alpha activity, and their relationship to post-stroke neuropathology and cognitive functions in the subacute and chronic stages of minor strokes.MethodsWe included 10 patients with right middle cerebral artery (MCA) ischemic strokes and 11 healthy controls. All the assessments of stroke patients were done both in the subacute and chronic stages. Neurological impairment was measured using the National Institute of Health Stroke Scale (NIHSS), whereas cognitive functions were assessed using the Montreal Cognitive Assessment (MoCA) and MoCA memory index (MoCA-MIS). The EEG was recorded using a 19 channel EEG system with standard EEG electrode placement. In particular, we analyzed the EEGs derived from the four lateral frontal (F3, F7, F4, F8), and corresponding lateral posterior (P3, P4, T5, T6) electrodes. Quantitative EEG analysis included: the group FFT spectra, the weighted average of alpha frequency (αAVG), the group probability density distributions of all conventional EEG frequency band relative amplitudes (EEG microstructure), the inter- and intra-hemispheric coherences, and the topographic distribution of alpha carrier frequency phase potentials (PPs). Statistical analysis was done using a Kruskal–Wallis ANOVA with a post-hoc Mann–Whitney U two-tailed test, and Spearman’s correlation.ResultsWe demonstrated transient cognitive impairment alongside a slower alpha frequency (αAVG) in the subacute right MCA stroke patients vs. the controls. This slower alpha frequency showed no amplitude change, but was highly synchronized intra-hemispherically, overlying the ipsi-lesional hemisphere, and inter-hemispherically, overlying the frontal cortex. In addition, the disturbances in EEG alpha activity in subacute stroke patients were expressed as a decrease in alpha PPs over the frontal cortex and an altered “alpha flow”, indicating the sustained augmentation of inter-hemispheric interactions. Although the stroke induced slower alpha was a transient phenomenon, the increased alpha intra-hemispheric synchronization, overlying the ipsi-lesional hemisphere, the increased alpha F3–F4 inter-hemispheric synchronization, the delayed alpha waves, and the newly established inter-hemispheric “alpha flow” within the frontal cortex, remained as a permanent consequence of the minor stroke. This newly established frontal inter-hemispheric “alpha flow” represented a permanent consequence of the “hidden” stroke neuropathology, despite the fact that cognitive impairment has been returned to the control values. All the detected permanent changes at the EEG level with no cognitive impairment after a minor stroke could be a way for the brain to compensate for the lesion and restore the lost function. DiscussionOur study indicates slower EEG alpha generation, synchronization and “flow” as potential biomarkers of cognitive impairment onset and/or compensatory post-stroke re-organizational processes. creator: Jelena Petrovic creator: Vuk Milosevic creator: Miroslava Zivkovic creator: Dragan Stojanov creator: Olga Milojkovic creator: Aleksandar Kalauzi creator: Jasna Saponjic uri: https://doi.org/10.7717/peerj.3839 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Petrovic et al. title: Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data link: https://peerj.com/articles/3742 last-modified: 2017-09-28 description: We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone. creator: Tomasz Dzida creator: Mudassar Iqbal creator: Iryna Charapitsa creator: George Reid creator: Henk Stunnenberg creator: Filomena Matarese creator: Korbinian Grote creator: Antti Honkela creator: Magnus Rattray uri: https://doi.org/10.7717/peerj.3742 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dzida et al. title: Advances in the study of nodavirus link: https://peerj.com/articles/3841 last-modified: 2017-09-27 description: Nodaviruses are small bipartite RNA viruses which belong to the family of Nodaviridae. They are categorized into alpha-nodavirus, which infects insects, and beta-nodavirus, which infects fishes. Another distinct group of nodavirus infects shrimps and prawns, which has been proposed to be categorized as gamma-nodavirus. Our current review focuses mainly on recent studies performed on nodaviruses. Nodavirus can be transmitted vertically and horizontally. Recent outbreaks have been reported in China, Indonesia, Singapore and India, affecting the aquaculture industry. It also decreased mullet stock in the Caspian Sea. Histopathology and transmission electron microscopy (TEM) are used to examine the presence of nodaviruses in infected fishes and prawns. For classification, virus isolation followed by nucleotide sequencing are required. In contrast to partial sequence identification, profiling the whole transcriptome using next generation sequencing (NGS) offers a more comprehensive comparison and characterization of the virus. For rapid diagnosis of nodavirus, assays targeting the viral RNA based on reverse-transcription PCR (RT-PCR) such as microfluidic chips, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and RT-LAMP coupled with lateral flow dipstick (RT-LAMP-LFD) have been developed. Besides viral RNA detections, diagnosis based on immunological assays such as enzyme-linked immunosorbent assay (ELISA), immunodot and Western blotting have also been reported. In addition, immune responses of fish and prawn are also discussed. Overall, in fish, innate immunity, cellular type I interferon immunity and humoral immunity cooperatively prevent nodavirus infections, whereas prawns and shrimps adopt different immune mechanisms against nodavirus infections, through upregulation of superoxide anion, prophenoloxidase, superoxide dismutase (SOD), crustin, peroxinectin, anti-lipopolysaccharides and heat shock proteins (HSP). Potential vaccines for fishes and prawns based on inactivated viruses, recombinant proteins or DNA, either delivered through injection, oral feeding or immersion, are also discussed in detail. Lastly, a comprehensive review on nodavirus virus-like particles (VLPs) is presented. In recent years, studies on prawn nodavirus are mainly focused on Macrobrachium rosenbergii nodavirus (MrNV). Recombinant MrNV VLPs have been produced in prokaryotic and eukaryotic expression systems. Their roles as a nucleic acid delivery vehicle, a platform for vaccine development, a molecular tool for mechanism study and in solving the structures of MrNV are intensively discussed. creator: Chean Yeah Yong creator: Swee Keong Yeap creator: Abdul Rahman Omar creator: Wen Siang Tan uri: https://doi.org/10.7717/peerj.3841 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yong et al. title: A probe-based qRT-PCR method to profile immunological gene expression in blood of captive beluga whales (Delphinapterus leucas) link: https://peerj.com/articles/3840 last-modified: 2017-09-27 description: Cytokines are fundamental for a functioning immune system, and thus potentially serve as important indicators of animal health. Quantitation of mRNA using quantitative reverse transcription polymerase chain reaction (qRT-PCR) is an established immunological technique. It is particularly suitable for detecting the expression of proteins against which monoclonal antibodies are not available. In this study, we developed a probe-based quantitative gene expression assay for immunological assessment of captive beluga whales (Delphinapterus leucas) that is one of the most common cetacean species on display in aquariums worldwide. Six immunologically relevant genes (IL-2Rα, -4, -10, -12, TNFα, and IFNγ) were selected for analysis, and two validated housekeeping genes (PGK1 and RPL4) with stable expression were used as reference genes. Sixteen blood samples were obtained from four animals with different health conditions and stored in RNAlater™ solution. These samples were used for RNA extraction followed by qRT-PCR analysis. Analysis of gene transcripts was performed by relative quantitation using the comparative Cq method with the integration of amplification efficiency and two reference genes. The expression levels of each gene in the samples from clinically healthy animals were normally distributed. Transcript outliers for IL-2Rα, IL-4, IL-12, TNFα, and IFNγ were noticed in four samples collected from two clinically unhealthy animals. This assay has the potential to identify immune system deviation from normal state, which is caused by health problems. Furthermore, knowing the immune status of captive cetaceans could help both trainers and veterinarians in implementing preventive approaches prior to disease onset. creator: Ming-An Tsai creator: I-Hua Chen creator: Jiann-Hsiung Wang creator: Shih-Jen Chou creator: Tsung-Hsien Li creator: Ming-Yih Leu creator: Hsiao-Kuan Ho creator: Wei Cheng Yang uri: https://doi.org/10.7717/peerj.3840 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tsai et al. title: The Spanish version of the Fatigue Assessment Scale: reliability and validity assessment in postpartum women link: https://peerj.com/articles/3832 last-modified: 2017-09-27 description: BackgroundFatigue is the most widely reported symptom by women during pregnancy, labour, the postpartum period, and early parenting. The objective was to translate the Fatigue Assessment Scale (FAS) into Spanish and assess its psychometric properties.MethodsInstrumental Design. The FAS was translated into Spanish (FAS-e) using forward and back translation. A convenience sample was constituted with 870 postpartum women recruited at discharge from 17 public hospitals in Eastern Spain. Data was obtained from clinical records and self-administered questionnaires at discharge. Internal consistency, factor structure, comparisons between known groups and correlations with other variables were assessed.ResultsCronbach’s alpha coefficient was .80. Findings on the dimensionality of the FAS-e scale indicated that it was sufficiently unidimensional. FAS-e scores were higher among women who had undergone caesarean births (p < .05), had a higher level of postpartum pain (p < .01), experienced difficulties during breastfeeding (p < .01) and had lower levels of self-efficacy for breastfeeding (p < .01).ConclusionsAn equivalent Spanish version of the FAS was obtained with good reliability and validity properties. FAS-e is an appropriate tool to measure postpartum fatigue. creator: Antoni Cano-Climent creator: Antonio Oliver-Roig creator: Julio Cabrero-García creator: Jolanda de Vries creator: Miguel Richart-Martínez uri: https://doi.org/10.7717/peerj.3832 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cano-Climent et al. title: Estimating the age of Heliconius butterflies from calibrated photographs link: https://peerj.com/articles/3821 last-modified: 2017-09-27 description: Mating behaviour and predation avoidance in Heliconius involve visual colour signals; however, there is considerable inter-individual phenotypic variation in the appearance of colours. In particular, the red pigment varies from bright crimson to faded red. It has been thought that this variation is primarily due to pigment fading with age, although this has not been explicitly tested. Previous studies have shown the importance of red patterns in mate choice and that birds and butterflies might perceive these small colour differences. Using digital photography and calibrated colour images, we investigated whether the hue variation in the forewing dorsal red band of Heliconius melpomene rosina corresponds with age. We found that the red hue and age were highly associated, suggesting that red colour can indeed be used as a proxy for age in the study of wild-caught butterflies. creator: Denise Dalbosco Dell’Aglio creator: Derya Akkaynak creator: W. Owen McMillan creator: Chris D. Jiggins uri: https://doi.org/10.7717/peerj.3821 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dalbosco Dell’Aglio et al. title: Increased utilization of fructose has a positive effect on the development of breast cancer link: https://peerj.com/articles/3804 last-modified: 2017-09-27 description: Rapid proliferation and Warburg effect make cancer cells consume plenty of glucose, which induces a low glucose micro-environment within the tumor. Up to date, how cancer cells keep proliferating in the condition of glucose insufficiency still remains to be explored. Recent studies have revealed a close correlation between excessive fructose consumption and breast cancer genesis and progression, but there is no convincing evidence showing that fructose could directly promote breast cancer development. Herein, we found that fructose, not amino acids, could functionally replace glucose to support proliferation of breast cancer cells. Fructose endowed breast cancer cells with the colony formation ability and migratory capacity as effective as glucose. Interestingly, although fructose was readily used by breast cancer cells, it failed to restore proliferation of non-tumor cells in the absence of glucose. These results suggest that fructose could be relatively selectively employed by breast cancer cells. Indeed, we observed that a main transporter of fructose, GLUT5, was highly expressed in breast cancer cells and tumor tissues but not in their normal counterparts. Furthermore, we demonstrated that the fructose diet promoted metastasis of 4T1 cells in the mouse models. Taken together, our data show that fructose can be used by breast cancer cells specifically in glucose-deficiency, and suggest that the high-fructose diet could accelerate the progress of breast cancer in vivo. creator: Xiajing Fan creator: Hongru Liu creator: Miao Liu creator: Yuanyuan Wang creator: Li Qiu creator: Yanfen Cui uri: https://doi.org/10.7717/peerj.3804 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Fan et al. title: Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies link: https://peerj.com/articles/3726 last-modified: 2017-09-27 description: BackgroundTibetans have lived at high altitudes for thousands of years, and they have unique physiological traits that enable them to tolerate this hypoxic environment. However, the genetic basis of these traits is still unknown. As a sensitive and highly efficient technique, RT-qPCR is widely used in gene expression analyses to provide insight into the molecular mechanisms underlying environmental changes. However, the quantitative analysis of gene expression in blood is limited by a shortage of stable reference genes for the normalization of mRNA levels. Thus, systematic approaches were used to identify potential reference genes.ResultsThe expression levels of eight candidate human reference genes (GAPDH, ACTB, 18S RNA, β2-MG, PPIA, RPL13A, TBP and SDHA) were assessed in blood from hypoxic environments. The expression stability of these selected reference genes was evaluated using the geNorm, NormFinder and BestKeeper programs. Interestingly, RPL13A was identified as the ideal reference gene for normalizing target gene expression in human blood before and after exposure to high-altitude conditions.ConclusionThese results indicate that different reference genes should be selected for the normalization of gene expression in blood from different environmental settings. creator: Jun Xiao creator: Xiaowei Li creator: Juan Liu creator: Xiu Fan creator: Huifen Lei creator: Cuiying Li uri: https://doi.org/10.7717/peerj.3726 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Xiao et al. title: Estimated effects of implementing an open access policy for grantees at a private foundation link: https://peerj.com/articles/3853 last-modified: 2017-09-26 description: BackgroundThe Gordon and Betty Moore Foundation (GBMF) was interested in understanding the potential effects of requiring that grantees publish their peer-reviewed research in open access journals.MethodsWe collected data on more than 2,000 publications in over 500 journals that were generated by GBMF grantees since 2001. We then examined the journal policies to establish how two possible open access policies might have affected grantee publishing habits.ResultsWe found that 99.3% of the articles published by grantees would have complied with a policy that requires open access within 12 months of publication. We also estimated the maximum annual costs to GBMF for covering fees associated with “gold open access” to be between $400,000 and $2,600,000 annually.DiscussionBased in part on this study, GBMF has implemented a new open access policy that requires grantees make peer-reviewed publications fully available within 12 months. creator: Carly Strasser creator: Eesha Khare uri: https://doi.org/10.7717/peerj.3853 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Strasser and Khare title: Historical dynamics and current environmental effects explain the spatial distribution of species richness patterns of New World monkeys link: https://peerj.com/articles/3850 last-modified: 2017-09-26 description: BackgroundWhy biodiversity is not uniformly distributed on the Earth is a major research question of biogeography. One of the most striking patterns of disparity in species distribution are the biodiversity hotspots, which generally do not fit with the distribution of relevant components of the Neotropical biota. In this study, we assess the proximal causes of the species-richness pattern of one of the most conspicuous groups of Neotropical mammals, the New World monkeys the Platyrrhini. We test two complementary hypotheses: (1) there is a historical source-sink dynamic (addressed using macroevolutionary and macroecological approaches); (2) the large number of species in the Amazon basin is due to the constraints imposed by environmental variables occurring outside this area.MethodsWe first characterize spatial patterns of species richness and biodiversity hotspots using a new, objective protocol based on probabilities. Then we evaluate the source-sink hypothesis using BioGeoBEARS analysis and nestedness analysis of species richness patterns. Complementarily, to measure how often different species pairs appear in the same sites, we used null models to estimate the checkerboard score index (C-score). Finally, we evaluate the relationship between several climatic variables and species richness through ordinary least squares (OLS) and spatial autoregressive (SAR) models, and the potential environmental constraints on the pattern.ResultsWe found one significant cluster of high values for species richness in the Amazon basin. Most dispersal events occurred from the Amazonian subregion to other Neotropical areas. Temperature (T), discrepancy (BR), and NODF indexes show a significant nesting in the matrix ordered by species richness and available energy. The C-score observed was significantly smaller than the null expectation for all sites in the Neotropics where there are records of platyrrhine species. Ten climatic variables comprised the best-fitting model that explains species richness. OLS and SAR models show that this set of variables explains 69.9% and 64.2% of species richness, respectively. Potential of evapotranspiration is the most important variable within this model, showing a linear positive relationship with species richness, and clear lower and upper limits to the species richness distribution.DiscussionWe suggest that New World monkeys historically migrated from their biodiversity hotspot (energetically optimal areas for most platyrrine species) to adjacent, energetically suboptimal areas, and that the different dispersal abilities of these species, the lack of competitive interactions at a macroecological scale, and environmental constraints (i.e., energy availability, seasonality) are key elements which explain the non-uniform pattern of species richness for this clade. creator: Paulo Vallejos-Garrido creator: Reinaldo Rivera creator: Oscar Inostroza-Michael creator: Enrique Rodríguez-Serrano creator: Cristián E. Hernández uri: https://doi.org/10.7717/peerj.3850 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vallejos-Garrido et al. title: The Legionella pneumophila effector Lpg1137 is a homologue of mitochondrial SLC25 carrier proteins, not of known serine proteases link: https://peerj.com/articles/3849 last-modified: 2017-09-26 description: Many bacterial effector proteins that are delivered to host cells during infection are enzymes targeting host cell signalling. Recently, Legionella pneumophila effector Lpg1137 was experimentally characterised as a serine protease that cleaves human syntaxin 17. We present strong bioinformatic evidence that Lpg1137 is a homologue of mitochondrial carrier proteins and is not related to known serine proteases. We also discuss how this finding can be reconciled with the apparently contradictory experimental results. creator: Marcin Gradowski creator: Krzysztof Pawłowski uri: https://doi.org/10.7717/peerj.3849 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gradowski and Pawłowski title: Ananke: temporal clustering reveals ecological dynamics of microbial communities link: https://peerj.com/articles/3812 last-modified: 2017-09-26 description: Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that complements existing sequence-identity-based clustering approaches by clustering marker-gene data based on time-series profiles and provides interactive visualization of clusters, including highlighting of internal OTU inconsistencies. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke. creator: Michael W. Hall creator: Robin R. Rohwer creator: Jonathan Perrie creator: Katherine D. McMahon creator: Robert G. Beiko uri: https://doi.org/10.7717/peerj.3812 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hall et al. title: Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes link: https://peerj.com/articles/3810 last-modified: 2017-09-26 description: Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genus Diporeia and the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived from Diporeia were compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 106 genome copies organism−1). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, β-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential infection. creator: Kalia S.I. Bistolas creator: Lars G. Rudstam creator: Ian Hewson uri: https://doi.org/10.7717/peerj.3810 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Bistolas et al. title: Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood link: https://peerj.com/articles/3816 last-modified: 2017-09-25 description: BackgroundMelissococcus plutonius is an entomopathogenic bacterium that causes European foulbrood (EFB), a honeybee (Apis mellifera L.) disease that necessitates quarantine in some countries. In Czechia, positive evidence of EFB was absent for almost 40 years, until an outbreak in the Krkonose Mountains National Park in 2015. This occurrence of EFB gave us the opportunity to study the epizootiology of EFB by focusing on the microbiome of honeybee workers, which act as vectors of honeybee diseases within and between colonies.MethodsThe study included worker bees collected from brood combs of colonies (i) with no signs of EFB (EFB0), (ii) without clinical symptoms but located at an apiary showing clinical signs of EFB (EFB1), and (iii) with clinical symptoms of EFB (EFB2). In total, 49 samples from 27 honeybee colonies were included in the dataset evaluated in this study. Each biological sample consisted of 10 surface-sterilized worker bees processed for DNA extraction. All subjects were analyzed using conventional PCR and by metabarcoding analysis based on the 16S rRNA gene V1–V3 region, as performed through Illumina MiSeq amplicon sequencing.ResultsThe bees from EFB2 colonies with clinical symptoms exhibited a 75-fold-higher incidence of M. plutonius than those from EFB1 asymptomatic colonies. Melissococcus plutonius was identified in all EFB1 colonies as well as in some of the control colonies. The proportions of Fructobacillus fructosus, Lactobacillus kunkeei, Gilliamella apicola, Frischella perrara, and Bifidobacterium coryneforme were higher in EFB2 than in EFB1, whereas Lactobacillus mellis was significantly higher in EFB2 than in EFB0. Snodgrassella alvi and L. melliventris, L. helsingborgensis and, L. kullabergensis exhibited higher proportion in EFB1 than in EFB2 and EFB0. The occurrence of Bartonella apis and Commensalibacter intestini were higher in EFB0 than in EFB2 and EFB1. Enterococcus faecalis incidence was highest in EFB2.ConclusionsHigh-throughput Illumina sequencing permitted a semi-quantitative analysis of the presence of M. plutonius within the honeybee worker microbiome. The results of this study indicate that worker bees from EFB-diseased colonies are capable of transmitting M. plutonius due to the greatly increased incidence of the pathogen. The presence of M. plutonius sequences in control colonies supports the hypothesis that this pathogen exists in an enzootic state. The bacterial groups synergic to both the colonies with clinical signs of EFB and the EFB-asymptomatic colonies could be candidates for probiotics. This study confirms that E. faecalis is a secondary invader to M. plutonius; however, other putative secondary invaders were not identified in this study. creator: Tomas Erban creator: Ondrej Ledvinka creator: Martin Kamler creator: Bronislava Hortova creator: Marta Nesvorna creator: Jan Tyl creator: Dalibor Titera creator: Martin Markovic creator: Jan Hubert uri: https://doi.org/10.7717/peerj.3816 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Erban et al. title: Diversity of cultivated aerobic poly-hydrolytic bacteria in saline alkaline soils link: https://peerj.com/articles/3796 last-modified: 2017-09-25 description: Alkaline saline soils, known also as “soda solonchaks”, represent a natural soda habitat which differs from soda lake sediments by higher aeration and lower humidity. The microbiology of soda soils, in contrast to the more intensively studied soda lakes, remains poorly explored. In this work we investigate the diversity of culturable aerobic haloalkalitolerant bacteria with various hydrolytic activities from soda soils at different locations in Central Asia, Africa, and North America. In total, 179 pure cultures were obtained by using media with various polymers at pH 10 and 0.6 M total Na+. According to the 16S rRNA gene sequence analysis, most of the isolates belonged to Firmicutes and Actinobacteria. Most isolates possessed multiple hydrolytic activities, including endoglucanase, xylanase, amylase and protease. The pH profiling of selected representatives of actinobacteria and endospore-forming bacteria showed, that the former were facultative alkaliphiles, while the latter were mostly obligate alkaliphiles. The hydrolases of selected representatives from both groups were active at a broad pH range from six to 11. Overall, this work demonstrates the presence of a rich hydrolytic bacterial community in soda soils which might be explored further for production of haloalkalistable hydrolases. creator: Dimitry Y. Sorokin creator: Tatiana V. Kolganova creator: Tatiana V. Khijniak creator: Brian E. Jones creator: Ilya V. Kublanov uri: https://doi.org/10.7717/peerj.3796 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sorokin et al. title: Ecomorphological characterization of murines and non-arvicoline cricetids (Rodentia) from south-western Europe since the latest Middle Miocene to the Mio-Pliocene boundary (MN 7/8–MN13) link: https://peerj.com/articles/3646 last-modified: 2017-09-25 description: Rodents are the most speciose group of mammals and display a great ecological diversity. Despite the greater amount of ecomorphological information compiled for extant rodent species, studies usually lack of morphological data on dentition, which has led to difficulty in directly utilizing existing ecomorphological data of extant rodents for paleoecological reconstruction because teeth are the most common or often the only micromammal fossils. Here, we infer the environmental ranges of extinct rodent genera by extracting habitat information from extant relatives and linking it to extinct taxa based on the phenogram of the cluster analysis, in which variables are derived from the principal component analysis on outline shape of the upper first molars. This phenotypic “bracketing” approach is particularly useful in the study of the fossil record of small mammals, which is mostly represented by isolated teeth. As a case study, we utilize extinct genera of murines and non-arvicoline cricetids, ranging from the Iberoccitanian latest middle Miocene to the Mio-Pliocene boundary, and compare our results thoroughly with previous paleoecological reconstructions inferred by different methods. The resultant phenogram shows a predominance of ubiquitous genera among the Miocene taxa, and the presence of a few forest specialists in the two rodent groups (Murinae and Cricetidae), along with the absence of open environment specialists in either group of rodents. This appears to be related to the absence of enduring grassland biomes in the Iberian Peninsula during the late Miocene. High consistency between our result and previous studies suggests that this phenotypic “bracketing” approach is a very useful tool. creator: Ana R. Gomez Cano creator: Yuri Kimura creator: Fernando Blanco creator: Iris Menéndez creator: María A. Álvarez-Sierra creator: Manuel Hernández Fernández uri: https://doi.org/10.7717/peerj.3646 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gomez Cano et al. title: Rootstock influence on iron uptake responses in Citrus leaves and their regulation under the Fe paradox effect link: https://peerj.com/articles/3553 last-modified: 2017-09-25 description: Background and aimsThis work evaluates the regulation of iron uptake responses in Citrus leaves and their involvement in the Fe paradox effect.MethodsExperiments were performed in field-grown ‘Navelina’ trees grafted onto two Cleopatra mandarin × Poncirus trifoliata (L.) Raf. hybrids with different Fe-chlorosis symptoms: 030146 (non-chlorotic) and 030122 (chlorotic).ResultsChlorotic leaves were smaller than non-chlorotic ones for both dry weight (DW) and area basis, and exhibited marked photosynthetic state affection, but reduced catalase and peroxidase enzymatic activities. Although both samples had a similar total Fe concentration on DW, it was lower in chlorotic leaves when expressed on an area basis. A similar pattern was observed for the total Fe concentration in the apoplast and cell sap and in active Fe (Fe2+) concentration. FRO2 gene expression and ferric chelate reductase (FC-R) activity were also lower in chlorotic samples, while HA1 and IRT1 were more induced. Despite similar apoplasmic pH, K+/Ca2+ was higher in chlorotic leaves, and both citrate and malate concentrations in total tissue and apoplast fluid were lower.Conclusion(1) The rootstock influences Fe acquisition system in the leaf; (2) the increased sensitivity to Fe-deficiency as revealed by chlorosis and decreased biomass, was correlated with lower FC-R activity and lower organic acid level in leaf cells, which could cause a decreased Fe mobility and trigger other Fe-stress responses in this organ to enhance acidification and Fe uptake inside cells; and (3) the chlorosis paradox phenomenon in citrus likely occurs as a combination of a marked FC-R activity impairment in the leaf and the strong growth inhibition in this organ. creator: Mary-Rus Martinez-Cuenca creator: Amparo Primo-Capella creator: Ana Quiñones creator: Almudena Bermejo creator: Maria Angeles Forner-Giner uri: https://doi.org/10.7717/peerj.3553 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Martinez-Cuenca et al. title: Filtering out parasites: sand crabs (Lepidopa benedicti) are infected by more parasites than sympatric mole crabs (Emerita benedicti) link: https://peerj.com/articles/3852 last-modified: 2017-09-22 description: Two digging decapod crustaceans, the sand crab species Lepidopa benedicti and the mole crab species Emerita benedicti, both live in the swash zone of fine sand beaches. They were examined for two parasites that infect decapod crustaceans in the region, an unidentified nematode previously shown to infect L. benedicti, and cestode tapeworm larvae, Polypocephalus sp., previously shown to infect shrimp (Litopenaeus setiferus). Lepidopa benedicti were almost always infected with both parasite species, while E. benedicti were rarely infected with either parasite species. This difference in infection pattern suggests that tapeworms are ingested during sediment feeding in L. benedicti, which E. benedicti avoid by filter feeding. Larger L. benedicti had more Polypocephalus sp. larvae. The thoracic ganglia, which make up the largest proportion of neural tissue, contained the largest numbers of Polypocephalus sp. larvae. Intensity of Polypocephalus sp. infection was not correlated with how long L. benedicti remained above sand in behavioural tests, suggesting that Polypocephalus sp. do not manipulate the sand crabs in a way that facilitates trophic transmission of the parasite. Litopenaeus setiferus may be a primary host for Polypocephalus sp., and L. benedict may be a secondary, auxiliary host. creator: Zen Faulkes uri: https://doi.org/10.7717/peerj.3852 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Faulkes title: Functional modularity in lake-dwelling characin fishes of Mexico link: https://peerj.com/articles/3851 last-modified: 2017-09-22 description: Modular evolution promotes evolutionary change, allowing independent variation across morphological units. Recent studies have shown that under contrasting ecological pressures, patterns of modularity could be related to divergent evolution. The main goal of the present study was to evaluate the presence of modular evolution in two sister lacustrine species, Astyanax aeneus and A. caballeroi, which are differentiated by their trophic habits. Two different datasets were analyzed: (1) skull X-rays from 73 specimens (35 A. aeneus and 38 A. caballeroi) to characterize skull variation patterns, considering both species and sex effects. For this dataset, three different modularity hypotheses were tested, previously supported in other lacustrine divergent species; (2) a complete body shape dataset was also tested for four modularity hypotheses, which included a total of 196 individuals (110 Astyanax aeneus and 86 A. caballeroi). Skull shape showed significant differences among species and sex (P < 0.001), where Astyanax caballeroi species showed an upwardly projected mandible and larger preorbital region. For the skull dataset, the modularity hypothesis ranked first included three partitioning modules. While for the complete body dataset the best ranked hypothesis included two modules (head vs the rest of the body), being significant only for A. caballeroi. creator: Claudia Patricia Ornelas-García creator: Amando Bautista creator: Fabian Herder creator: Ignacio Doadrio uri: https://doi.org/10.7717/peerj.3851 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ornelas-García et al. title: The Dark Cube: dark character profiles and OCEAN link: https://peerj.com/articles/3845 last-modified: 2017-09-22 description: BackgroundThe Big Five traits (i.e., openness, conscientiousness, extraversion, agreeableness, and neuroticism: OCEAN) have been suggested to provide a meaningful taxonomy for studying the Dark Triad: Machiavellianism, narcissism, and psychopathy. Nevertheless, current research consists of mixed and inconsistent associations between the Dark Triad and OCEAN. Here we used the Dark Cube (Garcia & Rosenberg, 2016), a model of malevolent character theoretically based on Cloninger’s biopsychosocial model of personality and in the assumption of a ternary structure of malevolent character. We use the dark cube profiles to investigate differences in OCEAN between individuals who differ in one dark character trait while holding the other two constant (i.e., conditional relationships).MethodParticipants (N = 330) responded to the Short Dark Triad Inventory and the Big Five Inventory and were grouped according to the eight possible combinations using their dark trait scores (M, high Machiavellianism; m, low Machiavellianism; N, high narcissism; n, low narcissism; P, high psychopathy; p, low psychopathy): MNP “maleficent”, MNp “manipulative narcissistic”, MnP “anti-social”, Mnp “Machiavellian”, mNP “psychopathic narcissistic”, mNp “narcissistic”, mnP “psychopathic”, and mnp “benevolent”.ResultsHigh narcissism-high extraversion and high psychopathy-low agreeableness were consistently associated across comparisons. The rest of the comparisons showed a complex interaction. For example, high Machiavellianism-high neuroticism only when both narcissism and psychopathy were low (Mnp vs. mnp), high narcissism-high conscientiousness only when both Machiavellianism and psychopathy were also high (MNP vs. MnP), and high psychopathy-high neuroticism only when Machiavellianism was low and narcissism was high (mNP vs. mNp).ConclusionsWe suggest that the Dark Cube is a useful tool in the investigation of a consistent Dark Triad Theory. This approach suggests that the only clear relationships were narcissism-extraversion and psychopathy-agreeableness and that the malevolent character traits were associated to specific OCEAN traits only under certain conditions. Hence, explaining the mixed and inconsistent linear associations in the Dark Triad literature. creator: Danilo Garcia creator: Fernando R. González Moraga uri: https://doi.org/10.7717/peerj.3845 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Garcia and González Moraga title: Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene? link: https://peerj.com/articles/3815 last-modified: 2017-09-22 description: The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae. creator: Manuel Pimentel creator: Marcial Escudero creator: Elvira Sahuquillo creator: Miguel Ángel Minaya creator: Pilar Catalán uri: https://doi.org/10.7717/peerj.3815 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pimentel et al. title: Spontaneous reoccurrence of “scooping”, a wild tool-use behaviour, in naïve chimpanzees link: https://peerj.com/articles/3814 last-modified: 2017-09-22 description: Modern human technological culture depends on social learning. A widespread assumption for chimpanzee tool-use cultures is that they, too, are dependent on social learning. However, we provide evidence to suggest that individual learning, rather than social learning, is the driver behind determining the form of these behaviours within and across individuals. Low-fidelity social learning instead merely facilitates the reinnovation of these behaviours, and thus helps homogenise the behaviour across chimpanzees, creating the population-wide patterns observed in the wild (what here we call “socially mediated serial reinnovations”). This is the main prediction of the Zone of Latent Solutions (ZLS) hypothesis. This study directly tested the ZLS hypothesis on algae scooping, a wild chimpanzee tool-use behaviour. We provided naïve chimpanzees (n = 14, Mage = 31.33, SD = 10.09) with ecologically relevant materials of the wild behaviour but, crucially, without revealing any information on the behavioural form required to accomplish this task. This study found that naïve chimpanzees expressed the same behavioural form as their wild counterparts, suggesting that, as the ZLS theory predicts, individual learning is the driver behind the frequency of this behavioural form. As more behaviours are being found to be within chimpanzee’s ZLS, this hypothesis now provides a parsimonious explanation for chimpanzee tool cultures. creator: Elisa Bandini creator: Claudio Tennie uri: https://doi.org/10.7717/peerj.3814 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bandini and Tennie title: Selected nutritional habits of teenagers associated with overweight and obesity link: https://peerj.com/articles/3681 last-modified: 2017-09-22 description: IntroductionA balanced diet is at the heart of healthy growth and development of children and youth, whereas inappropriate eating habits considerably influence the incidence of disorders connected with nutrition, including overweight and obesity. This paper aims at studying nutritional factors of 18-year-old secondary school youth in the urban environment and their effect on the incidence of overweight and obesity.Materials and methodsThe survey was conducted among 1,999 secondary school students chosen at random. The research tool consisted an original survey questionnaire. The measurements of respondents’ height and body mass provided data for calculating the body mass index.Results and conclusionThe percentage of youth with deficient body mass was estimated at 8.4%. The percentage of normal weight students in the surveyed group was estimated at 77.6%. Overweight and obesity characterized 14.0% of the total number. As many as 21.8% of overweight and obese respondents would eat one or two meals as opposed to 16.8% of normal weight students. Three-fourths of the surveyed students would eat breakfast regardless of their nutritional habits. Lunch is eaten by 52.9% of normal weight 18-year-olds and 46.1% of overweight and obese students. The analysis of mealtimes suggests that overweight and obese students would have their breakfast and dinner at later hours than the rest of the surveyed. More than half of the participating students failed to eat lunch (53.9%), and one in four students within this group resigned from supper. Girls would eat fruit and vegetables more frequently than boys several times a day. The percentage of persons in the surveyed groups who would eat fast foods on a daily basis was similar regardless of their nutritional status. Sweetened carbonated beverages would be drunk more often by overweight and obese boys (81.2%) as compared with boys with proper body mass (75.8%). The same type of beverages would be popular with two-thirds of girls, and this result was similar regardless of their nutritional status. About 44.2% of overweight and obese girls and 20% of girls with proper body mass attempted to lose weight, and 5.7% of boys tried to go on a diet. Eating limitations were declared by 16.5% of overweight and obese boys and ca. 3% of normal weight boys.ConclusionWithin the surveyed group of youth, it was possible to indicate eating errors primarily consisting in irregular eating, too low a number of meals during the day, particularly skipping breakfast, which took place more frequently among overweight and obese students rather than normal weight ones. The survey points to the insufficient intake of vegetables and fruit as opposed to salty and sweet meals. It is essential to convey the knowledge on the causes of overweight and obesity as well as rules of a healthy diet as factors preventing civilization diseases. creator: Magdalena Zalewska creator: Elżbieta Maciorkowska uri: https://doi.org/10.7717/peerj.3681 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Zalewska and Maciorkowska title: The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data link: https://peerj.com/articles/3844 last-modified: 2017-09-21 description: The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships among stomatopods using phylogenetic analyses of three mitochondrial and two nuclear markers. Our analyses recovered the superfamily Gonodactyloidea as polyphyletic, with Hemisquilla as the sister group to all other extant stomatopods. A relaxed molecular clock, calibrated by seven fossil-based age constraints, was used to date the origin and major diversification events of stomatopods. Our estimates suggest that crown-group stomatopods (Unipeltata) diverged from their closest crustacean relatives about 340 Ma (95% CRI [401–313 Ma]). We found that the specialized smashing appendage arose after the spearing appendage ∼126 Ma (95% CRI [174–87 Ma]). Ancestral state reconstructions revealed that the most recent common ancestor of extant stomatopods had eyes with six midband rows of hexagonal ommatidia. Hexagonal ommatidia are interpreted as plesiomorphic in stomatopods, and this is consistent with the malacostracan ground-plan. Our study provides insight into the evolutionary timescale and systematics of Stomatopoda, although further work is required to resolve with confidence the phylogenetic relationships among its superfamilies. creator: Cara Van Der Wal creator: Shane T. Ahyong creator: Simon Y.W. Ho creator: Nathan Lo uri: https://doi.org/10.7717/peerj.3844 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Van Der Wal et al. title: MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations link: https://peerj.com/articles/3830 last-modified: 2017-09-21 description: Bacteria adapt to adverse environmental conditions by altering gene expression patterns. Recently, a novel stress adaptation mechanism has been described that allows Escherichia coli to alter gene expression at the post-transcriptional level. The key player in this regulatory pathway is the endoribonuclease MazF, the toxin component of the toxin-antitoxin module mazEF that is triggered by various stressful conditions. In general, MazF degrades the majority of transcripts by cleaving at ACA sites, which results in the retardation of bacterial growth. Furthermore, MazF can process a small subset of mRNAs and render them leaderless by removing their ribosome binding site. MazF concomitantly modifies ribosomes, making them selective for the translation of leaderless mRNAs. In this study, we employed fluorescent reporter-systems to investigate mazEF expression during stressful conditions, and to infer consequences of the mRNA processing mediated by MazF on gene expression at the single-cell level. Our results suggest that mazEF transcription is maintained at low levels in single cells encountering adverse conditions, such as antibiotic stress or amino acid starvation. Moreover, using the grcA mRNA as a model for MazF-mediated mRNA processing, we found that MazF activation promotes heterogeneity in the grcA reporter expression, resulting in a subpopulation of cells with increased levels of GrcA reporter protein. creator: Nela Nikolic creator: Zrinka Didara creator: Isabella Moll uri: https://doi.org/10.7717/peerj.3830 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nikolic et al. title: Benchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity link: https://peerj.com/articles/3817 last-modified: 2017-09-21 description: BackgroundViral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic sequence-to-ecological-inference pipeline, including (i) read pre-processing and metagenome assembly, (ii) thresholds applied to estimate viral relative abundances based on read mapping to assembled contigs, and (iii) normalization methods applied to the matrix of viral relative abundances for alpha and beta diversity estimates.ResultsTools specifically designed for metagenomes, specifically metaSPAdes, MEGAHIT, and IDBA-UD, were the most effective at assembling viromes. Read pre-processing, such as partitioning, had virtually no impact on assembly output, but may be useful when hardware is limited. Viral populations with 2–5 × coverage typically assembled well, whereas lesser coverage led to fragmented assembly. Strain heterogeneity within populations hampered assembly, especially when strains were closely related (average nucleotide identity, or ANI ≥97%) and when the most abundant strain represented <50% of the population. Viral community composition assessments based on read recruitment were generally accurate when the following thresholds for detection were applied: (i) ≥10 kb contig lengths to define populations, (ii) coverage defined from reads mapping at ≥90% identity, and (iii) ≥75% of contig length with ≥1 × coverage. Finally, although data are limited to the most abundant viruses in a community, alpha and beta diversity patterns were robustly estimated (±10%) when comparing samples of similar sequencing depth, but more divergent (up to 80%) when sequencing depth was uneven across the dataset. In the latter cases, the use of normalization methods specifically developed for metagenomes provided the best estimates.ConclusionsThese simulations provide benchmarks for selecting analysis cut-offs and establish that an optimized sample-to-ecological-inference viromics pipeline is robust for making ecological inferences from natural viral communities. Continued development to better accessing RNA, rare, and/or diverse viral populations and improved reference viral genome availability will alleviate many of viromics remaining limitations. creator: Simon Roux creator: Joanne B. Emerson creator: Emiley A. Eloe-Fadrosh creator: Matthew B. Sullivan uri: https://doi.org/10.7717/peerj.3817 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Roux et al. title: Human agency beliefs influence behaviour during virtual social interactions link: https://peerj.com/articles/3819 last-modified: 2017-09-20 description: In recent years, with the emergence of relatively inexpensive and accessible virtual reality technologies, it is now possible to deliver compelling and realistic simulations of human-to-human interaction. Neuroimaging studies have shown that, when participants believe they are interacting via a virtual interface with another human agent, they show different patterns of brain activity compared to when they know that their virtual partner is computer-controlled. The suggestion is that users adopt an “intentional stance” by attributing mental states to their virtual partner. However, it remains unclear how beliefs in the agency of a virtual partner influence participants’ behaviour and subjective experience of the interaction. We investigated this issue in the context of a cooperative “joint attention” game in which participants interacted via an eye tracker with a virtual onscreen partner, directing each other’s eye gaze to different screen locations. Half of the participants were correctly informed that their partner was controlled by a computer algorithm (“Computer” condition). The other half were misled into believing that the virtual character was controlled by a second participant in another room (“Human” condition). Those in the “Human” condition were slower to make eye contact with their partner and more likely to try and guide their partner before they had established mutual eye contact than participants in the “Computer” condition. They also responded more rapidly when their partner was guiding them, although the same effect was also found for a control condition in which they responded to an arrow cue. Results confirm the influence of human agency beliefs on behaviour in this virtual social interaction context. They further suggest that researchers and developers attempting to simulate social interactions should consider the impact of agency beliefs on user experience in other social contexts, and their effect on the achievement of the application’s goals. creator: Nathan Caruana creator: Dean Spirou creator: Jon Brock uri: https://doi.org/10.7717/peerj.3819 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Caruana et al. title: Taxonomic overview of the hyperdiverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in India with descriptions and X-ray microtomography of two new species from the Andaman Islands link: https://peerj.com/articles/3800 last-modified: 2017-09-20 description: With 600 described species, the ant genus Tetramorium represents one of the most species-rich ant radiations. However, much work remains to fully document the hyperdiversity of this remarkable group. Tetramorium, while globally distributed, is thought to have originated in the Afrotropics and is particularly diverse in the Old World. Here, we focus attention on the Tetramorium fauna of India, a region of high biodiversity value and interest for conservation. We overview Tetramorium diversity in India by providing a species list, accounts of all species groups present, an illustrated identification key to Indian Tetramorium species groups and notes on the Indian Tetramorium fauna. Further, we describe two new species, Tetramorium krishnani sp. n. and Tetramorium jarawa sp. n. from the Andaman Islands archipelago and embed them into currently recognized Tetramorium tonganum and Tetramorium inglebyi species groups. We also provide illustrated species level keys for these groups. Along with detailed species descriptions and high-resolution montage images of types, we provide 3D cybertypes of the new species derived from X-ray micro-computed tomography. creator: Gaurav Agavekar creator: Francisco Hita Garcia creator: Evan P. Economo uri: https://doi.org/10.7717/peerj.3800 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Agavekar et al. title: Evaluation of ddRADseq for reduced representation metagenome sequencing link: https://peerj.com/articles/3837 last-modified: 2017-09-19 description: BackgroundProfiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling.MethodsThis technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data.ResultsThe ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected.DiscussionAlthough ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies. creator: Michael Y. Liu creator: Paul Worden creator: Leigh G. Monahan creator: Matthew Z. DeMaere creator: Catherine M. Burke creator: Steven P. Djordjevic creator: Ian G. Charles creator: Aaron E. Darling uri: https://doi.org/10.7717/peerj.3837 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liu et al. title: CA1 pyramidal cells have diverse biophysical properties, affected by development, experience, and aging link: https://peerj.com/articles/3836 last-modified: 2017-09-19 description: Neuron types (e.g., pyramidal cells) within one area of the brain are often considered homogeneous, despite variability in their biophysical properties. Here we review literature demonstrating variability in the electrical activity of CA1 hippocampal pyramidal cells (PCs), including responses to somatic current injection, synaptic stimulation, and spontaneous network-related activity. In addition, we describe how responses of CA1 PCs vary with development, experience, and aging, and some of the underlying ionic currents responsible. Finally, we suggest directions that may be the most impactful in expanding this knowledge, including the use of text and data mining to systematically study cellular heterogeneity in more depth; dynamical systems theory to understand and potentially classify neuron firing patterns; and mathematical modeling to study the interaction between cellular properties and network output. Our goals are to provide a synthesis of the literature for experimentalists studying CA1 PCs, to give theorists an idea of the rich diversity of behaviors models may need to reproduce to accurately represent these cells, and to provide suggestions for future research. creator: Erin C. McKiernan creator: Diano F. Marrone uri: https://doi.org/10.7717/peerj.3836 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 McKiernan and Marrone title: Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens link: https://peerj.com/articles/3765 last-modified: 2017-09-19 description: BackgroundThe rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for Disease Prevention and Control have been considered a major threat due to the rise in nosocomial infections. Here, we compared putative drug binding pockets of twelve essential and mostly conserved metabolic enzymes in numerous bacterial pathogens including those of the ESKAPE group and Mycobacterium tuberculosis. The comparative analysis will provide guidelines for the likelihood of transferability of the inhibitors from one species to another.MethodsNine bacterial species including six ESKAPE pathogens, Mycobacterium tuberculosis along with Mycobacterium smegmatis and Eschershia coli, two non-pathogenic bacteria, have been selected for drug binding pocket analysis of twelve essential enzymes. The amino acid sequences were obtained from Uniprot, aligned using ICM v3.8-4a and matched against the Pocketome encyclopedia. We used known co-crystal structures of selected target enzyme orthologs to evaluate the location of their active sites and binding pockets and to calculate a matrix of pairwise sequence identities across each target enzyme across the different species. This was used to generate sequence maps.ResultsHigh sequence identity of enzyme binding pockets, derived from experimentally determined co-crystallized structures, was observed among various species. Comparison at both full sequence level and for drug binding pockets of key metabolic enzymes showed that binding pockets are highly conserved (sequence similarity up to 100%) among various ESKAPE pathogens as well as Mycobacterium tuberculosis. Enzymes orthologs having conserved binding sites may have potential to interact with inhibitors in similar way and might be helpful for design of similar class of inhibitors for a particular species. The derived pocket alignments and distance-based maps provide guidelines for drug discovery and repurposing. In addition they also provide recommendations for the relevant model bacteria that may be used for initial drug testing.DiscussionComparing ligand binding sites through sequence identity calculation could be an effective approach to identify conserved orthologs as drug binding pockets have shown higher level of conservation among various species. By using this approach we could avoid the problems associated with full sequence comparison. We identified essential metabolic enzymes among ESKAPE pathogens that share high sequence identity in their putative drug binding pockets (up to 100%), of which known inhibitors can potentially antagonize these identical pockets in the various species in a similar manner. creator: Sadia Naz creator: Tony Ngo creator: Umar Farooq creator: Ruben Abagyan uri: https://doi.org/10.7717/peerj.3765 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Naz et al. title: Morning surge in blood pressure and sympathetic activity in Mongolians and Han Chinese: a multimodality investigation of hypertension and dyssomnia link: https://peerj.com/articles/3758 last-modified: 2017-09-19 description: BackgroundHypertension and dyssomnia are increasing significantly in Mongolians, and the related factors of ethnic differences in hypertension and dyssomnia between Mongolians and Han Chinese are unclear. This study examined the relationship of morning surge in blood pressure (MBP) with ethnicity, sleep situation, and sympathetic activity throughout the day.MethodsOf 692 hypertensive patients screened, 202 subjects with dyssomnia were selected. They were then divided into Mongolian (n = 87) and Han (n = 115) groups. The differences in dyssomnia, 24-h blood pressure, and urinary catecholamine were analyzed in all subjects; they were then further divided according to the degree of dyssomnia (low, moderate, and severe) to determine the differences in blood pressure and catecholamine.ResultsMongolians had a lower history of smoking, daytime dysfunction, nocturnal heart rates, and dopamine levels, but their body mass index, triglyceride, fasting glucose, morning surge in systolic blood pressure (MSBP), nocturnal systolic blood pressure (NSBP), nocturnal diastolic blood pressure, daytime systolic blood pressure, daytime heart rates, and dopamine level (D-DA) were higher than those of Han Chinese. With the aggravation of dyssomnia, MSBP, NSBP, D-NE, daytime epinephrine, and D-DA of Mongolians and Han Chinese increased gradually, but the rate of increase was faster in the latter (p < 0.05). D-DA was entered into the MSBP regression model of Mongolians (intercept, 157 mmHg), whereas D-DA and D-NE were entered into the MSBP regression model of Han Chinese (intercept, 142 mmHg).ConclusionWorsened dyssomnia induces higher MSBP and augments sympathetic excitability in Mongolians and Han Chinese. Mongolians with hypertension and dyssomnia had higher MSBP baseline and D-DA but lower N-DA. With an increase in D-DA, MSBP in Han and Mongolian patients increased gradually. creator: Guanhua Huang creator: Xiaoming Yang creator: Jing Huang uri: https://doi.org/10.7717/peerj.3758 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Huang et al. title: Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris link: https://peerj.com/articles/3747 last-modified: 2017-09-19 description: Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses. creator: Weilong Kong creator: Shaozong Yang creator: Yulu Wang creator: Mohammed Bendahmane creator: Xiaopeng Fu uri: https://doi.org/10.7717/peerj.3747 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kong et al. title: Vascular anatomy is a determining factor of successful submental flap raising: a retrospective study of 70 clinical cases link: https://peerj.com/articles/3606 last-modified: 2017-09-19 description: The vascular anatomy of submental flaps (SFs) represents a determining factor in successful SF raising. However, little attention has been focused on the venous return of SFs. Thus, the present study aimed to investigate SF venous return. This study enrolled patients who underwent SF reconstructive surgery in a tertiary referral center between November 2009 and October 2016. The drainage pathway of the SF venous return was routinely identified during the course of our operations to prevent damage during head and neck surgery. The venous return data of 70 patients were reviewed. The size of the flaps ranged from 15 to 84 cm2, and total flap loss was not observed in the case series. All of the submental arteries originated from the facial artery; however, the submental veins of 70 patients returned to either the internal jugular vein (IJV, 72.9%) or the external jugular vein (EJV, 27.1%). Our data suggest that drainage of the submental vein into the EJV, which has been previously overlooked, should receive greater attention during SF surgeries. The results support mandatory preservation of the EJV and IJV and indicate that vascular anatomy is a determining factor for successful SF raising. creator: Hung-Che Lin creator: Yuahn-Sieh Huang creator: Yueng-Hsiang Chu creator: Shao-Cheng Liu creator: Wei-Chuan Shangkuan creator: Wen-Sen Lai creator: Jinn-Moon Yang creator: Yaoh-Shiang Lin creator: Kuo-Hsing Ma creator: Jih-Chin Lee uri: https://doi.org/10.7717/peerj.3606 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lin et al. title: Sylvatic host associations of Triatominae and implications for Chagas disease reservoirs: a review and new host records based on archival specimens link: https://peerj.com/articles/3826 last-modified: 2017-09-18 description: BackgroundThe 152 extant species of kissing bug include important vectors of the debilitating, chronic, and often fatal Chagas disease, which affects several million people mainly in Central and South America. An understanding of the natural hosts of this speciose group of blood-feeding insects has and will continue to aid ongoing efforts to impede the spread of Chagas disease. However, information on kissing bug biology is piecemeal and scattered, developed using methods with varying levels of accuracy over more than 100 years. Existing host records are heavily biased towards well-studied primary vector species and are derived from primarily three different types of observations, associational, immunological or DNA-based, with varying reliability.MethodsWe gather a comprehensive and unparalleled number of sources reporting host associations via rigorous targeted searches of publication databases to review all known natural, or sylvatic, host records including information on how each record was collected. We integrate this information with novel host records obtained via attempted amplification and sequencing of a ∼160 base pair (bp) region of the vertebrate 12S mitochondrial gene from the gastrointestinal tract of 64 archival specimens of Triatominae representing 19 species collected primarily in sylvatic habitats throughout the southern United States and Central and South America during the past 10 years. We show the utility of this method for uncovering novel and under-studied groups of Triatominae hosts, as well as detecting the presence of the Chagas disease pathogen via Polymerase Chain Reaction (PCR) of a ∼400 bp sequence of the trypanosome 18S gene.ResultsNew host associations for several groups of arboreal mammals were determined including sloths, New World monkeys, coatis, arboreal porcupines and, for the first time as a host of any Triatominae, tayras. A thorough review of previously documented sylvatic hosts, organized by triatomine species and the type of observation (associational, antibody-based, or DNA-based), is presented in a phylogenetic context and highlights large gaps in our knowledge of Triatominae biology.ConclusionThe application of DNA-based methods of host identification towards additional species of Triatominae, including rarely collected species that may require use of archival specimens, is the most efficient and promising way to resolve recognized shortfalls. creator: Anna Y. Georgieva creator: Eric R.L. Gordon creator: Christiane Weirauch uri: https://doi.org/10.7717/peerj.3826 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Georgieva et al. title: Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances link: https://peerj.com/articles/3828 last-modified: 2017-09-18 description: The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics) could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies. creator: Jose L. Horreo uri: https://doi.org/10.7717/peerj.3828 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Horreo title: The Parenting to Reduce Adolescent Depression and Anxiety Scale: Assessing parental concordance with parenting guidelines for the prevention of adolescent depression and anxiety disorders link: https://peerj.com/articles/3825 last-modified: 2017-09-18 description: BackgroundDespite substantial evidence demonstrating numerous parental risk and protective factors for the development of adolescent depression and anxiety disorders, there is currently no single measure that assesses these parenting factors. To address this gap, we developed the Parenting to Reduce Adolescent Depression and Anxiety Scale (PRADAS) as a criterion-referenced measure of parental concordance with a set of evidence-based parenting guidelines for the prevention of adolescent depression and anxiety disorders. In this paper, we used a sample of Australian parents of adolescents to: (1) validate the PRADAS as a criterion-referenced measure; (2) examine parental concordance with the guidelines in the sample; and (3) examine correlates of parental concordance with the guidelines.MethodsSeven hundred eleven parents completed the PRADAS, as well as two established parenting measures, and parent-report measures of adolescent depression and anxiety symptoms. Six hundred sixty adolescent participants (aged 12–15) also completed the symptom measures. Concordance with the guidelines was assessed via nine subscale scores and a total score. Reliability of the scores was assessed with an estimate of the agreement coefficient, as well as 1-month test-retest reliability. Convergent validity was examined via correlations between the scale and two established parenting measures.ResultsOne proposed subscale was removed from the final version of the scale, resulting in a total of eight subscales. Reliability was high for the total score, and acceptable to high for seven of the eight subscales. One-month test-retest reliability was acceptable to high for the total score. Convergent validity was supported by moderate to high correlations with two established measures of parenting. Overall, rates of parental concordance with the guidelines were low in our sample. Higher scores were associated with being female and higher levels of parental education. Greater parental concordance with the guidelines was associated with fewer symptoms of depression and anxiety in adolescent participants.DiscussionThis initial validation study provides preliminary support for the reliability and validity of the PRADAS. The scale has potential for use in both clinical and research settings. It may be used to identify parents’ strengths and potential targets for intervention, and as an outcome measure in studies of preventive parenting interventions. creator: Mairead C. Cardamone-Breen creator: Anthony F. Jorm creator: Katherine A. Lawrence creator: Andrew J. Mackinnon creator: Marie B.H. Yap uri: https://doi.org/10.7717/peerj.3825 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cardamone-Breen et al. title: The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species link: https://peerj.com/articles/3820 last-modified: 2017-09-18 description: Cinnamomum camphora, a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized as herbal medicines and essential oils. Here, we reported the complete sequencing of the chloroplast genome of Cinnamomum camphora using illumina technology. The chloroplast genome of Cinnamomum camphora is 152,570 bp in length and characterized by a relatively conserved quadripartite structure containing a large single copy region of 93,705 bp, a small single copy region of 19,093 bp and two inverted repeat (IR) regions of 19,886 bp. Overall, the genome contained 123 coding regions, of which 15 were repeated in the IR regions. An analysis of chloroplast sequence divergence revealed that the small single copy region was highly variable among the different genera in the Lauraceae family. A total of 40 repeat structures and 83 simple sequence repeats were detected in both the coding and non-coding regions. A phylogenetic analysis indicated that Calycanthus is most closely related to Lauraceae, both being members of Laurales, which forms a sister group to Magnoliids. The complete sequence of the chloroplast of Cinnamomum camphora will aid in in-depth taxonomical studies of the Lauraceae family in the future. The genetic sequence information will also have valuable applications for chloroplast genetic engineering. creator: Caihui Chen creator: Yongjie Zheng creator: Sian Liu creator: Yongda Zhong creator: Yanfang Wu creator: Jiang Li creator: Li-An Xu creator: Meng Xu uri: https://doi.org/10.7717/peerj.3820 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Chen et al. title: Can squirrel monkeys learn an ABnA grammar? A re-evaluation of Ravignani et al. (2013) link: https://peerj.com/articles/3806 last-modified: 2017-09-18 description: Ravignani et al. (2013) habituated squirrel monkeys to sound sequences conforming to an ABnA grammar (n = 1, 2, 3), then tested them for their reactions to novel grammatical and non-grammatical sequences. Although they conclude that the monkeys “consistently recognized and generalized the sequence ABnA,” I remark that this conclusion is not robust. The statistical significance of results depends on specific choices of data analysis, namely dichotomization of the response variable and omission of specific data points. Additionally, there is little evidence of generalization to novel patterns (n = 4, 5), which is important to conclude that the monkeys recognized the ABnA grammar beyond the habituation patterns. Lastly, many test sequences were perceptually similar to habituation sequences, raising the possibility that the monkeys may have generalized based on perceptual similarity rather than based on grammaticality. creator: Stefano Ghirlanda uri: https://doi.org/10.7717/peerj.3806 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ghirlanda title: Integrative taxonomy of the ornamental ‘peppermint’ shrimp public market and population genetics of Lysmata boggessi, the most heavily traded species worldwide link: https://peerj.com/articles/3786 last-modified: 2017-09-18 description: The ornamental trade is a worldwide industry worth >15 billion USD with a problem of rampant product misidentification. Minimizing misidentification is critical in the face of overexploitation of species in the trade. We surveyed the peppermint shrimp ornamental marketplace in the southeastern USA, the most intense market for peppermint shrimps worldwide, to characterize the composition of species in the trade, reveal the extent of misidentification, and describe the population genetics of the true target species. Shrimps were bought from aquarium shops in FL, GA, SC, and NC. We demonstrated, contrary to popular belief (information from dealers), that the most heavily traded species in the market was Lysmata boggessi, an endemic species to the eastern Gulf of Mexico, and not Lysmata wurdemanni. Importantly, only when color pattern or genetic markers in conjunction with morphological traits were employed, was it was possible to unequivocally identify L. boggessi as the only species in the trade. The intensity of the market for peppermint shrimps in the USA has led to L. boggessi being the most traded species worldwide. Misidentification in the shrimp aquarium trade is accidental and involuntary, and is explained by remarkable similarity among congeneric species. Using sequences of the 16S-mt-DNA marker, we found no indication of population genetic structure in the endemic L. boggessi across  550 km of linear coast. Therefore, this species can be considered genetically homogeneous and a single fished stock. Still, we argue in favor of additional studies using more powerful markers (e.g., SNPs) capable of revealing genetic structure at a finer spatial-scale. Our results will help advance management and conservation policies in this lucrative yet understudied fishery. Future studies of other ornamental fisheries will benefit from using an integrative taxonomic approach, as we demonstrate here. creator: J. Antonio Baeza creator: Donald C. Behringer uri: https://doi.org/10.7717/peerj.3786 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Baeza et al. title: Asymmetric responses to simulated global warming by populations of Colobanthus quitensis along a latitudinal gradient link: https://peerj.com/articles/3718 last-modified: 2017-09-18 description: The increase in temperature as consequence of the recent global warming has been reported to generate new ice-free areas in the Antarctic continent, facilitating the colonization and spread of plant populations. Consequently, Antarctic vascular plants have been observed extending their southern distribution. But as the environmental conditions toward southern localities become progressively more departed from the species’ physiological optimum, the ecophysiological responses and survival to the expected global warming could be reduced. However, if processes of local adaptation are the main cause of the observed southern expansion, those populations could appear constrained to respond positively to the expected global warming. Using individuals from the southern tip of South America, the South Shetland Islands and the Antarctic Peninsula, we assess with a long term experiment (three years) under controlled conditions if the responsiveness of Colobanthus quitensis populations to the expected global warming, is related with their different foliar traits and photoprotective mechanisms along the latitudinal gradient. In addition, we tested if the release of the stress condition by the global warming in these cold environments increases the ecophysiological performance. For this, we describe the latitudinal pattern of net photosynthetic capacity, biomass accumulation, and number of flowers under current and future temperatures respective to each site of origin after three growing seasons. Overall, was found a clinal trend was found in the foliar traits and photoprotective mechanisms in the evaluated C. quitensis populations. On the other hand, an asymmetric response to warming was observed for southern populations in all ecophysiological traits evaluated, suggesting that low temperature is limiting the performance of C. quitensis populations. Our results suggest that under a global warming scenario, plant populations that inhabiting cold zones at high latitudes could increase in their ecophysiological performance, enhancing the size of populations or their spread. creator: Ian S. Acuña-Rodríguez creator: Cristian Torres-Díaz creator: Rasme Hereme creator: Marco A. Molina-Montenegro uri: https://doi.org/10.7717/peerj.3718 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Acuña-Rodríguez et al. title: Candidate genes for shell colour polymorphism in Cepaea nemoralis link: https://peerj.com/articles/3715 last-modified: 2017-09-18 description: The characteristic ground colour and banding patterns on shells of the land snail Cepaea nemoralis form a classic study system for genetics and adaptation as it varies widely between individuals. We use RNAseq analysis to identify candidate genes underlying this polymorphism. We sequenced cDNA from the foot and the mantle (the shell-producing tissue) of four individuals of two phenotypes and produced a de novo transcriptome of 147,397 contigs. Differential expression analysis identified a set of 1,961 transcripts that were upregulated in mantle tissue. Sequence variant analysis resulted in a set of 2,592 transcripts with single nucleotide polymorphisms (SNPs) that differed consistently between the phenotypes. Inspection of the overlap between the differential expression analysis and SNP analysis yielded a set of 197 candidate transcripts, of which 38 were annotated. Four of these transcripts are thought to be involved in production of the shell’s nacreous layer. Comparison with morph-associated Restriction-site Associated DNA (RAD)-tags from a published study yielded eight transcripts that were annotated as metallothionein, a protein that is thought to inhibit the production of melanin in melanocytes. These results thus provide an excellent starting point for the elucidation of the genetic regulation of the Cepaea nemoralis shell colour polymorphism. creator: Jesse Kerkvliet creator: Tjalf de Boer creator: Menno Schilthuizen creator: Ken Kraaijeveld uri: https://doi.org/10.7717/peerj.3715 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kerkvliet et al. title: Genomic analysis of P elements in natural populations of Drosophila melanogaster link: https://peerj.com/articles/3824 last-modified: 2017-09-15 description: The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations. Here we compare estimates of genomic P element content with gonadal dysgenesis phenotypes for isofemale strains obtained from three worldwide populations of D. melanogaster to illuminate the molecular basis of natural variation in cytotype status. We show that P element abundance estimated from genome sequences of isofemale strains is highly correlated across different bioinformatics approaches, but that abundance estimates are sensitive to method and filtering strategies as well as incomplete inbreeding of isofemale strains. We find that P element content varies significantly across populations, with strains from a North American population having fewer P elements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences in P element abundance and structure, neither the number of P elements nor the ratio of full-length to internally-truncated copies is strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in P element abundance and structure across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Finally, we confirm that population differences in the abundance and structure of P elements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. Our work supports the view that genomic P element content alone is not sufficient to explain variation in gonadal dysgenesis across strains of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes. creator: Casey M. Bergman creator: Shunhua Han creator: Michael G. Nelson creator: Vladyslav Bondarenko creator: Iryna Kozeretska uri: https://doi.org/10.7717/peerj.3824 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bergman et al. title: Association of rs1801157 single nucleotide polymorphism of CXCL12 gene in breast cancer in Pakistan and in-silico expression analysis of CXCL12–CXCR4 associated biological regulatory network link: https://peerj.com/articles/3822 last-modified: 2017-09-15 description: BackgroundC-X-C chemokine ligand 12 (CXCL12) has important implications in breast cancer (BC) pathogenesis. It is selectively expressed on B and T lymphocytes and is involved in hematopoiesis, thymocyte trafficking, stem cell motility, neovascularization, and tumorigenesis. The single nucleotide polymorphism (SNP) rs1801157 of CXCL12 gene has been found to be associated with higher risk of BC.MethodsOur study focuses on the genotypic and allelic distribution of SNP (rs1801157; G/A) in Pakistani population as well as its association with the clinico-pathological features. The association between rs1801157 genotypes (G/A) and BC risks was assessed by a multivariate logistic regression (MLR) analysis. Genotyping was performed in both healthy individuals and patients of BC using PCR-restriction fragment length polymorphism (PCR-RFLP) method. Furthermore, in-silico approaches were adapted to investigate the association of CXCL12 and its receptor CXCR4 with genes/proteins involved in BC signalling.ResultsSignificant differences in allelic and genotypic distribution between BC patients and healthy individuals of genotype (G/G) and (A/G) (p < 0.05) were observed. The frequency of the allele G in the BC group (77%) was significantly higher as compared to control group (61%) (p = 0.01). The association of genotype GG with clinico-pathological features including age, stages of cancer and organ (lung, liver, bones and brain) metastasis (p > 0.05) was assessed. In a MLR analysis, a number of variables including age, weight of an individual, affected lymph nodes, hormonal status (estrogen and progesterone receptor), alcohol consumption and family history associated with the GG genotype (GG:AA, odds ratio (OR) = 1.30, 95% CI [1.06–1.60]) were found to be independent risk factors for BC. Our in-vitro results suggest that genotype GG is possibly increasing the risk of BC in Pakistani cohorts. in-silico analysis finds that CXCL12–CXCR4 is associated with an increased expression of PDZK1, PI3k and Akt which lead the breast tumor towards metastasis.ConclusionMultiple targets such as CXCL12, CXCR4, PDZK1, PI3k and Akt can be inhibited in combined strategies to treat BC metastasis. creator: Samra Khalid creator: Rumeza Hanif uri: https://doi.org/10.7717/peerj.3822 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Khalid and Hanif title: Fish Ontology framework for taxonomy-based fish recognition link: https://peerj.com/articles/3811 last-modified: 2017-09-15 description: Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. creator: Najib M. Ali creator: Haris A. Khan creator: Amy Y-Hui Then creator: Chong Ving Ching creator: Manas Gaur creator: Sarinder Kaur Dhillon uri: https://doi.org/10.7717/peerj.3811 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ali et al. title: The distribution shifts of Pinus armandii and its response to temperature and precipitation in China link: https://peerj.com/articles/3807 last-modified: 2017-09-15 description: BackgroundThe changing climate, particularly in regard to temperature and precipitation, is already affecting tree species’ distributions. Pinus armandii, which dominates on the Yungui Plateau and in the Qinba Mountains in China, is of economic, cultural and ecological value. We wish to test the correlations between the distribution shift of P. armandii and changing climate, and figure out how it tracks future climate change.MethodsWe sampled the surface soil at sites throughout the distribution of P. armandii to compare the relative abundance of pollen to the current percent cover of plant species. This was used to determine possible changes in the distribution P. armandii. Given the hilly terrain, elevation was considered together with temperature and precipitation as variables correlated with distribution shifts of P. armandii.ResultsWe show that P. armandii is undergoing change in its geographic range, including retraction, a shift to more northern areas and from the upper high part of the mountains to a lower-altitude part in hilly areas. Temperature was the strongest correlate of this distribution shift. Elevation and precipitation were also both significantly correlated with distribution change of P. armandii, but to a lesser degree than temperature.ConclusionThe geographic range of P. armandii has been gradually decreasing under the influence of climate change. This provides evidence of the effect of climate change on trees at the species level and suggests that at least some species will have a limited ability to track the changing climate. creator: Xiaofeng Zheng creator: Pengxiang Gao creator: ShuoXin Zhang uri: https://doi.org/10.7717/peerj.3807 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zheng et al. title: Effects of long-term preservation on amphibian body conditions: implications for historical morphological research link: https://peerj.com/articles/3805 last-modified: 2017-09-15 description: Measurements of historical specimens are widely applied in studies of taxonomy, systematics, and ecology, but biologists often assume that the effects of preservative chemicals on the morphology of amphibian specimens are minimal in their analyses. We compared the body length and body mass of 182 samples of 13 live and preserved (up to 10 years) anuran species and found that the body length and body mass of preserved specimens significantly decreased by 6.1% and 24.8%, respectively, compared to those measurements of their live counterparts. The changes in body length and mass also exhibited highly significant variations between species. Similarly, there were significant differences in shrinkage of body length and body mass between sexes, where males showed greater shrinkage in body length and body mass compared to females. Preservation distorted the magnitude of the interspecific differences in body length observed in the fresh specimens. Overall, the reduction in body length or mass was greater in longer or heavier individuals. Due to the effects of preservation on amphibian morphology, we propose two parsimonious conversion equations to back-calculate the original body length and body mass of studied anurans for researchers working with historical data, since morphological data from preserved specimens may lead to incorrect biological interpretations when comparing to fresh specimens. Therefore, researchers should correct for errors due to preservation effects that may lead to the misinterpretation of results. creator: Guocheng Shu creator: Yuzhou Gong creator: Feng Xie creator: Nicholas C. Wu creator: Cheng Li uri: https://doi.org/10.7717/peerj.3805 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shu et al. title: Inferring ‘weak spots’ in phylogenetic trees: application to mosasauroid nomenclature link: https://peerj.com/articles/3782 last-modified: 2017-09-15 description: Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the ‘weak spots’ in the phylogeny of mosasauroids, we revise the nomenclature of the ‘traditionally’ recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support. creator: Daniel Madzia creator: Andrea Cau uri: https://doi.org/10.7717/peerj.3782 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Madzia and Cau title: Impacts of land use and invasive species on native avifauna of Mo’orea, French Polynesia link: https://peerj.com/articles/3761 last-modified: 2017-09-15 description: Oceanic islands are among the most endemically biodiverse ecosystems in the world. They have been adversely impacted by human expansion, which affects regional biodiversity by altering the natural habitats of vulnerable, indigenous species. Birds represent a valuable indicator species of environmental change due to their ability to adapt quickly. Investigating the relationship between environmental change, abundance, and behaviors of birds can help us better anticipate potential impacts to island ecosystems. In addition, we can understand the population trends and restricted ranges of native avifauna, identify the regions needing protection, and assess habitat vulnerability linked to anthropogenic activities. In Mo’orea, French Polynesia, we studied nine passerine bird species using automated acoustic recording devices placed in agricultural, forested, and mixed habitats. Based on call counts per unit time and occupancy modeling, we found evidence that three non-native species preferred agricultural areas and low-canopy cover over dense forested areas. Furthermore, native bird detectability and possibly abundance was significantly lower than non-native birds. Using hierarchical cluster analysis to support inferences regarding behavioral differences, we found that native bird calling activity was negatively associated with non-native bird calling activity. Altogether, these results suggest native bird populations are at risk in all of the habitats studied, but forests serve as a potential refuge. creator: Vanessa M. ZoBell creator: Brett J. Furnas uri: https://doi.org/10.7717/peerj.3761 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 ZoBell and Furnas title: Meta-analysis of biomarkers for severe dengue infections link: https://peerj.com/articles/3589 last-modified: 2017-09-15 description: BackgroundDengue viral infection is an acute infection that has the potential to have severe complications as its major sequela. Currently, there is no routine laboratory biomarker with which to predict the severity of dengue infection or monitor the effectiveness of standard management. Hence, this meta-analysis compared biomarker levels between dengue fever (DF) and severe dengue infections (SDI) to identify potential biomarkers for SDI.MethodsData concerning levels of cytokines, chemokines, and other potential biomarkers of DF, dengue hemorrhagic fever, dengue shock syndrome, and severe dengue were obtained for patients of all ages and populations using the Scopus, PubMed, and Ovid search engines. The keywords “(IL1* or IL-1*) AND (dengue*)” were used and the same process was repeated for other potential biomarkers, according to Medical Subject Headings terms suggested by PubMed and Ovid. Meta-analysis of the mean difference in plasma or serum level of biomarkers between DF and SDI patients was performed, separated by different periods of time (days) since fever onset. Subgroup analyses comparing biomarker levels of healthy plasma and sera controls, biomarker levels of primary and secondary infection samples were also performed, as well as analyses of different levels of severity and biomarker levels upon infection by different dengue serotypes.ResultsFifty-six studies of 53 biomarkers from 3,739 dengue cases (2,021 DF and 1,728 SDI) were included in this meta-analysis. Results showed that RANTES, IL-7, IL-8, IL-10, IL-18, TGF-b, and VEGFR2 levels were significantly different between DF and SDI. IL-8, IL-10, and IL-18 levels increased during SDI (95% CI, 18.1–253.2 pg/mL, 3–13 studies, n = 177–1,909, I2 = 98.86%–99.75%). In contrast, RANTES, IL-7, TGF-b, and VEGFR2 showed a decrease in levels during SDI (95% CI, −3238.7 to −3.2 pg/mL, 1–3 studies, n = 95–418, I2 = 97.59%–99.99%). Levels of these biomarkers were also found to correlate with the severity of the dengue infection, in comparison to healthy controls. Furthermore, the results showed that IL-7, IL-8, IL-10, TGF-b, and VEGFR2 display peak differences between DF and SDI during or before the critical phase (day 4–5) of SDI.DiscussionThis meta-analysis suggests that IL-7, IL-8, IL-10, TGF-b, and VEGFR2 may be used as potential early laboratory biomarkers in the diagnosis of SDI. This can be used to predict the severity of dengue infection and to monitor the effectiveness of treatment. Nevertheless, methodological and reporting limitations must be overcome in future research to minimize variables that affect the results and to confirm the findings. creator: Kuan-Meng Soo creator: Bahariah Khalid creator: Siew-Mooi Ching creator: Chau Ling Tham creator: Rusliza Basir creator: Hui-Yee Chee uri: https://doi.org/10.7717/peerj.3589 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Soo et al. title: Curcumin longa extract-loaded nanoemulsion improves the survival of endotoxemic mice by inhibiting nitric oxide-dependent HMGB1 release link: https://peerj.com/articles/3808 last-modified: 2017-09-14 description: BackgroundHigh mobility group box 1 (HMGB1) is a well-known damage-related alarmin that participates in cellular inflammatory responses. However, the mechanisms leading to HMGB1 release in inflammatory conditions and the therapeutic agents that could prevent it remain poorly understood. This study attempted to examine whether the Curcumin longa herb, which is known to have anti-inflammatory property, can modulate cellular inflammatory responses by regulating HMGB1 release.MethodsThe murine macrophage RAW264.7 cells were treated with lipopolysaccharide (LPS) and/or a C. longa extract-loaded nanoemulsion (CLEN). The levels of released HMGB1, nitric oxide (NO) production, inducible NO synthase (iNOS) expression, and phosphorylation of mitogen-activated protein kinases were analyzed in RAW264.7 macrophages. The effects of CLEN on survival of endotoxemic model mice, circulating HMGB1 levels, and tissue iNOS expression were also evaluated.ResultsWe have shown that a nanoemulsion loaded with an extract from the C. longa rhizome regulates cellular inflammatory responses and LPS-induced systemic inflammation by suppressing the release of HMGB1 by macrophages. First, treatment of RAW264.7 macrophages with the nanoemulsion significantly attenuated their LPS-induced release of HMGB1: this effect was mediated by inhibiting c-Jun N-terminal kinase activation, which in turn suppressed the NO production and iNOS expression of the cells. The nanoemulsion did not affect LPS-induced p38 or extracellular signal-regulated kinase activation. Second, intraperitoneal administration of the nanoemulsion improved the survival rate of LPS-injected endotoxemic mice. This associated with marked reductions in circulating HMGB1 levels and tissue iNOS expression.DiscussionThe present study shows for the first time the mechanism by which C. longa ameliorates sepsis, namely, by suppressing NO signaling and thereby inhibiting the release of the proinflammatory cytokine HMGB1. These observations suggest that identification of agents, including those in the herb C. longa, that can inhibit HMGB1 production and/or activity may aid the treatment of endotoxemia. creator: Min Young Ahn creator: Jung Seok Hwang creator: Su Bi Lee creator: Sun Ah Ham creator: Jinwoo Hur creator: Jun Tae Kim creator: Han Geuk Seo uri: https://doi.org/10.7717/peerj.3808 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ahn et al. title: A dark past, a restrained present, and an apocalyptic future: time perspective, personality, and life satisfaction among anorexia nervosa patients link: https://peerj.com/articles/3801 last-modified: 2017-09-14 description: BackgroundDespite reporting low levels of well-being, anorexia nervosa patients express temperament traits (e.g., extraversion and persistence) necessary for high levels of life satisfaction. Nevertheless, among individuals without eating disorders, a balanced organization of the flow of time, influences life satisfaction beyond temperamental dispositions. A balanced time perspective is defined as: high past positive, low past negative, high present hedonistic, low present fatalistic, and high future. We investigated differences in time perspective dimensions, personality traits, and life satisfaction between anorexia nervosa patients and matched controls. We also investigated if the personality traits and the outlook on time associated to positive levels of life satisfaction among controls also predicted anorexia patients’ life satisfaction. Additionally, we investigated if time perspective dimensions predicted life satisfaction beyond personality traits among both patients and controls.MethodA total of 88 anorexia nervosa patients from a clinic in the West of Sweden and 111 gender-age matched controls from a university in the West of Sweden participated in the Study. All participants responded to the Zimbardo Time Perspective Inventory, the Ten Item Personality Inventory, and the Temporal Satisfaction with Life Scale.ResultsA t-test showed that patients scored higher in the past negative, the present fatalistic, and the future dimensions, lower in the past positive and the present hedonistic dimensions, higher in conscientiousness, extraversion, and agreeableness, and lower in life satisfaction. Regression analyses showed that life satisfaction was predicted by openness to experience and emotional stability for controls and by emotional stability among patients. When time dimensions were entered in the regression, emotional stability and the past negative and past positive time dimensions predicted life satisfaction among controls, but only the past positive and present hedonistic time dimensions predicted life satisfaction among patients.ConclusionAnorexia patients were less satisfied with life despite being more conscientious, social, and agreeable than controls. Moreover, compared to controls, patients had an unbalanced time perspective: a dark view of the past (i.e., high past negative), a restrained present (i.e., low present hedonistic) and an apocalyptic view of the future (i.e., high present fatalistic). It is plausible to suggest that, therapeutic interventions should focus on empowering patients to cultivate a sentimental and positive view of the past (i.e., high past positive) and the desire to experience pleasure without concern for future consequences (i.e., high present hedonistic) so that they can make self-directed and flexible choices for their own well-being. Such interventions might have effects on life satisfaction beyond the patients’ temperamental disposition. creator: Danilo Garcia creator: Alexandre Granjard creator: Suzanna Lundblad creator: Trevor Archer uri: https://doi.org/10.7717/peerj.3801 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Garcia et al. title: Hydrology controls recruitment of two invasive cyprinids: bigheaded carp reproduction in a navigable large river link: https://peerj.com/articles/3641 last-modified: 2017-09-14 description: In the Mississippi River Basin of North America, invasive bigheaded carp (silver carp Hypophthalmichthys molitrix and bighead carp H. nobilis, also referred to as Asian carp) have spread rapidly over the past several decades. In the Illinois River, an important tributary of the Upper Mississippi River, reproduction appears to be sporadic and frequently unsuccessful, yet bigheaded carp densities in this river are among the highest recorded on the continent. Understanding the causative factors behind erratic recruitment in this commercially-harvested invasive species is important for both limiting their spread and managing their harvest. We analyzed weekly catch records from 15 years of a standardized monitoring program to document the emergence of age-0 bigheaded carp in relation to environmental conditions. The appearance of age-0 fish was generally linked to hydrographic attributes, which probably serve as a cue for spawning. However, we found profound differences in the number of age-0 fish among years, which varied by as much as five orders of magnitude in successive years. The strong link between summer flooding and age-0 fish production we observed emphasizes the importance of understanding the hydrologic context in which sustained invasions occur. Despite evidence of sporadic recruitment, bigheaded carp populations in the Illinois River appear to be consistent or increasing because of particularly strong, episodic year classes. creator: Daniel K. Gibson-Reinemer creator: Levi E. Solomon creator: Richard M. Pendleton creator: John H. Chick creator: Andrew F. Casper uri: https://doi.org/10.7717/peerj.3641 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gibson-Reinemer et al. title: The postcranial skeleton of Boreogomphodon (Cynodontia: Traversodontidae) from the Upper Triassic of North Carolina, USA and the comparison with other traversodontids link: https://peerj.com/articles/3521 last-modified: 2017-09-14 description: Postcranial remains of Boreogomphodon from the Upper Triassic of North Carolina are described and compared to those of other known traversodontid cynodonts. The postcranial skeleton of Boreogomphodon is characterized by four sacral ribs, simple ribs lacking costal plates, the extension of the scapular neck below the acromion process, a short scapular facet on the procoracoid, a concave anterior margin of the procoracoid, humerus entepicondyle with smooth corner, and the presence of a fifth distal carpal. Four types of ribs are identified among traversodontids: ‘normal’ form, tubercular rib, costal plate, and Y-shaped rib. Fossorial behavior is suggested for traversodontids with elaborate costal plates. Within Traversodontidae, the procoracoid is relatively small; the anterior process of the iliac blade extends anteroventrally to different degrees in different taxa, which facilitates retraction of the femur; and the limb bones show allometric growth in terms of length and width. creator: Jun Liu creator: Vincent P. Schneider creator: Paul E. Olsen uri: https://doi.org/10.7717/peerj.3521 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liu et al. title: The role of polycarbonate monomer bisphenol-A in insulin resistance link: https://peerj.com/articles/3809 last-modified: 2017-09-13 description: Bisphenol A (BPA) is a synthetic unit of polycarbonate polymers and epoxy resins, the types of plastics that could be found in essentially every human population and incorporated into almost every aspect of the modern human society. BPA polymers appear in a wide range of products, from liquid storages (plastic bottles, can and glass linings, water pipes and tanks) and food storages (plastics wraps and containers), to medical and dental devices. BPA polymers could be hydrolyzed spontaneously or in a photo- or temperature-catalyzed process, providing widespread environmental distribution and chronic exposure to the BPA monomer in contemporary human populations. Bisphenol A is also a xenoestrogen, an endocrine-disrupting chemical (EDC) that interferes with the endocrine system mimicking the effects of an estrogen and could potentially keep our endocrine system in a constant perturbation that parallels endocrine disruption arising during pregnancy, such as insulin resistance (IR). Gestational insulin resistance represents a natural biological phenomenon of higher insulin resistance in peripheral tissues of the pregnant females, when nutrients are increasingly being directed to the embryo instead of being stored in peripheral tissues. Gestational diabetes mellitus may appear in healthy non-diabetic females, due to gestational insulin resistance that leads to increased blood sugar levels and hyperinsulinemia (increased insulin production from the pancreatic beta cells). The hypothesis states that unnoticed and constant exposure to this environmental chemical might potentially lead to the formation of chronic low-level endocrine disruptive state that resembles gestational insulin resistance, which might contribute to the development of diabetes. The increasing body of evidence supports the major premises of this hypothesis, as exemplified by the numerous publications examining the association of BPA and insulin resistance, both epidemiological and mechanistic. However, to what extent BPA might contribute to the development of diabetes in the modern societies still remains unknown. In this review, I discuss the chemical properties of BPA and the sources of BPA contamination found in the environment and in human tissues. I provide an overview of mechanisms for the proposed role of bisphenol A in insulin resistance and diabetes, as well as other related diseases, such as cardiovascular diseases. I describe the transmission of BPA effects to the offspring and postulate that gender related differences might originate from differences in liver enzyme levels, such as UDP-glucuronosyltransferase, which is involved in BPA processing and its elimination from the organism. I discuss the molecular mechanisms of BPA action through nuclear and membrane-bound ER receptors, non-monotonic dose response, epigenetic modifications of the DNA and propose that chronic exposure to weak binders, such as BPA, may mimic the effects of strong binders, such as estrogens. creator: Milos Pjanic uri: https://doi.org/10.7717/peerj.3809 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pjanic title: Allele specific expression and methylation in the bumblebee, Bombus terrestris link: https://peerj.com/articles/3798 last-modified: 2017-09-13 description: The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the as yet unquantified role of genetic cis effects in insect allele specific methylation and expression. creator: Zoë Lonsdale creator: Kate Lee creator: Maria Kiriakidu creator: Harindra Amarasinghe creator: Despina Nathanael creator: Catherine J. O’Connor creator: Eamonn B. Mallon uri: https://doi.org/10.7717/peerj.3798 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lonsdale et al. title: Heterologous expression of Plasmodium vivax apical membrane antigen 1 (PvAMA1) for binding peptide selection link: https://peerj.com/articles/3794 last-modified: 2017-09-13 description: BackgroundPlasmodium is an obligate intracellular parasite. Apical membrane antigen 1 (AMA1) is the most prominent and well characterized malarial surface antigen that is essential for parasite-host cell invasion, i.e., for sporozoite to invade and replicate within hepatocytes in the liver stage and merozoite to penetrate and replicate within erythrocytes in the blood stage. AMA1 has long served as a potent antimalarial drug target and is a pivotal vaccine candidate. A good understanding of the structure and molecular function of this Plasmodium protein, particularly its involvement in host-cell adhesion and invasion, is of great interest and hence it offers an attractive target for the development of novel therapeutics. The present study aims to heterologous express recombinant Plasmodium AMA1 ectodomain of P. vivax (rPvAMA1) for the selection of binding peptides.MethodsThe rPvAMA1 protein was heterologous expressed using a tag-free Profinity eXactTM system and codon optimized BL21-Codon Plus (DE3)-RIL Escherichia coli strain and further refolded by dialysis for renaturation. Binding peptides toward refolded rPvAMA1 were panned using a Ph.D.-12 random phage display library.ResultsThe rPvAMA1 was successfully expressed and refolded with three phage-displayed dodecapeptides designated as PdV1 (DLTFTVNPLSKA), PdV2 (WHWSWWNPNQLT), and PdV3 (TSVSYINNRHNL) with affinity towards rPvAMA1 identified. All of them exhibited positive binding signal to rPvAMA1 in both direct phage assays, i.e., phage ELISA binding assay and Western blot binding assay.DiscussionPhage display technology enables the mapping of protein-protein interactions based on a simple principle that a library of phage particles displaying peptides is used and the phage clones that bind to the target protein are selected and identified. The binding sites of each selected peptides toward PvAMA1 (Protein Data Bank, PDB ID: 1W8K) were in silico predicted using CABS-dock web server. In this case, the binding peptides provide a valuable starting point for the development of peptidomimetic as antimalarial antagonists directed at PvAMA1. creator: Ching Hoong Chew creator: Yvonne Ai Lian Lim creator: Kek Heng Chua uri: https://doi.org/10.7717/peerj.3794 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chew et al. title: Calcitonin receptor expression in medullary thyroid carcinoma link: https://peerj.com/articles/3778 last-modified: 2017-09-13 description: BackgroundCalcitonin expression is a well-established marker for medullary thyroid carcinoma (MTC); yet the role of calcitonin receptor (CTR), its seven-transmembrane G-protein coupled receptor, remains to be established in C-cells derived thyroid tumors. The aim of this work was to investigate CTR expression in MTC and to correlate such expression with clinicopathological features in order to evaluate its possible role as a prognostic indicator of disease aggressiveness and outcome.MethodsCalcitonin receptor expression was analyzed in a series of 75 MTCs by immunohistochemistry, and by qPCR mRNA quantification in specimens from four patients. Statistical tests were used to evaluate the correlation between CTR expression and the clinicopathological and molecular characteristics of patients and tumors.ResultsCalcitonin receptor expression was detected in 62 out of 75 samples (82.7%), whereas 13 of the 75 samples (17.3%) were completely negative. CTR expression was significantly associated with expression of cytoplasmatic phosphatase and tensin homologue deleted on chromosome 10 and osteopontin, as well as with wild type RET/RAS genes and absence of tumor stroma, suggesting that CTR expression do not associate with clinicopathological signs of worse prognosis.DiscussionCalcitonin receptor expression appears to be associated in MTC with more differentiated status of the neoplastic cells. creator: Virginia Cappagli creator: Catarina Soares Potes creator: Luciana Bueno Ferreira creator: Catarina Tavares creator: Catarina Eloy creator: Rossella Elisei creator: Manuel Sobrinho-Simões creator: Peter J. Wookey creator: Paula Soares uri: https://doi.org/10.7717/peerj.3778 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Cappagli et al. title: Constructing three emotion knowledge tests from the invariant measurement approach link: https://peerj.com/articles/3755 last-modified: 2017-09-13 description: BackgroundPsychological constructionist models like the Conceptual Act Theory (CAT) postulate that complex states such as emotions are composed of basic psychological ingredients that are more clearly respected by the brain than basic emotions. The objective of this study was the construction and initial validation of Emotion Knowledge measures from the CAT frame by means of an invariant measurement approach, the Rasch Model (RM). Psychological distance theory was used to inform item generation.MethodsThree EK tests—emotion vocabulary (EV), close emotional situations (CES) and far emotional situations (FES)—were constructed and tested with the RM in a community sample of 100 females and 100 males (age range: 18–65), both separately and conjointly.ResultsIt was corroborated that data-RM fit was sufficient. Then, the effect of type of test and emotion on Rasch-modelled item difficulty was tested. Significant effects of emotion on EK item difficulty were found, but the only statistically significant difference was that between “happiness” and the remaining emotions; neither type of test, nor interaction effects on EK item difficulty were statistically significant. The testing of gender differences was carried out after corroborating that differential item functioning (DIF) would not be a plausible alternative hypothesis for the results. No statistically significant sex-related differences were found out in EV, CES, FES, or total EK. However, the sign of d indicate that female participants were consistently better than male ones, a result that will be of interest for future meta-analyses.DiscussionThe three EK tests are ready to be used as components of a higher-level measurement process. creator: Ana R. Delgado creator: Gerardo Prieto creator: Debora I. Burin uri: https://doi.org/10.7717/peerj.3755 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Delgado et al. title: In rats fed high-energy diets, taste, rather than fat content, is the key factor increasing food intake: a comparison of a cafeteria and a lipid-supplemented standard diet link: https://peerj.com/articles/3697 last-modified: 2017-09-13 description: BackgroundFood selection and ingestion both in humans and rodents, often is a critical factor in determining excess energy intake and its related disorders.MethodsTwo different concepts of high-fat diets were tested for their obesogenic effects in rats; in both cases, lipids constituted about 40% of their energy intake. The main difference with controls fed standard lab chow, was, precisely, the lipid content. Cafeteria diets (K) were self-selected diets devised to be desirable to the rats, mainly because of its diverse mix of tastes, particularly salty and sweet. This diet was compared with another, more classical high-fat (HF) diet, devised not to be as tasty as K, and prepared by supplementing standard chow pellets with fat. We also analysed the influence of sex on the effects of the diets.ResultsK rats grew faster because of a high lipid, sugar and protein intake, especially the males, while females showed lower weight but higher proportion of body lipid. In contrast, the weight of HF groups were not different from controls. Individual nutrient’s intake were analysed, and we found that K rats ingested large amounts of both disaccharides and salt, with scant differences of other nutrients’ proportion between the three groups. The results suggest that the key differential factor of the diet eliciting excess energy intake was the massive presence of sweet and salty tasting food.ConclusionsThe significant presence of sugar and salt appears as a powerful inducer of excess food intake, more effective than a simple (albeit large) increase in the diet’s lipid content. These effects appeared already after a relatively short treatment. The differential effects of sex agree with their different hedonic and obesogenic response to diet. creator: Laia Oliva creator: Tània Aranda creator: Giada Caviola creator: Anna Fernández-Bernal creator: Marià Alemany creator: José Antonio Fernández-López creator: Xavier Remesar uri: https://doi.org/10.7717/peerj.3697 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Oliva et al. title: Awareness about antibiotic resistance in a self-medication user group from Eastern Romania: a pilot study link: https://peerj.com/articles/3803 last-modified: 2017-09-12 description: BackgroundAwareness about antibiotic resistance depends on the attitudes and information about antibiotic resistance of both patients and physicians. Persons who practice self-medication are at high risk of also self-medicating with antibiotics. The purpose of the present study was to evaluate the awareness about antibiotic resistance by investigating the practice in a group of self-medication users in a sample of adults in Romania and the variables associated with such practice.Material and MethodsA cross-sectional self-filled questionnaire based study was conducted from December 2016 through January 2017 amongst 218 self-medication users (SMUG). The attitudes, the level of knowledge, the perceptions, about antibiotic use (ABU) and about antibiotic resistance (ABR) were compared to a reference group represented by medical residents group in their specialty training (MRG) considered to have a higher level of knowledge and awareness about ABU and ABR.ResultsThe response rate was 87.2% in the SMUG group and 100% in the MRG group. The SMUG group reported self-medication practices for antibiotics with a high frequency at any time in life (72%), but with a very low frequency from the month previous to the date of the study (12%), comparative with the MRG group (75% and 7%, respectively). The multivariate logistic regression analysis showed that self-medication with antibiotics at any time in life in the SMUG group could be predicted by the answers to two questions regarding the practices and knowledge about ABU (Q13 and Q20). On the other hand, in the MRG group, a question about ABR perception (Q23), could be predictor for self-medication with antibiotics. Self-medication with antibiotics in the month previous to the date of the study in the SMUG group could be predicted with three questions: one about ABU practice (Q14), one about ABR perception (Q26) and one referring to ABR knowledge (Q28). On the other hand, in the MRG group, a question about ABR knowledge (Q32) could be predictor for self-medication with antibiotics. The reduced awareness about ABR in the SMUG group, is revealed by the reduced number of subjects (38%), who did not know that missing an antibiotic dose during a medical treatment contributes to ABR, comparative with the MRG group (84%). Indirectly, low ABR awareness in the SMUG group is revealed by the confusion about the appropriate use of antibiotics in bacterial or viral infections (that antibiotics are not used against viruses).ConclusionsThe findings from our study on the awareness about antibiotic resistance in the SMUG group might help the policy makers and regulatory authorities to develop educational programs directed to change the perceptions and attitudes about the appropriate use of antibiotics in order to diminish self-medication practices with antibiotics. creator: Gabi Topor creator: Ionela-Alina Grosu creator: Cristina Mihaela Ghiciuc creator: Aurel Lulu Strat creator: Cătălina Elena Lupuşoru uri: https://doi.org/10.7717/peerj.3803 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Topor et al. title: Automated classification of tropical shrub species: a hybrid of leaf shape and machine learning approach link: https://peerj.com/articles/3792 last-modified: 2017-09-12 description: Plants play a crucial role in foodstuff, medicine, industry, and environmental protection. The skill of recognising plants is very important in some applications, including conservation of endangered species and rehabilitation of lands after mining activities. However, it is a difficult task to identify plant species because it requires specialized knowledge. Developing an automated classification system for plant species is necessary and valuable since it can help specialists as well as the public in identifying plant species easily. Shape descriptors were applied on the myDAUN dataset that contains 45 tropical shrub species collected from the University of Malaya (UM), Malaysia. Based on literature review, this is the first study in the development of tropical shrub species image dataset and classification using a hybrid of leaf shape and machine learning approach. Four types of shape descriptors were used in this study namely morphological shape descriptors (MSD), Histogram of Oriented Gradients (HOG), Hu invariant moments (Hu) and Zernike moments (ZM). Single descriptor, as well as the combination of hybrid descriptors were tested and compared. The tropical shrub species are classified using six different classifiers, which are artificial neural network (ANN), random forest (RF), support vector machine (SVM), k-nearest neighbour (k-NN), linear discriminant analysis (LDA) and directed acyclic graph multiclass least squares twin support vector machine (DAG MLSTSVM). In addition, three types of feature selection methods were tested in the myDAUN dataset, Relief, Correlation-based feature selection (CFS) and Pearson’s coefficient correlation (PCC). The well-known Flavia dataset and Swedish Leaf dataset were used as the validation dataset on the proposed methods. The results showed that the hybrid of all descriptors of ANN outperformed the other classifiers with an average classification accuracy of 98.23% for the myDAUN dataset, 95.25% for the Flavia dataset and 99.89% for the Swedish Leaf dataset. In addition, the Relief feature selection method achieved the highest classification accuracy of 98.13% after 80 (or 60%) of the original features were reduced, from 133 to 53 descriptors in the myDAUN dataset with the reduction in computational time. Subsequently, the hybridisation of four descriptors gave the best results compared to others. It is proven that the combination MSD and HOG were good enough for tropical shrubs species classification. Hu and ZM descriptors also improved the accuracy in tropical shrubs species classification in terms of invariant to translation, rotation and scale. ANN outperformed the others for tropical shrub species classification in this study. Feature selection methods can be used in the classification of tropical shrub species, as the comparable results could be obtained with the reduced descriptors and reduced in computational time and cost. creator: Miraemiliana Murat creator: Siow-Wee Chang creator: Arpah Abu creator: Hwa Jen Yap creator: Kien-Thai Yong uri: https://doi.org/10.7717/peerj.3792 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Murat et al. title: Greater reproductive investment, but shorter lifespan, in agrosystem than in natural-habitat toads link: https://peerj.com/articles/3791 last-modified: 2017-09-12 description: Global amphibian decline is due to several factors: habitat loss, anthropization, pollution, emerging diseases, and global warming. Amphibians, with complex life cycles, are particularly susceptible to habitat alterations, and their survival may be impaired in anthropized habitats. Increased mortality is a well-known consequence of anthropization. Life-history theory predicts higher reproductive investment when mortality is increased. In this work, we compared age, body size, and different indicators of reproductive investment, as well as prey availability, in natterjack toads (Epidalea calamita) from agrosystems and adjacent natural pine groves in Southwestern Spain. Mean age was lower in agrosystems than in pine groves, possibly as a consequence of increased mortality due to agrosystem environmental stressors. Remarkably, agrosystem toads were larger despite being younger, suggesting accelerated growth rate. Although we detected no differences in prey availability between habitats, artificial irrigation could shorten aestivation in agrosystems, thus increasing energy trade. Moreover, agrosystem toads exhibited increased indicators of reproductive investment. In the light of life-history theory, agrosystem toads might compensate for lesser reproductive events—due to shorter lives—with a higher reproductive investment in each attempt. Our results show that agrosystems may alter demography, which may have complex consequences on both individual fitness and population stability. creator: Francisco Javier Zamora-Camacho creator: Mar Comas uri: https://doi.org/10.7717/peerj.3791 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zamora-Camacho and Comas title: Factors influencing healthcare provider respondent fatigue answering a globally administered in-app survey link: https://peerj.com/articles/3785 last-modified: 2017-09-12 description: BackgroundRespondent fatigue, also known as survey fatigue, is a common problem in the collection of survey data. Factors that are known to influence respondent fatigue include survey length, survey topic, question complexity, and open-ended question type. There is a great deal of interest in understanding the drivers of physician survey responsiveness due to the value of information received from these practitioners. With the recent explosion of mobile smartphone technology, it has been possible to obtain survey data from users of mobile applications (apps) on a question-by-question basis. The author obtained basic demographic survey data as well as survey data related to an anesthesiology-specific drug called sugammadex and leveraged nonresponse rates to examine factors that influenced respondent fatigue.MethodsPrimary data were collected between December 2015 and February 2017. Surveys and in-app analytics were collected from global users of a mobile anesthesia calculator app. Key independent variables were user country, healthcare provider role, rating of importance of the app to personal practice, length of time in practice, and frequency of app use. Key dependent variable was the metric of respondent fatigue.ResultsProvider role and World Bank country income level were predictive of the rate of respondent fatigue for this in-app survey. Importance of the app to the provider and length of time in practice were moderately associated with fatigue. Frequency of app use was not associated. This study focused on a survey with a topic closely related to the subject area of the app. Respondent fatigue rates will likely change dramatically if the topic does not align closely.DiscussionAlthough apps may serve as powerful platforms for data collection, responses rates to in-app surveys may differ on the basis of important respondent characteristics. Studies should be carefully designed to mitigate fatigue as well as powered with the understanding of the respondent characteristics that may have higher rates of respondent fatigue. creator: Vikas N. O’Reilly-Shah uri: https://doi.org/10.7717/peerj.3785 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 O’Reilly-Shah title: Identification and analysis of CYP450 genes from transcriptome of Lonicera japonica and expression analysis of chlorogenic acid biosynthesis related CYP450s link: https://peerj.com/articles/3781 last-modified: 2017-09-12 description: BackgroundLonicera japonica is an important medicinal plant that has been widely used in traditional Chinese medicine for thousands of years. The pharmacological activities of L. japonica are mainly due to its rich natural active ingredients, most of which are secondary metabolites. CYP450s are a large, complex, and widespread superfamily of proteins that participate in many endogenous and exogenous metabolic reactions, especially secondary metabolism. Here, we identified CYP450s in L. japonica transcriptome and analyzed CYP450s that may be involved in chlorogenic acid (CGA) biosynthesis.MethodsThe recent availability of L. japonica transcriptome provided opportunity to identify CYP450s in this herb. BLAST based method and HMM based method were used to identify CYP450s in L. japonica transcriptome. Then, phylogenetic analysis, conserved motifs analysis, GO annotation, and KEGG annotation analyses were conducted to characterize the identified CYP450s. qRT-PCR was used to explore expression patterns of five CGA biosynthesis related CYP450s.ResultsIn this study, 151 putative CYP450s with complete cytochrome P450 domain, which belonged to 10 clans, 45 families and 76 subfamilies, were identified in L. japonica transcriptome. Phylogenetic analysis classified these CYP450s into two major branches, A-type (47%) and non-A type (53%). Both types of CYP450s had conserved motifs in L. japonica. The differences of typical motif sequences between A-type and non-A type CYP450s in L. japonica were similar with other plants. GO classification indicated that non-A type CYP450s participated in more molecular functions and biological processes than A-type. KEGG pathway annotation totally assigned 47 CYP450s to 25 KEGG pathways. From these data, we cloned two LjC3Hs (CYP98A subfamily) and three LjC4Hs (CYP73A subfamily) that may be involved in biosynthesis of CGA, the major ingredient for pharmacological activities of L. japonica. qRT-PCR results indicated that two LjC3Hs exhibited oppositing expression patterns during the flower development and LjC3H2 exhibited a similar expression pattern with CGA concentration measured by HPLC. The expression patterns of three LjC4Hs were quite different and the expression pattern of LjC4H3 was quite similar with that of LjC3H1.DiscussionOur results provide a comprehensive identification and characterization of CYP450s in L. japonica. Five CGA biosynthesis related CYP450s were cloned and their expression patterns were explored. The different expression patterns of two LjC3Hs and three LjC4Hs may be due to functional divergence of both substrate and catalytic specificity during plant evolution. The co-expression pattern of LjC3H1 and LjC4H3 strongly suggested that they were under coordinated regulation by the same transcription factors due to same cis elements in their promoters. In conclusion, this study provides insight into CYP450s and will effectively facilitate the research of biosynthesis of CGA in L. japonica. creator: Xiwu Qi creator: Xu Yu creator: Daohua Xu creator: Hailing Fang creator: Ke Dong creator: Weilin Li creator: Chengyuan Liang uri: https://doi.org/10.7717/peerj.3781 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Qi et al. title: Comparison of polybrominated diphenyl ethers (PBDEs) and polychlorinated biphenyls (PCBs) in the serum of hypothyroxinemic and euthyroid dogs link: https://peerj.com/articles/3780 last-modified: 2017-09-12 description: ObjectiveTo determine the profile of 14 polybrominated diphenyl ethers (PBDEs) and 23 polychlorinated biphenyls (PCBs) in serum of domestic canines and whether this was predictive of thyroid hormone status.SamplesSerum samples were collected from 51 client-owned dogs visiting the University of California Davis William R. Pritchard Veterinary Medical Teaching Hospital during 2012 to 2016 for routine appointments. Fifteen dogs were diagnosed with hypothyroxinemia while 36 were euthyroid.ProceduresConcentrations of PBDEs and PCBs in canine serum samples were measured by gas chromatography mass spectrometry. Logistic regression analysis was used to determine the association between the presence/absence of canine hypothyroxinemia and the serum concentration of individual PBDE or PCB congeners.ResultsThe median concentrations of total PBDE and PCB congeners in the hypothyroxinemic group were 660 and 1,371 ng/g lipid, respectively, which were higher than concentrations detected in the control group. However, logistic regression analysis determined that current concentrations of PBDEs and PCBs in canines were not significantly associated with hypothyroxinemia. BDE 183 was the only congener showing near significance (p = 0.068).ConclusionsPBDE and PCB congeners were detected in all canine samples confirming ongoing exposure to these pollutants. Because household dogs share the human environment, they may serve as biosentinels of human exposure to these contaminants. creator: Grace Lau creator: Kyla Walter creator: Philip Kass creator: Birgit Puschner uri: https://doi.org/10.7717/peerj.3780 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lau et al. title: The landscape of fear conceptual framework: definition and review of current applications and misuses link: https://peerj.com/articles/3772 last-modified: 2017-09-12 description: Landscapes of Fear (LOF), the spatially explicit distribution of perceived predation risk as seen by a population, is increasingly cited in ecological literature and has become a frequently used “buzz-word”. With the increase in popularity, it became necessary to clarify the definition for the term, suggest boundaries and propose a common framework for its use. The LOF, as a progeny of the “ecology of fear” conceptual framework, defines fear as the strategic manifestation of the cost-benefit analysis of food and safety tradeoffs. In addition to direct predation risk, the LOF is affected by individuals’ energetic-state, inter- and intra-specific competition and is constrained by the evolutionary history of each species. Herein, based on current applications of the LOF conceptual framework, I suggest the future research in this framework will be directed towards: (1) finding applied management uses as a trait defining a population’s habitat-use and habitat-suitability; (2) studying multi-dimensional distribution of risk-assessment through time and space; (3) studying variability between individuals within a population; (4) measuring eco-neurological implications of risk as a feature of environmental heterogeneity and (5) expanding temporal and spatial scales of empirical studies. creator: Sonny S. Bleicher uri: https://doi.org/10.7717/peerj.3772 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bleicher title: Habitat suitability—density relationship in an endangered woodland species: the case of the Blue Chaffinch (Fringilla polatzeki) link: https://peerj.com/articles/3771 last-modified: 2017-09-12 description: BackgroundUnderstanding constraints to the distribution of threatened species may help to ascertain whether there are other suitable sectors for reducing the risks associated with species that are recorded in only one protected locality, and to inform about the suitability of other areas for reintroduction or translocation programs.MethodsWe studied the Gran Canaria blue chaffinch (Fringilla polatzeki), a habitat specialist endemic of the Canary Islands restricted to the pine forest of Inagua, the only area where the species has been naturally present as a regular breeder in the last 25 years. A suitability distribution model using occurrences with demographic relevance (i.e., nest locations of successful breeding attempts analysed using boosted classification trees) was built considering orographic, climatic and habitat structure predictors. By means of a standardized survey program we monitored the yearly abundance of the species in 100 sectors since the declaration of Inagua as a Strict Nature Reserve in 1994.ResultsThe variables with the highest relative importance in blue chaffinch habitat preferences were pine height, tree cover, altitude, and rainfall during the driest trimester (July–September). The observed local abundance of the blue chaffinch in Inagua (survey data) was significantly correlated with habitat suitability derived from modelling the location of successful nesting attempts (using linear and quantile regressions). The outcomes of the habitat suitability model were used to quantify the suitability of other natural, historic, pine forests of Gran Canaria. Tamadaba is the forest with most suitable woodland patches for the species. We estimated a population size of 195–430 blue chaffinches in Inagua since 2011 (95% CI), the smallest population size of a woodland passerine in the Western Palearctic.DiscussionHabitat suitability obtained from modelling the location of successful breeding attempts is a good surrogate of the observed local abundance during the reproductive season. The outcomes of these models can be used for the identification of potential areas for the reintroduction of the species in other suitable pine forests and to inform forest management practices. creator: Luis M. Carrascal creator: Ángel C. Moreno creator: Alejandro Delgado creator: Víctor Suárez creator: Domingo Trujillo uri: https://doi.org/10.7717/peerj.3771 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Carrascal et al. title: Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data link: https://peerj.com/articles/3729 last-modified: 2017-09-12 description: High sensitivity methods such as next generation sequencing and polymerase chain reaction (PCR) are adversely impacted by organismal and DNA contaminants. Current methods for detecting contaminants in microbial materials (genomic DNA and cultures) are not sensitive enough and require either a known or culturable contaminant. Whole genome sequencing (WGS) is a promising approach for detecting contaminants due to its sensitivity and lack of need for a priori assumptions about the contaminant. Prior to applying WGS, we must first understand its limitations for detecting contaminants and potential for false positives. Herein we demonstrate and characterize a WGS-based approach to detect organismal contaminants using an existing metagenomic taxonomic classification algorithm. Simulated WGS datasets from ten genera as individuals and binary mixtures of eight organisms at varying ratios were analyzed to evaluate the role of contaminant concentration and taxonomy on detection. For the individual genomes the false positive contaminants reported depended on the genus, with Staphylococcus, Escherichia, and Shigella having the highest proportion of false positives. For nearly all binary mixtures the contaminant was detected in the in-silico datasets at the equivalent of 1 in 1,000 cells, though F. tularensis was not detected in any of the simulated contaminant mixtures and Y. pestis was only detected at the equivalent of one in 10 cells. Once a WGS method for detecting contaminants is characterized, it can be applied to evaluate microbial material purity, in efforts to ensure that contaminants are characterized in microbial materials used to validate pathogen detection assays, generate genome assemblies for database submission, and benchmark sequencing methods. creator: Nathan D. Olson creator: Justin M. Zook creator: Jayne B. Morrow creator: Nancy J. Lin uri: https://doi.org/10.7717/peerj.3729 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Adaptations to different habitats in sexual and asexual populations of parasitoid wasps: a meta-analysis link: https://peerj.com/articles/3699 last-modified: 2017-09-12 description: BackgroundCoexistence of sexual and asexual populations remains a key question in evolutionary ecology. We address the question how an asexual and a sexual form of the parasitoid Venturia canescens can coexist in southern Europe. We test the hypothesis that both forms are adapted to different habitats within their area of distribution. Sexuals inhabit natural environments that are highly unpredictable, and where density of wasps and their hosts is low and patchily distributed. Asexuals instead are common in anthropic environments (e.g., grain stores) where host outbreaks offer periods when egg-load is the main constraint on reproductive output.MethodsWe present a meta-analysis of known adaptations to these habitats. Differences in behavior, physiology and life-history traits between sexual and asexual wasps were standardized in term of effect size (Cohen’s d value; Cohen, 1988).ResultsSeeking consilience from the differences between multiple traits, we found that sexuals invest more in longevity at the expense of egg-load, are more mobile, and display higher plasticity in response to thermal variability than asexual counterparts.DiscussionThus, each form has consistent multiple adaptations to the ecological circumstances in the contrasting environments. creator: Isabelle Amat creator: Jacques J.M. van Alphen creator: Alex Kacelnik creator: Emmanuel Desouhant creator: Carlos Bernstein uri: https://doi.org/10.7717/peerj.3699 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Amat et al. title: The evolutionary history of plant T2/S-type ribonucleases link: https://peerj.com/articles/3790 last-modified: 2017-09-11 description: A growing number of T2/S-RNases are being discovered in plant genomes. Members of this protein family have a variety of known functions, but the vast majority are still uncharacterized. We present data and analyses of phylogenetic relationships among T2/S-RNases, and pay special attention to the group that contains the female component of the most widespread system of self-incompatibility in flowering plants. The returned emphasis on the initially identified component of this mechanism yields important conjectures about its evolutionary context. First, we find that the clade involved in self-rejection (class III) is found exclusively in core eudicots, while the remaining clades contain members from other vascular plants. Second, certain features, such as intron patterns, isoelectric point, and conserved amino acid regions, help differentiate S-RNases, which are necessary for expression of self-incompatibility, from other T2/S-RNase family members. Third, we devise and present a set of approaches to clarify new S-RNase candidates from existing genome assemblies. We use genomic features to identify putative functional and relictual S-loci in genomes of plants with unknown mechanisms of self-incompatibility. The widespread occurrence of possible relicts suggests that the loss of functional self-incompatibility may leave traces long after the fact, and that this manner of molecular fossil-like data could be an important source of information about the history and distribution of both RNase-based and other mechanisms of self-incompatibility. Finally, we release a public resource intended to aid the search for S-locus RNases, and help provide increasingly detailed information about their taxonomic distribution. creator: Karolis Ramanauskas creator: Boris Igić uri: https://doi.org/10.7717/peerj.3790 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ramanauskas and Igić title: Biochemical and structural characterization of a novel arginine kinase from the spider Polybetes pythagoricus link: https://peerj.com/articles/3787 last-modified: 2017-09-11 description: Energy buffering systems are key for homeostasis during variations in energy supply. Spiders are the most important predators for insects and therefore key in terrestrial ecosystems. From biomedical interest, spiders are important for their venoms and as a source of potent allergens, such as arginine kinase (AK, EC 2.7.3.3). AK is an enzyme crucial for energy metabolism, keeping the pool of phosphagens in invertebrates, and also an allergen for humans. In this work, we studied AK from the Argentininan spider Polybetes pythagoricus (PpAK), from its complementary DNA to the crystal structure. The PpAK cDNA from muscle was cloned, and it is comprised of 1068 nucleotides that encode a 384-amino acids protein, similar to other invertebrate AKs. The apparent Michaelis-Menten kinetic constant (Km) was 1.7 mM with a kcat of 75 s−1. Two crystal structures are presented, the apoPvAK and PpAK bound to arginine, both in the open conformation with the active site lid (residues 310–320) completely disordered. The guanidino group binding site in the apo structure appears to be organized to accept the arginine substrate. Finally, these results contribute to knowledge of mechanistic details of the function of arginine kinase. creator: Aldana Laino creator: Alonso A. Lopez-Zavala creator: Karina D. Garcia-Orozco creator: Jesus S. Carrasco-Miranda creator: Marianela Santana creator: Vivian Stojanoff creator: Rogerio R. Sotelo-Mundo creator: Carlos Fernando Garcia uri: https://doi.org/10.7717/peerj.3787 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Laino et al. title: Genome-wide identification of the MADS-box transcription factor family in pear (Pyrus bretschneideri) reveals evolution and functional divergence link: https://peerj.com/articles/3776 last-modified: 2017-09-11 description: MADS-box transcription factors play significant roles in plant developmental processes such as floral organ conformation, flowering time, and fruit development. Pear (Pyrus), as the third-most crucial temperate fruit crop, has been fully sequenced. However, there is limited information about the MADS family and its functional divergence in pear. In this study, a total of 95 MADS-box genes were identified in the pear genome, and classified into two types by phylogenetic analysis. Type I MADS-box genes were divided into three subfamilies and type II genes into 14 subfamilies. Synteny analysis suggested that whole-genome duplications have played key roles in the expansion of the MADS family, followed by rearrangement events. Purifying selection was the primary force driving MADS-box gene evolution in pear, and one gene pairs presented three codon sites under positive selection. Full-scale expression information for PbrMADS genes in vegetative and reproductive organs was provided and proved by transcriptional and reverse transcription PCR analysis. Furthermore, the PbrMADS11(12) gene, together with partners PbMYB10 and PbbHLH3 was confirmed to activate the promoters of the structural genes in anthocyanin pathway of red pear through dual luciferase assay. In addition, the PbrMADS11 and PbrMADS12 were deduced involving in the regulation of anthocyanin synthesis response to light and temperature changes. These results provide a solid foundation for future functional analysis of PbrMADS genes in different biological processes, especially of pigmentation in pear. creator: Runze Wang creator: Meiling Ming creator: Jiaming Li creator: Dongqing Shi creator: Xin Qiao creator: Leiting Li creator: Shaoling Zhang creator: Jun Wu uri: https://doi.org/10.7717/peerj.3776 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau link: https://peerj.com/articles/3770 last-modified: 2017-09-11 description: The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species. creator: Bin Wang creator: Feng Xie creator: Jiannan Li creator: Gang Wang creator: Cheng Li creator: Jianping Jiang uri: https://doi.org/10.7717/peerj.3770 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Wang et al. title: Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine link: https://peerj.com/articles/3698 last-modified: 2017-09-11 description: BackgroundThe microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.MethodsThe genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC.ResultsWe present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.DiscussionThis revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available. creator: Jacoline Gerritsen creator: Bastian Hornung creator: Bernadette Renckens creator: Sacha A.F.T. van Hijum creator: Vitor A.P. Martins dos Santos creator: Ger T. Rijkers creator: Peter J. Schaap creator: Willem M. de Vos creator: Hauke Smidt uri: https://doi.org/10.7717/peerj.3698 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gerritsen et al. title: Development and evaluation of rapid novel isothermal amplification assays for important veterinary pathogens: Chlamydia psittaci and Chlamydia pecorum link: https://peerj.com/articles/3799 last-modified: 2017-09-08 description: BackgroundChlamydia psittaci and Chlamydia pecorum are important veterinary pathogens, with the former also being responsible for zoonoses, and the latter adversely affecting koala populations in Australia and livestock globally. The rapid detection of these organisms is still challenging, particularly at the point-of-care (POC). In the present study, we developed and evaluated rapid, sensitive and robust C. psittaci-specific and C. pecorum-specific Loop Mediated Isothermal Amplification (LAMP) assays for detection of these pathogens.Methods and MaterialsThe LAMP assays, performed in a Genie III real-time fluorometer, targeted a 263 bp region of the C. psittaci-specific Cps_0607 gene or a 209 bp region of a C. pecorum-specific conserved gene CpecG_0573, and were evaluated using a range of samples previously screened using species-specific quantitative PCRs (qPCRs). Species-specificity for C. psittaci and C. pecorum LAMP targets was tested against DNA samples from related chlamydial species and a range of other bacteria. In order to evaluate pathogen detection in clinical samples, C. psittaci LAMP was evaluated using a total of 26 DNA extracts from clinical samples from equine and avian hosts, while for C. pecorum LAMP, we tested a total of 63 DNA extracts from clinical samples from koala, sheep and cattle hosts. A subset of 36 C. pecorum samples was also tested in a thermal cycler (instead of a real-time fluorometer) using newly developed LAMP and results were determined as an end point detection. We also evaluated rapid swab processing (without DNA extraction) to assess the robustness of these assays.ResultsBoth LAMP assays were demonstrated to species-specific, highly reproducible and to be able to detect as little as 10 genome copy number/reaction, with a mean amplification time of 14 and 24 min for C. psittaci and C. pecorum, respectively. When testing clinical samples, the overall congruence between the newly developed LAMP assays and qPCR was 92.3% for C. psittaci (91.7% sensitivity and 92.9% specificity); and 84.1% for C. pecorum (90.6% sensitivity and 77.4% specificity). For a subset of 36 C. pecorum samples tested in a thermal cycler using newly developed LAMP, we observed 34/36 (94.4%) samples result being congruent between LAMP performed in fluorometer and in thermal cycler. Rapid swab processing method evaluated in this study also allows for chlamydial DNA detection using LAMP.DiscussionIn this study, we describe the development of novel, rapid and robust C. psittaci-specific and C. pecorum-specific LAMP assays that are able to detect these bacteria in clinical samples in either the laboratory or POC settings. With further development and a focus on the preparation of these assays at the POC, it is anticipated that both tests may fill an important niche in the repertoire of ancillary diagnostic tools available to clinicians. creator: Martina Jelocnik creator: Md. Mominul Islam creator: Danielle Madden creator: Cheryl Jenkins creator: James Branley creator: Scott Carver creator: Adam Polkinghorne uri: https://doi.org/10.7717/peerj.3799 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Jelocnik et al. title: Variance component testing for identifying differentially expressed genes in RNA-seq data link: https://peerj.com/articles/3797 last-modified: 2017-09-08 description: RNA sequencing (RNA-Seq) enables the measurement and comparison of gene expression with isoform-level quantification. Differences in the effect of each isoform may make traditional methods, which aggregate isoforms, ineffective. Here, we introduce a variance component-based test that can jointly test multiple isoforms of one gene to identify differentially expressed (DE) genes, especially those with isoforms that have differential effects. We model isoform-level expression data from RNA-Seq using a negative binomial distribution and consider the baseline abundance of isoforms and their effects as two random terms. Our approach tests the global null hypothesis of no difference in any of the isoforms. The null distribution of the derived score statistic is investigated using empirical and theoretical methods. The results of simulations suggest that the performance of the proposed set test is superior to that of traditional algorithms and almost reaches optimal power when the variance of covariates is large. This method is also applied to analyze real data. Our algorithm, as a supplement to traditional algorithms, is superior at selecting DE genes with sparse or opposite effects for isoforms. creator: Sheng Yang creator: Fang Shao creator: Weiwei Duan creator: Yang Zhao creator: Feng Chen uri: https://doi.org/10.7717/peerj.3797 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yang et al. title: Age, growth, mortality and reproductive seasonality of jolthead porgy, Calamus bajonado, from Florida waters link: https://peerj.com/articles/3774 last-modified: 2017-09-08 description: Ages of jolthead porgy (Calamus bajonado Schneider 1801) (n = 635) from Florida commercial and recreational fisheries from 2008–2016 were determined using sectioned sagittal otoliths. We determined, using edge-type analysis, that opaque zones were annular, forming March–June (peaking in April). Jolthead porgy ranged from 1–13 years, and the largest fish measured 680 mm TL (total length, mm). Body size relationships for jolthead porgy were TL = 1.09FL + 20.44 (n = 622, r2 = 0.99), FL = 0.90 TL –14.26 (n = 622, r2 = 0.99), and W = 1.1 × 10−5 TL3.06 (n = 577), where W is total weight (grams, g) and FL is fork length (mm). The von Bertalanffy growth equation for jolthead porgy was Lt = 737(1 − e−0.14(t+2.02)) (n = 635). Point estimate of natural mortality was M = 0.32, while age-specific estimates of M ranged from 0.58–0.17 y−1 for ages 1–13. Catch curve analysis estimated the instantaneous rate of total mortality Z = 0.70, while instantaneous rate of fishing mortality F was 0.38. Macroscopic staging of female gonads indicated the presence of hydrated oocytes from December–March, and GSI data indicates that peak spawning in females occurs during March. This study presents the first published findings of life history parameters for jolthead porgy from the Atlantic waters off the southeastern United States. creator: Michael L. Burton creator: Jennifer C. Potts creator: Jordan Page creator: Ariel Poholek uri: https://doi.org/10.7717/peerj.3774 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Burton et al. title: Current practice in the management of new-onset atrial fibrillation in critically ill patients: a UK-wide survey link: https://peerj.com/articles/3716 last-modified: 2017-09-08 description: BackgroundNew-onset atrial fibrillation (AF) is the most common arrhythmia in critically ill patients. Although evidence base and expert consensus opinion for management have been summarised in several international guidelines, no specific considerations for critically ill patients have been included. We aimed to establish current practice of management of critically ill patients with new-onset AF.MethodsWe designed a short user-friendly online questionnaire. All members of the Intensive Care Society were invited via email containing a link to the questionnaire, which comprised 21 questions. The online survey was conducted between November 2016 and December 2016.ResultsThe response rate was 397/3152 (12.6%). The majority of respondents (81.1%) worked in mixed Intensive Care Units and were consultants (71.8%). Most respondents (39.5%) would start intervention on patients with fast new-onset AF and stable blood pressure at a heart rate between 120 and 139 beats/min. However, 34.8% of participants would treat all patients who developed new-onset fast AF. Amiodarone and beta-blockers (80.9% and 11.6% of answers) were the most commonly used anti-arrhythmics. A total of 63.8% of respondents do not regularly anti-coagulate critically ill patients with new-onset fast AF, while 30.8% anti-coagulate within 72 hours. A total of 68.0% of survey respondents do not routinely use stroke risk scores in critically ill patients with new-onset AF. A total of 85.4% of participants would consider taking part in a clinical trial investigating treatment of new-onset fast AF in the critically ill.DiscussionOur results suggest a considerable disparity between contemporary practice of management of new-onset AF in critical illness and treatment recommendations for the general patient population suffering from AF, particularly with regard to anti-arrhythmics and anti-coagulation used. Amongst intensivists, there is a substantial interest in research for management of new-onset AF in critically ill patients. creator: Chung Shen Chean creator: Daniel McAuley creator: Anthony Gordon creator: Ingeborg Dorothea Welters uri: https://doi.org/10.7717/peerj.3716 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chean et al. title: Early-branching euteleost relationships: areas of congruence between concatenation and coalescent model inferences link: https://peerj.com/articles/3548 last-modified: 2017-09-08 description: Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements. We report and examine a dataset of thirty-four OTUs with 17,957 aligned characters from fifty-three nuclear loci. Phylogenetic analysis is conducted in concatenated, joint gene trees and species tree estimation and summary coalescent frameworks. All analytical frameworks yield supporting evidence for existing hypotheses of relationship for the placement of Lepidogalaxias salamandroides, monophyly of the Stomiatii and the presence of an esociform + salmonid clade. Lepidogalaxias salamandroides and the Esociformes + Salmoniformes are successive sister lineages to all other euteleosts in the majority of analyses. The concatenated and joint gene trees and species tree analysis types produce high support values for this arrangement. However, inter-relationships of Argentiniformes, Stomiatii and Neoteleostei remain uncertain as they varied by analysis type while receiving strong and contradictory indices of support. Topological differences between analysis types are also apparent within the otomorph and the percomorph taxa in the data set. Our results identify concordant areas with strong support for relationships within and between early-branching euteleost lineages but they also reveal limitations in the ability of larger datasets to conclusively resolve other aspects of that phylogeny. creator: Matthew A. Campbell creator: Michael E. Alfaro creator: Max Belasco creator: J. Andrés López uri: https://doi.org/10.7717/peerj.3548 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Campbell et al. title: A comparison of the morphological and biochemical characteristics of Chlorella sorokiniana and Chlorella zofingiensis cultured under photoautotrophic and mixotrophic conditions link: https://peerj.com/articles/3473 last-modified: 2017-09-08 description: The responses of two species of microalgae, Chlorella sorokiniana and Chlorella zofingiensis, were compared regarding their morphological and biochemical properties under photoautotrophic and mixotrophic conditions. These microalgae were cultured under both conditions, and their crude ethanolic extracts were examined for their pigment and total phenolic contents. In addition, the microalgae’s antioxidant activities were determined using a DPPH radical scavenging assay and a ferric reducing antioxidant power (FRAP) assay. Both strains showed increases in cell size due to the accumulation of lipid bodies and other cell contents, especially carotenoids, under the mixotrophic condition. Notably, reductions in phenolic and chlorophyll contents were observed to be associated with lower antioxidant activity. C. zofingiensis compared with C. sorokiniana, demonstrated higher antioxidant activity and carotenoid content. This study showed that different species of microalgae responded differently to varying conditions by producing different types of metabolites, as evidenced by the production of higher levels of phenolic compounds under the photoautotrophic condition and the production of the same levels of carotenoids under both photoautotrophic and mixotrophic conditions. creator: Siti Nor Ani Azaman creator: Norio Nagao creator: Fatimah M. Yusoff creator: Sheau Wei Tan creator: Swee Keong Yeap uri: https://doi.org/10.7717/peerj.3473 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Azaman et al. title: MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes link: https://peerj.com/articles/3788 last-modified: 2017-09-07 description: Clustered regularly interspaced short palindromic repeat (CRISPR) systems are the adaptive immune systems of bacteria and archaea against viral infection. While CRISPRs have been exploited as a tool for genetic engineering, their spacer sequences can also provide valuable insights into microbial ecology by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR spacer detection tool (Metagenomic CRISPR Reference-Aided Search Tool—MetaCRAST) that constrains searches based on user-specified direct repeats (DRs). These DRs could be expected from assembly or taxonomic profiles of metagenomes. We compared the performance of MetaCRAST to those of two existing metagenomic CRISPR detection tools—Crass and MinCED—using both real and simulated acid mine drainage (AMD) and enhanced biological phosphorus removal (EBPR) metagenomes. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to the de novo CRISPR detection methods Crass and MinCED. Evaluation on simulated metagenomes show it performs better than de novo tools for Illumina metagenomes and comparably for 454 metagenomes. It also has comparable performance dependence on read length and community composition, run time, and accuracy to these tools. MetaCRAST is implemented in Perl, parallelizable through the Many Core Engine (MCE), and takes metagenomic sequence reads and direct repeat queries (FASTA or FASTQ) as input. It is freely available for download at https://github.com/molleraj/MetaCRAST. creator: Abraham G. Moller creator: Chun Liang uri: https://doi.org/10.7717/peerj.3788 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Moller and Liang title: Lectins: an effective tool for screening of potential cancer biomarkers link: https://peerj.com/articles/3784 last-modified: 2017-09-07 description: In recent years, the use of lectins for screening of potential biomarkers has gained increased importance in cancer research, given the development in glycobiology that highlights altered structural changes of glycans in cancer associated processes. Lectins, having the properties of recognizing specific carbohydrate moieties of glycoconjugates, have become an effective tool for detection of new cancer biomarkers in complex bodily fluids and tissues. The specificity of lectins provides an added advantage of selecting peptides that are differently glycosylated and aberrantly expressed in cancer patients, many of which are not possibly detected using conventional methods because of their low abundance in bodily fluids. When coupled with mass spectrometry, research utilizing lectins, which are mainly from plants and fungi, has led to identification of numerous potential cancer biomarkers that may be used in the future. This article reviews lectin-based methods that are commonly adopted in cancer biomarker discovery research. creator: Onn Haji Hashim creator: Jaime Jacqueline Jayapalan creator: Cheng-Siang Lee uri: https://doi.org/10.7717/peerj.3784 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hashim et al. title: Particle bombardment and subcellular protein localization analysis in the aquatic plant Egeria densa link: https://peerj.com/articles/3779 last-modified: 2017-09-07 description: Particle bombardment is a powerful and relatively easy method for transient expression of genes of interest in plant cells, especially those that are recalcitrant to other transformation methods. This method has facilitated numerous analyses of subcellular localization of fluorescent fusion protein constructs. Particle bombardment delivers genes to the first layer of plant tissue. In leaves of higher plants, epidermal cells are the first cell layer. Many studies have used the epidermal cell layer of onion bulb (Allium cepa) as the experimental tissue, because these cells are relatively large. However, onion epidermal cells lack developed plastids (i.e., chloroplasts), thereby precluding subcellular localization analysis of chloroplastic proteins. In this study, we developed a protocol for particle bombardment of the aquatic plant Egeria densa, and showed that it is a useful system for subcellular localization analysis of higher plant proteins. E. densa leaflets contain only two cell layers, and cells in the adaxial layer are sufficiently large for observation. The cells in both layers contain well-developed chloroplasts. We fused fluorescent proteins to conventional plant localization signals for the nucleus, cytosol, mitochondria, peroxisome, and chloroplast, and used particle bombardment to transiently express these fusion constructs in E. densa leaves. The plant subcellular localization signals functioned normally and displayed the expected distributions in transiently transformed E. densa cells, and even chloroplastic structures could be clearly visualized. creator: Yasuhide Osaki creator: Yutaka Kodama uri: https://doi.org/10.7717/peerj.3779 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Osaki and Kodama title: Impact of litter quantity on the soil bacteria community during the decomposition of Quercus wutaishanica litter link: https://peerj.com/articles/3777 last-modified: 2017-09-07 description: The forest ecosystem is the main component of terrestrial ecosystems. The global climate and the functions and processes of soil microbes in the ecosystem are all influenced by litter decomposition. The effects of litter decomposition on the abundance of soil microorganisms remain unknown. Here, we analyzed soil bacterial communities during the litter decomposition process in an incubation experiment under treatment with different litter quantities based on annual litterfall data (normal quantity, 200 g/(m2/yr); double quantity, 400 g/(m2/yr) and control, no litter). The results showed that litter quantity had significant effects on soil carbon fractions, nitrogen fractions, and bacterial community compositions, but significant differences were not found in the soil bacterial diversity. The normal litter quantity enhanced the relative abundance of Actinobacteria and Firmicutes and reduced the relative abundance of Bacteroidetes, Plantctomycets and Nitrospiare. The Beta-, Gamma-, and Deltaproteobacteria were significantly less abundant in the normal quantity litter addition treatment, and were subsequently more abundant in the double quantity litter addition treatment. The bacterial communities transitioned from Proteobacteria-dominant (Beta-, Gamma-, and Delta) to Actinobacteria-dominant during the decomposition of the normal quantity of litter. A cluster analysis showed that the double litter treatment and the control had similar bacterial community compositions. These results suggested that the double quantity litter limited the shift of the soil bacterial community. Our results indicate that litter decomposition alters bacterial dynamics under the accumulation of litter during the vegetation restoration process, which provides important significant guidelines for the management of forest ecosystems. creator: Quanchao Zeng creator: Yang Liu creator: Shaoshan An uri: https://doi.org/10.7717/peerj.3777 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zeng et al. title: Anthropometric, physical function and general health markers of Masters athletes: a cross-sectional study link: https://peerj.com/articles/3768 last-modified: 2017-09-07 description: Once the general decline in muscle mass, muscle strength and physical performance falls below specific thresholds, the middle aged or older adult will be diagnosed as having sarcopenia (a loss of skeletal muscle mass and strength). Sarcopenia contributes to a range of adverse events in older age including disability, hospitalisation, institutionalisation and falls. One potentially relevant but understudied population for sarcopenia researchers would be Masters athletes. Masters sport is becoming more common as it allows athletes (typically 40 years and older) the opportunity to participate in individual and/or team sports against individuals of similar age. This study examined a variety of measures of anthropometric, physical function and general health markers in the male and female Masters athletes who competed at the 2014 Pan Pacific Masters Games held on the Gold Coast, Australia. Bioelectrical impedance analysis was used to collect body fat percentage, fat mass and fat-free mass; with body mass, height, body mass index (BMI) and sarcopenic status also recorded. Physical function was quantified by handgrip strength and habitual walking speed; with general health described by the number of chronic diseases and prescribed medications. Between group analyses utilised ANOVA and Tukey’s post-hoc tests to examine the effect of age group (40–49, 50–59, 60–69 and >70 years old) on the outcome measures for the entire sample as well as the male and female sub-groups. A total of 156 athletes (78 male, 78 female; mean 55.7 years) provided informed consent to participate in this study. These athletes possessed substantially better anthropometric, physical function and general health characteristics than the literature for their less physically active age-matched peers. No Masters athletes were categorised as being sarcopenic, although one participant had below normal physical performance and six participants had below normal muscle strength. In contrast, significant age-related reductions in handgrip strength and increases in the number of chronic diseases and prescribed medications were observed for the overall cohort as well as the male and female sub-groups. Nevertheless, even those aged over 70 years only averaged one chronic disease and one prescribed medication. These results may suggest that participation in Masters sport helps to maintain anthropometry, physical function and general health in middle-aged and older adults. However, it is also possible that only healthier middle-aged and older adults with favourable body composition and physical function may be able to participate in Masters sport. Future research should therefore utilise longitudinal research designs to determine the health and functional benefits of Master sports participation for middle-aged and older adults. creator: Samantha Fien creator: Mike Climstein creator: Clodagh Quilter creator: Georgina Buckley creator: Timothy Henwood creator: Josie Grigg creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.3768 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Fien et al. title: Contrast based circular approximation for accurate and robust optic disc segmentation in retinal images link: https://peerj.com/articles/3763 last-modified: 2017-09-07 description: A new method for automatic optic disc localization and segmentation is presented. The localization procedure combines vascular and brightness information to provide the best estimate of the optic disc center which is the starting point for the segmentation algorithm. A detection rate of 99.58% and 100% was achieved for the Messidor and ONHSD databases, respectively. A simple circular approximation to the optic disc boundary is proposed based on the maximum average contrast between the inner and outer ring of a circle centered on the estimated location. An average overlap coefficient of 0.890 and 0.865 was achieved for the same datasets, outperforming other state of the art methods. The results obtained confirm the advantages of using a simple circular model under non-ideal conditions as opposed to more complex deformable models. creator: Jose Sigut creator: Omar Nunez creator: Francisco Fumero creator: Marta Gonzalez creator: Rafael Arnay uri: https://doi.org/10.7717/peerj.3763 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sigut et al. title: Is there genetic variation in mycorrhization of Medicago truncatula? link: https://peerj.com/articles/3713 last-modified: 2017-09-07 description: Differences in the plant’s response among ecotypes or accessions are often used to identify molecular markers for the respective process. In order to analyze genetic diversity of Medicago truncatula in respect to interaction with the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis, mycorrhizal colonization was evaluated in 32 lines of the nested core collection representing the genetic diversity of the SARDI collection. All studied lines and the reference line Jemalong A17 were inoculated with R. irregularis and the mycorrhization rate was determined at three time points after inoculation. There were, however, no reliable and consistent differences in mycorrhization rates among all lines. To circumvent possible overlay of potential differences by use of the highly effective inoculum, native sandy soil was used in an independent experiment. Here, significant differences in mycorrhization rates among few of the lines were detectable, but the overall high variability in the mycorrhization rate hindered clear conclusions. To narrow down the number of lines to be tested in more detail, root system architecture (RSA) of in vitro-grown seedlings of all lines under two different phosphate (Pi) supply condition was determined in terms of primary root length and number of lateral roots. Under high Pi supply (100 µM), only minor differences were observed, whereas in response to Pi-limitation (3 µM) several lines exhibited a drastically changed number of lateral roots. Five lines showing the highest alterations or deviations in RSA were selected and inoculated with R. irregularis using two different Pi-fertilization regimes with either 13 mM or 3 mM Pi. Mycorrhization rate of these lines was checked in detail by molecular markers, such as transcript levels of RiTubulin and MtPT4. Under high phosphate supply, the ecotypes L000368 and L000555 exhibited slightly increased fungal colonization and more functional arbuscules, respectively. To address the question, whether capability for mycorrhizal colonization might be correlated to general invasion by microorganisms, selected lines were checked for infection by the root rot causing pathogen, Aphanoymces euteiches. The mycorrhizal colonization phenotype, however, did not correlate with the resistance phenotype upon infection with two strains of A. euteiches as L000368 showed partial resistance and L000555 exhibited high susceptibility as determined by quantification of A. euteiches rRNA within infected roots. Although there is genetic diversity in respect to pathogen infection, genetic diversity in mycorrhizal colonization of M. truncatula is rather low and it will be rather difficult to use it as a trait to access genetic markers. creator: Dorothée Dreher creator: Heena Yadav creator: Sindy Zander creator: Bettina Hause uri: https://doi.org/10.7717/peerj.3713 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dreher et al. title: Divergence of compost extract and bio-organic manure effects on lucerne plant and soil link: https://peerj.com/articles/3775 last-modified: 2017-09-06 description: AimApplication of organic materials into agricultural systems enhances plant growth and yields, and improves soil fertility and structure. This study aimed to examine the effects of “compost extract (CE)”, a soil conditioner, and bio-organic manure (BOM) on the growth of lucerne (Medicago sativa), and compare the efficiency between BOM (including numbers of microorganisms) and CE (including no added microorganisms).MethodA greenhouse experiment was conducted with four soil amendment treatments (control, BOM, CE and CEBOM), and was arranged in a completely randomized design with 10 replicates for each treatment. Plant biomass, nutritive value and rhizobia efficacy as well as soil characteristics were monitored.ResultCE rather than BOM application showed a positive effect on plant growth and soil properties when compared with the control. Lucerne nodulation responded equally to CE addition and rhizobium inoculation. CE alone and in combination with BOM significantly increased plant growth and soil microbial activities and improved soil structure. The synergistic effects of CE and BOM indicate that applying CE and BOM together could increase their efficiency, leading to higher economic returns and improved soil health. However, CE alone is more effective for legume growth since nodulation was suppressed by nitrogen input from BOM. CE had a higher efficiency than BOM for enriching soil indigenous microorganisms instead of adding microorganisms and favouring plant nodulation. creator: Haiyan Ren creator: Jian Hu creator: Yifei Hu creator: Gaowen Yang creator: Yingjun Zhang uri: https://doi.org/10.7717/peerj.3775 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ren et al. title: Canopy soil bacterial communities altered by severing host tree limbs link: https://peerj.com/articles/3773 last-modified: 2017-09-06 description: Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities. creator: Cody R. Dangerfield creator: Nalini M. Nadkarni creator: William J. Brazelton uri: https://doi.org/10.7717/peerj.3773 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dangerfield et al. title: Re-examination of the contribution of substrates to energy expenditure during high-intensity intermittent exercise in endurance athletes link: https://peerj.com/articles/3769 last-modified: 2017-09-06 description: BackgroundIt has been believed that the contribution of fat oxidation to total energy expenditure is becoming negligible at higher exercise intensities (about 85% VO2max). The aim of the present study was to examine the changes in substrate oxidation during high-intensity interval exercise in young adult men.MethodsA total of 18 healthy well-trained (aged 19.60 ± 0.54 years, BMI = 22.19 ± 0.64 kg/m2, n = 10) and untrained (aged 20.25 ± 0.41 years, BMI = 22.78 ± 0.38 kg/m2, n = 8) young men volunteered to participate in this study. After an overnight fast, subjects were tested on a cycle ergometer and completed six 4-min bouts of cycling (at ∼80% VO2max) with 2 min of rests between intervals. Energy expenditure and the substrate oxidation rate were measured during the experiment by using indirect calorimetry. The blood lactate concentration was collected immediately after each interval workout.ResultsThe fat oxidation rate during each workout was significantly different between the untrained and the athlete groups (p < 0.05), and the carbohydrate (CHO) oxidation rate during the experiment was similar between groups (p > 0.05). Moreover, lactate concentration significantly increased in the untrained group (p < 0.05), whereas it did not significantly change in the athlete group during the workouts (p > 0.05). Fat contribution to energy expenditure was significantly higher in the athlete group (∼25%) than in the untrained group (∼2%).ConclusionsThe present study indicates that 17 times more fat oxidation was measured in the athlete group compared to the untrained group. However, the athletes had the same CHO oxidation rate as the recreationally active subjects during high-intensity intermittent exercise. Higher fat oxidation rate despite the same CHO oxidation rate may be related to higher performance in the trained group. creator: Zübeyde Aslankeser creator: Şükrü Serdar Balcı uri: https://doi.org/10.7717/peerj.3769 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Aslankeser and Balcı title: Status of gastrointestinal parasites in Red Panda of Nepal link: https://peerj.com/articles/3767 last-modified: 2017-09-06 description: Red pandas are known to be highly susceptible to endoparasites, which can have a prominent impact on the population dynamics of this endangered species. There are very limited published reports on prevalence and risk of parasites in wild populations of red panda, especially localized reports. This study attempts to provide an in-depth insight of the status of endoparasites in red pandas, which is critical for strengthening conservation efforts. A total of 272 fecal samples were collected through systematic sampling across the red panda distribution range in Nepal and coprological examination was completed using standard techniques. It was followed by an estimation of prevalence and mean intensity of parasites, as well as statistical analysis, which was carried out using R statistical software. Parasite prevalence was documented in 90.80% (n = 247) out of 272 samples examined which includes seven different species along with three genera of parasites belonging to Protozoans (3 species), Cestodes (1 genus, 1 species) and Nematodes (2 genera, 3 species). Nematodes predominated in all infected samples (87.62%). Prevalence of Ancyclostoma duodenale (n = 227, 70.06%), having a mean intensity of 3.45 ± 2.88 individuals per sample, was observed, followed by Ascaris lumbricoides (n = 19, 5.86%) and Entamoeba histolytica (n = 24, 7.41%). Eight variables for assessing the determinants of infestation were tested: protected areas; non-protected areas; aspect; elevation; slope; and distance to water sources, herding stations, and settlements. Only the settlement displayed significant association (β = −1534e−04, t =  − 2.192, p = 0.0293) though each parasite species displayed dissimilar association with different variables. This study indicates the urgent need of improving existing herding practice through habitat zonation, rotational grazing, medication of livestock, and prohibition of open defecation within and around red panda habitat. creator: Damber Bista creator: Saroj Shrestha creator: Ajaya Jang Kunwar creator: Sakshi Acharya creator: Shant Raj Jnawali creator: Krishna Prasad Acharya uri: https://doi.org/10.7717/peerj.3767 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bista et al. title: Laboratory evaluation of different formulations of Stress Coat® for slime production in goldfish (Carassius auratus) and koi (Cyprinus carpio) link: https://peerj.com/articles/3759 last-modified: 2017-09-06 description: A study was carried out to assess the effect of Stress Coat® on slime production in goldfish (Carassius auratus) and koi (Cyprinus carpio). The study also investigated histological changes that might be associated with slime producing cells, and wound healing in koi. Several formulations of Stress Coat® were investigated and the results showed that polyvinylpyrrolidone (PVP), also known as povidone, an ingredient of Stress Coat®, when used alone, showed significantly higher slime production in goldfish than salt and Stress Coat® without PVP after 25 h. The results also showed that koi treated with compounds containing PVP showed better wound healing than those not exposed to PVP. Histology results showed no difference between compounds tested with regards to density and number of slime producing cells. creator: Raghunath B. Shivappa creator: Larry S. Christian creator: Jerry M. Law creator: Gregory A. Lewbart uri: https://doi.org/10.7717/peerj.3759 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shivappa et al. title: Coral larvae for restoration and research: a large-scale method for rearing Acropora millepora larvae, inducing settlement, and establishing symbiosis link: https://peerj.com/articles/3732 last-modified: 2017-09-06 description: Here we describe an efficient and effective technique for rearing sexually-derived coral propagules from spawning through larval settlement and symbiont uptake with minimal impact on natural coral populations. We sought to maximize larval survival while minimizing expense and daily husbandry maintenance by experimentally determining optimized conditions and protocols for gamete fertilization, larval cultivation, induction of larval settlement by crustose coralline algae, and inoculation of newly settled juveniles with their dinoflagellate symbiont Symbiodinium. Larval rearing densities at or below 0.2 larvae mL−1 were found to maximize larval survival and settlement success in culture tanks while minimizing maintenance effort. Induction of larval settlement via the addition of a ground mixture of diverse crustose coralline algae (CCA) is recommended, given the challenging nature of in situ CCA identification and our finding that non settlement-inducing CCA assemblages do not inhibit larval settlement if suitable assemblages are present. Although order of magnitude differences in infectivity were found between common Great Barrier Reef Symbiodinium clades C and D, no significant differences in Symbiodinium uptake were observed between laboratory-cultured and wild-harvested symbionts in each case. The technique presented here for Acropora millepora can be adapted for research and restoration efforts in a wide range of broadcast spawning coral species. creator: F. Joseph Pollock creator: Sefano M. Katz creator: Jeroen A.J.M. van de Water creator: Sarah W. Davies creator: Margaux Hein creator: Gergely Torda creator: Mikhail V. Matz creator: Victor H. Beltran creator: Patrick Buerger creator: Eneour Puill-Stephan creator: David Abrego creator: David G. Bourne creator: Bette L. Willis uri: https://doi.org/10.7717/peerj.3732 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pollock et al. title: Fungi found in Mediterranean and North Sea sponges: how specific are they? link: https://peerj.com/articles/3722 last-modified: 2017-09-06 description: Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community. creator: Mohd Azrul Naim creator: Hauke Smidt creator: Detmer Sipkema uri: https://doi.org/10.7717/peerj.3722 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Naim et al. title: The semi-aquatic pondweed bugs of a Cretaceous swamp link: https://peerj.com/articles/3760 last-modified: 2017-09-05 description: Pondweed bugs (Hemiptera: Mesoveliidae), considered a sister group to all other Gerromorpha, are exceedingly rare as fossils. Therefore, each new discovery of a fossil mesoveliid is of high interest, giving new insight into their early evolutionary history and diversity and enabling the testing of their proposed relationships. Here, we report the discovery of new mesoveliid material from Spanish Lower Cretaceous (Albian) amber, which is the first such find in Spanish amber. To date, fossil records of this family only include one species from French Kimmeridgian as compression fossils, two species in French amber (Albian-Cenomanian boundary), and one in Dominican amber (Miocene). The discovery of two males and one female described and figured as Glaesivelia pulcherrima Sánchez-García & Solórzano Kraemer gen. et sp. n., and a single female described and figured as Iberovelia quisquilia Sánchez-García & Nel, gen. et sp. n., reveals novel combinations of traits related to some genera currently in the subfamily Mesoveliinae. Brief comments about challenges facing the study of fossil mesoveliids are provided, showing the necessity for a revision of the existing phylogenetic hypotheses. Some of the specimens were studied using infrared microscopy, a promising alternative to the systematic study of organisms preserved in amber that cannot be clearly visualised. The new taxa significantly expand the fossil record of the family and shed new light on its palaeoecology. The fossils indicate that Mesoveliidae were certainly diverse by the Cretaceous and that numerous tiny cryptic species living in humid terrestrial to marginal aquatic habitats remain to be discovered. Furthermore, the finding of several specimens as syninclusions suggests aggregative behaviour, thereby representing the earliest documented evidence of such ethology. creator: Alba Sánchez-García creator: André Nel creator: Antonio Arillo creator: Mónica M. Solórzano Kraemer uri: https://doi.org/10.7717/peerj.3760 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sánchez-García et al. title: Effects of tire leachate on the invasive mosquito Aedes albopictus and the native congener Aedes triseriatus link: https://peerj.com/articles/3756 last-modified: 2017-09-05 description: Discarded vehicle tire casings are an important artificial habitat for the developmental stages of numerous vector mosquitoes. Discarded vehicle tires degrade under ultraviolet light and leach numerous soluble metals (e.g., barium, cadmium, zinc) and organic substances (e.g., benzothiazole and its derivatives [BZTs], polyaromatic hydrocarbons [PAHs]) that could affect mosquito larvae that inhabit the tire casing. This study examined the relationship between soluble zinc, a common marker of tire leachate, on mosquito densities in tire habitats in the field, and tested the effects of tire leachate on the survival and development of newly hatched Aedes albopictus and Aedes triseriatus larvae in a controlled laboratory dose-response experiment. In the field, zinc concentrations were as high as 7.26 mg/L in a single tire and averaged as high as 2.39 (SE ± 1.17) mg/L among tires at a single site. Aedes albopictus (37/42 tires, 81.1%) and A. triseriatus (23/42, 54.8%) were the most widespread mosquito species, co-occurred in over half (22/42, 52.4%) of all tires, and A. triseriatus was only collected without A. albopictus in one tire. Aedes triseriatus was more strongly negatively associated with zinc concentration than A. albopictus, and another common mosquito, C. pipiens, which was found in 17 tires. In the laboratory experiment, A. albopictus per capita rate of population change (λ′) was over 1.0, indicating positive population growth, from 0–8.9 mg/L zinc concentration (0–10,000 mg/L tire leachate), but steeply declined to zero from 44.50–89.00 mg/L zinc (50,000–100,000 mg/L tire leachate). In contrast, A. triseriatus λ′ declined at the lower concentration of 0.05 mg/L zinc (100 mg/L tire leachate), and was zero at 0.45, 8.90, 44.50, and 89.00 mg/L zinc (500, 10,000, 50,000 and 100,000 mg/L tire leachate). These results indicate that tire leachate can have severe negative effects on populations of container-utilizing mosquitoes at concentrations commonly found in the field. Superior tolerance to tire leachate of A. albopictus compared to A. triseriatus, and possibly other native mosquito species, may have facilitated the replacement of these native species as A. albopictus has invaded North America and other regions around the world. creator: Oswaldo C. Villena creator: Ivana Terry creator: Kayoko Iwata creator: Edward R. Landa creator: Shannon L. LaDeau creator: Paul T. Leisnham uri: https://doi.org/10.7717/peerj.3756 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Villena et al. title: Quantitative comparison of the spreading and invasion of radial growth phase and metastatic melanoma cells in a three-dimensional human skin equivalent model link: https://peerj.com/articles/3754 last-modified: 2017-09-05 description: BackgroundStandard two-dimensional (2D) cell migration assays do not provide information about vertical invasion processes, which are critical for melanoma progression. We provide information about three-dimensional (3D) melanoma cell migration, proliferation and invasion in a 3D melanoma skin equivalent (MSE) model. In particular, we pay careful attention to compare the structure of the tissues in the MSE with similarly-prepared 3D human skin equivalent (HSE) models. The HSE model is identically prepared to the MSE model except that melanoma cells are omitted. Using the MSE model, we examine melanoma migration, proliferation and invasion from two different human melanoma cell lines. One cell line, WM35, is associated with the early phase of the disease where spreading is thought to be confined to the epidermis. The other cell line, SK-MEL-28, is associated with the later phase of the disease where spreading into the dermis is expected.Methods3D MSE and HSE models are constructed using human de-epidermised dermis (DED) prepared from skin tissue. Primary fibroblasts and primary keratinocytes are used in the MSE and HSE models to ensure the formation of a stratified epidermis, with a well-defined basement membrane. Radial spreading of cells across the surface of the HSE and MSE models is observed. Vertical invasion of melanoma cells downward through the skin is observed and measured using immunohistochemistry. All measurements of invasion are made at day 0, 9, 15 and 20, providing detailed time course data.ResultsBoth HSE and MSE models are similar to native skin in vivo, with a well-defined stratification of the epidermis that is separated from the dermis by a basement membrane. In the HSE and MSE we find fibroblast cells confined to the dermis, and differentiated keratinocytes in the epidermis. In the MSE, melanoma cells form colonies in the epidermis during the early part of the experiment. In the later stage of the experiment, the melanoma cells in the MSE invade deeper into the tissues. Interestingly, both the WM35 and SK-MEL-28 melanoma cells lead to a breakdown of the basement membrane and eventually enter the dermis. However, these two cell lines invade at different rates, with the SK-MEL-28 melanoma cells invading faster than the WM35 cells.DiscussionThe MSE and HSE models are a reliable platform for studying melanoma invasion in a 3D tissue that is similar to native human skin. Interestingly, we find that the WM35 cell line, that is thought to be associated with radial spreading only, is able to invade into the dermis. The vertical invasion of melanoma cells into the dermal region appears to be associated with a localised disruption of the basement membrane. Presenting our results in terms of time course data, along with images and quantitative measurements of the depth of invasion extends previous 3D work that has often been reported without these details. creator: Parvathi Haridas creator: Jacqui A. McGovern creator: Sean D.L. McElwain creator: Matthew J. Simpson uri: https://doi.org/10.7717/peerj.3754 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Haridas et al. title: Growth, stoichiometry and cell size; temperature and nutrient responses in haptophytes link: https://peerj.com/articles/3743 last-modified: 2017-09-05 description: Temperature and nutrients are key factors affecting the growth, cell size, and physiology of marine phytoplankton. In the ocean, temperature and nutrient availability often co-vary because temperature drives vertical stratification, which further controls nutrient upwelling. This makes it difficult to disentangle the effects of temperature and nutrients on phytoplankton purely from observational studies. In this study, we carried out a factorial experiment crossing two temperatures (13°and 19°C) with two growth regimes (P-limited, semi-continuous batch cultures [“−P”] and nutrient replete batch cultures in turbidostat mode [“+P”]) for three species of common marine haptophytes (Emiliania huxleyi, Chrysochromulina rotalis and Prymnesium polylepis) to address the effects of temperature and nutrient limitation on elemental content and stoichiometry (C:N:P), total RNA, cell size, and growth rate. We found that the main gradient in elemental content and RNA largely was related to nutrient regime and the resulting differences in growth rate and degree of P-limitation, and observed reduced cell volume-specific content of P and RNA (but also N and C in most cases) and higher N:P and C:P in the slow growing −P cultures compared to the fast growing +P cultures. P-limited cells also tended to be larger than nutrient replete cells. Contrary to other recent studies, we found lower N:P and C:P ratios at high temperature. Overall, elemental content and RNA increased with temperature, especially in the nutrient replete cultures. Notably, however, temperature had a weaker–and in some cases a negative–effect on elemental content and RNA under P-limitation. This interaction indicates that the effect of temperature on cellular composition may differ between nutrient replete and nutrient limited conditions, where cellular uptake and storage of excess nutrients may overshadow changes in resource allocation among the non-storage fractions of biomass (e.g. P-rich ribosomes and N-rich proteins). Cell size decreased at high temperature, which is in accordance with general observations. creator: Lars Fredrik Skau creator: Tom Andersen creator: Jan-Erik Thrane creator: Dag Olav Hessen uri: https://doi.org/10.7717/peerj.3743 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Skau et al. title: The contribution of Nintendo Wii Fit series in the field of health: a systematic review and meta-analysis link: https://peerj.com/articles/3600 last-modified: 2017-09-05 description: BackgroundWii Fit was originally designed as a health and fitness interactive training experience for the general public. There are, however, many examples of Wii Fit being utilized in clinical settings. This article aims to identify the contribution of Wii Fit in the field of health promotion and rehabilitation by: (1) identifying the health-related domains for which the Wii Fit series has been tested, (2) clarifying the effect of Wii Fit in those identified health-related domains and (3) quantifying this effect.MethodA systematic literature review was undertaken. The MEDLINE database and Games for Health Journal published content were explored using the search term “Wii-Fit.” Occurrences resulting from manual searches on Google and material suggested by experts in the field were also considered. Included articles were required to have measurements from Wii Fit activities for at least one relevant health indicator. The effect of Wii Fit interventions was assessed using meta-analyses for the following outcomes: activity-specific balance confidence score, Berg balance score (BBC) and time-up-and-go test (TUG).FindingsA total of 115 articles highlighted that the Wii Fit has been tested in numerous healthy and pathological populations. Out of these, only a few intervention studies have focused on the prevention of chronic diseases. A large proportion of the studies focus on balance training (N = 55). This systematic review highlights several potential benefits of Wii Fit interventions and these positive observations are supported by meta-analyses data (N = 25). For example, the BBC and the TUG respond to a similar extend to Wii Fit interventions compared with traditional training.ConclusionWii Fit has the potential to be used as a rehabilitation tool in different clinical situations. However, the current literature includes relatively few randomized controlled trials in each population. Further research is therefore required. creator: Julien Tripette creator: Haruka Murakami creator: Katie Rose Ryan creator: Yuji Ohta creator: Motohiko Miyachi uri: https://doi.org/10.7717/peerj.3600 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Tripette et al. title: Urbanization alters communities of flying arthropods in parks and gardens of a medium-sized city link: https://peerj.com/articles/3620 last-modified: 2017-09-04 description: Urbanization transforms undeveloped landscapes into built environments, causing changes in communities and ecological processes. Flying arthropods play important roles in these processes as pollinators, decomposers, and predators, and can be important in structuring food webs. The goal of this study was to identify associations between urbanization and the composition of communities of flying (and floating) arthropods within gardens and parks in a medium-sized mesic city. We predicted that flying arthropod abundance and diversity would respond strongly to percent impervious surface and distance to city center, measurements of urbanization. Flying arthropods were sampled from 30 gardens and parks along an urbanization gradient in Toledo, Ohio, during July and August 2016, using elevated pan traps. A variety of potential predictor variables were also recorded at each site. We collected a total of 2,369 individuals representing nine orders. We found that flying arthropod community composition was associated with percent impervious surface and canopy cover. Overall flying arthropod abundance was negatively associated with percent impervious surface and positively associated with distance to city center. Hymenoptera (bees, wasps, ants), Lepidoptera (moths, butterflies), and Araneae (spiders) were positively associated with distance to city center. Hemiptera (true bugs), Diptera (flies), and Araneae were negatively associated with percent impervious surface. Both distance to city center and percent impervious surface are metrics of urbanization, and this study shows how these factors influence flying arthropod communities in urban gardens and city parks, including significant reductions in taxa that contain pollinators and predators important to urban agriculture and forestry. A variety of environmental factors also showed significant associations with responses (e.g. canopy cover and soil moisture), suggesting these factors may underlie or modulate the urbanization effects. More research is needed to determine mechanisms of change. creator: Edward Lagucki creator: Justin D. Burdine creator: Kevin E. McCluney uri: https://doi.org/10.7717/peerj.3620 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Lagucki et al. title: How long should the fully hillside-closed forest protection be implemented on the Loess Plateau, Shaanxi, China? link: https://peerj.com/articles/3764 last-modified: 2017-09-04 description: BackgroundRestoration of degraded forest ecosystem is crucial for regional sustainable development. To protect the country’s fragile and fragmented environment, the Chinese government initiated an ecological engineering project, the Natural Forest Protection Program, in seventeen provinces in China beginning in 1998. Fully hillside-closed forest protection (vegetation restoration naturally without any artificial disturbance) was one of vital measures of the Natural Forest Protection Program applied nation wide. Whether plant diversity, biomass and age structure of dominant tree species and soil nutrients in protected stands may become better with increase of protected period are still open problems.MethodsWe investigated community diversity, biomass of dominant tree species, age structures, and analyzed soil chemical properties of a Pinus tabulaeformis population at protected sites representing different protected ages at Huanglongshan Forest Bureau on the Loess Plateau, Shaanxi, China.ResultsPlant species richness of Pinus tabulaeformis community was significantly affected (p < 0.05) by forest protection and the effect attenuated with protection age. Shannon evenness index of plant species generally increased with protection age. Stands protected for 45 years had the highest tree biomass and considerable natural regeneration capacity. Contents of organic carbon, available phosphorus and available potassium in top soil increased in protected stands less than 45 years, however decreased significantly thereafter. Long-term forest protection also decreased the content of mineral nitrogen in top soil.DiscussionWe found that the richness of shrubs and herbs was significantly affected by forest protection, and evenness indices of tree, shrub and herb increased inconsistently with protected ages. Forest protection created more complex age structures and tree densities with increasing age of protection. Content of soil mineral nitrogen at 0–20 cm soil depth showed a decreasing trend in stands of up to 30 years. Soil available phosphorus and potassium contents were higher in stands with greater proportions of big and medium trees. Long-term protection (>45 years) of Pinus tabulaeformis stands in southeast Loess Plateau, China, may be associated with decreasing plant species richness, proportion of medium to large trees, dominant biomass of Pinus tabulaeformis and soil nutrients. creator: Lin Hou creator: Sijia Hou uri: https://doi.org/10.7717/peerj.3764 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hou and Hou title: Preferences for achromatic horizontal, vertical, and square patterns in zebrafish (Danio rerio) link: https://peerj.com/articles/3748 last-modified: 2017-09-04 description: The zebrafish (Danio rerio) is gaining popularity as a laboratory organism and is used to model many human diseases. Many behavioural measures of locomotion and cognition have been developed that involve the processing of visual stimuli. However, the innate preference for vertical and horizontal stripes in zebrafish is unknown. We tested the preference of adult zebrafish for three achromatic patterns (vertical stripes, horizontal stripes, and squares) at three different size conditions (1, 5, and 10 mm). Each animal was tested once in a rectangular arena, which had a different pattern of the same size condition on the walls of either half of the arena. We show that zebrafish have differential preferences for patterned stimuli at each of the three size conditions. These results suggest that zebrafish have naïve preferences that should be carefully considered when testing zebrafish in paradigms using visual stimuli. creator: Lisa A. Rimstad creator: Adam Holcombe creator: Alicia Pope creator: Trevor J. Hamilton creator: Melike P. Schalomon uri: https://doi.org/10.7717/peerj.3748 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Rimstad et al. title: Stress responses to conspecific visual cues of predation risk in zebrafish link: https://peerj.com/articles/3739 last-modified: 2017-09-04 description: Chemical communication relating to predation risk is a trait common among fish species. Prey fish under threat of predation can signal risk to conspecific fish, which then exhibit defensive responses. Fish also assess predation risk by visual cues and change their behavior accordingly. Here, we explored whether these behavioral changes act as visual alarm signals to conspecific fish that are not initially under risk. We show that shoals of zebrafish (Danio rerio) visually exposed to a predator display antipredator behaviors. In addition, these defensive maneuvers trigger antipredator reactions in conspecifics and, concomitantly, stimulate the hypothalamus-pituitary-interrenal axis, leading to cortisol increase. Thus, we conclude that zebrafish defensive behaviors act as visual alarm cues that induce antipredator and stress response in conspecific fish. creator: Thiago Acosta Oliveira creator: Renan Idalencio creator: Fabiana Kalichak creator: João Gabriel dos Santos Rosa creator: Gessi Koakoski creator: Murilo Sander de Abreu creator: Ana Cristina Varrone Giacomini creator: Darlan Gusso creator: Denis Brook Rosemberg creator: Rodrigo Egydio Barreto creator: Leonardo José Gil Barcellos uri: https://doi.org/10.7717/peerj.3739 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Oliveira et al. title: Minimum infusion rate and adrenocortical function after continuous infusion of the novel etomidate analog ET-26-HCl in rats link: https://peerj.com/articles/3693 last-modified: 2017-09-04 description: BackgroundBecause etomidate induces prolonged adrenal suppression, even following a single bolus, its use as an infused anesthetic is limited. Our previous study indicated that a single administration of the novel etomidate analog methoxyethyletomidate hydrochloride (ET-26-HCl) shows little suppression of adrenocortical function. The aims of the present study were to (1) determine the minimum infusion rate of ET-26-HCl and compare it with those for etomidate and cyclopropyl-methoxycarbonylmetomidate (CPMM), a rapidly metabolized etomidate analog that is currently in clinical trials and (2) to evaluate adrenocortical function after a continuous infusion of ET-26-HCl as part of a broader study investigating whether this etomidate analog is suitable for long infusion in the maintenance of anesthesia.MethodThe up-and-down method was used to determine the minimum infusion rates for ET-26-HCl, etomidate and CPMM. Sprague-Dawley rats (n = 32) were then randomly divided into four groups: etomidate, ET-26-HCl, CPMM, and vehicle control. Rats in each group were infused for 60 min with one of the drugs at its predetermined minimum infusion rate. Blood samples were drawn initially and then every 30 min after drug infusion to determine the adrenocorticotropic hormone-stimulated concentration of serum corticosterone as a measure of adrenocortical function.ResultsThe minimum infusion rates for etomidate, ET-26-HCl and CPMM were 0.29, 0.62, and 0.95 mg/kg/min, respectively. Compared with controls, etomidate decreased serum corticosterone, as expected, whereas serum corticosterone concentrations following infusion with the etomidate analogs ET-26-HCl or CPMM were not significantly different from those in the control group.ConclusionThe corticosterone concentrations tended to be reduced for the first hour following ET-26-HCl infusion (as compared to vehicle infusion); however, this reduction did not reach statistical significance. Thus, further studies are warranted examining the practicability of using ET-26-HCl as an infused anesthetic. creator: Junli Jiang creator: Bin Wang creator: Zhaoqiong Zhu creator: Jun Yang creator: Jin Liu creator: Wensheng Zhang uri: https://doi.org/10.7717/peerj.3693 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Jiang et al. title: Trophic analysis of the fish community in the Ciénega Churince, Cuatro Ciénegas, Coahuila link: https://peerj.com/articles/3637 last-modified: 2017-09-04 description: Fish diets were analyzed to evaluate the dynamic trophs of the fish community in the Churince wetland system of the Cuatro Ciénegas, where the fauna consists of nine species: endemic, native and introduced. In nine sampling events (between February 2011 and May 2014) 556 specimens of all nine species were collected. Stomach contents were analyzed and the Relative Importance Index (IRI) was calculated. The feed coefficient (Q) of the diets and the accumulated trophic diversity (Hk), as well as the amplitude of the trophic niche were evaluated. Feeding strategies in the fish community were found to be eurifagic. The main foods in general were insects, crustaceans, gastropods, plants and teleosts. According to the average linkage method, four functional trophic groups were defined, with no higher consumption species; nevertheless all were regulators, mainly invertebrates. Therefore, the chain reaction in food control was higher from top to bottom, meaning a downwards dietary control. creator: Ariana Hernández creator: Hector S. Espinosa-Pérez creator: Valeria Souza uri: https://doi.org/10.7717/peerj.3637 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hernández et al. title: Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine link: https://peerj.com/articles/3561 last-modified: 2017-09-04 description: BackgroundThe endoplasmic reticulum plays an important role in many cellular processes, which includes protein synthesis, folding and post-translational processing of newly synthesized proteins. It is also the site for quality control of misfolded proteins and entry point of extracellular proteins to the secretory pathway. Hence at any given point of time, endoplasmic reticulum contains two different cohorts of proteins, (i) proteins involved in endoplasmic reticulum-specific function, which reside in the lumen of the endoplasmic reticulum, called as endoplasmic reticulum resident proteins and (ii) proteins which are in process of moving to the extracellular space. Thus, endoplasmic reticulum resident proteins must somehow be distinguished from newly synthesized secretory proteins, which pass through the endoplasmic reticulum on their way out of the cell. Approximately only 50% of the proteins used in this study as training data had endoplasmic reticulum retention signal, which shows that these signals are not essentially present in all endoplasmic reticulum resident proteins. This also strongly indicates the role of additional factors in retention of endoplasmic reticulum-specific proteins inside the endoplasmic reticulum.MethodsThis is a support vector machine based method, where we had used different forms of protein features as inputs for support vector machine to develop the prediction models. During training leave-one-out approach of cross-validation was used. Maximum performance was obtained with a combination of amino acid compositions of different part of proteins.ResultsIn this study, we have reported a novel support vector machine based method for predicting endoplasmic reticulum resident proteins, named as ERPred. During training we achieved a maximum accuracy of 81.42% with leave-one-out approach of cross-validation. When evaluated on independent dataset, ERPred did prediction with sensitivity of 72.31% and specificity of 83.69%. We have also annotated six different proteomes to predict the candidate endoplasmic reticulum resident proteins in them. A webserver, ERPred, was developed to make the method available to the scientific community, which can be accessed at http://proteininformatics.org/mkumar/erpred/index.html.DiscussionWe found that out of 124 proteins of the training dataset, only 66 proteins had endoplasmic reticulum retention signals, which shows that these signals are not an absolute necessity for endoplasmic reticulum resident proteins to remain inside the endoplasmic reticulum. This observation also strongly indicates the role of additional factors in retention of proteins inside the endoplasmic reticulum. Our proposed predictor, ERPred, is a signal independent tool. It is tuned for the prediction of endoplasmic reticulum resident proteins, even if the query protein does not contain specific ER-retention signal. creator: Ravindra Kumar creator: Bandana Kumari creator: Manish Kumar uri: https://doi.org/10.7717/peerj.3561 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kumar et al. title: Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface link: https://peerj.com/articles/3685 last-modified: 2017-09-01 description: BackgroundPreterm birth is a main determinant of neonatal mortality and morbidity and a major contributor to the overall mortality and burden of disease. However, research of the preterm birth is hindered by the imprecise definition of the clinical phenotype and complexity of the molecular phenotype due to multiple pregnancy tissue types and molecular processes that may contribute to the preterm birth. Here we comprehensively evaluate the mRNA transcriptome that characterizes preterm and term labor in tissues comprising the pregnancy using precisely phenotyped samples. The four complementary phenotypes together provide comprehensive insight into preterm and term parturition.MethodsSamples of maternal blood, chorion, amnion, placenta, decidua, fetal blood, and myometrium from the uterine fundus and lower segment (n = 183) were obtained during cesarean delivery from women with four complementary phenotypes: delivering preterm with (PL) and without labor (PNL), term with (TL) and without labor (TNL). Enrolled were 35 pregnant women with four precisely and prospectively defined phenotypes: PL (n = 8), PNL (n = 10), TL (n = 7) and TNL (n = 10). Gene expression data were analyzed using shrunken centroid analysis to identify a minimal set of genes that uniquely characterizes each of the four phenotypes. Expression profiles of 73 genes and non-coding RNA sequences uniquely identified each of the four phenotypes. The shrunken centroid analysis and 10 times 10-fold cross-validation was also used to minimize false positive finings and overfitting. Identified were the pathways and molecular processes associated with and the cis-regulatory elements in gene’s 5′ promoter or 3′-UTR regions of the set of genes which expression uniquely characterized the four phenotypes.ResultsThe largest differences in gene expression among the four groups occurred at maternal fetal interface in decidua, chorion and amnion. The gene expression profiles showed suppression of chemokines expression in TNL, withdrawal of this suppression in TL, activation of multiple pathways of inflammation in PL, and an immune rejection profile in PNL. The genes constituting expression signatures showed over-representation of three putative regulatory elements in their 5′and 3′ UTR regions.ConclusionsThe results suggest that pregnancy is maintained by downregulation of chemokines at the maternal-fetal interface. Withdrawal of this downregulation results in the term birth and its overriding by the activation of multiple pathways of the immune system in the preterm birth. Complications of the pregnancy associated with impairment of placental function, which necessitated premature delivery of the fetus in the absence of labor, show gene expression patterns associated with immune rejection. creator: Radek Bukowski creator: Yoel Sadovsky creator: Hani Goodarzi creator: Heping Zhang creator: Joseph R. Biggio creator: Michael Varner creator: Samuel Parry creator: Feifei Xiao creator: Sean M. Esplin creator: William Andrews creator: George R. Saade creator: John V. Ilekis creator: Uma M. Reddy creator: Donald A. Baldwin uri: https://doi.org/10.7717/peerj.3685 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bukowski et al. title: Measuring coral calcification under ocean acidification: methodological considerations for the 45Ca-uptake and total alkalinity anomaly technique link: https://peerj.com/articles/3749 last-modified: 2017-09-01 description: As the oceans become less alkaline due to rising CO2 levels, deleterious consequences are expected for calcifying corals. Predicting how coral calcification will be affected by on-going ocean acidification (OA) requires an accurate assessment of CaCO3 deposition and an understanding of the relative importance that decreasing calcification and/or increasing dissolution play for the overall calcification budget of individual corals. Here, we assessed the compatibility of the 45Ca-uptake and total alkalinity (TA) anomaly techniques as measures of gross and net calcification (GC, NC), respectively, to determine coral calcification at pHT 8.1 and 7.5. Considering the differing buffering capacity of seawater at both pH values, we were also interested in how strongly coral calcification alters the seawater carbonate chemistry under prolonged incubation in sealed chambers, potentially interfering with physiological functioning. Our data indicate that NC estimates by TA are erroneously ∼5% and ∼21% higher than GC estimates from 45Ca for ambient and reduced pH, respectively. Considering also previous data, we show that the consistent discrepancy between both techniques across studies is not constant, but largely depends on the absolute value of CaCO3 deposition. Deriving rates of coral dissolution from the difference between NC and GC was not possible and we advocate a more direct approach for the future by simultaneously measuring skeletal calcium influx and efflux. Substantial changes in carbonate system parameters for incubation times beyond two hours in our experiment demonstrate the necessity to test and optimize experimental incubation setups when measuring coral calcification in closed systems, especially under OA conditions. creator: Stephanie Cohen creator: Thomas Krueger creator: Maoz Fine uri: https://doi.org/10.7717/peerj.3749 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cohen et al. title: The influence of fundamental frequency on perceived duration in spectrally comparable sounds link: https://peerj.com/articles/3734 last-modified: 2017-09-01 description: The perceived duration of a sound is affected by its fundamental frequency and intensity: higher sounds are judged to be longer, as are sounds with greater intensity. Since increasing intensity lengthens the perceived duration of the auditory object, and increasing the fundamental frequency increases the sound’s perceived loudness (up to ca. 3 kHz), frequency modulation of duration could be potentially explained by a confounding effect where the primary cause of the modulation would be variations in intensity. Here, a series of experiments are described that were designed to disentangle the contributions of fundamental frequency, intensity, and duration to perceived loudness and duration. In two forced-choice tasks, participants judged duration and intensity differences between two sounds varying simultaneously in intensity, fundamental frequency, fundamental frequency gliding range, and duration. The results suggest that fundamental frequency and intensity each have an impact on duration judgments, while frequency gliding range did not influence the present results. We also demonstrate that the modulation of perceived duration by sound fundamental frequency cannot be fully explained by the confounding relationship between frequency and intensity. creator: Caitlin Dawson creator: Daniel Aalto creator: Juraj Simko creator: Martti Vainio uri: https://doi.org/10.7717/peerj.3734 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dawson et al. title: A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes link: https://peerj.com/articles/3703 last-modified: 2017-09-01 description: BackgroundHeterocyclic aromatic amines (HAA) are environmental and food contaminants that are potentially carcinogenic for humans. 2-Amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) is one of the most abundant HAA formed in cooked meat. MeIQx is metabolized by cytochrome P450 1A2 in the human liver into detoxificated and bioactivated products. Once bioactivated, MeIQx metabolites can lead to DNA adduct formation responsible for further genome instability.MethodsUsing a computational approach, we developed a numerical model for MeIQx metabolism in the liver that predicts the MeIQx biotransformation into detoxification or bioactivation pathways according to the concentration of MeIQx.ResultsOur results demonstrate that (1) the detoxification pathway predominates, (2) the ratio between detoxification and bioactivation pathways is not linear and shows a maximum at 10 µM of MeIQx in hepatocyte cell models, and (3) CYP1A2 is a key enzyme in the system that regulates the balance between bioactivation and detoxification. Our analysis suggests that such a ratio could be considered as an indicator of MeIQx genotoxicity at a low concentration of MeIQx.ConclusionsOur model permits the investigation of the balance between bioactivation (i.e., DNA adduct formation pathway through the prediction of potential genotoxic compounds) and detoxification of MeIQx in order to predict the behaviour of this environmental contaminant in the human liver. It highlights the importance of complex regulations of enzyme competitions that should be taken into account in any further multi-organ models. creator: Victorien Delannée creator: Sophie Langouët creator: Nathalie Théret creator: Anne Siegel uri: https://doi.org/10.7717/peerj.3703 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Delannée et al. title: A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog link: https://peerj.com/articles/3702 last-modified: 2017-09-01 description: Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki. creator: Santiago Montero-Mendieta creator: Manfred Grabherr creator: Henrik Lantz creator: Ignacio De la Riva creator: Jennifer A. Leonard creator: Matthew T. Webster creator: Carles Vilà uri: https://doi.org/10.7717/peerj.3702 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Montero-Mendieta et al.