title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1637 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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.