title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2017-11 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Examining publication bias—a simulation-based evaluation of statistical tests on publication bias link: https://peerj.com/articles/4115 last-modified: 2017-11-30 description: BackgroundPublication bias is a form of scientific misconduct. It threatens the validity of research results and the credibility of science. Although several tests on publication bias exist, no in-depth evaluations are available that examine which test performs best for different research settings.MethodsFour tests on publication bias, Egger’s test (FAT), p-uniform, the test of excess significance (TES), as well as the caliper test, were evaluated in a Monte Carlo simulation. Two different types of publication bias and its degree (0%, 50%, 100%) were simulated. The type of publication bias was defined either as file-drawer, meaning the repeated analysis of new datasets, or p-hacking, meaning the inclusion of covariates in order to obtain a significant result. In addition, the underlying effect (β = 0, 0.5, 1, 1.5), effect heterogeneity, the number of observations in the simulated primary studies (N = 100, 500), and the number of observations for the publication bias tests (K = 100, 1,000) were varied.ResultsAll tests evaluated were able to identify publication bias both in the file-drawer and p-hacking condition. The false positive rates were, with the exception of the 15%- and 20%-caliper test, unbiased. The FAT had the largest statistical power in the file-drawer conditions, whereas under p-hacking the TES was, except under effect heterogeneity, slightly better. The CTs were, however, inferior to the other tests under effect homogeneity and had a decent statistical power only in conditions with 1,000 primary studies.DiscussionThe FAT is recommended as a test for publication bias in standard meta-analyses with no or only small effect heterogeneity. If two-sided publication bias is suspected as well as under p-hacking the TES is the first alternative to the FAT. The 5%-caliper test is recommended under conditions of effect heterogeneity and a large number of primary studies, which may be found if publication bias is examined in a discipline-wide setting when primary studies cover different research problems. creator: Andreas Schneck uri: https://doi.org/10.7717/peerj.4115 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Schneck title: A tyrannosauroid metatarsus from the Merchantville Formation of Delaware increases the diversity of non-tyrannosaurid tyrannosauroids on Appalachia link: https://peerj.com/articles/4123 last-modified: 2017-11-30 description: During the Late Cretaceous, the continent of North America was divided into two sections: Laramidia in the west and Appalachia in the east. Although the sediments of Appalachia recorded only a sparse fossil record of dinosaurs, the dinosaur faunas of this landmass were different in composition from those of Laramidia. Represented by at least two taxa (Appalachiosaurus montgomeriensis and Dryptosaurus aquilunguis), partial and fragmentary skeletons, and isolated bones, the non-tyrannosaurid tyrannosauroids of the landmass have attracted some attention. Unfortunately, these eastern tyrants are poorly known compared to their western contemporaries. Here, one specimen, the partial metatarsus of a tyrannosauroid from the Campanian Merchantville Formation of Delaware, is described in detail. The specimen can be distinguished from A. montgomeriensis and D. aquilunguis by several morphological features. As such, the specimen represents a potentially previously unrecognized taxon of tyrannosauroid from Appalachia, increasing the diversity of the clade on the landmass. Phylogenetic analysis and the morphology of the bones suggest the Merchantville specimen is a tyrannosauroid of “intermediate” grade, thus supporting the notion that Appalachia was a refugium for relict dinosaur clades. creator: Chase D. Brownstein uri: https://doi.org/10.7717/peerj.4123 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Brownstein title: Acute ischemic preconditioning does not influence high-intensity intermittent exercise performance link: https://peerj.com/articles/4118 last-modified: 2017-11-30 description: This study evaluated the acute effect of ischemic preconditioning (IPC) on a high-intensity intermittent exercise performance and physiological indicators in amateur soccer players. Thirteen players (21.5 ± 2 yrs) attended three trials separated by 3–5 days in a counterbalanced randomized cross-over design: IPC (4 × 5-min occlusion 220 mmHg/reperfusion 0 mmHg) in each thigh; SHAM (similar to the IPC protocol but “occlusion” at 20 mmHg) and control (seated during the same time of IPC). After 6-min of each trial (IPC, SHAM or control), the players performed the YoYo Intermittent Endurance Test level 2 (YoYoIE2). The distance covered in the YoYoIE2 (IPC 867 ± 205 m; SHAM 873 ± 212 m; control 921 ± 206 m) was not different among trials (p = 0.10), furthermore, lactate concentration and rate of perceived exertion did not differ (P > 0.05) among protocols. There were also no significant differences in either mean heart rate (HR) or peak HR (p > 0.05) for both IPC and SHAM compared to control. Therefore, we conclude that acute IPC does not influence high-intensity intermittent exercise performance in amateur soccer players and that rate of perceived exertion, heart rate and lactate do not differ between the intervention IPC, SHAM and control. creator: Isabela Coelho Marocolo creator: Gustavo Ribeiro da Mota creator: André Monteiro Londe creator: Stephen D. Patterson creator: Octávio Barbosa Neto creator: Moacir Marocolo uri: https://doi.org/10.7717/peerj.4118 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Marocolo et al. title: Ability to predict repetitions to momentary failure is not perfectly accurate, though improves with resistance training experience link: https://peerj.com/articles/4105 last-modified: 2017-11-30 description: ‘Repetitions in Reserve’ (RIR) scales in resistance training (RT) are used to control effort but assume people accurately predict performance a priori (i.e. the number of possible repetitions to momentary failure (MF)). This study examined the ability of trainees with different experience levels to predict number of repetitions to MF. One hundred and forty-one participants underwent a full body RT session involving single sets to MF and were asked to predict the number of repetitions they could complete before reaching MF on each exercise. Participants underpredicted the number of repetitions they could perform to MF (Standard error of measurements [95% confidence intervals] for combined sample ranged between 2.64 [2.36–2.99] and 3.38 [3.02–3.83]). There was a tendency towards improved accuracy with greater experience. Ability to predict repetitions to MF is not perfectly accurate among most trainees though may improve with experience. Thus, RIR should be used cautiously in prescription of RT. Trainers and trainees should be aware of this as it may have implications for the attainment of training goals, particularly muscular hypertrophy. creator: James Steele creator: Andreas Endres creator: James Fisher creator: Paulo Gentil creator: Jürgen Giessing uri: https://doi.org/10.7717/peerj.4105 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Steele et al. title: Diagnosis value of aberrantly expressed microRNA profiles in lung squamous cell carcinoma: a study based on the Cancer Genome Atlas link: https://peerj.com/articles/4101 last-modified: 2017-11-30 description: BackgroundLung cancer is considered as one of the most frequent and deadly cancers with high mortality all around the world. It is critical to find new biomarkers for early diagnosis of lung cancer, especially lung squamous cell carcinoma (LUSC). The Cancer Genome Atlas (TCGA) is a database which provides both cancer and clinical information. This study is a comprehensive analysis of a novel diagnostic biomarker for LUSC, based on TCGA.Methods and ResultsThe present study investigated LUSC-specific key microRNAs (miRNAs) from large-scale samples in TCGA. According to exclusion criteria and inclusion criteria, the expression profiles of miRNAs with related clinical information of 332 LUSC patients were obtained. Most aberrantly expressed miRNAs were identified between tumor and normal samples. Forty-two LUSC-specific intersection miRNAs (fold change >2, p < 0.05) were obtained by an integrative computational method, among them six miRNAs were found to be aberrantly expressed concerning characteristics of patients (gender, lymphatic metastasis, patient outcome assessment) through Student t-test. Five miRNAs correlated with overall survival (log-rank p < 0.05) were obtained through the univariate Cox proportional hazards regression model and Mantel–Haenszel test. Then, five miRNAs were randomly selected to validate the expression in 47 LUSC patient tissues using quantitative real-time polymerase chain reaction. The results showed that the test findings were consistent with the TCGA findings. Also, the diagnostic value of the specific key miRNAs was determined by areas under receiver operating characteristic curves. Finally, 577 interaction mRNAs as the targets of 42 LUSC-specific intersection miRNAs were selected for further bioinformatics analysis.ConclusionThis study indicates that this novel microRNA expression signature may be a useful biomarker of the diagnosis for LUSC patients, based on bioinformatics analysis. creator: Sheng Yang creator: Jing Sui creator: Geyu Liang uri: https://doi.org/10.7717/peerj.4101 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Yang et al. title: Ordinary kriging vs inverse distance weighting: spatial interpolation of the sessile community of Madagascar reef, Gulf of Mexico link: https://peerj.com/articles/4078 last-modified: 2017-11-30 description: Information about the distribution and abundance of the habitat-forming sessile organisms in marine ecosystems is of great importance for conservation and natural resource managers. Spatial interpolation methodologies can be useful to generate this information from in situ sampling points, especially in circumstances where remote sensing methodologies cannot be applied due to small-scale spatial variability of the natural communities and low light penetration in the water column. Interpolation methods are widely used in environmental sciences; however, published studies using these methodologies in coral reef science are scarce. We compared the accuracy of the two most commonly used interpolation methods in all disciplines, inverse distance weighting (IDW) and ordinary kriging (OK), to predict the distribution and abundance of hard corals, octocorals, macroalgae, sponges and zoantharians and identify hotspots of these habitat-forming organisms using data sampled at three different spatial scales (5, 10 and 20 m) in Madagascar reef, Gulf of Mexico. The deeper sandy environments of the leeward and windward regions of Madagascar reef were dominated by macroalgae and seconded by octocorals. However, the shallow rocky environments of the reef crest had the highest richness of habitat-forming groups of organisms; here, we registered high abundances of octocorals and macroalgae, with sponges, Millepora alcicornis and zoantharians dominating in some patches, creating high levels of habitat heterogeneity. IDW and OK generated similar maps of distribution for all the taxa; however, cross-validation tests showed that IDW outperformed OK in the prediction of their abundances. When the sampling distance was at 20 m, both interpolation techniques performed poorly, but as the sampling was done at shorter distances prediction accuracies increased, especially for IDW. OK had higher mean prediction errors and failed to correctly interpolate the highest abundance values measured in situ, except for macroalgae, whereas IDW had lower mean prediction errors and high correlations between predicted and measured values in all cases when sampling was every 5 m. The accurate spatial interpolations created using IDW allowed us to see the spatial variability of each taxa at a biological and spatial resolution that remote sensing would not have been able to produce. Our study sets the basis for further research projects and conservation management in Madagascar reef and encourages similar studies in the region and other parts of the world where remote sensing technologies are not suitable for use. creator: Salvador Zarco-Perello creator: Nuno Simões uri: https://doi.org/10.7717/peerj.4078 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zarco-Perello and Simões title: Hermit crab response to a visual threat is sensitive to looming cues link: https://peerj.com/articles/4058 last-modified: 2017-11-30 description: Prior work in our lab has shown that an expanding image on a computer screen elicits a hiding response in the Caribbean terrestrial hermit crab (Coenobita clypeatus). We conducted two experiments to identify what properties of the expanding stimulus contribute to its effectiveness as a visual threat. First we found that an expanding geometric star evoked a strong hiding response while a contracting or full-sized stationary star did not. A second experiment revealed that the more quickly the stimulus expanded the shorter the latency to hide. These findings suggest that the anti-predator response to looming stimulus relies heavily on visual cues relating to the manner of approach. The simulated visual threat on a computer screen captures key features of a real looming object that elicits hiding behavior in crabs in the wild. creator: Talya Shragai creator: Xiaoge Ping creator: Cameron Arakaki creator: Dennis Garlick creator: Daniel T. Blumstein creator: Aaron P. Blaisdell uri: https://doi.org/10.7717/peerj.4058 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shragai et al. title: Reference standards to assess physical fitness of children and adolescents of Brazil: an approach to the students of the Lake Itaipú region—Brazil link: https://peerj.com/articles/4032 last-modified: 2017-11-30 description: BackgroundThe importance of assessing body fat variables and physical fitness tests plays an important role in monitoring the level of activity and physical fitness of the general population. The objective of this study was to develop reference norms to evaluate the physical fitness aptitudes of children and adolescents based on age and sex from the lake region of Itaipú, Brazil.MethodsA descriptive cross-sectional study was carried out with 5,962 students (2,938 males and 3,024 females) with an age range of 6.0 and 17.9 years. Weight (kg), height (cm), and triceps (mm), and sub-scapular skinfolds (mm) were measured. Body Mass Index (BMI kg/m2) was calculated. To evaluate the four physical fitness aptitude dimensions (morphological, muscular strength, flexibility, and cardio-respiratory), the following physical education tests were given to the students: sit-and-reach (cm), push-ups (rep), standing long jump (cm), and 20-m shuttle run (m).Results and DiscussionFemales showed greater flexibility in the sit-and-reach test and greater body fat than the males. No differences were found in BMI. Percentiles were created for the four components for the physical fitness aptitudes, BMI, and skinfolds by using the LMS method based on age and sex. The proposed reference values may be used for detecting talents and promoting health in children and adolescents. creator: Edilson Hobold creator: Vitor Pires-Lopes creator: Rossana Gómez-Campos creator: Miguel de Arruda creator: Cynthia Lee Andruske creator: Jaime Pacheco-Carrillo creator: Marco Antonio Cossio-Bolaños uri: https://doi.org/10.7717/peerj.4032 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hobold et al. title: Kullback Leibler divergence in complete bacterial and phage genomes link: https://peerj.com/articles/4026 last-modified: 2017-11-30 description: The amino acid content of the proteins encoded by a genome may predict the coding potential of that genome and may reflect lifestyle restrictions of the organism. Here, we calculated the Kullback–Leibler divergence from the mean amino acid content as a metric to compare the amino acid composition for a large set of bacterial and phage genome sequences. Using these data, we demonstrate that (i) there is a significant difference between amino acid utilization in different phylogenetic groups of bacteria and phages; (ii) many of the bacteria with the most skewed amino acid utilization profiles, or the bacteria that host phages with the most skewed profiles, are endosymbionts or parasites; (iii) the skews in the distribution are not restricted to certain metabolic processes but are common across all bacterial genomic subsystems; (iv) amino acid utilization profiles strongly correlate with GC content in bacterial genomes but very weakly correlate with the G+C percent in phage genomes. These findings might be exploited to distinguish coding from non-coding sequences in large data sets, such as metagenomic sequence libraries, to help in prioritizing subsequent analyses. creator: Sajia Akhter creator: Ramy K. Aziz creator: Mona T. Kashef creator: Eslam S. Ibrahim creator: Barbara Bailey creator: Robert A. Edwards uri: https://doi.org/10.7717/peerj.4026 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Akhter et al. title: BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters link: https://peerj.com/articles/3948 last-modified: 2017-11-30 description: Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily. creator: Gong Cheng creator: Quan Lu creator: Ling Ma creator: Guocai Zhang creator: Liang Xu creator: Zongshan Zhou uri: https://doi.org/10.7717/peerj.3948 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Cheng et al. title: On the relationship between tumour growth rate and survival in non-small cell lung cancer link: https://peerj.com/articles/4111 last-modified: 2017-11-29 description: A recurrent question within oncology drug development is predicting phase III outcome for a new treatment using early clinical data. One approach to tackle this problem has been to derive metrics from mathematical models that describe tumour size dynamics termed re-growth rate and time to tumour re-growth. They have shown to be strong predictors of overall survival in numerous studies but there is debate about how these metrics are derived and if they are more predictive than empirical end-points. This work explores the issues raised in using model-derived metric as predictors for survival analyses. Re-growth rate and time to tumour re-growth were calculated for three large clinical studies by forward and reverse alignment. The latter involves re-aligning patients to their time of progression. Hence, it accounts for the time taken to estimate re-growth rate and time to tumour re-growth but also assesses if these predictors correlate to survival from the time of progression. I found that neither re-growth rate nor time to tumour re-growth correlated to survival using reverse alignment. This suggests that the dynamics of tumours up until disease progression has no relationship to survival post progression. For prediction of a phase III trial I found the metrics performed no better than empirical end-points. These results highlight that care must be taken when relating dynamics of tumour imaging to survival and that bench-marking new approaches to existing ones is essential. creator: Hitesh B. Mistry uri: https://doi.org/10.7717/peerj.4111 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Mistry title: Transcriptomic profiling of mTOR and ryanodine receptor signaling molecules in developing zebrafish in the absence and presence of PCB 95 link: https://peerj.com/articles/4106 last-modified: 2017-11-29 description: The mechanistic target of rapamycin (mTOR) and ryanodine receptor (RyR) signaling pathways regulate fundamental processes of neurodevelopment, and genetic mutations within these pathways have been linked to neurodevelopmental disorders. While previous studies have established that these signaling molecules are expressed in developing zebrafish, a detailed characterization of the ontogenetic profile of these signaling molecules is lacking. Thus, we evaluated the spatiotemporal expression of key transcripts in mTOR and RyR signaling pathways in wildtype zebrafish at 24, 72 and 120 hours post fertilization (hpf). We further determined whether transcriptional profiles of a subset of genes in both pathways were altered by exposure to PCB 95 (2,2′,3,5′,6-pentachlorobiphenyl), a pervasive environmental contaminant known to cause developmental neurotoxicity in mammalian systems via RyR-dependent mechanisms. Quantitative PCR revealed that transcription generally increased across development. Genes in the signaling pathway upstream of the mTORC1 complex, and the RyR-paralogs, ryr2a and ryr3, were robustly upregulated, and in situ hybridization of ryr3 coincided with a transcriptional shift from muscle to neuronal tissue after 24 hpf. Static waterborne exposure to PCB 95 beginning at 6 hpf significantly altered transcription of genes in both pathways. These changes were concentration- and time-dependent, and included downregulation of rptor, a member of the mTORC1 complex, at both 72 and 120 hpf, and increased transcript levels of the RyR paralog ryr2b and downstream target of RyR signaling, Wingless-type 2ba (wnt2ba) at 72 hpf. The detailed transcriptomic profiling of key genes within these two signaling pathways provides a baseline for identifying other environmental factors that modify normal spatiotemporal expression patterns of mTOR and RyR signaling pathways in the developing zebrafish, as illustrated here for PCB 95. creator: Daniel F. Frank creator: Galen W. Miller creator: Richard E. Connon creator: Juergen Geist creator: Pamela J. Lein uri: https://doi.org/10.7717/peerj.4106 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Frank et al. title: Age-based and reproductive biology of the Pacific Longnose Parrotfish Hipposcarus longiceps from Guam link: https://peerj.com/articles/4079 last-modified: 2017-11-29 description: The Pacific longnose parrotfish Hipposcarus longiceps (Valenciennes 1840) represents a prime fishery resource throughout much of the tropical Pacific. In this study, we sampled the species from the Guam commercial fishery market across five consecutive years to characterize reproductive and age-based demographic information imperative for informed fishery management. Compared with other parrotfishes, this species was found to be large-bodied, but has only a moderate life span of 10 + years. Hipposcarus longiceps was confirmed as a diandric protogynous hermaphrodite with highly sex-specific growth patterns and an overall mean asymptotic length of 434 mm fork length (FL). Females were estimated to reach median maturity at 329 mm FL (2.4 years) and have a median length at female-to-male sex change of 401 mm FL. Life-history trait values derived here were used to update previous models relating life history and vulnerability to overexploitation. We found that enhancement of just one species’ trait values improved model fits considerably, which strengthens the conclusion that life-history traits are a strong determinant of species’ vulnerability in the parrotfishes. This information is an imperative complement to other data sources facilitating formal stock assessment of a key fishery target. creator: Brett M. Taylor creator: Eric Cruz uri: https://doi.org/10.7717/peerj.4079 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Taylor and Cruz title: An exceptionally preserved armored dinosaur reveals the morphology and allometry of osteoderms and their horny epidermal coverings link: https://peerj.com/articles/4066 last-modified: 2017-11-29 description: Although the evolution and function of “exaggerated” bony projections in ornithischian dinosaurs has been subject to significant debate recently, our understanding of the structure and morphology of their epidermal keratinized coverings is greatly limited. The holotype of Borealopelta, a new nodosaurid ankylosaur, preserves osteoderms and extensive epidermal structures (dark organic residues), in anatomic position across the entire precaudal length. Contrasting previous specimens, organic epiosteodermal scales, often in the form of horn-like (keratinous) sheaths, cap and exaggerate nearly all osteoderms, allowing for morphometric and allometric analyses of both the bony osteoderms and their horny sheaths. A total of 172 osteoderms were quantified, with osteoderm spine length and height being positively allometric with respect to basal length and width. Despite tight correlations between the different measures amongst all other osteoderms, the large parascapular spines represent consistent outliers. Thickness and relative contribution of the keratinized epiosteodermal scales/sheaths varies greatly by region, ranging from 2% to 6% for posterior thoracics, to ∼25% (1.3×) for the parascapular spines—similar to horn sheaths in some bovid analogues. Relative to the bony cores, the horny portions of the spines are strongly positively allometric (slope = 2.3, CI = 1.8–2.8). Strong allometric scaling, species-specific morphology, and significant keratinous extension of the cervicoscapular spines is consistent with elaboration under socio-sexual selection. This marks the first allometric analysis of ornithischian soft tissues. creator: Caleb M. Brown uri: https://doi.org/10.7717/peerj.4066 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Brown title: Facilitative and competitive interaction components among New England salt marsh plants link: https://peerj.com/articles/4049 last-modified: 2017-11-29 description: Intra- and interspecific interactions can be broken down into facilitative and competitive components. The net interaction between two organisms is simply the sum of these counteracting elements. Disentangling the positive and negative components of species interactions is a critical step in advancing our understanding of how the interaction between organisms shift along physical and biotic gradients. We performed a manipulative field experiment to quantify the positive and negative components of the interactions between a perennial forb, Aster tenuifolius, and three dominant, matrix-forming grasses and rushes in a New England salt marsh. Specifically, we asked whether positive and negative interaction components: (1) are unique or redundant across three matrix-forming species (two grasses; Distichlis spicata and Spartina patens, and one rush; Juncus gerardi), and (2) change across Aster life stages (seedling, juvenile, and adult). For adult Aster the strength of the facilitative component of the matrix-forb interaction was stronger than the competitive component for two of the three matrix species, leading to net positive interactions. There was no statistically significant variation among matrix species in their net or component effects. We found little difference in the effects of J. gerardi on Aster at later life-history stages; interaction component strengths did not differ between juveniles and adults. However, mortality of seedlings in neighbor removal plots was 100%, indicating a particularly strong and critical facilitative effect of matrix species on this forb during the earliest life stages. Overall, our results indicate that matrix forming grasses and rushes have important, yet largely redundant, positive net effects on Aster performance across its life cycle. Studies that untangle various components of interactions and their contingencies are critical to both expanding our basic understanding of community organization, and predicting how natural communities and their component parts will respond to environmental change. creator: John F. Bruno creator: Tatyana A. Rand creator: Nancy C. Emery creator: Mark D. Bertness uri: https://doi.org/10.7717/peerj.4049 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bruno et al. title: DNA barcoding reveals the mislabeling of fish in a popular tourist destination in Brazil link: https://peerj.com/articles/4006 last-modified: 2017-11-29 description: The consumption of raw fish has increased considerably in the West, since it is said to be potentially healthier than processed fish (for containing omega 3 and 6, essential amino acids and vitamins). However this potential benefit, as well as the taste, value and even the risk of extinction are not the same for all species of fish, constituting grounds for fraud. Using the principles of the DNA barcode we revealed mislabelling of fish in Japanese restaurants and fishmarkets in Florianópolis, a popular tourist capital in Brazil. We sequenced the COI gene of 65 samples from fisheries and 80 from restaurants and diagnosed 30% of mislabeled samples in fisheries and 26% in restaurants. We discussed that frauds may have occurred for different reasons: to circumvent surveillance on threatened species; to sell fish with sizes smaller than allowed or abundant species as being a much rarer species (law of supply); to induce product consumption using species with better taste. It should be noted that some substitutions are derived from incorrect identification and are not a fraud per se; they are due to confusion of popular names or misunderstanding by the sellers. Therefore, we suggest the implementation of a systematic regulatory program conducted by governmental agencies to reduce mislabelling in order to avoid further damage to the community (in health and financial issues) and fish stocks. creator: Clisten Fátima Staffen creator: Mari Dalva Staffen creator: Mariana Londero Becker creator: Sara Emelie Löfgren creator: Yara Costa Netto Muniz creator: Renato Hajenius Aché de Freitas creator: Andrea Rita Marrero uri: https://doi.org/10.7717/peerj.4006 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Staffen et al. title: Genomic characterization of a new endophytic Streptomyces kebangsaanensis identifies biosynthetic pathway gene clusters for novel phenazine antibiotic production link: https://peerj.com/articles/3738 last-modified: 2017-11-29 description: BackgroundStreptomyces are well known for their capability to produce many bioactive secondary metabolites with medical and industrial importance. Here we report a novel bioactive phenazine compound, 6-((2-hydroxy-4-methoxyphenoxy) carbonyl) phenazine-1-carboxylic acid (HCPCA) extracted from Streptomyces kebangsaanensis, an endophyte isolated from the ethnomedicinal Portulaca oleracea.MethodsThe HCPCA chemical structure was determined using nuclear magnetic resonance spectroscopy. We conducted whole genome sequencing for the identification of the gene cluster(s) believed to be responsible for phenazine biosynthesis in order to map its corresponding pathway, in addition to bioinformatics analysis to assess the potential of S. kebangsaanensis in producing other useful secondary metabolites.ResultsThe S. kebangsaanensis genome comprises an 8,328,719 bp linear chromosome with high GC content (71.35%) consisting of 12 rRNA operons, 81 tRNA, and 7,558 protein coding genes. We identified 24 gene clusters involved in polyketide, nonribosomal peptide, terpene, bacteriocin, and siderophore biosynthesis, as well as a gene cluster predicted to be responsible for phenazine biosynthesis.DiscussionThe HCPCA phenazine structure was hypothesized to derive from the combination of two biosynthetic pathways, phenazine-1,6-dicarboxylic acid and 4-methoxybenzene-1,2-diol, originated from the shikimic acid pathway. The identification of a biosynthesis pathway gene cluster for phenazine antibiotics might facilitate future genetic engineering design of new synthetic phenazine antibiotics. Additionally, these findings confirm the potential of S. kebangsaanensis for producing various antibiotics and secondary metabolites. creator: Juwairiah Remali creator: Nurul ‘Izzah Mohd Sarmin creator: Chyan Leong Ng creator: John J.L. Tiong creator: Wan M. Aizat creator: Loke Kok Keong creator: Noraziah Mohamad Zin uri: https://doi.org/10.7717/peerj.3738 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Remali et al. title: Geological duration of ammonoids controlled their geographical range of fossil distribution link: https://peerj.com/articles/4108 last-modified: 2017-11-28 description: The latitudinal distributions in Devonian–Cretaceous ammonoids were analyzed at the genus level, and were compared with the hatchling sizes (i.e., ammonitella diameters) and the geological durations. The results show that (1) length of temporal ranges of ammonoids effected broader ranges of fossil distribution and paleobiogeography of ammonoids, and (2) the hatchling size was not related to the geographical range of fossil distribution of ammonoids. Reducing the influence of geological duration in this analysis implies that hatchling size was one of the controlling factors that determined the distribution of ammonoid habitats at any given period in time: ammonoids with smaller hatchling sizes tended to have broader ammonoid habitat ranges. These relationships were somewhat blurred in the Devonian, Carboniferous, Triassic, and Jurassic, which is possibly due to (1) the course of development of a reproductive strategy with smaller hatchling sizes in the Devonian and (2) the high origination rates after the mass extinction events. creator: Ryoji Wani uri: https://doi.org/10.7717/peerj.4108 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wani title: Denitrifying metabolism of the methylotrophic marine bacterium Methylophaga nitratireducenticrescens strain JAM1 link: https://peerj.com/articles/4098 last-modified: 2017-11-28 description: BackgroundMethylophaga nitratireducenticrescens strain JAM1 is a methylotrophic, marine bacterium that was isolated from a denitrification reactor treating a closed-circuit seawater aquarium. It can sustain growth under anoxic conditions by reducing nitrate (${\mathrm{NO}}_{3}^{-}$NO3−) to nitrite (${\mathrm{NO}}_{2}^{-}$NO2−). These physiological traits are attributed to gene clusters that encode two dissimilatory nitrate reductases (Nar). Strain JAM1 also contains gene clusters encoding two nitric oxide (NO) reductases and one nitrous oxide (N2O) reductase, suggesting that NO and N2O can be reduced by strain JAM1. Here we characterized further the denitrifying activities of M. nitratireducenticrescens JAM1.MethodsSeries of oxic and anoxic cultures of strain JAM1 were performed with N2O, ${\mathrm{NO}}_{3}^{-}$NO3− or sodium nitroprusside, and growth and N2O, ${\mathrm{NO}}_{3}^{-}$NO3−, ${\mathrm{NO}}_{2}^{-}$NO2− and N2 concentrations were measured. Ammonium (${\mathrm{NH}}_{4}^{+}$NH4+)-free cultures were also tested to assess the dynamics of N2O, ${\mathrm{NO}}_{3}^{-}$NO3− and ${\mathrm{NO}}_{2}^{-}$NO2−. Isotopic labeling of N2O was performed in 15NH4+-amended cultures. Cultures with the JAM1ΔnarG1narG2 double mutant were performed to assess the involvement of the Nar systems on N2O production. Finally, RT-qPCR was used to measure the gene expression levels of the denitrification genes cytochrome bc-type nitric oxide reductase (cnorB1 and cnorB2) and nitrous oxide reductase (nosZ), and also nnrS and norR that encode NO-sensitive regulators.ResultsStrain JAM1 can reduce NO to N2O and N2O to N2 and can sustain growth under anoxic conditions by reducing N2O as the sole electron acceptor. Although strain JAM1 lacks a gene encoding a dissimilatory ${\mathrm{NO}}_{2}^{-}$NO2− reductase, ${\mathrm{NO}}_{3}^{-}$NO3−-amended cultures produce N2O, representing up to 6% of the N-input. ${\mathrm{NO}}_{2}^{-}$NO2− was shown to be the key intermediate of this production process. Upregulation in the expression of cnorB1, cnorB2, nnrS and norR during the growth and the N2O accumulation phases suggests NO production in strain JAM1 cultures.DiscussionBy showing that all the three denitrification reductases are active, this demonstrates that M. nitratireducenticrescens JAM1 is one of many bacteria species that maintain genes associated primarily with denitrification, but not necessarily related to the maintenance of the entire pathway. The reason to maintain such an incomplete pathway could be related to the specific role of strain JAM1 in the denitrifying biofilm of the denitrification reactor from which it originates. The production of N2O in strain JAM1 did not involve Nar, contrary to what was demonstrated in Escherichia coli. M. nitratireducenticrescens JAM1 is the only reported Methylophaga species that has the capacity to grow under anoxic conditions by using ${\mathrm{NO}}_{3}^{-}$NO3− and N2O as sole electron acceptors for its growth. It is also one of a few marine methylotrophs that is studied at the physiological and genetic levels in relation to its capacity to perform denitrifying activities. creator: Florian Mauffrey creator: Alexandra Cucaita creator: Philippe Constant creator: Richard Villemur uri: https://doi.org/10.7717/peerj.4098 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Mauffrey et al. title: The presence of genes encoding enzymes that digest carbohydrates in coral genomes and analysis of their activities link: https://peerj.com/articles/4087 last-modified: 2017-11-28 description: Numerous enzymes that digest carbohydrates, such as cellulases and chitinases, are present in various organisms (e.g., termites, nematodes, and so on). Recently, the presence of cellulases and chitinases has been reported in marine organisms such as urchin and bivalves, and their several roles in marine ecosystems have been proposed. In this study, we reported the presence of genes predicted to encode proteins similar to cellulases and chitinases in the genome of the coral Acropora digitifera, their gene expression patterns at various life stages, and cellulose- and chitin-degrading enzyme activities in several coral species (A. digitifera, Galaxea fascicularis, Goniastrea aspera, Montipora digitata, Pavona divaricata, Pocillopora damicornis, and Porites australiensis). Our gene expression analysis demonstrated the expressions of these cellulase- and chitinase-like genes during various life stages, including unfertilized eggs, fertilized eggs, zygotes, planula larvae, primary polyps and adults of A. digitifera. Agar plate assays confirmed cellulase and chitinase activities in the tissues extracted from adult branches of several coral species. These results suggested that corals are able to utilize cellulases and chitinases in their life histories. creator: Yuki Yoshioka creator: Toshiaki Tanabe creator: Akira Iguchi uri: https://doi.org/10.7717/peerj.4087 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yoshioka et al. title: Evaluation of potential reference genes for real-time qPCR analysis in a biparental beetle, Lethrus apterus (Coleoptera: Geotrupidae) link: https://peerj.com/articles/4047 last-modified: 2017-11-28 description: Hormones play an important role in the regulation of physiological, developmental and behavioural processes. Many of these mechanisms in insects, however, are still not well understood. One way to investigate hormonal regulation is to analyse gene expression patterns of hormones and their receptors by real-time quantitative polymerase chain reaction (RT-qPCR). This method, however, requires stably expressed reference genes for normalisation. In the present study, we evaluated 11 candidate housekeeping genes as reference genes in samples of Lethrus apterus, an earth-boring beetle with biparental care, collected from a natural population. For identifying the most stable genes we used the following computational methods: geNorm, NormFinder, BestKeeper, comparative delta Ct method and RefFinder. Based on our results, the two body regions sampled (head and thorax) differ in which genes are most stably expressed. We identified two candidate reference genes for each region investigated: ribosomal protein L7A and RP18 in samples extracted from the head, and ribosomal protein L7A and RP4 extracted from the muscles of the thorax. Additionally, L7A and RP18 appear to be the best reference genes for normalisation in all samples irrespective of body region. These reference genes can be used to study the hormonal regulation of reproduction and parental care in Lethrus apterus in the future. creator: Nikoletta A. Nagy creator: Zoltán Németh creator: Edit Juhász creator: Szilárd Póliska creator: Rita Rácz creator: András Kosztolányi creator: Zoltán Barta uri: https://doi.org/10.7717/peerj.4047 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nagy et al. title: Phylogeographic and population insights of the Asian common toad (Bufo gargarizans) in Korea and China: population isolation and expansions as response to the ice ages link: https://peerj.com/articles/4044 last-modified: 2017-11-28 description: The effects of ice ages on speciation have been well documented for many European and North American taxa. In contrast, very few studies have addressed the consequences of such environmental and topographical changes in North East Asian species. More precisely, the Korean Peninsula offers a unique model to assess patterns and processes of speciation as it hosts the northern- and eastern-most distribution limit of some widespread Asian taxa. Despite this, studies addressing phylogeographic patterns and population genetics in the peninsula and surrounding countries are few and studies for most families are lacking. Here we inferred the phylogenetic relationships of the common toad (Bufo gargarizans) from South Korea and their North East Asian counterpart populations, based on mitochondrial data. Korean B. gargarizans GenBank BLASTs matched few individuals from nearby China, but the presence of a Korean clade suggests isolation on the Korean Peninsula, previous to the last glacial maximum, linked to sea level resurgence. Molecular clock calibrations within this group were used to date the divergence between clades and their relationship to paleo-climatic events in the area. Lack of genetic structure among South Korean populations and strong homogeneity between the Korean and some Chinese localities suggest weak isolation and recent expansion. Geographical projection of continuous coalescent maximum-clade-credibility trees shows an original Chinese expansion towards the Korean Peninsula through the Yellow Sea circa two million years ago with colonisation events dating circa 800 thousand years ago (K. y. a.). Following this colonisation, the data point to outgoing Korean Peninsula dispersal events throughout different periods, towards the North through land, and West through land bridge formations over the Yellow Sea during sea level falls. In accordance, demographic analyses revealed a population expansion in the Koran Peninsula circa 300 K. y. a., likely attributed to glacial cycle fluctuations. creator: Amaël Borzée creator: Joana L. Santos creator: Santiago Sánchez-RamÍrez creator: Yoonhyuk Bae creator: Kyongman Heo creator: Yikweon Jang creator: Michael Joseph Jowers uri: https://doi.org/10.7717/peerj.4044 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Borzée et al. title: Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits link: https://peerj.com/articles/4100 last-modified: 2017-11-27 description: Diarrhea is a syndrome of digestive disorders in young rabbits and may lead to secondary infections resulting in reduced immunity and higher mortality in baby rabbits, with serious impacts on rabbit farming. In this study, we investigated the effects of diarrhea on the health of baby rabbits in terms of intestinal mucosal development, immune function, and intestinal microbial diversity. We found that the duodenal villus length and the villus/crypt ratio in rabbits with diarrhea were significantly reduced compared with those in healthy rabbits (P < 0.01). Rabbits with diarrhea had significantly lower concentrations of acetic acid (P < 0.05), higher pH levels (P < 0.05), and higher levels of ammonia nitrogen (P < 0.01) in the cecum. Moreover, diarrhea in baby rabbits led to significantly reduced levels of total serum protein (P < 0.05) and markedly increased levels of alkaline phosphatase, urea nitrogen, TNF-α, and IL-6 (P < 0.05). Transcriptional analysis of peptidoglycan recognition proteins (PGRPs, including PGLYRP-1, PGLYRP-2, and PGLYRP-3) using real-time PCR revealed that diarrhea induced the upregulation of PGRPs in the cecum and duodenum. Furthermore, through pyrosequencing of the 16S rRNA V4 region in cecum samples, we found that the total number and diversity of microbes were not significantly different between healthy rabbits and those with diarrhea, though there were noticeable differences in the prevalences of Clostridium, Roseburia, and Alistipes. Our results will contribute to a better understanding of the pathological mechanisms of diarrhea in young rabbits. creator: Yang Chen creator: Bohao Zhao creator: Yuwei Wu creator: Shuaishuai Hu creator: Lin Mu creator: Cigen Zhu creator: Yulai Pan creator: Xinsheng Wu uri: https://doi.org/10.7717/peerj.4100 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chen et al. title: Diagnostic value of serum procalcitonin, lactate, and high-sensitivity C-reactive protein for predicting bacteremia in adult patients in the emergency department link: https://peerj.com/articles/4094 last-modified: 2017-11-27 description: BackgroundFew studies compared the diagnostic value of procalcitonin with a combination of other tests including lactate and high-sensitivity C-reactive protein in the prediction of pathogenic bacteremia in emergency department adult patients.MethodsWe performed a retrospective study assessing the differences in performances of procalcitonin at a cutoff of 0.5 ng/mL, lactate at a cutoff of 19.8 mg/dL, high-sensitivity C-reactive protein at a cutoff of 0.8 mg/dL and their combinations for predicting bacteremia in emergency department adult patients. Sensitivity, specificity, overall accuracy, positive-test and negative-test likelihood, and diagnostic odds ratio with 95% confidence interval for each test combination were calculated for comparison. The receiver operating characteristic curve for every single test were compared using DeLong’s method. We also performed a sensitivity analysis in two expanded patient cohorts to assess the discriminative ability of procalcitonin or test combination.ResultsA total of 886 patients formed the initial patient cohort. The area under the receiver operating characteristic curve for discriminating positive blood culture was: procalcitonin = 0.72 (95% CI [0.69–0.75]) with a derived optimal cutoff at 3.9 ng/mL; lactate 0.69 (0.66–0.72) with an optimal cutoff at 17.9 mg/dL; high-sensitivity C-reactive protein 0.56 (0.53–0.59) with an optimal cutoff of 13 mg/dL; with pairwise comparisons showing statistically significant better performance of either procalcitonin or lactate outperforming high-sensitivity C-reactive protein. To predict positive blood cultures, the diagnostic odds ratio for procalcitonin was 3.64 (95% CI [2.46–5.51]), lactate 2.93 (2.09–4.14), and high-sensitivity C-reactive protein 0.91 (0.55–1.55; P = 0.79). About combined tests, the diagnostic odds ratio for procalcitonin and lactate increases were 3.98 (95% CI [2.81–5.63]) for positive blood culture prediction. Elevated procalcitonin level rendered a six-fold increased risk of positive gram-negative bacteremia with a diagnostic odds ratio of 6.44 (95% CI [3.65–12.15]), which showed no further improvement in any test combinations. In the sensitivity analysis, as a single test to predict unspecified, gram-negative and gram-positive bacteremia, procalcitonin performed even better in an expanded cohort of 2,234 adult patients in terms of the diagnostic odds ratio.DiscussionsFor adult emergency patients, procalcitonin has an acceptable discriminative ability for bacterial blood culture and a better discriminative ability for gram-negative bacteremia when compared with lactate and high-sensitivity C-reactive protein. High-sensitivity C-reactive protein at a cutoff of 0.8 mg/dL performed poorly for the prediction of positive bacterial culture. creator: Chiung-Tsung Lin creator: Jang-Jih Lu creator: Yu-Ching Chen creator: Victor C. Kok creator: Jorng-Tzong Horng uri: https://doi.org/10.7717/peerj.4094 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lin et al. title: The zebrafish as a model system for analyzing mammalian and native α-crystallin promoter function link: https://peerj.com/articles/4093 last-modified: 2017-11-27 description: Previous studies have used the zebrafish to investigate the biology of lens crystallin proteins and their roles in development and disease. However, little is known about zebrafish α-crystallin promoter function, how it compares to that of mammals, or whether mammalian α-crystallin promoter activity can be assessed using zebrafish embryos. We injected a variety of α-crystallin promoter fragments from each species combined with the coding sequence for green fluorescent protein (GFP) into zebrafish zygotes to determine the resulting spatiotemporal expression patterns in the developing embryo. We also measured mRNA levels and protein abundance for all three zebrafish α-crystallins. Our data showed that mouse and zebrafish αA-crystallin promoters generated similar GFP expression in the lens, but with earlier onset when using mouse promoters. Expression was also found in notochord and skeletal muscle in a smaller percentage of embryos. Mouse αB-crystallin promoter fragments drove GFP expression primarily in zebrafish skeletal muscle, with less common expression in notochord, lens, heart and in extraocular regions of the eye. A short fragment containing only a lens-specific enhancer region increased lens and notochord GFP expression while decreasing muscle expression, suggesting that the influence of mouse promoter control regions carries over into zebrafish embryos. The two paralogous zebrafish αB-crystallin promoters produced subtly different expression profiles, with the aBa promoter driving expression equally in notochord and skeletal muscle while the αBb promoter resulted primarily in skeletal muscle expression. Messenger RNA for zebrafish αA increased between 1 and 2 days post fertilization (dpf), αBa increased between 4 and 5 dpf, but αBb remained at baseline levels through 5 dpf. Parallel reaction monitoring (PRM) mass spectrometry was used to detect αA, aBa, and αBb peptides in digests of zebrafish embryos. In whole embryos, αA-crystallin was first detected by 2 dpf, peaked in abundance by 4–5 dpf, and was localized to the eye. αBa was detected in whole embryo at nearly constant levels from 1–6 dpf, was also localized primarily to the eye, and its abundance in extraocular tissues decreased from 4–7 dpf. In contrast, due to its low abundance, no αBb protein could be detected in whole embryo, or dissected eye and extraocular tissues. Our results show that mammalian α-crystallin promoters can be efficiently screened in zebrafish embryos and that their controlling regions are well conserved. An ontogenetic shift in zebrafish aBa-crystallin promoter activity provides an interesting system for examining the evolution and control of tissue specificity. Future studies that combine these promoter based approaches with the expanding ability to engineer the zebrafish genome via techniques such as CRISPR/Cas9 will allow the manipulation of protein expression to test hypotheses about lens crystallin function and its relation to lens biology and disease. creator: Mason Posner creator: Kelly L. Murray creator: Matthew S. McDonald creator: Hayden Eighinger creator: Brandon Andrew creator: Amy Drossman creator: Zachary Haley creator: Justin Nussbaum creator: Larry L. David creator: Kirsten J. Lampi uri: https://doi.org/10.7717/peerj.4093 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Posner et al. title: The relationship between egg size and helper number in cooperative breeders: a meta-analysis across species link: https://peerj.com/articles/4028 last-modified: 2017-11-24 description: BackgroundLife history theory predicts that mothers should adjust reproductive investment depending on benefits of current reproduction and costs of reduced future reproductive success. These costs and benefits may in turn depend on the breeding female’s social environment. Cooperative breeders provide an ideal system to test whether changes in maternal investment are associated with the social conditions mothers experience. As alloparental helpers assist in offspring care, larger groups might reduce reproductive costs for mothers or alternatively indicate attractive conditions for reproduction. Thus, mothers may show reduced (load-lightening) or increased (differential allocation) reproductive investment in relation to group size. A growing number of studies have investigated how cooperatively breeding mothers adjust pre-natal investment depending on group size. Our aim was to survey these studies to assess, first, whether mothers consistently reduce or increase pre-natal investment when in larger groups and, second, whether these changes relate to variation in post-natal investment.MethodsWe extracted data on the relationship between helper number and maternal pre-natal investment (egg size) from 12 studies on 10 species of cooperatively breeding vertebrates. We performed meta-analyses to calculate the overall estimated relationship between egg size and helper number, and to quantify variation among species. We also tested whether these relationships are stronger in species in which the addition of helpers is associated with significant changes in maternal and helper post-natal investment.ResultsAcross studies, there is a significant negative relationship between helper number and egg size, suggesting that in most instances mothers show reduced reproductive investment in larger groups, in particular in species in which mothers also show a significant reduction in post-natal investment. However, even in this limited sample, substantial variation exists in the relationship between helper number and egg size, and the overall effect appears to be driven by a few well-studied species.DiscussionOur results, albeit based on a small sample of studies and species, indicate that cooperatively breeding females tend to produce smaller eggs in larger groups. These findings on prenatal investment accord with previous studies showing similar load-lightening reductions in postnatal parental effort (leading to concealed helper effects), but do not provide empirical support for differential allocation. However, the considerable variation in effect size across studies suggests that maternal investment is mitigated by additional factors. Our findings indicate that variation in the social environment may influence life-history strategies and suggest that future studies investigating within-individual changes in maternal investment in cooperative breeders offer a fruitful avenue to study the role of adaptive plasticity. creator: Tanmay Dixit creator: Sinead English creator: Dieter Lukas uri: https://doi.org/10.7717/peerj.4028 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dixit et al. title: The impact of self-incompatibility systems on the prevention of biparental inbreeding link: https://peerj.com/articles/4085 last-modified: 2017-11-24 description: Inbreeding in hermaphroditic plants can occur through two different mechanisms: biparental inbreeding, when a plant mates with a related individual, or self-fertilization, when a plant mates with itself. To avoid inbreeding, many hermaphroditic plants have evolved self-incompatibility (SI) systems which prevent or limit self-fertilization. One particular SI system—homomorphic SI—can also reduce biparental inbreeding. Homomorphic SI is found in many angiosperm species, and it is often assumed that the additional benefit of reduced biparental inbreeding may be a factor in the success of this SI system. To test this assumption, we developed a spatially-explicit, individual-based simulation of plant populations that displayed three different types of homomorphic SI. We measured the total level of inbreeding avoidance by comparing each population to a self-compatible population (NSI), and we measured biparental inbreeding avoidance by comparing to a population of self-incompatible plants that were free to mate with any other individual (PSI). Because biparental inbreeding is more common when offspring dispersal is limited, we examined the levels of biparental inbreeding over a range of dispersal distances. We also tested whether the introduction of inbreeding depression affected the level of biparental inbreeding avoidance. We found that there was a statistically significant decrease in autozygosity in each of the homomorphic SI populations compared to the PSI population and, as expected, this was more pronounced when seed and pollen dispersal was limited. However, levels of homozygosity and inbreeding depression were not reduced. At low dispersal, homomorphic SI populations also suffered reduced female fecundity and had smaller census population sizes. Overall, our simulations showed that the homomorphic SI systems had little impact on the amount of biparental inbreeding in the population especially when compared to the overall reduction in inbreeding compared to the NSI population. With further study, this observation may have important consequences for research into the origin and evolution of homomorphic self-incompatibility systems. creator: Tara N. Furstenau creator: Reed A. Cartwright uri: https://doi.org/10.7717/peerj.4085 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Furstenau and Cartwright title: Characteristics and risk factors of rheumatoid arthritis in the United States: an NHANES analysis link: https://peerj.com/articles/4035 last-modified: 2017-11-24 description: BackgroundWe examined the United States National Health and Nutrition Examination Survey (NHANES) database to determine factors associated with rheumatoid arthritis (RA) in adults 20 to 55 years of age.MethodsNHANES data collected between 2007 and 2014, excluding the 2011–2012 period, were used. Subjects were divided into those with and without RA. Demographic, clinical, and lifestyle factors were compared between the groups.ResultsAfter applying inclusion/exclusion criteria, 8,789 persons were included in the study (8,483 without RA, 306 with RA). Multivariable analysis indicated that advanced age (odds ratio [OR] = 1.09, 95% CI [1.07–1.11], P < 0.001), regular smoking (OR = 2.19, 95% CI [1.49–3.21], P < 0.001), diabetes (OR = 2.00, 95% CI [1.35–2.95], P = 0.001), obesity (reference, normal or underweight; OR = 3.31, 95% CI [2.05–5.36], P < 0.001), and osteoporosis (OR = 3.68, 95% CI [1.64–8.22], P = 0.002) were positively associated with RA. Covered by health insurance (OR = 1.81, 95% CI [1.12–2.93], P = 0.016) and living in poverty (OR = 2.96, 95% CI [1.88–4.65], P < 0.001) were also associated with having RA. Mexican American, Hispanic white or other Hispanic ethnicity (reference, non-Hispanic white; OR = 0.54, 95% CI [0.31–0.96], P = 0.036), appropriate sleep duration (about 6–11 h, OR = 0.46, 95% CI [0.32–0.65], P < 0.001), and insufficient vitamin A intake (reference, recommended; OR = 0.70, 95% CI [0.50–0.98], P = 0.036) were negatively associated with RA.DiscussionSome factors associated with RA are potentially modifiable. creator: Bei Xu creator: Jin Lin uri: https://doi.org/10.7717/peerj.4035 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Xu and Lin title: Forelimb muscle and joint actions in Archosauria: insights from Crocodylus johnstoni (Pseudosuchia) and Mussaurus patagonicus (Sauropodomorpha) link: https://peerj.com/articles/3976 last-modified: 2017-11-24 description: Many of the major locomotor transitions during the evolution of Archosauria, the lineage including crocodiles and birds as well as extinct Dinosauria, were shifts from quadrupedalism to bipedalism (and vice versa). Those occurred within a continuum between more sprawling and erect modes of locomotion and involved drastic changes of limb anatomy and function in several lineages, including sauropodomorph dinosaurs. We present biomechanical computer models of two locomotor extremes within Archosauria in an analysis of joint ranges of motion and the moment arms of the major forelimb muscles in order to quantify biomechanical differences between more sprawling, pseudosuchian (represented the crocodile Crocodylus johnstoni) and more erect, dinosaurian (represented by the sauropodomorph Mussaurus patagonicus) modes of forelimb function. We compare these two locomotor extremes in terms of the reconstructed musculoskeletal anatomy, ranges of motion of the forelimb joints and the moment arm patterns of muscles across those ranges of joint motion. We reconstructed the three-dimensional paths of 30 muscles acting around the shoulder, elbow and wrist joints. We explicitly evaluate how forelimb joint mobility and muscle actions may have changed with postural and anatomical alterations from basal archosaurs to early sauropodomorphs. We thus evaluate in which ways forelimb posture was correlated with muscle leverage, and how such differences fit into a broader evolutionary context (i.e. transition from sprawling quadrupedalism to erect bipedalism and then shifting to graviportal quadrupedalism). Our analysis reveals major differences of muscle actions between the more sprawling and erect models at the shoulder joint. These differences are related not only to the articular surfaces but also to the orientation of the scapula, in which extension/flexion movements in Crocodylus (e.g. protraction of the humerus) correspond to elevation/depression in Mussaurus. Muscle action is highly influenced by limb posture, more so than morphology. Habitual quadrupedalism in Mussaurus is not supported by our analysis of joint range of motion, which indicates that glenohumeral protraction was severely restricted. Additionally, some active pronation of the manus may have been possible in Mussaurus, allowing semi-pronation by a rearranging of the whole antebrachium (not the radius against the ulna, as previously thought) via long-axis rotation at the elbow joint. However, the muscles acting around this joint to actively pronate it may have been too weak to drive or maintain such orientations as opposed to a neutral position in between pronation and supination. Regardless, the origin of quadrupedalism in Sauropoda is not only linked to manus pronation but also to multiple shifts of forelimb morphology, allowing greater flexion movements of the glenohumeral joint and a more columnar forelimb posture. creator: Alejandro Otero creator: Vivian Allen creator: Diego Pol creator: John R. Hutchinson uri: https://doi.org/10.7717/peerj.3976 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Otero et al. title: Do rotational shear-cushioning shoes influence horizontal ground reaction forces and perceived comfort during basketball cutting maneuvers? link: https://peerj.com/articles/4086 last-modified: 2017-11-23 description: BackgroundCourt shoe designs predominantly focus on reducing excessive vertical ground reaction force, but shear force cushioning has received little attention in the basketball population. We aimed to examine the effect of a novel shoe-cushioning design on both resultant horizontal ground reaction forces and comfort perception during two basketball-specific cutting movements.MethodsFifteen university team basketball players performed lateral shuffling and 45-degree sidestep cutting at maximum effort in basketball shoes with and without the shear-cushioning system (SCS). Paired t-tests were used to examine the differences in kinetics and comfort perception between two shoes.ResultsSCS shoe allowed for larger rotational material deformation compared with control shoes, but no significant shoe differences were found in braking phase kinetics during both cutting movements (P = 0.35). Interestingly, a greater horizontal propulsion impulse was found with the SCS during 45-degree cutting (P < 0.05), when compared with the control. In addition, players wearing SCS shoes perceived better forefoot comfort (P = 0.012). During lateral shuffling, there were no significant differences in horizontal GRF and comfort perception between shoe conditions (P > 0.05).DiscussionThe application of a rotational shear-cushioning structure allowed for better forefoot comfort and enhanced propulsion performance in cutting, but did not influence the shear impact. Understanding horizontal ground reaction force information may be useful in designing footwear to prevent shear-related injuries in sport populations. creator: Wing-Kai Lam creator: Yi Qu creator: Fan Yang creator: Roy T.H. Cheung uri: https://doi.org/10.7717/peerj.4086 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lam et al. title: Associations of IGF2 and DRD2 polymorphisms with laying traits in Muscovy duck link: https://peerj.com/articles/4083 last-modified: 2017-11-23 description: Insulin-like growth factor 2 (IGF2) and dopamine receptor 2 (DRD2) play important roles in ovarian follicular development. In this study, we analyzed tissue-specific expression of the Muscovy duck IGF2 and DRD2 genes and cloned those genes transcripts. Polymorphisms in these genes were tightly linked with egg production traits and both genes were highly expressed in the ovary. Moreover, we identified five single nucleotide polymorphisms (SNPs) for IGF1 and 28 for DRD2. Mutations A-1864G and C-1704G of IGF2 were positively correlated with increased egg laying at 59 weeks (E59W) (P < 0.05). The C+7T and C+364G mutations of DRD2 were highly and significantly associated with first-egg age (FEA) and egg numbers at 300 days (E300D) (P < 0.01). Moreover, C+3301G and C+3545G of DRD2 were highly significantly associated with FEA, E59W and E300D (P < 0.01). Other mutations were positively associated with FEA or E300D or E59W (P < 0.05). These data suggest specific roles for IGF1 and DRD2 polymorphisms in egg production in Muscovy ducks. creator: Qiao Ye creator: Jiguo Xu creator: Xinfeng Gao creator: Hongjia Ouyang creator: Wei Luo creator: Qinghua Nie uri: https://doi.org/10.7717/peerj.4083 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ye et al. title: An update on anticancer drug development and delivery targeting carbonic anhydrase IX link: https://peerj.com/articles/4068 last-modified: 2017-11-23 description: The expression of carbonic anhydrase (CA) IX is up-regulated in many types of solid tumors in humans under hypoxic and acidic microenvironment. Inhibition of CA IX enzymatic activity with selective inhibitors, antibodies or labeled probes has been shown to reverse the acidic environment of solid tumors and reduce the tumor growth establishing the significant role of CA IX in tumorigenesis. Thus, the development of potent antitumor drugs targeting CA IX with minimal toxic effects is important for the target-specific tumor therapy. Recently, several promising antitumor agents against CA IX have been developed to treat certain types of cancers in combination with radiation and chemotherapy. Here we review the inhibition of CA IX by small molecule compounds and monoclonal antibodies. The methods of enzymatic assays, biophysical methods, animal models including zebrafish and Xenopus oocytes, and techniques of diagnostic imaging to detect hypoxic tumors using CA IX-targeted conjugates are discussed with the aim to overview the recent progress related to novel therapeutic agents that target CA IX in hypoxic tumors. creator: Justina Kazokaitė creator: Ashok Aspatwar creator: Seppo Parkkila creator: Daumantas Matulis uri: https://doi.org/10.7717/peerj.4068 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kazokaitė et al. title: Antibodies to Bordetella pertussis antigens in maternal and cord blood pairs: a Thai cohort study link: https://peerj.com/articles/4043 last-modified: 2017-11-23 description: BackgroundPertussis is a vaccine-preventable disease, yet an increasing incidence of pertussis occurs in many countries. Thailand has a long-standing pertussis vaccination policy, therefore most expectant mothers today had received vaccines as children. The resurgence of pertussis among Thai infants in recent years led us to examine the pre-existing antibodies to Bordetella pertussis antigens in a cohort of 90 pregnant women.MethodsWe evaluated the IgG to the Pertussis toxin (PT), filamentous hemagglutinin (FHA) and pertactin (PRN) in maternal and cord blood sera using commercial enzyme-linked immunosorbent assays (ELISA).ResultsWhen values of >10 IU/ml were accepted as potential protective concentrations, we found that the percentages of unprotected infants were 73.3%, 43.3% and 75.5% for anti-PT, anti-FHA and anti-PRN IgG, respectively.DiscussionThese results may explain the susceptibility for pertussis among newborn infants in Thailand and support the requirement for a pertussis booster vaccine during pregnancy, which may contribute to the passive seroprotection among newborns during the first months of life. creator: Nasamon Wanlapakorn creator: Thanunrat Thongmee creator: Preeyaporn Vichaiwattana creator: Elke Leuridan creator: Sompong Vongpunsawad creator: Yong Poovorawan uri: https://doi.org/10.7717/peerj.4043 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wanlapakorn et al. title: Morphological and molecular data confirm the transfer of homostylous species in the typically distylous genus Galianthe (Rubiaceae), and the description of the new species Galianthe vasquezii from Peru and Colombia link: https://peerj.com/articles/4012 last-modified: 2017-11-23 description: Galianthe (Rubiaceae) is a neotropical genus comprising 50 species divided into two subgenera, Galianthe subgen. Galianthe, with 39 species and Galianthe subgen. Ebelia, with 11 species. The diagnostic features of the genus are: usually erect habit with xylopodium, distylous flowers arranged in lax thyrsoid inflorescences, bifid stigmas, 2-carpellate and longitudinally dehiscent fruits, with dehiscent valves or indehiscent mericarps, plump seeds or complanate with a wing-like strophiole, and pollen with double reticulum, rarely with a simple reticulum. This study focused on two species that were originally described under Diodia due to the occurrence of fruits indehiscent mericarps: Diodia palustris and D. spicata. In the present study, classical taxonomy is combined with molecular analyses. As a result, we propose that both Diodia species belong to Galianthe subgen. Ebelia. The molecular position within Galianthe, based on ITS and ETS sequences, has been supported by the following morphological characters: thyrsoid, spiciform or cymoidal inflorescences, bifid stigmas, pollen grains with a double reticulum, and indehiscent mericarps. However, both species, unlike the remainder of the genus Galianthe, have homostylous flowers, so the presence of this type of flower significantly modifies the generic concept. In this framework, a third homostylous species, Galianthe vasquezii, from the Andean region is also described. Until now, this species remained cryptic under specimens of Galianthe palustris It differs however from the latter by having longer calyx lobes, the presence of dispersed trichomes inside the corolla lobes (vs. glabrous), fruits that are acropetally dehiscent (vs. basipetally dehiscent), and its Andean geographical distribution (vs. Paranaense). Additionally, a lectotype has been chosen for Diodia palustris, Borreria pterophora has been placed under synonymy of Galianthe palustris, and Galianthe boliviana is reported for the first time from Peru. A key of all Galianthe species with indehiscent mericarps is also provided. creator: Javier Elias Florentín creator: Andrea Alejandra Cabaña Fader creator: Roberto Manuel Salas creator: Steven Janssens creator: Steven Dessein creator: Elsa Leonor Cabral uri: https://doi.org/10.7717/peerj.4012 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Florentín et al. title: Modus operandi and affect in Sweden: the Swedish version of the Regulatory Mode Questionnaire link: https://peerj.com/articles/4092 last-modified: 2017-11-22 description: BackgroundThe Regulatory Mode Questionnaire (RMQ) is the most used and internationally well-known instrument for the measurement of individual differences in the two self-regulatory modes: locomotion (i.e., the aspect of self-regulation that is concerned with movement from state to state) and assessment (i.e., the comparative aspect of self-regulation). The aim of the present study was to verify the independence of the two regulatory modes, as postulated by the Regulatory Mode Theory (Kruglanski et al., 2000), and the psychometric properties of the RMQ in the Swedish context. Furthermore, we investigated the relationship between regulatory modes (locomotion and assessment) and affective well-being (i.e., positive affect and negative affect).MethodA total of 655 university and high school students in the West of Sweden (males = 408 females = 242, and five participants who didn’t report their gender; agemean = 21.93 ± 6.51) responded to the RMQ and the Positive Affect Negative Affect Schedule. We conducted two confirmatory factor analyses using structural equation modeling (SEM). A third SEM was conducted to test the relationship between locomotion and assessment to positive affect and negative affect.ResultsThe first analyses confirmed the unidimensional factor structure of locomotion and assessment and both scales showed good reliability. The assessment scale, however, was modified by dropping item 10 (“I don’t spend much time thinking about ways others could improve themselves”.) because it showed low loading (.07, p = .115). Furthermore, the effect of locomotion on positive affect was stronger than the effect of assessment on positive affect (Z = −15.16, p < .001), while the effect of assessment on negative affect was stronger than the effect of locomotion on negative affect (Z = 10.73, p < .001).ConclusionThe factor structure of the Swedish version of the RMQ is, as Regulatory Mode Theory suggests, unidimensional and it showed good reliability. The scales discriminated between the two affective well-being dimensions. We suggest that the Swedish version of the RMQ, with only minor modifications, is a useful instrument to tap individual differences in locomotion and assessment. Hence, the present study contributes to the validation of the RMQ in the Swedish culture and adds support to the theoretical framework of self-regulatory mode. creator: Clara Amato creator: Ali Al Nima creator: Marko Mihailovic creator: Danilo Garcia uri: https://doi.org/10.7717/peerj.4092 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Amato et al. title: I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples link: https://peerj.com/articles/4040 last-modified: 2017-11-22 description: Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome profiling of clinical samples. With this advancement in technology, we are now accumulating ATAC-seq samples from clinical samples at an unprecedented rate. These epigenomic profiles hold the key to uncovering how transcriptional programs are established in diverse human cells and are disrupted by genetic or environmental factors. Thus, the barrier to deriving important clinical insights from clinical epigenomic samples is no longer one of data generation but of data analysis. Specifically, we are still missing easy-to-use software tools that will enable non-computational scientists to analyze their own ATAC-seq samples. To facilitate systematic pre-processing and management of ATAC-seq samples, we developed an interactive, cross-platform, user-friendly and customized desktop application: interactive-ATAC (I-ATAC). I-ATAC integrates command-line data processing tools (FASTQC, Trimmomatic, BWA, Picard, ATAC_BAM_shiftrt_gappedAlign.pl, Bedtools and Macs2) into an easy-to-use platform with user interface to automatically pre-process ATAC-seq samples with parallelized and customizable pipelines. Its performance has been tested using public ATAC-seq datasets in GM12878 and CD4+T cells and a feature-based comparison is performed with some available interactive LIMS (Galaxy, SMITH, SeqBench, Wasp, NG6, openBIS). I-ATAC is designed to empower non-computational scientists to process their own datasets and to break to exclusivity of data analyses to computational scientists. Additionally, I-ATAC is capable of processing WGS and ChIP-seq samples, and can be customized by the user for one-independent or multiple-sequential operations. creator: Zeeshan Ahmed creator: Duygu Ucar uri: https://doi.org/10.7717/peerj.4040 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ahmed and Ucar title: Assessment of brain functional connectome alternations and correlation with depression and anxiety in major depressive disorders link: https://peerj.com/articles/3147 last-modified: 2017-11-22 description: Major depressive disorder (MDD) is highly prevalent, recurrent, and associated with functional impairment, morbidity, and mortality. Herein, we aimed to identify disruptions in functional connectomics among subjects with MDD by using resting-state functional magnetic resonance imaging (rs-fMRI). Sixteen subjects with MDD and thirty health controls completed resting-state fMRI scans and clinical assessments (e.g., Hamilton Depression Rating Scale (HAMD) and Hospital Anxiety and Depression Scale (HADS)). We found higher amplitude of low frequency fluctuations (ALFF) bilaterally in the hippocampus and amygdala among MDD subjects when compared to healthy controls. Using graph theoretical analysis, we found decreased clustering coefficient, local efficiency, and transitivity in the MDD patients. Our findings suggest a potential biomarker for differentiating individuals with MDD from individuals without MDD. creator: Vincent Chin-Hung Chen creator: Chao-Yu Shen creator: Sophie Hsin-Yi Liang creator: Zhen-Hui Li creator: Ming-Hong Hsieh creator: Yeu-Sheng Tyan creator: Mong-Liang Lu creator: Yena Lee creator: Roger S. McIntyre creator: Jun-Cheng Weng uri: https://doi.org/10.7717/peerj.3147 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chen et al. title: Morphological convergence in ‘river dolphin’ skulls link: https://peerj.com/articles/4090 last-modified: 2017-11-21 description: Convergent evolution can provide insights into the predictability of, and constraints on, the evolution of biodiversity. One striking example of convergence is seen in the ‘river dolphins’. The four dolphin genera that make up the ‘river dolphins’ (Inia geoffrensis, Pontoporia blainvillei, Platanista gangetica and Lipotes vexillifer) do not represent a single monophyletic group, despite being very similar in morphology. This has led many to using the ‘river dolphins’ as an example of convergent evolution. We investigate whether the skulls of the four ‘river dolphin’ genera are convergent when compared to other toothed dolphin taxa in addition to identifying convergent cranial and mandibular features. We use geometric morphometrics to uncover shape variation in the skulls of the ‘river dolphins’ and then apply a number of phylogenetic techniques to test for convergence. We find significant convergence in the skull morphology of the ‘river dolphins’. The four genera seem to have evolved similar skull shapes, leading to a convergent morphotype characterised by elongation of skull features. The cause of this morphological convergence remains unclear. However, the features we uncover as convergent, in particular elongation of the rostrum, support hypotheses of shared feeding mode or diet and thus provide the foundation for future work into convergence within the Odontoceti. creator: Charlotte E. Page creator: Natalie Cooper uri: https://doi.org/10.7717/peerj.4090 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Page and Cooper title: Diversity of bacterial communities on the facial skin of different age-group Thai males link: https://peerj.com/articles/4084 last-modified: 2017-11-21 description: BackgroundSkin microbiome varies from person to person due to a combination of various factors, including age, biogeography, sex, cosmetics and genetics. Many skin disorders appear to be related to the resident microflora, yet databases of facial skin microbiome of many biogeographies, including Thai, are limited.MethodsMetagenomics derived B-RISA and 16S rRNA gene sequencing was utilized to identify the culture-independent bacterial diversity on Thai male faces (cheek and forehead areas). Skin samples were categorized (grouped) into (i) normal (teenage.hea) and (ii) acne-prone (teenage.acn) young adults, and normal (iii) middle-aged (middle.hea) and (iv) elderly (elderly.hea) adults.ResultsThe 16S rRNA gene sequencing was successful as the sequencing depth had an estimated >98% genus coverage of the true community. The major diversity was found between the young and elderly adults in both cheek and forehead areas, followed by that between normal and acne young adults. Detection of representative characteristics indicated that bacteria from the order Rhizobiales, genera Sphingomonas and Pseudoalteromonas, distinguished the elderly.hea microbiota, along the clinical features of wrinkles and pores. Prediction of the metabolic potential revealed reduced metabolic pathways involved in replication and repair, nucleotide metabolism and genetic translation in the elderly.hea compared with that in the teenage.hea. For young adults, some unique compositions such as abundance of Propionibacterium acnes and Staphylococcus epidermidis, with a minor diversity between normal and acne skins, were detected. The metabolic potentials of the acne vs. normal young adults showed that teenage.acn was low in many cellular processes (e.g., cell motility and environmental adaptation), but high in carbohydrate metabolism, which could support acne growth. Moreover, comparison with the age-matched males from the US (Boulder, Colorado) to gain insight into the diversity across national biogeography, revealed differences in the distribution pattern of species, although common bacteria were present in both biogeographical samples. Furthermore, B-RISA served as a crosscheck result to the 16S rRNA gene sequencing (i.e., differences between teenage and elderly microbiota).ConclusionsThis study revealed and compared the microbial diversity on different aged Thai male faces, and included analyses for representing the bacterial flora, the clinical skin characteristics, and comparison with the US age-matched. The results represent the first skin microbiota of Thai males, and helps the design of a large-scale skin microbiome study of Thais. The findings of the diversity among ages, skin type and national biogeography supported the importance of these traits in the skin microbiome and in developing a safe and sustainable treatment for acne and aging skin diseases. creator: Alisa Wilantho creator: Pamornya Deekaew creator: Chutika Srisuttiyakorn creator: Sissades Tongsima creator: Naraporn Somboonna uri: https://doi.org/10.7717/peerj.4084 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wilantho et al. title: Development of medical informatics in China over the past 30 years from a conference perspective and a Sino-American comparison link: https://peerj.com/articles/4082 last-modified: 2017-11-21 description: BackgroundAs the world’s second-largest economy, China has launched health reforms for the second time and invested significant funding in medical informatics (MI) since 2010; however, few studies have been conducted on the outcomes of this ambitious cause.ObjectiveThis study analyzed the features of major MI meetings held in China and compared them with similar MI conferences in the United States, aiming at informing researchers on the outcomes of MI in China and the US from the professional conference perspective and encouraging greater international cooperation for the advancement of the field of medical informatics in China and, ultimately, the promotion of China’s health reform.MethodsQualitative and quantitative analyses of four MI meetings in China (i.e., CMIAAS, CHINC, CHITEC, and CPMI) and two in the US (i.e., AMIA and HIMSS) were conducted. Furthermore, the size, constituent parts and regional allocation of participants, topics, and fields of research for each meeting were determined and compared.ResultsFrom 1985 to 2016, approximately 45,000 individuals attended the CMIAAS and CPMI (academic), CHINC and CHITEC (industry), resulting in 5,085 documented articles. In contrast, in 2015, 38,000 and 3,700 individuals, respectively, attended the American HIMSS (industry) and AMIA (academic) conferences and published 1,926 papers in the latter. Compared to those of HIMSS in 2015, the meeting duration of Chinese industry CHITEC was 3 vs. 5 days, the number of vendors was 100 vs. 1,500+, the number of sub-forums was 10 vs. 250; while compared to those of AMIA, the meeting duration of Chinese CMIAAS was 2 vs. 8 days, the number of vendors was 5 vs. 65+, the number of sub-forums was 4 vs. 26. HIMSS and AMIA were more open, international, and comprehensive in comparison to the aforementioned Chinese conferences.ConclusionsThe current MI in China can be characterized as “hot in industry application, and cold in academic research.” Taking into consideration the economic scale together with the huge investment in MI, conference yield and attendee diversity are still low in China. This study demonstrates an urgent necessity to elevate the medical informatics discipline in China and to expand research fields in order to maintain pace with the development of medical informatics in the US and other countries. creator: Jun Liang creator: Kunyan Wei creator: Qun Meng creator: Zhenying Chen creator: Jiajie Zhang creator: Jianbo Lei uri: https://doi.org/10.7717/peerj.4082 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liang et al. title: Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata link: https://peerj.com/articles/4077 last-modified: 2017-11-21 description: The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species. creator: Meghann K. Devlin-Durante creator: Iliana B. Baums uri: https://doi.org/10.7717/peerj.4077 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Devlin-Durante and Baums title: The ability of laying pullets to negotiate two ramp designs as measured by bird preference and behaviour link: https://peerj.com/articles/4069 last-modified: 2017-11-21 description: BackgroundLaying hens are often kept in barn or free-range systems where they must negotiate level changes in the house to access resources. However, collisions and resultant keel fractures are commonplace. Producers sometimes add ramps to make raised areas more accessible but designs vary and very little research has investigated bird preference or behaviour when using different ramp designs, or the effect of ramp design on falls and collisions.MethodsTwo ramp designs were studied in an experimental setting—a ramp made of plastic poultry slats (grid ramp, GR) and a ramp made of wooden rungs (ladder ramp, LR). Sixty-four young female hens were trained to move to a food reward and this was used to test their behavioural responses when first negotiating the two different ramps during individual tests. Both upward and downward transitions were studied. Ramp preference was also tested using a room that replicated a commercial single-tier system with both types of ramp available. Birds were placed in this room in groups of 16 for three days and their use of the ramps studied.ResultsA greater percentage of birds successfully completed (reached the reward bowl) on the GR than the LR during both upward (58% vs 37%) and downward (83% vs 73%) transitions, and a smaller percentage of birds made zero attempts to use the GR than the LR (upwards: 13% vs 56%, downwards: 8% vs 26%). When making a downward transition, more hesitation behaviours were seen (head orientations, stepping on the spot, moving away) for the LR. However, more head orientations were seen for the GR during the upward transition. Birds were more likely to abort attempts (an attempt began when a bird placed both feet on the ramp) to move up the GR than the LR. Birds took longer to negotiate the LR than the GR in both directions, and more pauses were seen during a successful upward transition on the LR. Birds were more likely to move down the GR by walking/running whereas birds tended to jump over the entire LR. More collisions with the food reward bowl were seen for the LR. In the group tests, birds preferred to use the GR, with more transitions seen at all timepoints. However, in these tests, birds preferred to rest on the LR with greater numbers of birds counted on this type of ramp during scan sampling at all timepoints.DiscussionBehavioural results suggest that the GR was easier for the birds to use than the LR, particularly on the downward transition. The GR was also less likely to result in collisions. However, the upward transition may be more difficult on the GR for some birds, potentially because of the inability to pause on a level surface during the transition. The results suggest that the GR was preferred by pullets for moving between a raised area and the ground but the LR was preferred for resting. creator: Isabelle C. Pettersson creator: Claire A. Weeks creator: Kate I. Norman creator: Christine J. Nicol uri: https://doi.org/10.7717/peerj.4069 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pettersson et al. title: Levels of detail analysis of microwave scattering from human head models for brain stroke detection link: https://peerj.com/articles/4061 last-modified: 2017-11-21 description: In this paper, we have presented a microwave scattering analysis from multiple human head models. This study incorporates different levels of detail in the human head models and its effect on microwave scattering phenomenon. Two levels of detail are taken into account; (i) Simplified ellipse shaped head model (ii) Anatomically realistic head model, implemented using 2-D geometry. In addition, heterogenic and frequency-dispersive behavior of the brain tissues has also been incorporated in our head models. It is identified during this study that the microwave scattering phenomenon changes significantly once the complexity of head model is increased by incorporating more details using magnetic resonance imaging database. It is also found out that the microwave scattering results match in both types of head model (i.e., geometrically simple and anatomically realistic), once the measurements are made in the structurally simplified regions. However, the results diverge considerably in the complex areas of brain due to the arbitrary shape interface of tissue layers in the anatomically realistic head model.After incorporating various levels of detail, the solution of subject microwave scattering problem and the measurement of transmitted and backscattered signals were obtained using finite element method. Mesh convergence analysis was also performed to achieve error free results with a minimum number of mesh elements and a lesser degree of freedom in the fast computational time. The results were promising and the E-Field values converged for both simple and complex geometrical models. However, the E-Field difference between both types of head model at the same reference point differentiated a lot in terms of magnitude. At complex location, a high difference value of 0.04236 V/m was measured compared to the simple location, where it turned out to be 0.00197 V/m. This study also contributes to provide a comparison analysis between the direct and iterative solvers so as to find out the solution of subject microwave scattering problem in a minimum computational time along with memory resources requirement.It is seen from this study that the microwave imaging may effectively be utilized for the detection, localization and differentiation of different types of brain stroke. The simulation results verified that the microwave imaging can be efficiently exploited to study the significant contrast between electric field values of the normal and abnormal brain tissues for the investigation of brain anomalies. In the end, a specific absorption rate analysis was carried out to compare the ionizing effects of microwave signals to different types of head model using a factor of safety for brain tissues. It is also suggested after careful study of various inversion methods in practice for microwave head imaging, that the contrast source inversion method may be more suitable and computationally efficient for such problems. creator: Awais Munawar Qureshi creator: Zartasha Mustansar uri: https://doi.org/10.7717/peerj.4061 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Qureshi and Mustansar title: Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach link: https://peerj.com/articles/4042 last-modified: 2017-11-21 description: BackgroundTartary buckwheat (TB), a crop rich in protein, dietary fiber, and flavonoids, has been reported to have an effect on Type II diabetes (T2D), hypertension (HT), and hyperlipidemia (HL). However, limited information is available about the relationship between Tartary buckwheat and these three diseases. The mechanisms of how TB impacts these diseases are still unclear.MethodsIn this study, network pharmacology was used to investigate the relationship between the herb as well as the diseases and the mechanisms of how TB might impact these diseases.ResultsA total of 97 putative targets of 20 compounds found in TB were obtained. Then, an interaction network of 97 putative targets for these compounds and known therapeutic targets for the treatment of the three diseases was constructed. Based on the constructed network, 28 major nodes were identified as the key targets of TB due to their importance in network topology. The targets of ATK2, IKBKB, RAF1, CHUK, TNF, JUN, and PRKCA were mainly involved in fluid shear stress and the atherosclerosis and PI3K-Akt signaling pathways. Finally, molecular docking simulation showed that 174 pairs of chemical components and the corresponding key targets had strong binding efficiencies.ConclusionFor the first time, a comprehensive systemic approach integrating drug target prediction, network analysis, and molecular docking simulation was developed to reveal the relationships and mechanisms between the putative targets in TB and T2D, HT, and HL. creator: Chao-Long Lu creator: Qi Zheng creator: Qi Shen creator: Chi Song creator: Zhi-Ming Zhang uri: https://doi.org/10.7717/peerj.4042 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lu et al. title: Transcriptome sequencing reveals high isoform diversity in the ant Formica exsecta link: https://peerj.com/articles/3998 last-modified: 2017-11-21 description: Transcriptome resources for social insects have the potential to provide new insight into polyphenism, i.e., how divergent phenotypes arise from the same genome. Here we present a transcriptome based on paired-end RNA sequencing data for the ant Formica exsecta (Formicidae, Hymenoptera). The RNA sequencing libraries were constructed from samples of several life stages of both sexes and female castes of queens and workers, in order to maximize representation of expressed genes. We first compare the performance of common assembly and scaffolding software (Trinity, Velvet-Oases, and SOAPdenovo-trans), in producing de novo assemblies. Second, we annotate the resulting expressed contigs to the currently published genomes of ants, and other insects, including the honeybee, to filter genes that have annotation evidence of being true genes. Our pipeline resulted in a final assembly of altogether 39,262 mRNA transcripts, with an average coverage of >300X, belonging to 17,496 unique genes with annotation in the related ant species. From these genes, 536 genes were unique to one caste or sex only, highlighting the importance of comprehensive sampling. Our final assembly also showed expression of several splice variants in 6,975 genes, and we show that accounting for splice variants affects the outcome of downstream analyses such as gene ontologies. Our transcriptome provides an outstanding resource for future genetic studies on F. exsecta and other ant species, and the presented transcriptome assembly can be adapted to any non-model species that has genomic resources available from a related taxon. creator: Kishor Dhaygude creator: Kalevi Trontti creator: Jenni Paviala creator: Claire Morandin creator: Christopher Wheat creator: Liselotte Sundström creator: Heikki Helanterä uri: https://doi.org/10.7717/peerj.3998 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dhaygude et al. title: The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification link: https://peerj.com/articles/3995 last-modified: 2017-11-21 description: Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus. creator: Tao Pan creator: Yanan Zhang creator: Hui Wang creator: Jun Wu creator: Xing Kang creator: Lifu Qian creator: Jinyun Chen creator: Dingqi Rao creator: Jianping Jiang creator: Baowei Zhang uri: https://doi.org/10.7717/peerj.3995 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pan et al. title: PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks link: https://peerj.com/articles/4013 last-modified: 2017-11-20 description: This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license. creator: Jonathan Barnoud creator: Hubert Santuz creator: Pierrick Craveur creator: Agnel Praveen Joseph creator: Vincent Jallu creator: Alexandre G. de Brevern creator: Pierre Poulain uri: https://doi.org/10.7717/peerj.4013 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Barnoud et al. title: Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation link: https://peerj.com/articles/4080 last-modified: 2017-11-17 description: Morphological differentiation among closely related species provides opportunities to study mechanisms shaping natural phenotypic variation. Here, we address variation in the orientation of melanin-colored body stripes in three cichlid species of the tribe Haplochromini. Melanochromis auratus displays a common pattern of dark, straight horizontal body stripes, whereas in Aristochromis christyi and Buccochromis rhoadesii, oblique stripes extend from the anterior dorsal to the posterior mid-lateral trunk. We first validated a stably reference gene, and then, investigated the chromatophore distribution in the skin by assessing the expression levels of the iridophore and melanophore marker genes, ltk and slc24a5, respectively, as well as pmel, a melanophore pigmentation marker gene. We found anterior-posterior differences in the expression levels of the three genes in the oblique-striped species. The higher anterior expression of ltk, indicates increased iridophore density in the anterior region, i.e., uneven horizontal distribution of iridophores, which coincides with the anterior dorsalization of melanophore stripe in these species. The obliqueness of the horizontal body stripes might be a result of distinct migratory or patterning abilities of melanophores in anterior and posterior stripe regions which could be reflected by variation in the expression of genes involved in melanophore patterning. To address this, we investigated anterior-posterior expression levels of a primary set of candidate target genes with known functions in melanophore migration and stripe patterning in the adult zebrafish, and their related gene regulatory network. Among these genes, those with differences in anterior-posterior expression showed only species-specific differential expression, e.g., sdf1a, col14a1a, ifitm5, and agpat3, with the exception of fbxw4/hagoromo (differentially expressed in an oblique-and the straight-striped species). In summary, distinct anterior-posterior gradients in iridophore density found to be more similar characteristic between the two oblique-striped species. Furthermore, the species-specific differential expression of genes involved in stripe patterning might also implicate distinct molecular processes underlying the obliqueness of body stripe in two closely related cichlid species. creator: Ehsan Pashay Ahi creator: Kristina M. Sefc uri: https://doi.org/10.7717/peerj.4080 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ahi and Sefc title: The role of biomaterials in the treatment of meniscal tears link: https://peerj.com/articles/4076 last-modified: 2017-11-17 description: Extensive investigations over the recent decades have established the anatomical, biomechanical and functional importance of the meniscus in the knee joint. As a functioning part of the joint, it serves to prevent the deterioration of articular cartilage and subsequent osteoarthritis. To this end, meniscus repair and regeneration is of particular interest from the biomaterial, bioengineering and orthopaedic research community. Even though meniscal research is previously of a considerable volume, the research community with evolving material science, biology and medical advances are all pushing toward emerging novel solutions and approaches to the successful treatment of meniscal difficulties. This review presents a tactical evaluation of the latest biomaterials, experiments to simulate meniscal tears and the state-of-the-art materials and strategies currently used to treat tears. creator: Crystal O. Kean creator: Robert J. Brown creator: James Chapman uri: https://doi.org/10.7717/peerj.4076 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kean et al. title: Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast link: https://peerj.com/articles/4073 last-modified: 2017-11-17 description: Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast). creator: Simon M. Dittami creator: Erwan Corre uri: https://doi.org/10.7717/peerj.4073 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Dittami and Corre title: NDUFA4L2 is associated with clear cell renal cell carcinoma malignancy and is regulated by ELK1 link: https://peerj.com/articles/4065 last-modified: 2017-11-17 description: BackgroundClear cell renal cell carcinoma (ccRCC) is the most common and lethal cancer of the adult kidney. However, its pathogenesis has not been fully understood till now, which hinders the therapeutic development of ccRCC. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) was found to be upregulated and play an important role in ccRCC. We aimed to further investigate the underlying mechanisms by which NDUFA4L2 exerted function and its expression level was upregulated.MethodsThe Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data were mined to verify the change of NDUFA4L2 expression level in ccRCC tissues. The correlation between expression level of NDUFA4L2 and cell proliferation/apoptosis was explored by Gene Set Enrichment Analysis (GSEA). Protein-protein interaction (PPI) network of NDUFA4L2 was constructed. Biological process and involved pathways of NDUFA4L2 were analyzed by gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The transcription factors (TFs) which can induce the expression of NDUFA4L2 were explored in clinical samples by correlation analysis and its regulation on the expression of NDUFA4L2 was verified by knockdown experiment.ResultsNDUFA4L2 was verified to be overexpressed in ccRCC tissues and its expression level was increased accordingly as the American Joint Committee on Cancer (AJCC) stage progressed. A high NDUFA4L2 level predicted the poor prognosis of ccRCC patients and correlated with enhanced cell proliferation and anti-apoptosis. NDUFA4L2 may interact with 14 tumor-related proteins, participate in growth and death processes and be involved in ccRCC-related pathways, such as insulin-like growth factor 1 (IGF-1), mammalian target of Rapamycin (mTOR) and phosphoinositide 3 kinase serine/threonine protein kinase (PI3K/AKT). ETS domain-containing protein ELK1 level positively correlated with the level of NDUFA4L2 in ccRCC tissues and ELK1 could regulate the expression of NDUFA4L2 in ccRCC cells.DiscussionNDUFA4L2 upregulation was associated with ccRCC malignancy. NDUFA4L2 expression was regulated by ELK1 in ccRCC cells. Our study provided potential mechanisms by which NDUFA4L2 affected ccRCC occurrence and progression. creator: Lei Wang creator: Zhiqiang Peng creator: Kaizhen Wang creator: Yijun Qi creator: Ying Yang creator: Yue Zhang creator: Xinyuan An creator: Shudong Luo creator: Junfang Zheng uri: https://doi.org/10.7717/peerj.4065 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: A 16-gene signature predicting prognosis of patients with oral tongue squamous cell carcinoma link: https://peerj.com/articles/4062 last-modified: 2017-11-17 description: BackgroundOral tongue squamous cell carcinoma (OTSCC) is the most common subtype of oral cancer. A predictive gene signature is necessary for prognosis of OTSCC.MethodsFive microarray data sets of OTSCC from the Gene Expression Omnibus (GEO) and one data set from The Cancer Genome Atlas (TCGA) were obtained. Differentially expressed genes (DEGs) of GEO data sets were identified by integrated analysis. The DEGs associated with prognosis were screened in the TCGA data set by univariate survival analysis to obtain a gene signature. A risk score was calculated as the summation of weighted expression levels with coefficients by Cox analysis. The signature was used to distinguish carcinoma, estimated by receiver operator characteristic curves and the area under the curve (AUC). All were validated in the GEO and TCGA data sets.ResultsIntegrated analysis of GEO data sets revealed 300 DEGs. A 16-gene signature and a risk score were developed after survival analysis. The risk score was effective to stratify patients into high-risk and low-risk groups in the TCGA data set (P < 0.001). The 16-gene signature was valid to distinguish the carcinoma from normal samples (AUC 0.872, P < 0.001).DiscussionWe identified a useful 16-gene signature for prognosis of OTSCC patients, which could be applied to clinical practice. Further studies were needed to prove the findings. creator: Zeting Qiu creator: Wei Sun creator: Shaowei Gao creator: Huaqiang Zhou creator: Wulin Tan creator: Minghui Cao creator: Wenqi Huang uri: https://doi.org/10.7717/peerj.4062 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Qiu et al. title: Comparative analysis of prophages in Streptococcus mutans genomes link: https://peerj.com/articles/4057 last-modified: 2017-11-17 description: Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages. creator: Tiwei Fu creator: Xiangyu Fan creator: Quanxin Long creator: Wanyan Deng creator: Jinlin Song creator: Enyi Huang uri: https://doi.org/10.7717/peerj.4057 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Fu et al. title: Coral-associated viral communities show high levels of diversity and host auxiliary functions link: https://peerj.com/articles/4054 last-modified: 2017-11-17 description: Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae, as well as Retroviridae and Polydnaviridae. Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis. Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis (psbA, psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species. creator: Karen D. Weynberg creator: Patrick W. Laffy creator: Elisha M. Wood-Charlson creator: Dmitrij Turaev creator: Thomas Rattei creator: Nicole S. Webster creator: Madeleine J.H. van Oppen uri: https://doi.org/10.7717/peerj.4054 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Weynberg et al. title: Assessment of perioperative stress in colorectal cancer by use of in vitro cell models: a systematic review link: https://peerj.com/articles/4033 last-modified: 2017-11-17 description: BackgroundThe perioperative period is important for patient outcome. Colorectal cancer surgery can lead to metastatic disease due to release of disseminated tumor cells and the induction of surgical stress response. To explore the overall effects on surgically-induced changes in serum composition, in vitro model systems are useful.MethodsA systematic search in PubMed and EMBASE was performed to identify studies describing in vitro models used to investigate cancer cell growth/proliferation, cell migration, cell invasion and cell death of serum taken pre- and postoperatively from patients undergoing colorectal tumor resection.ResultsTwo authors (MG and TK) independently reviewed 984 studies and identified five studies, which fulfilled the inclusion criteria. Disagreements were solved by discussion. All studies investigated cell proliferation and cell invasion, whereas three studies investigated cell migration, and only one study investigated cell death/apoptosis. One study investigated postoperative peritoneal infection due to anastomotic leak, one study investigated mode of anesthesia (general anesthesia with volatile or intravenous anesthetics), and one study investigated preoperative intervention with granulocyte macrophage colony stimulating factor (GMCSF). In all studies an increased proliferation, cell migration and invasion was demonstrated after surgery. Anesthetics with propofol and intervention with GMCSF significantly reduced postoperative cell proliferation, whereas peritoneal infection enhanced the invasive capability of tumor cells.ConclusionThis study suggests that in vitro cell models are useful and reliable tools to explore the effect of surgery on colorectal cancer cell proliferation and metastatic ability. The models should therefore be considered as additional tests to investigate the effects of perioperative interventions. creator: Tove Kirkegaard creator: Mikail Gögenur creator: Ismail Gögenur uri: https://doi.org/10.7717/peerj.4033 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kirkegaard et al. title: Ginsenoside Rk1 bioactivity: a systematic review link: https://peerj.com/articles/3993 last-modified: 2017-11-17 description: Ginsenoside Rk1 (G-Rk1) is a unique component created by processing the ginseng plant (mainly Sung Ginseng (SG)) at high temperatures. The aim of our study was to systematically review the pharmacological effects of G-Rk1. We utilized and manually searched eight databases to select in vivo and in vitro original studies that provided information about biological, pharmaceutical effects of G-Rk1 and were published up to July 2017 with no restriction on language or study design. Out of the 156 papers identified, we retrieved 28 eligible papers in the first skimming phase of research. Several articles largely described the G-Rk1 anti-cancer activity investigating “cell viability”, “cell proliferation inhibition”, “apoptotic activity”, and “effects of G-Rk1 on G1 phase and autophagy in tumor cells” either alone or in combination with G-Rg5. Others proved that it has antiplatelet aggregation activities, anti-inflammatory effects, anti-insulin resistance, nephroprotective effect, antimicrobial effect, cognitive function enhancement, lipid accumulation reduction and prevents osteoporosis. In conclusion, G-Rk1 has a significant anti-tumor effect on liver cancer, melanoma, lung cancer, cervical cancer, colon cancer, pancreatic cancer, gastric cancer, and breast adenocarcinoma against in vitro cell lines. In vivo experiments are further warranted to confirm these effects. creator: Abdelrahman Elshafay creator: Ngo Xuan Tinh creator: Samar Salman creator: Yara Saber Shaheen creator: Eman Bashir Othman creator: Mohamed Tamer Elhady creator: Aswin Ratna Kansakar creator: Linh Tran creator: Le Van creator: Kenji Hirayama creator: Nguyen Tien Huy uri: https://doi.org/10.7717/peerj.3993 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Elshafay et al. title: Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion link: https://peerj.com/articles/4075 last-modified: 2017-11-16 description: The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attributable to dietary specialization. Several populations discriminated between the koala and wombat fecal communities, most notably S24-7 and Synergistaceae in the koala, and Christensenellaceae and RF39 in the wombat. As expected for herbivores, both communities contained the genes necessary for lignocellulose degradation and urea recycling partitioned and redundantly encoded across multiple populations. Secondary metabolism was overrepresented in the koala fecal samples, consistent with the need to process Eucalyptus secondary metabolites. The Synergistaceae population encodes multiple pathways potentially relevant to Eucalyptus compound metabolism, and is predicted to be a key player in detoxification of the koala’s diet. Notably, characterized microbial isolates from the koala gut appear to be minor constituents of this habitat, and the metagenomes provide the opportunity for genome-directed isolation of more representative populations. Metagenomic analysis of other obligate and facultative Eucalyptus folivores will reveal whether putatively detoxifying bacteria identified in the koala are shared across these marsupials. creator: Miriam E. Shiffman creator: Rochelle M. Soo creator: Paul G. Dennis creator: Mark Morrison creator: Gene W. Tyson creator: Philip Hugenholtz uri: https://doi.org/10.7717/peerj.4075 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Shiffman et al. title: Antimicrobial consumption on Austrian dairy farms: an observational study of udder disease treatments based on veterinary medication records link: https://peerj.com/articles/4072 last-modified: 2017-11-16 description: BackgroundAntimicrobial use in livestock production is an important contemporary issue, which is of public interest worldwide. Antimicrobials are not freely available to Austrian farmers and can only be administered to livestock by veterinarians, or by farmers who are trained members of the Animal Health Service. Since 2015, veterinarians have been required by law to report antimicrobials dispensed to farmers for use in food-producing animals. The study presented here went further than the statutory framework, and collected data on antimicrobials dispensed to farmers and those administered by veterinarians.MethodsSeventeen veterinary practices were enrolled in the study via convenience sampling. These veterinarians were asked to contact interested dairy farmers regarding participation in the study (respondent-driven sampling). Data were collected from veterinary practice software between 1st October 2015 and 30th September 2016. Electronic data (89.4%) were transferred via an online interface and paper records (10.6%) were entered by the authors. Antimicrobial treatments with respect to udder disease were analysed by number of defined daily doses per cow and year (nDDDvet/cow/year), based on the European Medicines Agency technical unit, Defined Daily Dose for animals (DDDvet). Descriptive statistics and the Wilcoxon rank sum test were used to analyse the results.ResultsAntimicrobial use data from a total of 248 dairy farms were collected during the study, 232 of these farms treated cows with antibiotics; dry cow therapy was excluded from the current analysis. The mean number of DDDvet/cow/year for the antimicrobial treatment of all udder disease was 1.33 DDDvet/cow/year. Of these treatments, 0.73 DDDvet/cow/year were classed as highest priority critically important antimicrobials (HPCIAs), according to the World Health Organization (WHO) definition. The Wilcoxon rank sum test determined a statistically significant difference between the median number of DDDvet/cow/year for acute and chronic mastitis treatment (W = 10,734, p < 0.001). The most commonly administered antimicrobial class for the treatment of acute mastitis was beta-lactams. Intramammary penicillin was used at a mean of 0.63 DDDvet/cow/year, followed by the third generation cephalosporin, cefoperazone, (a HPCIA) at 0.60 DDDvet/cow/year. Systemic antimicrobial treatments were used at a lower overall level than intramammary treatments for acute mastitis.DiscussionThis study demonstrated that Austrian dairy cows in the study population were treated with antimicrobial substances for udder diseases at a relatively low frequency, however, a substantial proportion of these treatments were with substances considered critically important for human health. While it is vital that sick cows are treated, reductions in the overall use of antimicrobials, and critically important substances in particular, are still possible. creator: Clair L. Firth creator: Annemarie Käsbohrer creator: Corina Schleicher creator: Klemens Fuchs creator: Christa Egger-Danner creator: Martin Mayerhofer creator: Hermann Schobesberger creator: Josef Köfer creator: Walter Obritzhauser uri: https://doi.org/10.7717/peerj.4072 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Firth et al. title: HRV-derived data similarity and distribution index based on ensemble neural network for measuring depth of anaesthesia link: https://peerj.com/articles/4067 last-modified: 2017-11-16 description: Evaluation of depth of anaesthesia (DoA) is critical in clinical surgery. Indices derived from electroencephalogram (EEG) are currently widely used to quantify DoA. However, there are known to be inaccurate under certain conditions; therefore, experienced anaesthesiologists rely on the monitoring of vital signs such as body temperature, pulse rate, respiration rate, and blood pressure to control the procedure. Because of the lack of an ideal approach for quantifying level of consciousness, studies have been conducted to develop improved methods of measuring DoA. In this study, a short-term index known as the similarity and distribution index (SDI) is proposed. The SDI is generated using heart rate variability (HRV) in the time domain and is based on observations of data distribution differences between two consecutive 32 s HRV data segments. A comparison between SDI results and expert assessments of consciousness level revealed that the SDI has strong correlation with anaesthetic depth. To optimise the effect, artificial neural network (ANN) models were constructed to fit the SDI, and ANN blind cross-validation was conducted to overcome random errors and overfitting problems. An ensemble ANN was then employed and was discovered to provide favourable DoA assessment in comparison with commonly used Bispectral Index. This study demonstrated the effectiveness of this method of DoA assessment, and the results imply that it is feasible and meaningful to use the SDI to measure DoA with the additional use of other measurement methods, if appropriate. creator: Quan Liu creator: Li Ma creator: Ren-Chun Chiu creator: Shou-Zen Fan creator: Maysam F. Abbod creator: Jiann-Shing Shieh uri: https://doi.org/10.7717/peerj.4067 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Liu et al. title: Increased risk of periodontitis in patients with psoriatic disease: a nationwide population-based retrospective cohort study link: https://peerj.com/articles/4064 last-modified: 2017-11-16 description: AimsPeriodontitis and psoriatic disease, including psoriasis (PS) and psoriatic arthritis (PsA), share the common risk factors and co-morbidities. However, the risk of periodontitis in patients with psoriatic disease still needs further investigation. This study was a nationwide population-based retrospective cohort study assessing the risk of periodontitis from psoriatic disease exposure.Materials and MethodsPatients with newly diagnosed psoriatic disease from 2003 to 2012 were identified from the Taiwanese National Health Insurance Research Database. The 1:4 ratio propensity score matched controls were selected from no psoriatic disease participations. The subsequent risk of periodontitis was evaluated in exposure and comparison groups. Multiple Cox proportional hazard models were used for the estimation.ResultsA total of 3,487 psoriatic disease patients and 13,948 controls were identified. Incidence rate of periodontitis was higher in patients with PsA. The adjusted hazard ratio (aHRs) for moderate/severe periodontitis were 0.85 (95% CI [0.65–1.11]) in PS group and 1.66 (95% CI [0.99–2.78]) in PsA group. The aHRs of PsA were increased over time, aHRs was changed from 0.65 (0–11 months from index date) to 1.34 (≥12 months from index date) in all types of periodontitis and from 1.09 to 1.79 in moderate/severe periodontitis group, respectively.ConclusionsThe increased risk of periodontitis was observed, especially the association between PsA and moderate/severe periodontitis. The patients with psoriatic disease should receive regular periodontal evaluation. creator: Ni-Yu Su creator: Jing-Yang Huang creator: Chien-Jen Hu creator: Hui-Chieh Yu creator: Yu-Chao Chang uri: https://doi.org/10.7717/peerj.4064 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Su et al. title: Adult zebra finches rehearse highly variable song patterns during sleep link: https://peerj.com/articles/4052 last-modified: 2017-11-16 description: Brain activity during sleep is fairly ubiquitous and the best studied possible function is a role in memory consolidation, including motor memory. One suggested mechanism of how neural activity effects these benefits is through reactivation of neurons in patterns resembling those of the preceding experience. The specific patterns of motor activation replayed during sleep are largely unknown for any system. Brain areas devoted to song production in the songbird brain exhibit spontaneous song-like activity during sleep, but single cell neural recordings did not permit detection of the specific song patterns. We have now discovered that this sleep activation can be detected in the muscles of the vocal organ, thus providing a unique window into song-related brain activity at night. We show that male zebra finches (Taeniopygia guttata) frequently exhibit spontaneous song-like activity during the night, but that the fictive song patterns are highly variable and uncoordinated compared to the highly stereotyped day-time song production. This substantial variability is not consistent with the idea that night-time activity replays day-time experiences for consolidation. Although the function of this frequent activation is unknown, it may represent a mechanism for exploring motor space or serve to generate internal error signals that help maintain the high stereotypy of day-time song. In any case, the described activity supports the emerging insight that brain activity during sleep may serve a variety of functions. creator: Brent K. Young creator: Gabriel B. Mindlin creator: Ezequiel Arneodo creator: Franz Goller uri: https://doi.org/10.7717/peerj.4052 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Young et al. title: Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans” link: https://peerj.com/articles/4046 last-modified: 2017-11-16 description: Hörnig, Haug & Haug (2017) published a description of a new specimen of Santanmantis axelrodi MB.I.2068, an extinct species of praying mantis from the Crato Formation of Brazil. According to Hörnig, Haug & Haug (2017), the discovery of this new specimen brought with it implications for praying mantis character evolution and predatory behavior; it is with these lines of reasoning that we find fault. More specifically, we point to four flawed assumptions in their study that led to their unsubstantiated conclusion that S. axelrodi employed their mesothoracic legs in prey capture. creator: Sydney K. Brannoch creator: Gavin J. Svenson uri: https://doi.org/10.7717/peerj.4046 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Brannoch and Svenson title: 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro link: https://peerj.com/articles/4017 last-modified: 2017-11-16 description: Gastrointestinal mucositis is a debilitating side effect of chemotherapy treatment, with currently no treatment available. As changes in microbial composition have been reported upon chemotherapy treatment in vivo, it is thought that gut microbiota dysbiosis contribute to the mucositis etiology. Yet it is not known whether chemotherapeutics directly cause microbial dysbiosis, thereby increasing mucositis risk, or whether the chemotherapeutic subjected host environment disturbs the microbiome thereby aggravating the disease. To address this question, we used the M-SHIME®, an in vitro mucosal simulator of the human intestinal microbial ecosystem, as an experimental setup that excludes the host factor. The direct impact of two chemotherapeutics, 5-fluorouracil (5-FU) and SN-38 (active metabolite of irinotecan), on the luminal and mucosal gut microbiota from several human donors was investigated through monitoring fermentation activity and next generation sequencing. At a dose of 10 µM in the mucosal environment, 5-FU impacted the functionality and composition of the colon microbiota to a minor extent. Similarly, a daily dose of 10 µM SN-38 in the luminal environment did not cause significant changes in the functionality or microbiome composition. As our mucosal model does not include a host-compartment, our findings strongly indicate that a putative microbial contribution to mucositis is initially triggered by an altered host environment upon chemotherapy. creator: Eline Vanlancker creator: Barbara Vanhoecke creator: Andrea Stringer creator: Tom Van de Wiele uri: https://doi.org/10.7717/peerj.4017 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vanlancker et al. title: Sediment tolerance mechanisms identified in sponges using advanced imaging techniques link: https://peerj.com/articles/3904 last-modified: 2017-11-16 description: Terrestrial runoff, resuspension events and dredging can affect filter-feeding sponges by elevating the concentration of suspended sediments, reducing light intensity, and smothering sponges with sediments. To investigate how sponges respond to pressures associated with increased sediment loads, the abundant and widely distributed Indo-Pacific species Ianthella basta was exposed to elevated suspended sediment concentrations, sediment deposition, and light attenuation for 48 h (acute exposure) and 4 weeks (chronic exposure). In order to visualise the response mechanisms, sponge tissue was examined by 3D X-ray microscopy and scanning electron microscopy (SEM). Acute exposures resulted in sediment rapidly accumulating in the aquiferous system of I. basta, although this sediment was fully removed within three days. Sediment removal took longer (>2 weeks) following chronic exposures, and I. basta also exhibited tissue regression and a smaller aquiferous system. The application of advanced imaging approaches revealed that I. basta employs a multilevel system for sediment rejection and elimination, containing both active and passive components. Sponges responded to sediment stress through (i) mucus production, (ii) exclusion of particles by incurrent pores, (iii) closure of oscula and pumping cessation, (iv) expulsion of particles from the aquiferous system, and (v) tissue regression to reduce the volume of the aquiferous system, thereby entering a dormant state. These mechanisms would result in tolerance and resilience to exposure to variable and high sediment loads associated with both anthropogenic impacts like dredging programs and natural pressures like flood events. creator: Brian W. Strehlow creator: Mari-Carmen Pineda creator: Alan Duckworth creator: Gary A. Kendrick creator: Michael Renton creator: Muhammad Azmi Abdul Wahab creator: Nicole S. Webster creator: Peta L. Clode uri: https://doi.org/10.7717/peerj.3904 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Strehlow et al. title: Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts link: https://peerj.com/articles/4063 last-modified: 2017-11-15 description: Specific regulation and activation of focal adhesion kinase (FAK) are thought to be important for focal adhesion formation, and activation of Rho-kinase has been suggested to play a role in determining the effects of FAK on the formation of stress fibers and focal adhesions. To clarify the role of FAK in stress fiber formation and focal adhesion organization, the author examined the formation of new stress fibers and focal adhesions by activation of Rho-kinase in FAK knockout (FAK–/–) fibroblasts. FAK–/– cells were elliptical in shape, and showed reduced numbers of stress fibers and focal adhesions in the central part of the cells along with large focal adhesions in the peripheral regions. Activation of Rho-kinase in FAK–/– cells transiently increased the actin filaments in the cell center, but these did not form typical thick stress fibers. Moreover, only plaque-like structures as the origins of newly formed focal adhesions were observed in the center of the cell. Furthermore, introduction of an exogenous GFP-labeled FAK gene into FAK–/– cells resulted in increased numbers of stress fibers and focal adhesions in the center of the cells, which showed typical fibroblast morphology. These results indicated that FAK plays an important role in the formation of stress fibers and focal adhesions as well as in regulation of cell shape and morphology with the activation of Rho-kinase. creator: Kazuo Katoh uri: https://doi.org/10.7717/peerj.4063 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Katoh title: Lowland extirpation of anuran populations on a tropical mountain link: https://peerj.com/articles/4059 last-modified: 2017-11-15 description: BackgroundClimate change and infectious diseases threaten animal and plant species, even in natural and protected areas. To cope with these changes, species may acclimate, adapt, move or decline. Here, we test for shifts in anuran distributions in the Luquillo Mountains (LM), a tropical montane forest in Puerto Rico by comparing species distributions from historical (1931–1989)and current data (2015/2016).MethodsHistorical data, which included different methodologies, were gathered through the Global Biodiversity Information Facility (GBIF) and published literature, and the current data were collected using acoustic recorders along three elevational transects.ResultsIn the recordings, we detected the 12 native frog species known to occur in LM. Over a span of ∼25 years, two species have become extinct and four species suffered extirpation in lowland areas. As a consequence, low elevation areas in the LM (<300 m) have lost at least six anuran species.DiscussionWe hypothesize that these extirpations are due to the effects of climate change and infectious diseases, which are restricting many species to higher elevations and a much smaller area. Land use change is not responsible for these changes because LM has been a protected reserve for the past 80 years. However, previous studies indicate that (1) climate change has increased temperatures in Puerto Rico, and (2) Batrachochytrium dendrobatidis (Bd) was found in 10 native species and early detection of Bd coincides with anurans declines in the LM. Our study confirms the general impressions of amphibian population extirpations at low elevations, and corroborates the levels of threat assigned by IUCN. creator: Marconi Campos-Cerqueira creator: T. Mitchell Aide uri: https://doi.org/10.7717/peerj.4059 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Campos-Cerqueira and Aide title: Virus like particles as a platform for cancer vaccine development link: https://peerj.com/articles/4053 last-modified: 2017-11-15 description: Cancers have killed millions of people in human history and are still posing a serious health problem worldwide. Therefore, there is an urgent need for developing preventive and therapeutic cancer vaccines. Among various cancer vaccine development platforms, virus-like particles (VLPs) offer several advantages. VLPs are multimeric nanostructures with morphology resembling that of native viruses and are mainly composed of surface structural proteins of viruses but are devoid of viral genetic materials rendering them neither infective nor replicative. In addition, they can be engineered to display multiple, highly ordered heterologous epitopes or peptides in order to optimize the antigenicity and immunogenicity of the displayed entities. Like native viruses, specific epitopes displayed on VLPs can be taken up, processed, and presented by antigen-presenting cells to elicit potent specific humoral and cell-mediated immune responses. Several studies also indicated that VLPs could overcome the immunosuppressive state of the tumor microenvironment and break self-tolerance to elicit strong cytotoxic lymphocyte activity, which is crucial for both virus clearance and destruction of cancerous cells. Collectively, these unique characteristics of VLPs make them optimal cancer vaccine candidates. This review discusses current progress in the development of VLP-based cancer vaccines and some potential drawbacks of VLPs in cancer vaccine development. Extracellular vesicles with close resembling to viral particles are also discussed and compared with VLPs as a platform in cancer vaccine developments. creator: Hui Kian Ong creator: Wen Siang Tan creator: Kok Lian Ho uri: https://doi.org/10.7717/peerj.4053 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ong et al. title: Genome-wide in silico identification of membrane-bound transcription factors in plant species link: https://peerj.com/articles/4051 last-modified: 2017-11-15 description: Membrane-bound transcription factors (MTFs) are located in cellular membranes due to their transmembrane domains. In plants, proteolytic processing is considered to be the main mechanism for MTF activation, which ensures the liberation of MTFs from membranes and further their translocation into the nucleus to regulate gene expression; this process skips both the transcriptional and translational stages, and thus it guarantees the prompt responses of plants to various stimuli. Currently, information concerning plant MTFs is limited to model organisms, including Arabidopsis thaliana and Oryza sativa, and little is known in other plant species at the genome level. In the present study, seven membrane topology predictors widely used by the research community were employed to establish a reliable workflow for MTF identification. Genome-wide in silico analysis of MTFs was then performed in 14 plant species spanning the chlorophytes, bryophytes, gymnosperms, monocots and eudicots. A total of 1,089 MTFs have been identified from a total of 25,850 transcription factors in these 14 plant species. These MTFs belong to 52 gene family, and the top six most abundant families are the NAC (128), SBP (77), C2H2 (70), bZIP (67), MYB-related (65) and bHLH (63) families. The MTFs have transmembrane spans ranging from one to thirteen, and 71.5% and 21.1% of the MTFs have one and two transmembrane motifs, respectively. Most of the MTFs in this study have transmembrane motifs located in either N- or C-terminal regions, indicating that proteolytic cleavage could be a conserved mechanism for MTF activation. Additionally, approximately half of the MTFs in the genome of either Arabidopsis thaliana or Gossypium raimondii could be potentially regulated by alternative splicing, indicating that alternative splicing is another conserved activation mechanism for MTFs. The present study performed systematic analyses of MTFs in plant lineages at the genome level, and provides invaluable information for the research community. creator: Shixiang Yao creator: Lili Deng creator: Kaifang Zeng uri: https://doi.org/10.7717/peerj.4051 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yao et al. title: Fitness implications of sex-specific catch-up growth in Nephila senegalensis, a spider with extreme reversed SSD link: https://peerj.com/articles/4050 last-modified: 2017-11-15 description: BackgroundAnimal growth is often constrained by unfavourable conditions and divergences from optimal body size can be detrimental to an individual’s fitness, particularly in species with determinate growth and a narrow time-frame for life-time reproduction. Growth restriction in early juvenile stages can later be compensated by means of plastic developmental responses, such as adaptive catch-up growth (the compensation of growth deficits through delayed development). Although sex differences regarding the mode and degree of growth compensation have been coherently predicted from sex-specific fitness payoffs, inconsistent results imply a need for further research. We used the African Nephila senegalensis, representing an extreme case of female-biased sexual size dimorphism (SSD), to study fitness implications of sex-specific growth compensation. We predicted effective catch-up growth in early food-restricted females to result in full compensation of growth deficits and a life-time fecundity (LTF) equivalent to unrestricted females. Based on a stronger trade-off between size-related benefits and costs of a delayed maturation, we expected less effective catch-up growth in males.MethodsWe tracked the development of over one thousand spiders in different feeding treatments, e.g., comprising a fixed period of early low feeding conditions followed by unrestricted feeding conditions, permanent unrestricted feeding conditions, or permanent low feeding conditions as a control. In a second experimental section, we assessed female fitness by measuring LTF in a subset of females. In addition, we tested whether compensatory development affected the reproductive lifespan in both sexes and analysed genotype-by-treatment interactions as a potential cause of variation in life-history traits.ResultsBoth sexes delayed maturation to counteract early growth restriction, but only females achieved full compensation of adult body size. Female catch-up growth resulted in equivalent LTF compared to unrestricted females. We found significant interactions between experimental treatments and sex as well as between treatments and family lineage, suggesting that family-specific responses contribute to the unusually large variation of life-history traits in Nephila spiders. Our feeding treatments had no effect on the reproductive lifespan in either sex.DiscussionOur findings are in line with predictions of life-history theory and corroborate strong fecundity selection to result in full female growth compensation. Males showed incomplete growth compensation despite a delayed development, indicating relaxed selection on large size and a stronger trade-off between late maturation and size-related benefits. We suggest that moderate catch-up growth in males is still adaptive as a ‘bet-hedging’ strategy to disperse unavoidable costs between life-history traits affected by early growth restriction (the duration of development and adult size). creator: Rainer Neumann creator: Nicole Ruppel creator: Jutta M. Schneider uri: https://doi.org/10.7717/peerj.4050 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Neumann et al. title: Mitochondrial genomes of three Tetrigoidea species and phylogeny of Tetrigoidea link: https://peerj.com/articles/4002 last-modified: 2017-11-15 description: The mitochondrial genomes (mitogenomes) of Formosatettix qinlingensis, Coptotettix longjiangensis and Thoradonta obtusilobata (Orthoptera: Caelifera: Tetrigoidea) were sequenced in this study, and almost the entire mitogenomes of these species were determined. The mitogenome sequences obtained for the three species were 15,180, 14,495 and 14,538 bp in length, respectively, and each sequence included 13 protein-coding genes (PCGs), partial sequences of rRNA genes (rRNAs), tRNA genes (tRNAs) and a A + T-rich region. The order and orientation of the gene arrangement pattern were identical to that of most Tetrigoidea species. Some conserved spacer sequences between trnS(UCN) and nad1 were useful to identify Tetrigoidea and Acridoidea. The Ka/Ks value of atp8 between Trachytettix bufo and other four Tetrigoidea species indicated that some varied sites in this gene might be related with the evolution of T. bufo. The three Tetrigoidea species were compared with other Caelifera. At the superfamily level, conserved sequences were observed in intergenic spacers, which can be used for superfamily level identification between Tetrigoidea and Acridoidea. Furthermore, a phylogenomic analysis was conducted based on the concatenated data sets from mitogenome sequences of 24 species of Orthoptera in the superorders Caelifera and Ensifera. Both maximum likelihood and bayesian inference analyses strongly supported Acridoidea and Tetrigoidea as forming monophyletic groups. The relationships among six Tetrigoidea species were (((((Tetrix japonica, Alulatettix yunnanensis), Formosatettix qinlingensis), Coptotettix longjiangensis), Trachytettix bufo), Thoradonta obtusilobata). creator: Li-Liang Lin creator: Xue-Juan Li creator: Hong-Li Zhang creator: Zhe-Min Zheng uri: https://doi.org/10.7717/peerj.4002 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lin et al. title: The Furvela tent-trap Mk 1.1 for the collection of outdoor biting mosquitoes link: https://peerj.com/articles/3848 last-modified: 2017-11-15 description: Outdoor transmission of malaria and other vector borne diseases remains a problem. The WHO has recently recognized the need for suitable methods for assessing vector density outdoors and a number of tent-traps have been developed. Only one such trap, the Furvela tent-trap, does not require an ‘entry’ behavior on the part of the mosquito. It remains the cheapest and lightest tent-trap described. It takes less than two minutes to install and is the only trap that uses readily available components. Here we describe recent modifications to the trap, which make it even easier to set up in the field, provide a standard operating procedure (SOP) and describe some recent experiments examining the effect of the addition of light and door placement to working of the trap. The trap provides the closest approximation to CDC light-traps, widely used to collect indoor biting mosquitoes. This enables the effect of both indoor and outdoor interventions on mosquito density and behavior to be determined. creator: Jacques D. Charlwood creator: Mark Rowland creator: Natacha Protopopoff creator: Corey Le Clair uri: https://doi.org/10.7717/peerj.3848 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Charlwood et al. title: North Atlantic Oscillation drives the annual occurrence of an isolated, peripheral population of the brown seaweed Fucus guiryi in the Western Mediterranean Sea link: https://peerj.com/articles/4048 last-modified: 2017-11-14 description: The canopy-forming, intertidal brown (Phaeophyceae) seaweed Fucus guiryi is distributed along the cold-temperate and warm-temperate coasts of Europe and North Africa. Curiously, an isolated population develops at Punta Calaburras (Alboran Sea, Western Mediterranean) but thalli are not present in midsummer every year, unlike the closest (ca. 80 km), perennial populations at the Strait of Gibraltar. The persistence of the alga at Punta Calaburras could be due to the growth of resilient, microscopic stages as well as the arrival of few–celled stages originating from neighbouring localities, and transported by the permanent Atlantic Jet flowing from the Atlantic Ocean into the Mediterranean. A twenty-six year time series (from 1990 to 2015) of midsummer occurrence of F. guiryi thalli at Punta Calaburras has been analysed by correlating with oceanographic (sea surface temperature, an estimator of the Atlantic Jet power) and climatic factors (air temperature, rainfall, and North Atlantic Oscillation –NAO-, and Arctic Oscillation –AO- indexes). The midsummer occurrence of thalli clustered from 1990–1994 and 1999–2004, with sporadic occurrences in 2006 and 2011. Binary logistic regression showed that the occurrence of thalli at Punta Calaburras in midsummer is favoured under positive NAO index from April to June. It has been hypothesized that isolated population of F. guiryi should show greater stress than their congeners of permanent populations, and to this end, two approaches were used to evaluate stress: one based on the integrated response during ontogeny (developmental instability, based on measurements of the fractal branching pattern of algal thalli) and another based on the photosynthetic response. Although significant differences were detected in photosynthetic quantum yield and water loss under emersion conditions, with thalli from Punta Calaburras being more affected by emersion than those from Tarifa, the developmental instability showed that the population from Tarifa suffers higher stress during ontogeny than that from Punta Calaburras. In conclusion, this study demonstrates the teleconnection between atmospheric oscillations and survival and proliferation of marine macroalgae. creator: Ignacio J. Melero-Jiménez creator: A. Enrique Salvo creator: José C. Báez creator: Elena Bañares-España creator: Andreas Reul creator: Antonio Flores-Moya uri: https://doi.org/10.7717/peerj.4048 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Melero-Jiménez et al. title: Zebrafish swimming in the flow: a particle image velocimetry study link: https://peerj.com/articles/4041 last-modified: 2017-11-14 description: Zebrafish is emerging as a species of choice for the study of a number of biomechanics problems, including balance development, schooling, and neuromuscular transmission. The precise quantification of the flow physics around swimming zebrafish is critical toward a mechanistic understanding of the complex swimming style of this fresh-water species. Although previous studies have elucidated the vortical structures in the wake of zebrafish swimming in placid water, the flow physics of zebrafish swimming against a water current remains unexplored. In an effort to illuminate zebrafish swimming in a dynamic environment reminiscent of its natural habitat, we experimentally investigated the locomotion and hydrodynamics of a single zebrafish swimming in a miniature water tunnel using particle image velocimetry. Our results on zebrafish locomotion detail the role of flow speed on tail beat undulations, heading direction, and swimming speed. Our findings on zebrafish hydrodynamics offer a precise quantification of vortex shedding during zebrafish swimming and demonstrate that locomotory patterns play a central role on the flow physics. This knowledge may help clarify the evolutionary advantage of burst and cruise swimming movements in zebrafish. creator: Violet Mwaffo creator: Peng Zhang creator: Sebastián Romero Cruz creator: Maurizio Porfiri uri: https://doi.org/10.7717/peerj.4041 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Mwaffo et al. title: The sensitivity of the yeast, Saccharomyces cerevisiae, to acetic acid is influenced by DOM34 and RPL36A link: https://peerj.com/articles/4037 last-modified: 2017-11-14 description: The presence of acetic acid during industrial alcohol fermentation reduces the yield of fermentation by imposing additional stress on the yeast cells. The biology of cellular responses to stress has been a subject of vigorous investigations. Although much has been learned, details of some of these responses remain poorly understood. Members of heat shock chaperone HSP proteins have been linked to acetic acid and heat shock stress responses in yeast. Both acetic acid and heat shock have been identified to trigger different cellular responses including reduction of global protein synthesis and induction of programmed cell death. Yeast HSC82 and HSP82 code for two important heat shock proteins that together account for 1–2% of total cellular proteins. Both proteins have been linked to responses to acetic acid and heat shock. In contrast to the overall rate of protein synthesis which is reduced, the expression of HSC82 and HSP82 is induced in response to acetic acid stress. In the current study we identified two yeast genes DOM34 and RPL36A that are linked to acetic acid and heat shock sensitivity. We investigated the influence of these genes on the expression of HSP proteins. Our observations suggest that Dom34 and RPL36A influence translation in a CAP-independent manner. creator: Bahram Samanfar creator: Kristina Shostak creator: Houman Moteshareie creator: Maryam Hajikarimlou creator: Sarah Shaikho creator: Katayoun Omidi creator: Mohsen Hooshyar creator: Daniel Burnside creator: Imelda Galván Márquez creator: Tom Kazmirchuk creator: Thet Naing creator: Paula Ludovico creator: Anna York-Lyon creator: Kama Szereszewski creator: Cindy Leung creator: Jennifer Yixin Jin creator: Rami Megarbane creator: Myron L. Smith creator: Mohan Babu creator: Martin Holcik creator: Ashkan Golshani uri: https://doi.org/10.7717/peerj.4037 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Samanfar et al. title: Intraspecific variation in the diet of the Mexican garter snake Thamnophis eques link: https://peerj.com/articles/4036 last-modified: 2017-11-14 description: The Mexican Garter Snake (Thamnophis eques) is a terrestrial-aquatic generalist that feeds on both aquatic and terrestrial prey. We describe size-related variation and sexual variation in the diet of T. eques through analysis of 262 samples of identifiable stomach contents in snakes from 23 locations on the Mexican Plateau. The snake T. eques we studied consumed mostly fish, followed in lesser amounts by leeches, earthworms, frogs, and tadpoles. Correspondence analysis suggested that the frequency of consumption of various prey items differed between the categories of age but not between sex of snakes, and the general pattern was a reduction of prey item diversity with size of snake. Snake length was correlated positively with mass of ingested prey. Large snakes consumed large prey and continued to consume smaller prey. In general, no differences were found between the prey taxa of male and female snakes, although males ate two times more tadpoles than females. Males and females did not differ in the mass of leeches, earthworms, fishes, frogs and tadpoles that they ate, and males and females that ate each prey taxon were similar in length. We discuss proximate and functional determinants of diet and suggest that the observed intraspecific variation in T. eques could be explored by temporal variation in prey availability, proportions of snake size classes and possible sexual dimorphism in head traits and prey dimensions to assess the role of intersexual resource competition. creator: Javier Manjarrez creator: Martha Pacheco-Tinoco creator: Crystian S. Venegas-Barrera uri: https://doi.org/10.7717/peerj.4036 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Manjarrez et al. title: Whole genome sequencing of Rhodotorula mucilaginosa isolated from the chewing stick (Distemonanthus benthamianus): insights into Rhodotorula phylogeny, mitogenome dynamics and carotenoid biosynthesis link: https://peerj.com/articles/4030 last-modified: 2017-11-14 description: In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte R. mucilaginosa RIT389 isolated from Distemonanthus benthamianus, a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of R. mucilaginosa RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to supporting the monophyly of the currently sequenced Rhodotorula species. Further, we report for the first time, the recovery of the complete mitochondrial genome of R. mucilaginosa using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of Rhodotorula taiwanensis which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in R. mucilaginosa RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts. creator: Han Ming Gan creator: Bolaji N. Thomas creator: Nicole T. Cavanaugh creator: Grace H. Morales creator: Ashley N. Mayers creator: Michael A. Savka creator: André O. Hudson uri: https://doi.org/10.7717/peerj.4030 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gan et al. title: Science responses to IUCN Red Listing link: https://peerj.com/articles/4025 last-modified: 2017-11-14 description: The IUCN Red List of Threatened Species is often advocated as a tool to assist decision-making in conservation investment and research focus. It is frequently suggested that research efforts should prioritize species in higher threat categories and those that are Data Deficient (DD). We assessed the linkage between IUCN listing and research effort in DD and Critically Endangered (CR) species, two groups generally advocated as research priorities. The analysis of the change in the research output following species classification indicated a listing effect in DD species, while such effect was observed in only a minority of CR species groups. DD species, while chronically understudied, seem to be recognized as research priorities, while research effort for endangered species appears to be driven by various factors other than the IUCN listing. Optimized conservation research focus would require international science planning efforts, harmonized through international mechanisms and promoted by financial and other incentives. creator: Ivan Jarić creator: David L. Roberts creator: Jörn Gessner creator: Andrew R. Solow creator: Franck Courchamp uri: https://doi.org/10.7717/peerj.4025 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Jarić et al. title: Short-term effects of CO2 leakage on the soil bacterial community in a simulated gas leakage scenario link: https://peerj.com/articles/4024 last-modified: 2017-11-14 description: The technology of carbon dioxide (CO2) capture and storage (CCS) has provided a new option for mitigating global anthropogenic emissions with unique advantages. However, the potential risk of gas leakage from CO2 sequestration and utilization processes has attracted considerable attention. Moreover, leakage might threaten soil ecosystems and thus cannot be ignored. In this study, a simulation experiment of leakage from CO2 geological storage was designed to investigate the short-term effects of different CO2 leakage concentration (from 400 g m−2 day−1 to 2,000 g m−2 day−1) on soil bacterial communities. A shunt device and adjustable flow meter were used to control the amount of CO2 injected into the soil. Comparisons were made between soil physicochemical properties, soil enzyme activities, and microbial community diversity before and after injecting different CO2 concentrations. Increasing CO2 concentration decreased the soil pH, and the largest variation ranged from 8.15 to 7.29 (p < 0.05). Nitrate nitrogen content varied from 1.01 to 4.03 mg/Kg, while Olsen-phosphorus and total phosphorus demonstrated less regular downtrends. The fluorescein diacetate (FDA) hydrolytic enzyme activity was inhibited by the increasing CO2 flux, with the average content varying from 22.69 to 11.25 mg/(Kg h) (p < 0.05). However, the increasing activity amplitude of the polyphenol oxidase enzyme approached 230%, while the urease activity presented a similar rising trend. Alpha diversity results showed that the Shannon index decreased from 7.66 ± 0.13 to 5.23 ± 0.35 as the soil CO2 concentration increased. The dominant phylum in the soil samples was Proteobacteria, whose proportion rose rapidly from 28.85% to 67.93%. In addition, the proportion of Acidobacteria decreased from 19.64% to 9.29% (p < 0.01). Moreover, the abundances of genera Methylophilus, Methylobacillus, and Methylovorus increased, while GP4, GP6 and GP7 decreased. Canonical correlation analysis results suggested that there was a correlation between the abundance variation of Proteobacteria, Acidobacteria, and the increasing nitrate nitrogen, urease and polyphenol oxidase enzyme activities, as well as the decreasing FDA hydrolytic enzyme activity, Olsen-phosphorus and total phosphorus contents. These results might be useful for evaluating the risk of potential CO2 leakages on soil ecosystems. creator: Jing Ma creator: Wangyuan Zhang creator: Shaoliang Zhang creator: Qianlin Zhu creator: Qiyan Feng creator: Fu Chen uri: https://doi.org/10.7717/peerj.4024 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ma et al. title: The ultimate legs of Chilopoda (Myriapoda): a review on their morphological disparity and functional variability link: https://peerj.com/articles/4023 last-modified: 2017-11-14 description: The arthropodium is the key innovation of arthropods. Its various modifications are the outcome of multiple evolutionary transformations, and the foundation of nearly endless functional possibilities. In contrast to hexapods, crustaceans, and even chelicerates, the spectrum of evolutionary transformations of myriapod arthropodia is insufficiently documented and rarely scrutinized. Among Myriapoda, Chilopoda (centipedes) are characterized by their venomous forcipules—evolutionarily transformed walking legs of the first trunk segment. In addition, the posterior end of the centipedes’ body, in particular the ultimate legs, exhibits a remarkable morphological heterogeneity. Not participating in locomotion, they hold a vast functional diversity. In many centipede species, elongation and annulation in combination with an augmentation of sensory structures indicates a functional shift towards a sensory appendage. In other species, thickening, widening and reinforcement with a multitude of cuticular protuberances and glandular systems suggests a role in both attack and defense. Moreover, sexual dimorphic characteristics indicate that centipede ultimate legs play a pivotal role in intraspecific communication, mate finding and courtship behavior. We address ambiguous identifications and designations of podomeres in order to point out controversial aspects of homology and homonymy. We provide a broad summary of descriptions, illustrations, ideas and observations published in past 160 years, and propose that studying centipede ultimate legs is not only essential in itself for filling gaps of knowledge in descriptive morphology, but also provides an opportunity to explore diverse pathways of leg transformations within Myriapoda. creator: Matthes Kenning creator: Carsten H.G. Müller creator: Andy Sombke uri: https://doi.org/10.7717/peerj.4023 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kenning et al. title: Snapshot recordings provide a first description of the acoustic signatures of deeper habitats adjacent to coral reefs of Moorea link: https://peerj.com/articles/4019 last-modified: 2017-11-14 description: Acoustic recording has been recognized as a valuable tool for non-intrusive monitoring of the marine environment, complementing traditional visual surveys. Acoustic surveys conducted on coral ecosystems have so far been restricted to barrier reefs and to shallow depths (10–30 m). Since they may provide refuge for coral reef organisms, the monitoring of outer reef slopes and describing of the soundscapes of deeper environment could provide insights into the characteristics of different biotopes of coral ecosystems. In this study, the acoustic features of four different habitats, with different topographies and substrates, located at different depths from 10 to 100 m, were recorded during day-time on the outer reef slope of the north Coast of Moorea Island (French Polynesia). Barrier reefs appeared to be the noisiest habitats whereas the average sound levels at other habitats decreased with their distance from the reef and with increasing depth. However, sound levels were higher than expected by propagation models, supporting that these habitats possess their own sound sources. While reef sounds are known to attract marine larvae, sounds from deeper habitats may then also have a non-negligible attractive potential, coming into play before the reef itself. creator: Frédéric Bertucci creator: Eric Parmentier creator: Cécile Berthe creator: Marc Besson creator: Anthony D. Hawkins creator: Thierry Aubin creator: David Lecchini uri: https://doi.org/10.7717/peerj.4019 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bertucci et al. title: Attribute amnesia is greatly reduced with novel stimuli link: https://peerj.com/articles/4016 last-modified: 2017-11-14 description: Attribute amnesia is the counterintuitive phenomenon where observers are unable to report a salient aspect of a stimulus (e.g., its colour or its identity) immediately after the stimulus was presented, despite both attending to and processing the stimulus. Almost all previous attribute amnesia studies used highly familiar stimuli. Our study investigated whether attribute amnesia would also occur for unfamiliar stimuli. We conducted four experiments using stimuli that were highly familiar (colours or repeated animal images) or that were unfamiliar to the observers (unique animal images). Our results revealed that attribute amnesia was present for both sets of familiar stimuli, colour (p < .001) and repeated animals (p = .001); but was greatly attenuated, and possibly eliminated, when the stimuli were unique animals (p = .02). Our data shows that attribute amnesia is greatly reduced for novel stimuli. creator: Weijia Chen creator: Piers D.L. Howe uri: https://doi.org/10.7717/peerj.4016 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chen and Howe title: Bed site selection by a subordinate predator: an example with the cougar (Puma concolor) in the Greater Yellowstone Ecosystem link: https://peerj.com/articles/4010 last-modified: 2017-11-14 description: As technology has improved, our ability to study cryptic animal behavior has increased. Bed site selection is one such example. Among prey species, bed site selection provides thermoregulatory benefits and mitigates predation risk, and may directly influence survival. We conducted research to test whether a subordinate carnivore also selected beds with similar characteristics in an ecosystem supporting a multi-species guild of competing predators. We employed a model comparison approach in which we tested whether cougar (Puma concolor) bed site attributes supported the thermoregulatory versus the predator avoidance hypotheses, or exhibited characteristics supporting both hypotheses. Between 2012–2016, we investigated 599 cougar bed sites in the Greater Yellowstone Ecosystem and examined attributes at two scales: the landscape (second-order, n = 599) and the microsite (fourth order, n = 140). At the landscape scale, cougars selected bed sites in winter that supported both the thermoregulatory and predator avoidance hypotheses: bed sites were on steeper slopes but at lower elevations, closer to the forest edge, away from sagebrush and meadow habitat types, and on southern, eastern, and western-facing slopes. In the summer, bed attributes supported the predator avoidance hypothesis over the thermoregulation hypothesis: beds were closer to forest edges, away from sagebrush and meadow habitat classes, and on steeper slopes. At the microsite scale, cougar bed attributes in both the winter and summer supported both the predator avoidance and thermoregulatory hypotheses: they selected bed sites with high canopy cover, high vegetative concealment, and in a rugged habitat class characterized by cliff bands and talus fields. We found that just like prey species, a subordinate predator selected bed sites that facilitated both thermoregulatory and anti-predator functions. In conclusion, we believe that measuring bed site attributes may provide a novel means of measuring the use of refugia by subordinate predators, and ultimately provide new insights into the habitat requirements and energetics of subordinate carnivores. creator: Anna Kusler creator: L. Mark Elbroch creator: Howard Quigley creator: Melissa Grigione uri: https://doi.org/10.7717/peerj.4010 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kusler et al. title: Colour change of twig-mimicking peppered moth larvae is a continuous reaction norm that increases camouflage against avian predators link: https://peerj.com/articles/3999 last-modified: 2017-11-14 description: Camouflage, and in particular background-matching, is one of the most common anti-predator strategies observed in nature. Animals can improve their match to the colour/pattern of their surroundings through background selection, and/or by plastic colour change. Colour change can occur rapidly (a few seconds), or it may be slow, taking hours to days. Many studies have explored the cues and mechanisms behind rapid colour change, but there is a considerable lack of information about slow colour change in the context of predation: the cues that initiate it, and the range of phenotypes that are produced. Here we show that peppered moth (Biston betularia) larvae respond to colour and luminance of the twigs they rest on, and exhibit a continuous reaction norm of phenotypes. When presented with a heterogeneous environment of mixed twig colours, individual larvae specialise crypsis towards one colour rather than developing an intermediate colour. Flexible colour change in this species has likely evolved in association with wind dispersal and polyphagy, which result in caterpillars settling and feeding in a diverse range of visual environments. This is the first example of visually induced slow colour change in Lepidoptera that has been objectively quantified and measured from the visual perspective of natural predators. creator: Amy Eacock creator: Hannah M. Rowland creator: Nicola Edmonds creator: Ilik J. Saccheri uri: https://doi.org/10.7717/peerj.3999 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Eacock et al. title: Grassland habitat restoration: lessons learnt from long term monitoring of Swanworth Quarry, UK, 1997–2014 link: https://peerj.com/articles/3942 last-modified: 2017-11-14 description: Habitat restoration projects are often conducted when prior use or extraction of natural resources results in land degradation. The success of restoration programmes, however, is variable, and studies that provide evidence of long term outcomes are valuable for evaluation purposes. This study focused on the restoration of vegetation within a limestone quarry in Dorset, UK between 1997 and 2014. Using a randomised block design, the effect of seed mix and seed rate on the development of community assemblage was investigated in comparison to a nearby target calcareous grassland site. We hypothesised that seed mix composition and sowing rate would influence both the trajectory of the grassland assemblage and final community composition. We found that species composition (in relation to both richness and community assemblage) was strongly influenced by time and to some extent by seed rate and seed mix. However, no treatments achieved strong resemblance to the calcareous grassland target vegetation; rather they resembled mesotrophic communities. We conclude that (as with previous studies) there is no “quick fix” for the establishment of a grassland community; long-term monitoring provides useful information on the trajectory of community development; sowing gets you something (in our case mesotrophic grassland), but, it may not be the target vegetation (e.g., calcicolous grassland) you want that is difficult to establish and regenerate; it is important to sow a diverse mix as subsequent recruitment opportunities are probably limited; post-establishment management should be explored further and carefully considered as part of a restoration project. creator: Barbara Maria Smith creator: Anita Diaz creator: Linton Winder uri: https://doi.org/10.7717/peerj.3942 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Smith et al. title: Supradapedon revisited: geological explorations in the Triassic of southern Tanzania link: https://peerj.com/articles/4038 last-modified: 2017-11-13 description: The upper Triassic deposits of the Selous Basin in south Tanzania have not been prospected for fossil tetrapods since the middle of last century, when Gordon M. Stockley collected two rhynchosaur bone fragments from the so called “Tunduru beds”. Here we present the results of a field trip conducted in July 2015 to the vicinities of Tunduru and Msamara, Ruvuma Region, Tanzania, in search for similar remains. Even if unsuccessful in terms of fossil discoveries, the geological mapping conducted during the trip improved our knowledge of the deposition systems of the southern margin of the Selous Basin during the Triassic, allowing tentative correlations to its central part and to neighbouring basins. Moreover, we reviewed the fossil material previously collected by Gordon M. Stockley, confirming that the remains correspond to a valid species, Supradapedon stockleyi, which was incorporated into a comprehensive phylogeny of rhynchosaurs and found to represent an Hyperodapedontinae with a set of mostly plesiomorphic traits for the group. Data gathered form the revision and phylogenetic placement of Su. stockleyi helps understanding the acquisition of the typical dental traits of Late Triassic rhynchosaurs, corroborating the potential of hyperodapedontines as index fossils of the Carnian-earliest Norian. creator: Max C. Langer creator: Átila A.S. da Rosa creator: Felipe C. Montefeltro uri: https://doi.org/10.7717/peerj.4038 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Langer et al. title: Generation and characterization of cross neutralizing human monoclonal antibody against 4 serotypes of dengue virus without enhancing activity link: https://peerj.com/articles/4021 last-modified: 2017-11-13 description: BackgroundDengue disease is a leading cause of illness and death in the tropics and subtropics. Most severe cases occur among patients secondarily infected with a different dengue virus (DENV) serotype compared with that from the first infection, resulting in antibody-dependent enhancement activity (ADE). Our previous study generated the neutralizing human monoclonal antibody, D23-1B3B9 (B3B9), targeting the first domain II of E protein, which showed strong neutralizing activity (NT) against all four DENV serotypes. However, at sub-neutralizing concentrations, it showed ADE activity in vitro.MethodsIn this study, we constructed a new expression plasmid using the existing IgG heavy chain plasmid as a template for Fc modification at position N297Q by site-directed mutagenesis. The resulting plasmid was then co-transfected with a light chain plasmid to produce full recombinant IgG (rIgG) in mammalian cells (N297Q-B3B9). This rIgG was characterized for neutralizing and enhancing activity by using different FcγR bearing cells. To produce sufficient quantities of B3B9 rIgG for further characterization, CHO-K1 cells stably secreting N297Q-B3B9 rIgG were then established.ResultsThe generated N297Q-B3B9 rIgG which targets the conserved N-terminal fusion loop of DENV envelope protein showed the same cross-neutralizing activity to all four DENV serotypes as those of wild type rIgG. In both FcγRI- and RII-bearing THP-1 cells and FcγRII-bearing K562 cells, N297Q-B3B9 rIgG lacked ADE activity against all DENV serotypes at sub-neutralizing concentrations. Fortunately, the N297Q-B3B9 rIgG secreted from stable cells showed the same patterns of NT and ADE activities as those of the N297Q-B3B9 rIgG obtained from transient expression against DENV2. Thus, the CHO-K1 stably expressing N297Q-B3B9 HuMAb can be developed as high producer stable cells and used to produce sufficient amounts of antibody for further characterization as a promising dengue therapeutic candidate.DiscussionHuman monoclonal antibody, targeted to fusion loop of envelope domainII (EDII), was generated and showed cross-neutralizing activity to 4 serotypes of DENV, but did not cause any viral enhancement activity in vitro. This HuMAb could be further developed as therapeutic candidates. creator: Subenya Injampa creator: Nataya Muenngern creator: Chonlatip Pipattanaboon creator: Surachet Benjathummarak creator: Khwanchit Boonha creator: Hathairad Hananantachai creator: Waranya Wongwit creator: Pongrama Ramasoota creator: Pannamthip Pitaksajjakul uri: https://doi.org/10.7717/peerj.4021 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Injampa et al. title: Assessing Mongolian gerbil emotional behavior: effects of two shock intensities and response-independent shocks during an extended inhibitory-avoidance task link: https://peerj.com/articles/4009 last-modified: 2017-11-13 description: Despite step-down inhibitory avoidance procedures that have been widely implemented in rats and mice to study learning and emotion phenomena, performance of other species in these tasks has received less attention. The case of the Mongolian gerbil is of relevance considering the discrepancies in the parameters of the step-down protocols implemented, especially the wide range of foot-shock intensities (i.e., 0.4–4.0 mA), and the lack of information on long-term performance, extinction effects, and behavioral patterning during these tasks. Experiment 1 aimed to (a) characterize gerbils’ acquisition, extinction, and steady-state performance during a multisession (i.e., extended) step-down protocol adapted for implementation in a commercially-available behavioral package (Video Fear Conditioning System—MED Associates Fairfax, VT, USA), and (b) compare gerbils’ performance in this task with two shock intensities – 0.5 vs. 1.0 mA—considered in the low-to-mid range. Results indicated that the 1.0 mA protocol produced more reliable and clear evidence of avoidance learning, extinction, and reacquisition in terms of increments in freezing and on-platform time as well as suppression of platform descent. Experiment 2 aimed to (a) assess whether an alternate protocol consisting of a random delivery of foot shocks could replicate the effects of Experiment 1 and (b) characterize gerbils’ exploratory behavior during the step-down task (jumping, digging, rearing, and probing). Random shocks did not reproduce the effects observed with the first protocol. The data also indicated that a change from random to response-dependent shocks affects (a) the length of each visit to the platform, but not the frequency of platform descends or freezing time, and (b) the patterns of exploratory behavior, namely, suppression of digging and rearing, as well as increments in probing and jumping. Overall, the study demonstrated the feasibility of the extended step-down protocol for studying steady performance, extinction, and reacquisition of avoidance behavior in gerbils, which could be easily implemented in a commercially available system. The observation that 1.0 mA shocks produced a clear and consistent avoidance behavior suggests that implementation of higher intensities is unnecessary for reproducing aversive-conditioning effects in this species. The observed patterning of freezing, platform descents, and exploratory responses produced by the change from random to periodic shocks may relate to the active defensive system of the gerbil. Of special interest is the probing behavior, which could be interpreted as risk assessment and has not been reported in other rodent species exposed to step-down and similar tasks. creator: Camilo Hurtado-Parrado creator: Camilo González-León creator: Mónica A. Arias-Higuera creator: Angelo Cardona creator: Lucia G. Medina creator: Laura García-Muñoz creator: Christian Sánchez creator: Julián Cifuentes creator: Juan Carlos Forigua creator: Andrea Ortiz creator: Cesar A. Acevedo-Triana creator: Javier L. Rico uri: https://doi.org/10.7717/peerj.4009 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hurtado-Parrado et al. title: Microbial agents in macroscopically healthy mammary gland tissues of small ruminants link: https://peerj.com/articles/3994 last-modified: 2017-11-13 description: BackgroundHealth of mammary glands is fundamental for milk and dairy products hygiene and quality, with huge impacts on consumers welfare.MethodsThis study aims to investigate the microbial agents (bacteria, fungi and lentiviruses) isolated from 89 macroscopically healthy udders of regularly slaughtered small ruminants (41 sheep, 48 goats), also correlating their presence with the histological findings. Multinomial logistic regression was applied to evaluate the association between lesions and positivity for different microbial isolates, animal age and bacteria.ResultsTwenty-five samples were microbiologically negative; 138 different bacteria were isolated in 64 positive udders. Coagulase-negative staphylococci were the most prevalent bacteria isolated (46.42%), followed by environmental opportunists (34.76%), others (10.14%) and pathogens (8.68%). Most mammary glands showed coinfections (75%). Lentiviruses were detected in 39.3% of samples. Histologically, chronic non-suppurative mastitis was observed in 45/89 glands, followed by chronic mixed mastitis (12/89) and acute suppurative mastitis (4/89). Only 28 udders were normal. Histological lesions were significantly associated with the animal species and lentiviruses and coagulase-negative staphylococci infections. Goats had significantly higher risk to show chronic mixed mastitis compared to sheep. Goats showed a significantly lower risk (OR = 0.26; 95% CI [0.06–0.71]) of being infected by environmental opportunists compared to sheep, but higher risk (OR = 10.87; 95% CI [3.69–37.77]) of being infected with lentiviruses.DiscussionThe results of the present study suggest that macroscopically healthy glands of small ruminants could act as a reservoir of microbial agents for susceptible animals, representing a potential risk factor for the widespread of acute or chronic infection in the flock. creator: Liliana Spuria creator: Elena Biasibetti creator: Donal Bisanzio creator: Ilaria Biasato creator: Daniele De Meneghi creator: Patrizia Nebbia creator: Patrizia Robino creator: Paolo Bianco creator: Michele Lamberti creator: Claudio Caruso creator: Alessia Di Blasio creator: Simone Peletto creator: Loretta Masoero creator: Alessandro Dondo creator: Maria Teresa Capucchio uri: https://doi.org/10.7717/peerj.3994 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Spuria et al. title: Vegetation structure of plantain-based agrosystems determines numerical dominance in community of ground-dwelling ants link: https://peerj.com/articles/3917 last-modified: 2017-11-13 description: In tropics, ants can represent an important part of animal biomass and are known to be involved in ecosystem services, such as pest regulation. Understanding the mechanisms underlying the structuring of local ant communities is therefore important in agroecology. In the humid tropics of Africa, plantains are cropped in association with many other annual and perennial crops. Such agrosystems differ greatly in vegetation diversity and structure and are well-suited for studying how habitat-related factors affect the ant community. We analysed abundance data for the six numerically dominant ant taxa in 500 subplots located in 20 diversified, plantain-based fields. We found that the density of crops with foliage at intermediate and high canopy strata determined the numerical dominance of species. We found no relationship between the numerical dominance of each ant taxon with the crop diversity. Our results indicate that the manipulation of the densities of crops with leaves in the intermediate and high strata may help maintain the coexistence of ant species by providing different habitat patches. Further research in such agrosystems should be performed to assess if the effect of vegetation structure on ant abundance could result in efficient pest regulation. creator: Anicet Gbéblonoudo Dassou creator: Philippe Tixier creator: Sylvain Dépigny creator: Dominique Carval uri: https://doi.org/10.7717/peerj.3917 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Dassou et al. title: Overland movement in African clawed frogs (Xenopus laevis): empirical dispersal data from within their native range link: https://peerj.com/articles/4039 last-modified: 2017-11-10 description: Dispersal forms are an important component of the ecology of many animals, and reach particular importance for predicting ranges of invasive species. African clawed frogs (Xenopus laevis) move overland between water bodies, but all empirical studies are from invasive populations with none from their native southern Africa. Here we report on incidents of overland movement found through a capture-recapture study carried out over a three year period in Overstrand, South Africa. The maximum distance moved was 2.4 km with most of the 91 animals, representing 5% of the population, moving ∼150 m. We found no differences in distances moved by males and females, despite the former being smaller. Fewer males moved overland, but this was no different from the sex bias found in the population. In laboratory performance trials, we found that males outperformed females, in both distance moved and time to exhaustion, when corrected for size. Overland movement occurred throughout the year, but reached peaks in spring and early summer when temporary water bodies were drying. Despite permanent impoundments being located within the study area, we found no evidence for migrations of animals between temporary and permanent water bodies. Our study provides the first dispersal kernel for X. laevis and suggests that it is similar to many non-pipid anurans with respect to dispersal. creator: F. André De Villiers creator: John Measey uri: https://doi.org/10.7717/peerj.4039 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 De Villiers and Measey title: Foliar microbiome transplants confer disease resistance in a critically-endangered plant link: https://peerj.com/articles/4020 last-modified: 2017-11-10 description: There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped. Using the host/parasite system of Phyllostegia kaalaensis and Neoerysiphe galeopsidis, we conducted experiments to test total foliar microbiome transplants from healthy wild relatives onto fungicide-dependent endangered plants in an attempt to mitigate disease and reduce dependency on fungicides. Plants were treated with total microbiome transplants or cultured subsets of this community and monitored for disease severity. High-throughput DNA screening of fungal ITS1 rDNA was used to track the leaf-associated fungal communities and evaluate the effectiveness of transplantation methods. Individuals receiving traditionally isolated fungal treatments showed no improvement, but those receiving applications of a simple leaf slurry containing an uncultured fungal community showed significant disease reduction, to which we partially attribute an increase in the mycoparasitic Pseudozyma aphidis. These results were replicated in two independent experimental rounds. Treated plants have since been moved to a native habitat and, as of this writing, remain disease-free. Our results demonstrate the effectiveness of a simple low-tech method for transferring beneficial microbes from healthy wild plants to greenhouse-raised plants with reduced symbiotic microbiota. This technique was effective at reducing disease, and in conferring increased survival to an out-planted population of critically endangered plants. It was not effective in a closely related plant. Plant conservation efforts should strive to include foliar microbes as part of comprehensive management plans. creator: Geoffrey Zahn creator: Anthony S. Amend uri: https://doi.org/10.7717/peerj.4020 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zahn and Amend title: How can we reliably identify a taxon based on humeral morphology? Comparative morphology of desmostylian humeri link: https://peerj.com/articles/4011 last-modified: 2017-11-10 description: Desmostylia is a clade of marine mammals belonging to either Tethytheria or Perissodactyla. Rich fossil records of Desmostylia were found in the Oligocene to Miocene strata of the Northern Pacific Rim, especially in the northwestern region, which includes the Japanese archipelago. Fossils in many shapes and forms, including whole or partial skeletons, skulls, teeth, and fragmentary bones have been discovered from this region. Despite the prevalent availability of fossil records, detailed taxonomic identification based on fragmentary postcranial materials has been difficult owing to to our limited knowledge of the postcranial diagnostic features of many desmostylian taxa. In this study, I propose the utilization of diagnostic characters found in the humerus to identify desmostylian genus. These characters can be used to identify isolated desmostylian humeri at the genus level, contributing to a better understanding of the stratigraphic and geographic distributions of each genus. creator: Kumiko Matsui uri: https://doi.org/10.7717/peerj.4011 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Matsui title: A unified approach to model peripheral nerves across different animal species link: https://peerj.com/articles/4005 last-modified: 2017-11-10 description: Peripheral nerves are extremely complex biological structures. The knowledge of their response to stretch is crucial to better understand physiological and pathological states (e.g., due to overstretch). Since their mechanical response is deterministically related to the nature of the external stimuli, theoretical and computational tools were used to investigate their behaviour. In this work, a Yeoh-like polynomial strain energy function was used to reproduce the response of in vitro porcine nerve. Moreover, this approach was applied to different nervous structures coming from different animal species (rabbit, lobster, Aplysia) and tested for different amount of stretch (up to extreme ones). Starting from this theoretical background, in silico models of both porcine nerves and cerebro-abdominal connective of Aplysia were built to reproduce experimental data (R2 > 0.9). Finally, bi-dimensional in silico models were provided to reduce computational time of more than 90% with respect to the performances of fully three-dimensional models. creator: Elisabetta Giannessi creator: Maria Rita Stornelli creator: Pier Nicola Sergi uri: https://doi.org/10.7717/peerj.4005 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Giannessi et al. title: Anthropogenic water sources and the effects on Sonoran Desert small mammal communities link: https://peerj.com/articles/4003 last-modified: 2017-11-10 description: Anthropogenic water sources (AWS) are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012. A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse (Chaetodipus penicillatus) which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey’s pocket mouse (C. baileyi) and white-throated woodrat (Neotoma albigula), had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture. creator: Aaron B. Switalski creator: Heather L. Bateman uri: https://doi.org/10.7717/peerj.4003 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Switalski and Bateman title: Preoperative cervical sagittal alignment parameters and their impacts on myelopathy in patients with cervical spondylotic myelopathy: a retrospective study link: https://peerj.com/articles/4027 last-modified: 2017-11-09 description: BackgroundCervical sagittal alignment plays an important role in the pathogenesis of cervical spondylotic myelopathy (CSM), but there are limited studies on the cervical sagittal parameters in CSM patients and their correlations with myelopathy. The aim of this study is to investigate the correlations among the preoperative cervical sagittal alignment parameters and their correlations with the development of myelopathy in patients with CSM.MethodsWe retrospectively collected 212 patients with CSM who underwent surgical interventions. Gender, age, modified Japanese Orthopedic Association score (mJOA), cervical lordosis (CL), C2–C7 sagittal vertical axis (C2–C7 SVA), T1 slope (T1S), neck tilt (NT) and thoracic inlet angle (TIA) were collected before operation. Interobserver and intraobserver reliability were calculated for all measurements (intraclass correlation coefficient, ICC). Data were analyzed with Pearson and Spearman correlation tests and multiple linear regression analysis.ResultsA total of 212 patients with CSM were included in this study (male: 136, female: 76) with an average age of 54.5 ± 10.1 years old. Intraobserver and interobserver reliability for all included radiographic parameters presented good to excellent agreement (ICC > 0.7). No significant differences in demographic and radiological parameters have been observed between males and females (P > 0.05). We found statistically significant correlations among the following parameters: age with CL (r = 0.135, P = 0.049), age with T1S (r = 0.222, P = 0.001), CL with T1S (r = 0.291, P < 0.001), CL with C2-C7 SVA (r =  − 0.395, P < 0.001), mJOA with age (r =  − 0.274, P < 0.001), mJOA with C2–C7 SVA (r =  − 0.219, P < 0.001) and mJOA with T1S(r =  − 0.171, p = 0.013). Linear regression analysis showed that C2–C7 SVA was the predictor of CL (adjusted R2 = 0.152, P < 0.001) and multiple linear regression showed that age combined with C2–C7 SVA was a sensitive predictor of mJOA (adjusted R2 = 0.106, P < 0.001).DiscussionThere were significant correlations among certain preoperative cervical sagittal parameters in CSM patients. CL was the only predictor of C2–C7 SVA. Age combined with C2–C7 SVA could predict the severity of myelopathy. creator: Wei Yuan creator: Yue Zhu creator: Haitao Zhu creator: Cui Cui creator: Lei Pei creator: Zhuxi Huang uri: https://doi.org/10.7717/peerj.4027 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yuan et al. title: The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle link: https://peerj.com/articles/4014 last-modified: 2017-11-09 description: The wood frog (Rana sylvatica) can endure freezing of up to 65% of total body water during winter. When frozen, wood frogs enter a dormant state characterized by a cessation of vital functions (i.e., no heartbeat, blood circulation, breathing, brain activity, or movement). Wood frogs utilize various behavioural and biochemical adaptations to survive extreme freezing and component anoxia and dehydration stresses, including a global suppression of metabolic functions and gene expression. The stress-responsive myocyte enhancer factor-2 (MEF2) transcription factor family regulates the selective expression of genes involved in glucose transport, protein quality control, and phosphagen homeostasis. This study examined the role of MEF2A and MEF2C proteins as well as select downstream targets (glucose transporter-4, calreticulin, and muscle and brain creatine kinase isozymes) in 40% dehydration and 24 h anoxia exposure at the transcriptional, translational, and post-translational levels using qRT-PCR, immunoblotting, and subcellular localization. Mef2a/c transcript levels remained constant during dehydration and anoxia. Total, cytoplasmic, and nuclear MEF2A/C and phospho-MEF2A/C protein levels remained constant during dehydration, whereas a decrease in total MEF2C levels was observed during rehydration. Total and phospho-MEF2A levels remained constant during anoxia, whereas total MEF2C levels decreased during 24 h anoxia and P-MEF2C levels increased during 4 h anoxia. In contrast, cytoplasmic MEF2A levels and nuclear phospho-MEF2A/C levels were upregulated during anoxia. MEF2 downstream targets remained constant during dehydration and anoxia, with the exception of glut4 which was upregulated during anoxia. These results suggest that the upregulated MEF2 response reported in wood frogs during freezing may in part stem from their cellular responses to surviving prolonged anoxia, rather than dehydration, leading to an increase in GLUT4 expression which may have an important role during anoxia survival. creator: Myriam P. Hoyeck creator: Hanane Hadj-Moussa creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4014 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hoyeck et al. title: The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert link: https://peerj.com/articles/4007 last-modified: 2017-11-09 description: BackgroundSoil microbial communities (SMC) play a central role in the structure and function of desert ecosystems. However, the high variability of annual precipitation could results in the alteration of SMC and related biological processes depending on soil water potential. The nature of the physiological adjustments made by SMC in order to obtain energy and nutrients remains unclear under different soil resource availabilities in desert ecosystems. In order to examine this dynamic, the present study examined the effects of variation in annual precipitation on physiological adjustments by the SMC across two vegetation-soil systems of different soil organic matter input in an oligotrophic desert ecosystem.MethodsWe collected soil samples in the Cuatro Ciénegas Basin (Mexico) under two vegetation covers: rosetophylous scrub (RS) and grassland (G), that differ in terms of quantity and quality of organic matter. Collections were conducted during the years 2011, 2012, 2013 and 2014, over which a noticeable variation in the annual precipitation occurred. The ecoenzymatic activity involved in the decomposition of organic matter, and the concentration of dissolved, available and microbial biomass nutrients, were determined and compared between sites and years.ResultsIn 2011, we observed differences in bacterial taxonomic composition between the two vegetation covers. The lowest values of dissolved, available and microbial nutrients in both cover types were found in 2012. The G soil showed higher values of dissolved and available nutrients in the wet years. Significant positive correlations were detected between precipitation and the ratios Cmic:Nmic and Cmic:Pmic in the RS soil and Cmic:Pmic and Nmic:Pmic in the G soil. The slopes of the regression with Cmic and Nmic were higher in the G soil and lower in the RS soil. Moreover, the SMC under each vegetation cover were co-limited by different nutrients and responded to the sum of water stress and nutrient limitation.DiscussionSoil community within both sites (RS and G) may be vulnerable to drought. However, the community of the site with lower resources (RS) is well adapted to acquire P resources by ecoenzyme upregulation during years with adequate precipitation, suggesting that this community is resilient after drought occurs. Under the Global Climate Change scenarios for desert ecosystems that predict reduced annual precipitation and an increased intensity and frequency of torrential rains and drought events, the soil microbial communities of both sites could be vulnerable to drought through C and P co-limitation and reallocation of resources to physiological acclimatization strategies in order to survive. creator: Cristina Montiel-González creator: Yunuen Tapia-Torres creator: Valeria Souza creator: Felipe García-Oliva uri: https://doi.org/10.7717/peerj.4007 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Montiel-González et al. title: Mobile acoustic transects miss rare bat species: implications of survey method and spatio-temporal sampling for monitoring bats link: https://peerj.com/articles/3940 last-modified: 2017-11-09 description: Due to increasing threats facing bats, long-term monitoring protocols are needed to inform conservation strategies. Effective monitoring should be easily repeatable while capturing spatio-temporal variation. Mobile acoustic driving transect surveys (‘mobile transects’) have been touted as a robust, cost-effective method to monitor bats; however, it is not clear how well mobile transects represent dynamic bat communities, especially when used as the sole survey approach. To assist biologists who must select a single survey method due to resource limitations, we assessed the effectiveness of three acoustic survey methods at detecting species richness in a vast protected area (Everglades National Park): (1) mobile transects, (2) stationary surveys that were strategically located by sources of open water and (3) stationary surveys that were replicated spatially across the landscape. We found that mobile transects underrepresented bat species richness compared to stationary surveys across all major vegetation communities and in two distinct seasons (dry/cool and wet/warm). Most critically, mobile transects failed to detect three rare bat species, one of which is federally endangered. Spatially replicated stationary surveys did not estimate higher species richness than strategically located stationary surveys, but increased the rate at which species were detected in one vegetation community. The survey strategy that detected maximum species richness and the highest mean nightly species richness with minimal effort was a strategically located stationary detector in each of two major vegetation communities during the wet/warm season. creator: Elizabeth C. Braun de Torrez creator: Megan A. Wallrichs creator: Holly K. Ober creator: Robert A. McCleery uri: https://doi.org/10.7717/peerj.3940 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Braun de Torrez et al. title: HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities link: https://peerj.com/articles/4015 last-modified: 2017-11-08 description: The development and application of metagenomic approaches have provided an opportunity to study and define horizontal gene transfer (HGT) on the level of microbial communities. However, no current metagenomic data simulation tools offers the option to introduce defined HGT within a microbial community. Here, we present HgtSIM, a pipeline to simulate HGT event among microbial community members with user-defined mutation levels. It was developed for testing and benchmarking pipelines for recovering HGTs from complex microbial datasets. HgtSIM is implemented in Python3 and is freely available at: https://github.com/songweizhi/HgtSIM. creator: Weizhi Song creator: Kerrin Steensen creator: Torsten Thomas uri: https://doi.org/10.7717/peerj.4015 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Song et al. title: Indicators for the use of robotic labs in basic biomedical research: a literature analysis link: https://peerj.com/articles/3997 last-modified: 2017-11-08 description: Robotic labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments. In this article, we investigate whether these labs could be applicable in current experimental practice. We do this by text mining 1,628 papers for occurrences of methods that are supported by commercial robotic labs. Using two different concept recognition tools, we find that 86%–89% of the papers have at least one of these methods. This and our other results provide indications that robotic labs can serve as the foundation for performing many lab-based experiments. creator: Paul Groth creator: Jessica Cox uri: https://doi.org/10.7717/peerj.3997 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Groth and Cox title: Character drawing style in cartoons on empathy induction: an eye-tracking and EEG study link: https://peerj.com/articles/3988 last-modified: 2017-11-08 description: In its most basic form, empathy refers to the ability to understand another person’s feelings and emotions, representing an essential component of human social interaction. Owing to an increase in the use of mass media, which is used to distribute high levels of empathy-inducing content, media plays a key role in individual and social empathy induction. We investigated empathy induction in cartoons using eye movement, EEG and behavioral measures to explore whether empathy factors correlate with character drawing styles. Two different types of empathy-inducing cartoons that consisted of three stages and had the same story plot were used. One had an iconic style, while the other was realistic style. Fifty participants were divided into two groups corresponding to the individual cartoon drawing styles and were presented with only one type of drawing style. We found that there were no significant differences of empathy factors between iconic and realistic style. However, the Induced Empathy Score (IES) had a close relationship with subsequent attentional processing (total fixation length for gaze duration). Furthermore, iconic style suppressed the fronto-central area more than realistic style in the gamma power band. These results suggest that iconic cartoons have the advantage of abstraction during empathy induction, because the iconic cartoons induced the same level of empathy as realistic cartoons while using the same story plot (top-down process), even though lesser time and effort were required by the cartoon artist to draw them. This also means that the top-down process (story plot) is more important than the bottom-up process (drawing style) in empathy induction when viewing cartoons creator: Yong-il Lee creator: Yeojeong Choi creator: Jaeseung Jeong uri: https://doi.org/10.7717/peerj.3988 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Lee et al. title: Visual and acoustic components of courtship in the bird-of-paradise genus Astrapia (Aves: Paradisaeidae) link: https://peerj.com/articles/3987 last-modified: 2017-11-08 description: The distinctive and divergent courtship phenotypes of the birds-of-paradise make them an important group for gaining insights into the evolution of sexually selected phenotypic evolution. The genus Astrapia includes five long-tailed species that inhabit New Guinea’s montane forests. The visual and acoustic components of courtship among Astrapia species are very poorly known. In this study, we use audiovisual data from a natural history collection of animal behavior to fill gaps in knowledge about the visual and acoustic components of Astrapia courtship. We report seven distinct male behaviors and two female specific behaviors along with distinct vocalizations and wing-produced sonations for all five species. These results provide the most complete assessment of courtship in the genus Astrapia to date and provide a valuable baseline for future research, including comparative and evolutionary studies among these and other bird-of-paradise species. creator: Edwin Scholes creator: Julia M. Gillis creator: Timothy G. Laman uri: https://doi.org/10.7717/peerj.3987 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Scholes et al. title: EEG sensorimotor rhythms’ variation and functional connectivity measures during motor imagery: linear relations and classification approaches link: https://peerj.com/articles/3983 last-modified: 2017-11-08 description: Hands motor imagery (MI) has been reported to alter synchronization patterns amongst neurons, yielding variations in the mu and beta bands’ power spectral density (PSD) of the electroencephalography (EEG) signal. These alterations have been used in the field of brain-computer interfaces (BCI), in an attempt to assign distinct MI tasks to commands of such a system. Recent studies have highlighted that information may be missing if knowledge about brain functional connectivity is not considered. In this work, we modeled the brain as a graph in which each EEG electrode represents a node. Our goal was to understand if there exists any linear correlation between variations in the synchronization patterns—that is, variations in the PSD of mu and beta bands—induced by MI and alterations in the corresponding functional networks. Moreover, we (1) explored the feasibility of using functional connectivity parameters as features for a classifier in the context of an MI-BCI; (2) investigated three different types of feature selection (FS) techniques; and (3) compared our approach to a more traditional method using the signal PSD as classifier inputs. Ten healthy subjects participated in this study. We observed significant correlations (p < 0.05) with values ranging from 0.4 to 0.9 between PSD variations and functional network alterations for some electrodes, prominently in the beta band. The PSD method performed better for data classification, with mean accuracies of (90 ± 8)% and (87 ± 7)% for the mu and beta band, respectively, versus (83 ± 8)% and (83 ± 7)% for the same bands for the graph method. Moreover, the number of features for the graph method was considerably larger. However, results for both methods were relatively close, and even overlapped when the uncertainties of the accuracy rates were considered. Further investigation regarding a careful exploration of other graph metrics may provide better alternatives. creator: Carlos A. Stefano Filho creator: Romis Attux creator: Gabriela Castellano uri: https://doi.org/10.7717/peerj.3983 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Stefano Filho et al. title: Assemblage and functional categorization of dung beetles (Coleoptera: Scarabaeinae) from the Pantanal link: https://peerj.com/articles/3978 last-modified: 2017-11-08 description: The Pantanal is one of the world’s largest tropical wetland areas and harbors high mammal biomass. There is no formal list of dung beetle species, and studies on their functional roles have never being carried out in Pantanal. In this study, we identified dung beetle species occurring in the north Pantanal region (Poconé sub-region, Brazil) and studied their functional organization, by measuring morphological, behavioral and phenological traits. We collected 25,278 individuals belonging to 17 genera and 35 species. We identified eight functional groups in the habitat: Noturnal Telecoprids, Diurnal Telecoprids, Nesting Endocoprids, Small Nonrollers, Nocturnal Nester Paracoprids, Big Nesters Paracoprids, Non Nesters Paracoprids and Diurnal Nesters Paracoprids. The functional groups were defined mostly by two reproductive traits and two niche differentiation traits related to the use of fecal resources. This high diversification of both species and functional roles shows the importance of the group in a habitat with strong variation in availability of habitat and resources. creator: Marcelo B. Pessôa creator: Thiago J. Izzo creator: Fernando Z. Vaz-de-Mello uri: https://doi.org/10.7717/peerj.3978 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Pessôa et al. title: Genome-wide identification and characterization of GRAS transcription factors in tomato (Solanum lycopersicum) link: https://peerj.com/articles/3955 last-modified: 2017-11-08 description: Solanum lycopersicum, belonging to Solanaceae, is one of the commonly used model plants. The GRAS genes are transcriptional regulators, which play a significant role in plant growth and development, and the functions of several GRAS genes have been recognized, such as, axillary shoot meristem formation, radial root patterning, phytohormones (gibberellins) signal transduction, light signaling, and abiotic/biotic stress; however, only a few of these were identified and functionally characterized. In this study, a gene family was analyzed comprehensively with respect to phylogeny, gene structure, chromosomal localization, and expression pattern; the 54 GRAS members were screened from tomato by bioinformatics for the first time. The GRAS genes among tomato, Arabidopsis, rice, and grapevine were rebuilt to form a phylogenomic tree, which was divided into ten groups according to the previous classification of Arabidopsis and rice. A multiple sequence alignment exhibited the typical GRAS domain and conserved motifs similar to other gene families. Both the segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in tomato; the expression patterns across a variety of tissues and biotic conditions revealed potentially different functions of GRAS genes in tomato development and stress responses. Altogether, this study provides valuable information and robust candidate genes for future functional analysis for improving the resistance of tomato growth. creator: Yiling Niu creator: Tingting Zhao creator: Xiangyang Xu creator: Jingfu Li uri: https://doi.org/10.7717/peerj.3955 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Niu et al. title: A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus link: https://peerj.com/articles/4018 last-modified: 2017-11-07 description: The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58–62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species. creator: Hanghui Kong creator: Wanzhen Liu creator: Gang Yao creator: Wei Gong uri: https://doi.org/10.7717/peerj.4018 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kong et al. title: Metabarcoding analysis of the stomach contents of the Antarctic Toothfish (Dissostichus mawsoni) collected in the Antarctic Ocean link: https://peerj.com/articles/3977 last-modified: 2017-11-07 description: Stomach contents of the Antarctic toothfish, Dissostichus mawsoni, collected from subareas 58.4 and 88.3, were analyzed using next generation sequencing (NGS) technology. After processing the raw reads generated by the MiSeq platform, a total of 131,233 contigs (130 operational taxonomic units [OTUs]) were obtained from 163 individuals in subarea 58.4, and 75,961 contigs (105 OTUs) from 164 fish in subarea 88.3. At 98% sequence identity, species names were assigned to most OTUs in this study, indicating the quality of the DNA barcode database for the Antarctic Ocean was sufficient for molecular analysis, especially for fish species. A total of 19 species was identified from the stomach of D. mawsoni in this study, which included 14 fish species and five mollusks. More than 90% of contigs belonged to fish species, supporting the postulate that the major prey of D. mawsoni are fish. Two fish species, Macrourus whitsoni and Chionobathyscus dewitti, were the most important prey items (a finding similar to that of previous studies). We also obtained genotypes of prey items by NGS analysis, identifying an additional 17 representative haplotypes in this study. Comparison with three previous morphological studies and the NGS-based molecular identification in this study extended our knowledge regarding the prey of D. mawsoni, which previously was not possible. These results suggested that NGS-based diet studies are possible, if several current technical limitations, including the quality of the barcode database or the development of precise molecular quantification techniques to link them with morphological values, are overcome. To achieve this, additional studies should be conducted on various marine organisms. creator: Tae-Ho Yoon creator: Hye-Eun Kang creator: Soo Rin Lee creator: Jae-Bong Lee creator: Gun Wook Baeck creator: Hyun Park creator: Hyun-Woo Kim uri: https://doi.org/10.7717/peerj.3977 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Yoon et al. title: Male sex pheromone components in Heliconius butterflies released by the androconia affect female choice link: https://peerj.com/articles/3953 last-modified: 2017-11-07 description: Sex-specific pheromones are known to play an important role in butterfly courtship, and may influence both individual reproductive success and reproductive isolation between species. Extensive ecological, behavioural and genetic studies of Heliconius butterflies have made a substantial contribution to our understanding of speciation. Male pheromones, although long suspected to play an important role, have received relatively little attention in this genus. Here, we combine morphological, chemical and behavioural analyses of male pheromones in the Neotropical butterfly Heliconius melpomene. First, we identify putative androconia that are specialized brush-like scales that lie within the shiny grey region of the male hindwing. We then describe putative male sex pheromone compounds, which are largely confined to the androconial region of the hindwing of mature males, but are absent in immature males and females. Finally, behavioural choice experiments reveal that females of H. melpomene, H. erato and H. timareta strongly discriminate against conspecific males which have their androconial region experimentally blocked. As well as demonstrating the importance of chemical signalling for female mate choice in Heliconius butterflies, the results describe structures involved in release of the pheromone and a list of potential male sex pheromone compounds. creator: Kathy Darragh creator: Sohini Vanjari creator: Florian Mann creator: Maria F. Gonzalez-Rojas creator: Colin R. Morrison creator: Camilo Salazar creator: Carolina Pardo-Diaz creator: Richard M. Merrill creator: W. Owen McMillan creator: Stefan Schulz creator: Chris D. Jiggins uri: https://doi.org/10.7717/peerj.3953 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Darragh et al. title: HCV core antigen is an alternative marker to HCV RNA for evaluating active HCV infection: implications for improved diagnostic option in an era of affordable DAAs link: https://peerj.com/articles/4008 last-modified: 2017-11-06 description: The core antigen of the hepatitis C virus (HCV Ag) presents an alternative marker to HCV RNA when screening patients for HCV viremia. This study sought to evaluate the utility of HCV Ag as a marker to assess active HCV infection in individuals residing in an HCV-endemic area. From 298 HCV-seropositive individuals evaluated for the presence of anti-HCV antibody, HCV Ag and HCV RNA, anti-HCV antibody was detected in 252 individuals (signal-to-cutoff ratios ≥5), HCV RNA was detected in 222 individuals (88%), and HCV Ag was reactive (≥3 fmol/L) in 220 individuals (87%). HCV genotype 1, 3, and 6 were identified. HCV Ag significantly correlated with HCV RNA irrespective of HCV genotype and/or HBV co-infection (log HCV RNA = 2.67 + 0.95 [log HCV Ag], R2 = 0.890, p < 0.001). To predict HCV viremia (HCV Ag ≥ 3 fmol/L), the accuracy, sensitivity, specificity, positive predictive value, and negative predictive value were 99%, 99%, 100%, 100% and 97%, respectively. We concluded that HCV Ag was a good surrogate marker for HCV RNA and could be used to diagnose active HCV infection in a resource-limited setting. As a result, a cost-effective strategy for screening and identifying active HCV carriers using HCV Ag detection would enable more patients access to efficacious and increasingly affordable direct-acting antivirals (DAAs) for the treatment of HCV infection. creator: Rujipat Wasitthankasem creator: Preeyaporn Vichaiwattana creator: Chompoonut Auphimai creator: Nipaporn Siripon creator: Sirapa Klinfueng creator: Pisit Tangkijvanich creator: Sompong Vongpunsawad creator: Yong Poovorawan uri: https://doi.org/10.7717/peerj.4008 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wasitthankasem et al. title: Transcriptome dynamics along axolotl regenerative development are consistent with an extensive reduction in gene expression heterogeneity in dedifferentiated cells link: https://peerj.com/articles/4004 last-modified: 2017-11-06 description: Although in recent years the study of gene expression variation in the absence of genetic or environmental cues or gene expression heterogeneity has intensified considerably, many basic and applied biological fields still remain unaware of how useful the study of gene expression heterogeneity patterns might be for the characterization of biological systems and/or processes. Largely based on the modulator effect chromatin compaction has for gene expression heterogeneity and the extensive changes in chromatin compaction known to occur for specialized cells that are naturally or artificially induced to revert to less specialized states or dedifferentiate, I recently hypothesized that processes that concur with cell dedifferentiation would show an extensive reduction in gene expression heterogeneity. The confirmation of the existence of such trend could be of wide interest because of the biomedical and biotechnological relevance of cell dedifferentiation-based processes, i.e., regenerative development, cancer, human induced pluripotent stem cells, or plant somatic embryogenesis. Here, I report the first empirical evidence consistent with the existence of an extensive reduction in gene expression heterogeneity for processes that concur with cell dedifferentiation by analyzing transcriptome dynamics along forearm regenerative development in Ambystoma mexicanum or axolotl. Also, I briefly discuss on the utility of the study of gene expression heterogeneity dynamics might have for the characterization of cell dedifferentiation-based processes, and the engineering of tools that afforded better monitoring and modulating such processes. Finally, I reflect on how a transitional reduction in gene expression heterogeneity for dedifferentiated cells can promote a long-term increase in phenotypic heterogeneity following cell dedifferentiation with potential adverse effects for biomedical and biotechnological applications. creator: Carlos Díaz-Castillo uri: https://doi.org/10.7717/peerj.4004 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Díaz-Castillo title: Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages link: https://peerj.com/articles/3986 last-modified: 2017-11-06 description: Intestinal microbiota is an integral component of the host and plays important roles in host health. The pacific white shrimp is one of the most profitable aquaculture species commercialized in the world market with the largest production in shrimp consumption. Many studies revealed that the intestinal microbiota shifted significantly during host development in other aquaculture animals. In the present study, 22 shrimp samples were collected every 15 days from larval stage (15 day post-hatching, dph) to adult stage (75 dph) to investigate the intestinal microbiota at different culture stages by targeting the V4 region of 16S rRNA gene, and the microbial function prediction was conducted by PICRUSt. The operational taxonomic unit (OTU) was assigned at 97% sequence identity. A total of 2,496 OTUs were obtained, ranging from 585 to 1,239 in each sample. Forty-three phyla were identified due to the classifiable sequence. The most abundant phyla were Proteobacteria, Cyanobacteria, Tenericutes, Fusobacteria, Firmicutes, Verrucomicrobia, Bacteroidetes, Planctomycetes, Actinobacteria and Chloroflexi. OTUs belonged to 289 genera and the most abundant genera were Candidatus_Xiphinematobacter, Propionigenium, Synechococcus, Shewanella and Cetobacterium. Fifty-nine OTUs were detected in all samples, which were considered as the major microbes in intestine of shrimp. The intestinal microbiota was enriched with functional potentials that were related to transporters, ABC transporters, DNA repair and recombination proteins, two component system, secretion system, bacterial motility proteins, purine metabolism and ribosome. All the results showed that the intestinal microbial composition, diversity and functions varied significantly at different culture stages, which indicated that shrimp intestinal microbiota depended on culture stages. These findings provided new evidence on intestinal microorganism microecology and greatly enhanced our understanding of stage-specific community in the shrimp intestinal ecosystem. creator: Shenzheng Zeng creator: Zhijian Huang creator: Dongwei Hou creator: Jian Liu creator: Shaoping Weng creator: Jianguo He uri: https://doi.org/10.7717/peerj.3986 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zeng et al. title: Increasing evidence that bats actively forage at wind turbines link: https://peerj.com/articles/3985 last-modified: 2017-11-03 description: Although the ultimate causes of high bat fatalities at wind farms are not well understood, several lines of evidence suggest that bats are attracted to wind turbines. One hypothesis is that bats would be attracted to turbines as a foraging resource if the insects that bats prey upon are commonly present on and around the turbine towers. To investigate the role that foraging activity may play in bat fatalities, we conducted a series of surveys at a wind farm in the southern Great Plains of the US from 2011–2016. From acoustic monitoring we recorded foraging activity, including feeding buzzes indicative of prey capture, in the immediate vicinity of turbine towers from all six bat species known to be present at this site. From insect surveys we found Lepidoptera, Coleoptera, and Orthoptera in consistently high proportions over several years suggesting that food resources for bats were consistently available at wind turbines. We used DNA barcoding techniques to assess bat diet composition of (1) stomach contents from 47 eastern red bat (Lasiurus borealis) and 24 hoary bat (Lasiurus cinereus) carcasses collected in fatality searches, and (2) fecal pellets from 23 eastern red bats that were found on turbine towers, transformers, and tower doors. We found that the majority of the eastern red bat and hoary bat stomachs, the two bat species most commonly found in fatality searches at this site, were full or partially full, indicating that the bats were likely killed while foraging. Although Lepidoptera and Orthoptera dominated the diets of these two bat species, both consumed a range of prey items with individual bats having from one to six insect species in their stomachs at the time of death. The prey items identified from eastern red bat fecal pellets showed similar results. A comparison of the turbine insect community to the diet analysis results revealed that the most abundant insects at wind turbines, including terrestrial insects such as crickets and several important crop pests, were also commonly eaten by eastern red and hoary bats. Collectively, these findings suggest that bats are actively foraging around wind turbines and that measures to minimize bat fatalities should be broadly implemented at wind facilities. creator: Cecily F. Foo creator: Victoria J. Bennett creator: Amanda M. Hale creator: Jennifer M. Korstian creator: Alison J. Schildt creator: Dean A. Williams uri: https://doi.org/10.7717/peerj.3985 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Foo et al. title: Carbohydrates digestion and metabolism in the spiny lobster (Panulirus argus): biochemical indication for limited carbohydrate utilization link: https://peerj.com/articles/3975 last-modified: 2017-11-03 description: As other spiny lobsters, Panulirus argus is supposed to use preferentially proteins and lipids in energy metabolism, while carbohydrates are well digested but poorly utilized. The aim of this study was to evaluate the effect of dietary carbohydrate level on digestion and metabolism in the spiny lobster P. argus. We used complementary methodologies such as post-feeding flux of nutrients and metabolites, as well as measurements of α-amylase expression and activity in the digestive tract. Lobsters readily digested and absorbed carbohydrates with a time-course that is dependent on their content in diet. Lobster showed higher levels of free glucose and stored glycogen in different tissues as the inclusion of wheat flour increased. Modifications in intermediary metabolism revealed a decrease in amino acids catabolism coupled with a higher use of free glucose as carbohydrates rise up to 20%. However, this effect seems to be limited by the metabolic capacity of lobsters to use more than 20% of carbohydrates in diets. Lobsters were not able to tightly regulate α-amylase expression according to dietary carbohydrate level but exhibited a marked difference in secretion of this enzyme into the gut. Results are discussed to highlight the limitations to increasing carbohydrate utilization by lobsters. Further growout trials are needed to link the presented metabolic profiles with phenotypic outcomes. creator: Leandro Rodríguez-Viera creator: Erick Perera creator: Vivian Montero-Alejo creator: Rolando Perdomo-Morales creator: Tsai García-Galano creator: Gonzalo Martínez-Rodríguez creator: Juan M. Mancera uri: https://doi.org/10.7717/peerj.3975 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Rodríguez-Viera et al. title: New species of the endemic Neotropical caddisfly genus Contulma from the Andes of Ecuador (Trichoptera: Anomalopsychidae) link: https://peerj.com/articles/3967 last-modified: 2017-11-03 description: The genus Contulma Flint (Trichoptera: Anomalopsychidae) is composed mostly of regionally endemic species occurring above 2,000 m, with a few more widespread species and some that are found at lower elevations. Adults of three new species of Contulma are described and illustrated from the Andes of Ecuador, Contulma lina, new species, Contulma quito, new species, and Contulma sangay, new species. These species are similar to previously described species from the region, including C. paluguillensis, C. nevada, and C. lancelolata. New provincial records are provided for C. bacula, C. cataracta, and C. echinata. Contulma duffiOláh, 2016 is considered a junior, subjective synonym of C. penai, Holzenthal & Flint, 1995. Also, we provide an identification key to males of the 30 Contulma species now known. creator: Ralph W. Holzenthal creator: Blanca Ríos-Touma creator: Ernesto Rázuri-Gonzales uri: https://doi.org/10.7717/peerj.3967 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Holzenthal et al. title: Assessment of fine-scale resource selection and spatially explicit habitat suitability modelling for a re-introduced tiger (Panthera tigris) population in central India link: https://peerj.com/articles/3920 last-modified: 2017-11-03 description: BackgroundLarge carnivores influence ecosystem functions at various scales. Thus, their local extinction is not only a species-specific conservation concern, but also reflects on the overall habitat quality and ecosystem value. Species-habitat relationships at fine scale reflect the individuals’ ability to procure resources and negotiate intraspecific competition. Such fine scale habitat choices are more pronounced in large carnivores such as tiger (Panthera tigris), which exhibits competitive exclusion in habitat and mate selection strategies. Although landscape level policies and conservation strategies are increasingly promoted for tiger conservation, specific management interventions require knowledge of the habitat correlates at fine scale.MethodsWe studied nine radio-collared individuals of a successfully reintroduced tiger population in Panna Tiger Reserve, central India, focussing on the species-habitat relationship at fine scales. With 16 eco-geographical variables, we performed Manly’s selection ratio and K-select analyses to define population-level and individual-level variation in resource selection, respectively. We analysed the data obtained during the exploratory period of six tigers and during the settled period of eight tigers separately, and compared the consequent results. We further used the settled period characteristics to model and map habitat suitability based on the Mahalanobis D2 method and the Boyce index.ResultsThere was a clear difference in habitat selection by tigers between the exploratory and the settled period. During the exploratory period, tigers selected dense canopy and bamboo forests, but also spent time near villages and relocated village sites. However, settled tigers predominantly selected bamboo forests in complex terrain, riverine forests and teak-mixed forest, and totally avoided human settlements and agriculture areas. There were individual variations in habitat selection between exploratory and settled periods. Based on threshold limits of habitat selection by the Boyce Index, we established that 83% of core and 47% of buffer areas are now suitable habitats for tiger in this reserve.DiscussionTiger management often focuses on large-scale measures, but this study for the first time highlights the behaviour and fine-scale individual-specific habitat selection strategies. Such knowledge is vital for management of critical tiger habitats and specifically for the success of reintroduction programs. Our spatially explicit habitat suitability map provides a baseline for conservation planning and optimizing carrying capacity of the tiger population in this reserve. creator: Mriganka Shekhar Sarkar creator: Ramesh Krishnamurthy creator: Jeyaraj A. Johnson creator: Subharanjan Sen creator: Goutam Kumar Saha uri: https://doi.org/10.7717/peerj.3920 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Sarkar et al. title: Revisiting the tryptophan-serotonin deficiency and the inflammatory hypotheses of major depression in a biopsychosocial approach link: https://peerj.com/articles/3968 last-modified: 2017-11-02 description: BackgroundThe aim of this cross-sectional study was to identify important biopsychosocial correlates of major depression. Biological mechanisms, including the inflammatory and the tryptophan-serotonin deficiency hypotheses of major depression, were investigated alongside health-related quality of life, life satisfaction, and social support.MethodsThe concentrations of plasma tryptophan, plasma kynurenine, plasma kynurenic acid, serum quinolinic acid, and the tryptophan breakdown to kynurenine were determined alongside health-related quality of life (Medical Outcome Study Form, SF-36), life satisfaction (Life Satisfaction Questionnaire, FLZ), and social support (Social Support Survey, SSS) in 71 depressive patients at the time of their in-patient admittance and 48 healthy controls.ResultsCorresponding with the inflammatory hypothesis of major depression, our study results suggest a tryptophan breakdown to kynurenine in patients with major depression, and depressive patients had a lower concentration of neuroprotective kynurenic acid in comparison to the healthy controls (Mann–Whitney-U: 1315.0; p = 0.046). Contradicting the inflammatory theory, the concentrations of kynurenine (t: −0.945; df = 116; p = 0.347) and quinolinic acid (Mann-Whitney-U: 1376.5; p = 0.076) in depressive patients were not significantly different between depressed and healthy controls. Our findings tend to support the tryptophan-serotonin deficiency hypothesis of major depression, as the deficiency of the serotonin precursor tryptophan in depressive patients (t: −3.931; df = 116; p < 0.001) suggests dysfunction of serotonin neurotransmission. A two-step hierarchical linear regression model showed that low tryptophan concentrations, low social support (SSS), occupational requirements (FLZ), personality traits (FLZ), impaired physical role (SF-36), and impaired vitality (SF-36) predict higher Beck Depression Inventory (BDI-II) scores.DiscussionOur study results argue for the validity of a biopsychosocial model of major depression with multiple pathophysiological mechanisms involved. creator: Andreas Baranyi creator: Omid Amouzadeh-Ghadikolai creator: Dirk von Lewinski creator: Robert J. Breitenecker creator: Hans-Bernd Rothenhäusler creator: Christoph Robier creator: Maria Baranyi creator: Simon Theokas creator: Andreas Meinitzer uri: https://doi.org/10.7717/peerj.3968 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Baranyi et al. title: Comparative analysis of the microRNA transcriptome between yak and cattle provides insight into high-altitude adaptation link: https://peerj.com/articles/3959 last-modified: 2017-11-02 description: Extensive and in-depth investigations of high-altitude adaptation have been carried out at the level of morphology, anatomy, physiology and genomics, but few investigations focused on the roles of microRNA (miRNA) in high-altitude adaptation. We examined the differences in the miRNA transcriptomes of two representative hypoxia-sensitive tissues (heart and lung) between yak and cattle, two closely related species that live in high and low altitudes, respectively. In this study, we identified a total of 808 mature miRNAs, which corresponded to 715 pre-miRNAs in the two species. The further analysis revealed that both tissues showed relatively high correlation coefficient between yak and cattle, but a greater differentiation was present in lung than heart between the two species. In addition, miRNAs with significantly differentiated patterns of expression in two tissues exhibited co-operation effect in high altitude adaptation based on miRNA family and cluster. Functional analysis revealed that differentially expressed miRNAs were enriched in hypoxia-related pathways, such as the HIF-1α signaling pathway, the insulin signaling pathway, the PI3K-Akt signaling pathway, nucleotide excision repair, cell cycle, apoptosis and fatty acid metabolism, which indicated the important roles of miRNAs in high altitude adaptation. These results suggested the diverse degrees of miRNA transcriptome variation in different tissues between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation. creator: Jiuqiang Guan creator: Keren Long creator: Jideng Ma creator: Jinwei Zhang creator: Dafang He creator: Long Jin creator: Qianzi Tang creator: Anan Jiang creator: Xun Wang creator: Yaodong Hu creator: Shilin Tian creator: Zhi Jiang creator: Mingzhou Li creator: Xiaolin Luo uri: https://doi.org/10.7717/peerj.3959 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Guan et al. title: Genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry link: https://peerj.com/articles/3951 last-modified: 2017-11-02 description: BackgroundCurrently, there is limited knowledge about the genetics underlying pigmentary traits in East Asian populations. Here, we report the results of the first genome-wide association study of pigmentary traits (skin and iris color) in individuals of East Asian ancestry.MethodsWe obtained quantitative skin pigmentation measures (M-index) in the inner upper arm of the participants using a portable reflectometer (N = 305). Quantitative measures of iris color (expressed as L*, a* and b* CIELab coordinates) were extracted from high-resolution iris pictures (N = 342). We also measured the color differences between the pupillary and ciliary regions of the iris (e.g., iris heterochromia). DNA samples were genotyped with Illumina’s Infinium Multi-Ethnic Global Array (MEGA) and imputed using the 1000 Genomes Phase 3 samples as reference haplotypes.ResultsFor skin pigmentation, we did not observe any genome-wide significant signal. We followed-up in three independent Chinese samples the lead SNPs of five regions showing multiple common markers (minor allele frequency ≥ 5%) with good imputation scores and suggestive evidence of association (p-values < 10−5). One of these markers, rs2373391, which is located in an intron of the ZNF804B gene on chromosome 7, was replicated in one of the Chinese samples (p = 0.003). For iris color, we observed genome-wide signals in the OCA2 region on chromosome 15. This signal is driven by the non-synonymous rs1800414 variant, which explains 11.9%, 10.4% and 6% of the variation observed in the b*, a* and L* coordinates in our sample, respectively. However, the OCA2 region was not associated with iris heterochromia.DiscussionAdditional genome-wide association studies in East Asian samples will be necessary to further disentangle the genetic architecture of pigmentary traits in East Asian populations. creator: Lida Rawofi creator: Melissa Edwards creator: S Krithika creator: Phuong Le creator: David Cha creator: Zhaohui Yang creator: Yanyun Ma creator: Jiucun Wang creator: Bing Su creator: Li Jin creator: Heather L. Norton creator: Esteban J. Parra uri: https://doi.org/10.7717/peerj.3951 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Rawofi et al. title: Estrogen therapy offsets thermal impairment of vitellogenesis, but not zonagenesis, in maiden spawning female Atlantic salmon (Salmo salar) link: https://peerj.com/articles/3897 last-modified: 2017-11-02 description: In female Atlantic salmon (Salmo salar), exposure to warm summer temperatures causes a reduction in plasma 17β-estradiol (E2), which impairs downstream vitellogenesis and zonagenesis, and reduces egg fertility and embryo survival. The aim of the present study was to determine whether E2-treatment could offset thermal impairment of endocrine function and maintain egg quality in maiden (first-time-spawning) S. salar reared at 22 °C. Treatment with E2 at 22 °C stimulated vitellogenin (vtg) gene expression and subsequent protein synthesis which promoted oocyte growth and increased egg size relative to untreated fish at 14 and 22 °C. However, E2-treatment at 22 °C was not associated with an increase in egg fertility and embryo survival relative to untreated fish at 22 °C, despite the positive effects of E2-treatment on vitellogenesis and oocyte growth. As there was no evidence to suggest that the estrogen receptor alpha expression was suppressed by high temperature, this could be due to the lack of stimulation on zonagenesis by E2-treatment observed at high temperature during oocyte development. Our results demonstrate that treatment with E2 is not able to maintain zonagenesis or egg quality in maiden S. salar at high temperature, even when vtg gene expression, protein synthesis and subsequent oocyte growth is promoted. This implies that the mechanisms regulating zonagenesis, but not vitellogenesis are impaired at elevated temperature in female S. salar broodstock, and highlights the remarkable complexity of thermally induced endocrine disruption in fish. creator: Kelli Anderson creator: Ned Pankhurst creator: Harry King creator: Abigail Elizur uri: https://doi.org/10.7717/peerj.3897 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Anderson et al. title: Scaldiporia vandokkumi, a new pontoporiid (Mammalia, Cetacea, Odontoceti) from the Late Miocene to earliest Pliocene of the Westerschelde estuary (The Netherlands) link: https://peerj.com/articles/3991 last-modified: 2017-11-01 description: BackgroundThe family Pontoporiidae (Cetacea, Odontoceti, Inioidea) is currently represented in our oceans by just one species of diminutive dolphin (Pontoporia blainvillei, franciscana). Although P. blainvillei is limited to coastal waters of the South Atlantic along Brazil, Uruguay and Argentina, multiple Miocene and Pliocene fossils indicate the past presence of members of the family in the South Atlantic, South Paciifc and North Atlantic oceans. Our comprehension of the origin and diversity of this clade and of the relationships of its members with other inioids is hampered by the fact that part of the described fossil specimens, especially from the North Atlantic realm, are cranial fragments often associated to limited stratigraphic information.MethodsBased on an almost complete fossil cranium of pontoporiid from the Westerschelde estuary, The Netherlands, whose preservation allows for detailed morphological observations, we describe a new genus and species. The latter is compared to other pontoporiids, as well as a few non-pontoporiid inioids. A phylogenetic analysis is performed to investigate the relationship of S. vandokkumi with the best-known extinct and extant inioids. Palynological analysis of the sediment associated to the holotype is used to assess its geological age.Results and discussionThe new genus and species Scaldiporia vandokkumi is characterized among others by greatly thickened premaxillary eminences reaching the level of the antorbital notch. Palynologically dated from the late Tortonian—earliest Zanclean (7.6–5 Ma, Late Miocene—earliest Pliocene), this new pontoporiid confirms the surprising past diversity of marine inioids in the North Atlantic area. Finally the content of the pontoporiid subfamily Brachydelphininae is briefly discussed. creator: Klaas Post creator: Stephen Louwye creator: Olivier Lambert uri: https://doi.org/10.7717/peerj.3991 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Post et al. title: Self-medication practices and rational drug use habits among university students: a cross-sectional study from Kahramanmaraş, Turkey link: https://peerj.com/articles/3990 last-modified: 2017-11-01 description: BackgroundSelf-medication refers to the use of medicines to treat self-diagnosed diseases without consulting any healthcare professionals. Irrational drug use and self-medication have serious negative consequences both on health and economy. Therefore, the aim of this study is to assess the habits related to rational use of drugs (RUD) and to estimate the prevalence of self-medication practices among university students.MethodsThis cross-sectional study was conducted on university students in Kahramanmaraş. From May 2017 to June 2017 a total of 960 students filled a “Rational Use of Drugs Questionnaire”.ResultsThe prevalence of practicing self-medication in students was 63.4%. The most common medicines that the students had consumed without prescription were analgesics by 39.5%, antibiotics by 36.9% and cold remedies by 24.0%. The rate of students who declared that they were familiar with RUD and “rational use of antibiotics” (RUA) was 45.9%. Reading/checking the instructions in the prospectus (OR = 1.529, 95% CI [1.176–1.990]), understanding the context of the prospectus (OR = 1.893, 95% CI [1.387–2.584]), compliance with the duration of antibiotic treatment (OR = 1.597, 95% CI [1.231–2.071]) and consulting a physician in case of a side effect (OR = 1.350, 95% CI [1.037–1.757]) were significantly higher among students who were familiar with RUD as compared to who were not.DiscussionSince the awareness of RUD among university students was found to be inadequate, it has critical importance to hold educational activities with the cooperation of physicians, health organizations, universities, non-governmental organizations and media to avoid negative consequences of irrational drug use and self-medication. creator: Ramazan Azim Okyay creator: Ayşegül Erdoğan uri: https://doi.org/10.7717/peerj.3990 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Okyay and Erdoğan title: Mechanisms of oat (Avena sativa L.) acclimation to phosphate deficiency link: https://peerj.com/articles/3989 last-modified: 2017-11-01 description: BackgroundDeficiency of available forms of phosphorus is common in most soils and causes reduction of crop plants growth and yield. Recently, model plants responses to phosphate (Pi) deficiency have been intensively studied. However, acclimation mechanisms of cereals like oat (Avena sativa L.), to low Pi stress remains not fully understood. Oat plants have been usually cultured on poor soils, with a low nutrient content, but their responses to such conditions are not well known, therefore the main goal of the study was to investigate the mechanisms that enable oat plants to grow under low Pi conditions.MethodsFour oat cultivars (A. sativa, cv. Arab, Krezus, Rajtar and Szakal) were grown for three weeks in a nutrient media with various P sources: inorganic—KH2PO4 (control), organic—phytate (PA) and with no phosphate (−P). The effects of Pi deficiency on the level of P, oat growth parameters, intensity of photosynthesis, plant productivity, root exudation ability, localization, activity and isoforms of acid phosphatases, enzymes involved in Pi mobilization, were estimated. In addition, the effect of mycorrhization on plant growth was also observed.ResultsAll studied oat cultivars grown on Pi-deficient media had significantly decreased Pi content in the tissues. Pi deficiency caused inhibition of shoot growth, but generally it did not affect root elongation; root diameter was decreased, root/shoot ratios increased, whereas PA plants showed a similar growth to control. Photosynthesis rate and productivity parameters decreased under low Pi nutrition, however, sugar content generally increased. Studied oat cultivars did not respond to low Pi via increased exudation of carboxylates from the roots, as pH changes in the growth media were not observed. Pi starvation significantly increased the activity of extracellular and intracellular acid phosphatases (APases) in comparison to the control plants. Three major APase isoforms were detected in oat tissues and the isoform pattern was similar in all studied conditions, usually with a higher level of one of the isoforms under Pi starvation. Generally no significant effects of mycorrhizal colonization on growth of oat cultivars were observed.DiscussionWe postulated that acid phosphatases played the most important role in oat cultivars acclimation to Pi deficiency, especially extracellular enzymes involved in Pi acquisition from soil organic P esters. These APases are mainly located in the epidermis of young roots, and may be released to the rhizosphere. On the other hand, intracellular APases could be involved in fast Pi remobilization from internal sources. Our study showed that oat, in contrast to other plants, can use phytates as the sole source of P. The studied oat cultivars demonstrated similar acclimation mechanisms to Pi deficiency, however, depending on stress level, they can use different pools of acid phosphatases. creator: Ewa Żebrowska creator: Marta Milewska creator: Iwona Ciereszko uri: https://doi.org/10.7717/peerj.3989 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Żebrowska et al. title: Can 9q34.2 rs633862 polymorphism predict survival in epithelial ovarian cancer? link: https://peerj.com/articles/3946 last-modified: 2017-11-01 description: ObjectiveOur previous genome-wide association study (GWAS) identified that the ABO rs633862 variant in chromosome 9q34.2 was associated with the risk of epithelial ovarian cancer (EOC) in Chinese Han women. The aim of the present study was to evaluate its prognostic effect on EOC.MethodsA total of 669 EOC patients were enrolled for the genotyping of rs633862 variant in 9q34.2. We used Kaplan–Meier survival curves, univariate and multivariate Cox proportional hazard models to evaluate the association of rs633862 with overall survival (OS) in EOC patients.ResultsWe found that rs633862 variant AG/GG genotypes were significantly associated with a longer OS by using univariate Cox proportional hazards regression analysis, compared with the rs633862 AA genotype (HR = 0.69, 95% CI [0.49–0.98], p = 0.035), albeit with a boardline significance in the multivariate analysis. Similar findings were observed in the subgroup of high-grade serous ovarian carcinoma. Further expression quantitative trait loci (eQTL) analysis indicated that the rs633862 AA genotype was associated with an increased level of ABO mRNA expression (p = 1.8 × 10−11).ConclusionsSupplementary to the previous GWAS, our study provides additional evidence on the prognostic value of the 9q34.2 rs633862 variant in EOC patients, and this variant may function by regulating the ABO mRNA expression. creator: Rong Jiang creator: Yuan Xu creator: Pan Wang creator: Xi Cheng creator: Tingyan Shi creator: Rongyu Zang uri: https://doi.org/10.7717/peerj.3946 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Jiang et al. title: Effects of graded concentrations of supplemental lead on lead concentrations in tissues of pigs and prediction equations for estimating dietary lead intake link: https://peerj.com/articles/3936 last-modified: 2017-11-01 description: The objectives of this experiment were to determine the effects of graded dietary lead (Pb) concentrations on body weight and Pb concentrations in blood, hair, soft tissues, and urine from pigs and to generate equations for estimating daily Pb intake. Sixteen barrows with initial body weight 36.3 kg (standard deviation = 2.3) were allotted to four dietary treatments that consisted of graded supplemental Pb concentrations (0, 10, 25, and 250 mg/kg of diet). Daily feed allowances for each pig were 1 kg for first two weeks and 2 kg for last two weeks. The hair and blood of pigs were collected on d 14 and 28. At the end of experiment, the pigs were euthanized, and the liver, kidneys, muscle, and urine samples were collected. The prediction equations for estimating daily Pb intake of pigs were generated using Pb concentration of blood, hair, tissues, or urine as an independent variable. The Pb concentrations in the blood, hair, liver, kidneys, muscle, and urine linearly increased (P < 0.01) with increasing dietary Pb concentrations. There were quadratic effects (P < 0.05) of increasing dietary Pb concentration on Pb concentrations in the blood, hair, and muscle. There were highly positive correlations between dietary Pb concentration and Pb concentrations in the blood, hair, liver, kidneys, muscle, and urine (r > 0.83; P < 0.01). The equations were significant (P < 0.01) and showed high r2 (>0.83), except the equation using Pb concentration in the muscle as an independent variable. In conclusion, the dietary Pb concentration was highly correlated with Pb concentrations in the blood, hair, soft tissues, and urine of pigs. The total dietary Pb intake can be estimated from the Pb concentrations in the blood, hair, soft tissues, or urine for pigs. creator: Kondreddy Eswar Reddy creator: Kyu Ree Park creator: Sung Dae Lee creator: Ji-Hyock Yoo creator: Ah Reum Son creator: Hyun-Jung Lee uri: https://doi.org/10.7717/peerj.3936 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Reddy et al.