title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1938 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Photosynthetic response of Persian Gulf acroporid corals to summer versus winter temperature deviations link: https://peerj.com/articles/1062 last-modified: 2015-06-30 description: With on-going climate change, coral susceptibility to thermal stress constitutes a central concern in reefconservation. In the Persian Gulf, coral reefs are confronted with a high seasonal variability in water temperature, and both hot and cold extremes have been associated with episodes of coral bleaching and mortality. Using physiological performance as a measure of coral health, we investigated the thermal susceptibility of the common acroporid, Acropora downingi, near Hengam Island where the temperature oscillates seasonally in the range 20.2–34.2 °C. In a series of two short-term experiments comparing coral response in summer versus winter conditions, we exposed corals during each season (1) to the corresponding seasonal average and extreme temperature levels in a static thermal environment, and (2) to a progressive temperature deviation from the annual mean toward the corresponding extreme seasonal value and beyond in a dynamic thermal environment. We monitored four indictors of coral physiological performance: net photosynthesis (Pn), dark respiration (R), autotrophic capability (Pn/R), and survival. Corals exposed to warming during summer showed a decrease in net photosynthesis and ultimately died, while corals exposed to cooling during winter were not affected in their photosynthetic performance and survival. Coral autotrophic capability Pn/R was lower at the warmer thermal level within eachseason, and during summer compared to winter. Corals exposed to the maximum temperature of summer displayed Pn/R < 1, inferring that photosynthetic performance could not support basal metabolic needs under this environment. Our results suggest that the autotrophic performance of the Persian Gulf A. downingi is sensitive to the extreme temperatures endured in summer, and therefore its populations may be impacted by future increases in water temperature. creator: Jahangir Vajed Samiei creator: Abolfazl Saleh creator: Ali Mehdinia creator: Arash Shirvani creator: Mohsen Kayal uri: https://doi.org/10.7717/peerj.1062 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Vajed Samiei et al. title: HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases link: https://peerj.com/articles/1057 last-modified: 2015-06-30 description: Clustering algorithms are often used to find groups relevant in a specific context; however, they are not informed about this context. We present a simple algorithm, HOODS, which identifies context-specific neighborhoods of entities from a similarity matrix and a list of entities specifying the context. We illustrate its applicability by finding disease-specific neighborhoods of functionally associated proteins, kinase-specific neighborhoods of structurally similar inhibitors, and physiological-system-specific neighborhoods of interconnected diseases. HOODS can be used via a simple interface at http://hoods.jensenlab.org, from where the source code can also be downloaded. creator: Albert Palleja creator: Lars J. Jensen uri: https://doi.org/10.7717/peerj.1057 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2015 Palleja and Jensen title: Influence of rimonabant treatment on peripheral blood mononuclear cells; flow cytometry analysis and gene expression profiling link: https://peerj.com/articles/1056 last-modified: 2015-06-30 description: The cannabinoid receptor type 1 (CB1) antagonist rimonabant has been used as treatment for obesity. In addition, anti-proliferative effects on mitogen-activated leukocytes have been demonstrated in vitro. We have previously shown that rimonabant (SR141716A) induces cell death in ex vivo isolated malignant lymphomas with high expression of CB1 receptors. Since CB1 targeting may be part of a future lymphoma therapy, it was of interest to investigate possible effects on peripheral blood mononuclear cells (PBMC) in patients treated with rimonabant. We therefore evaluated leukocyte subsets by 6 color flow cytometry in eight patients before and at treatment with rimonabant for 4 weeks. Whole-transcript gene expression profiling in PBMC before and at 4 weeks of rimonabant treatment was done using Affymetrix Human Gene 1.0 ST Arrays. Our data show no significant changes of monocytes, B cells, total T cells or T cell subsets in PBMC during treatment with rimonabant. There was a small but significant increase in CD3–, CD16+ and/or CD56+ cells after rimonabant therapy. Gene expression analysis detected significant changes in expression of genes associated with innate immunity, cell death and metabolism. The present study shows that normal monocytes and leukocyte subsets in blood remain rather constant during rimonabant treatment. This is in contrast to the induction of cell death previously observed in CB1 expressing lymphoma cells in response to treatment with rimonabant in vitro. These differential effects observed on normal and malignant lymphoid cells warrant investigation of CB1 targeting as a potential lymphoma treatment. creator: Stefan Almestrand creator: Xiao Wang creator: Åsa Jeppsson-Ahlberg creator: Marcus Nordgren creator: Jenny Flygare creator: Birger Christensson creator: Stephan Rössner creator: Birgitta Sander uri: https://doi.org/10.7717/peerj.1056 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Almestrand et al. title: Comprehensive comparison of large-scale tissue expression datasets link: https://peerj.com/articles/1054 last-modified: 2015-06-30 description: For tissues to carry out their functions, they rely on the right proteins to be present. Several high-throughput technologies have been used to map out which proteins are expressed in which tissues; however, the data have not previously been systematically compared and integrated. We present a comprehensive evaluation of tissue expression data from a variety of experimental techniques and show that these agree surprisingly well with each other and with results from literature curation and text mining. We further found that most datasets support the assumed but not demonstrated distinction between tissue-specific and ubiquitous expression. By developing comparable confidence scores for all types of evidence, we show that it is possible to improve both quality and coverage by combining the datasets. To facilitate use and visualization of our work, we have developed the TISSUES resource (http://tissues.jensenlab.org), which makes all the scored and integrated data available through a single user-friendly web interface. creator: Alberto Santos creator: Kalliopi Tsafou creator: Christian Stolte creator: Sune Pletscher-Frankild creator: Seán I. O’Donoghue creator: Lars Juhl Jensen uri: https://doi.org/10.7717/peerj.1054 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Santos et al. title: US adolescents’ friendship networks and health risk behaviors: a systematic review of studies using social network analysis and Add Health data link: https://peerj.com/articles/1052 last-modified: 2015-06-30 description: Background. Documented trends in health-related risk behaviors among US adolescents have remained high over time. Studies indicate relationships among mutual friends are a major influence on adolescents’ risky behaviors. Social Network Analysis (SNA) can help understand friendship ties affecting individual adolescents’ engagement in these behaviors. Moreover, a systematic literature review can synthesize findings from a range of studies using SNA, as well as assess these studies’ methodological quality. Review findings also can help health educators and promoters develop more effective programs.Objective. This review systematically examined studies of the influence of friendship networks on adolescents’ risk behaviors, which utilized SNA and the Add Health data (a nationally representative sample).Methods. We employed the Matrix Method to synthesize and evaluate 15 published studies that met our inclusion and exclusion criteria, retrieved from the Add Health website and 3 major databases (Medline, Eric, and PsycINFO). Moreover, we assigned each study a methodological quality score (MQS).Results. In all studies, friendship networks among adolescents promoted their risky behaviors, including drinking alcohol, smoking, sexual intercourse, and marijuana use. The average MQS was 4.6, an indicator of methodological rigor (scale: 1–9).Conclusion. Better understanding of risky behaviors influenced by friends can be useful for health educators and promoters, as programs targeting friendships might be more effective. Additionally, the overall MQ of these reviewed studies was good, as average scores fell above the scale’s mid-point. creator: Kwon Chan Jeon creator: Patricia Goodson uri: https://doi.org/10.7717/peerj.1052 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Jeon and Goodson title: Attitudes of medical students in Lahore, Pakistan towards the doctor–patient relationship link: https://peerj.com/articles/1050 last-modified: 2015-06-30 description: Background. A good doctor–patient relationship is the centre stone of modern medicine. Patients are getting increasingly aware about exercising their autonomy and thus modern medicine cannot deliver all its advances to the patients if a good doctor–patient relationship is not established. We initiated this study with the aim to assess the leaning of medical students, who are the future physicians, towards either a doctor-centered or a patient-centered care, and to explore the effects of personal attributes on care such as gender, academic year, etc.Materials & Methods. A cross-sectional study was conducted between July and Sep 2013. CMH Lahore Medical and Dental College Ethical Review Committee approved the study questionnaire. The study population consisted of 1,181 medical students in years 1–5 from two medical colleges. The English version of Patient Practitioner Orientation Scale (PPOS) was used to assess attitudes of medical students towards doctor–patient relationship. PPOS yields a mean score range of 1–6, where 1 signifies tendency towards a doctor centered relationship and 6 signifies patient-centered relationship. The relationship between PPOS scores and individual characteristics like gender, academic year etc. were examined by multiple regression.Results. A total of 783 students formed the final sample (response rate = 92%). Mean PPOS score of the entire sample was 3.40 (± .49 S.D.). Mean sharing sub-scale score was 3.18 (± 0.62 S.D. Mean caring sub-scale score was 3.63 (± 0.56 S.D.). Characteristics associated with most patient-centered attitudes were advanced academic year, having a clinical rotation, foreign background and studying in a private college. Gender, having doctor parents, relationship and residence status had no bearing on the attitudes (p > 0.05).Conclusion. Despite ongoing debate and the emphasis on a patient-centered curriculum, our study suggests that the current curriculum and its teachings are not producing the results they are designed to achieve. Students should be adequately exposed to the patients from the beginning of their medical education in clinical settings which are more sympathetic to a patient-centered care. creator: Waqas Ahmad creator: Edward Krupat creator: Yumna Asma creator: Noor-E- Fatima creator: Rayan Attique creator: Umar Mahmood creator: Ahmed Waqas uri: https://doi.org/10.7717/peerj.1050 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ahmad et al. title: Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids link: https://peerj.com/articles/1040 last-modified: 2015-06-30 description: FadD catalyses the first step in E. coli beta-oxidation, the activation of free fatty acids into acyl-CoA thioesters. This activation makes fatty acids competent for catabolism and reduction into derivatives like alcohols and alkanes. Alcohols and alkanes derived from medium chain fatty acids (MCFAs, 6–12 carbons) are potential biofuels; however, FadD has low activity on MCFAs. Herein, we generate mutations in fadD that enhance its acyl-CoA synthetase activity on MCFAs. Homology modeling reveals that these mutations cluster on a face of FadD from which the co-product, AMP, is expected to exit. Using FadD homology models, we design additional FadD mutations that enhance E. coli growth rate on octanoate and provide evidence for a model wherein FadD activity on octanoate can be enhanced by aiding product exit. These studies provide FadD mutants useful for producing MCFA derivatives and a rationale to alter the substrate specificity of adenylating enzymes. creator: Tyler J. Ford creator: Jeffrey C. Way uri: https://doi.org/10.7717/peerj.1040 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Ford and Way title: Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas link: https://peerj.com/articles/1019 last-modified: 2015-06-30 description: Patterns of dispersal and connectivity of the Caribbean gorgonian Antillogorgia elisabethae in The Bahamas were assessed in both adults and recently settled recruits from 13 sites using microsatellite loci. Adult populations along the Little Bahama Bank (LBB) exhibited a clear pattern of isolation by distance (IBD) which described 86% of the variance in pairwise genetic distances. Estimates of dispersal based on the IBD model suggested dispersal distances along the LBB on the order of 100 m. Increasing the spatial scale to include sites separated by open ocean generated an apparent IBD signal but the relationship had a greater slope and explained less of the variance. This relationship with distance reflected both stepping stone based IBD and regional differentiation probably created by ocean currents and barriers to dispersal that are correlated with geographic distance. Analysis of recruits from 4 sites on the LBB from up to 6 years did not detect differences between years nor differences with adult populations. The result suggests that neither selection on recruits nor inter-annual variation in dispersal affected adult population structure. Assignment tests of recruits indicated the most likely sources of the recruits were the local or adjacent populations. Most of the patterning in population structure in the northern Bahamas can be explained by geographic distance and oceanographic connectivity. Recognition of these complex patterns is important in developing management plans for A. elisabethae and in understanding the effects of disturbance to adult populations of A. elisabethae and similar species with limited dispersal. creator: Howard R. Lasker creator: Isabel Porto-Hannes uri: https://doi.org/10.7717/peerj.1019 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lasker and Porto-Hannes title: HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors link: https://peerj.com/articles/1060 last-modified: 2015-06-25 description: The production of recombinant proteins such as the fibroblast growth factors (FGFs) is the key to establishing their function in cell communication. The production of recombinant FGFs in E. coli is limited, however, due to expression and solubility problems. HaloTag has been used as a fusion protein to introduce a genetically-encoded means for chemical conjugation of probes. We have expressed 11 FGF proteins with an N-terminal HaloTag, followed by a tobacco etch virus (TEV) protease cleavage site to allow release of the FGF protein. These were purified by heparin-affinity chromatography, and in some instances by further ion-exchange chromatography. It was found that HaloTag did not adversely affect the expression of FGF1 and FGF10, both of which expressed well as soluble proteins. The N-terminal HaloTag fusion was found to enhance the expression and yield of FGF2, FGF3 and FGF7. Moreover, whereas FGF6, FGF8, FGF16, FGF17, FGF20 and FGF22 were only expressed as insoluble proteins, their N-terminal HaloTag fusion counterparts (Halo-FGFs) were soluble, and could be successfully purified. However, cleavage of Halo-FGF6, -FGF8 and -FGF22 with TEV resulted in aggregation of the FGF protein. Measurement of phosphorylation of p42/44 mitogen-activated protein kinase and of cell growth demonstrated that the HaloTag fusion proteins were biologically active. Thus, HaloTag provides a means to enhance the expression of soluble recombinant proteins, in addition to providing a chemical genetics route for covalent tagging of proteins. creator: Changye Sun creator: Yong Li creator: Sarah E. Taylor creator: Xianqing Mao creator: Mark C. Wilkinson creator: David G. Fernig uri: https://doi.org/10.7717/peerj.1060 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sun et al. title: Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet link: https://peerj.com/articles/1047 last-modified: 2015-06-25 description: Understanding the role of predators in food webs can be challenging in highly diverse predator/prey systems composed of small cryptic species. DNA based dietary analysis can supplement predator removal experiments and provide high resolution for prey identification. Here we use a metabarcoding approach to provide initial insights into the diet and functional role of coral-dwelling predatory fish feeding on small invertebrates. Fish were collected in Moorea (French Polynesia) where the BIOCODE project has generated DNA barcodes for numerous coral associated invertebrate species. Pyrosequencing data revealed a total of 292 Operational Taxonomic Units (OTU) in the gut contents of the arc-eye hawkfish (Paracirrhites arcatus), the flame hawkfish (Neocirrhites armatus) and the coral croucher (Caracanthus maculatus). One hundred forty-nine (51%) of them had species-level matches in reference libraries (>98% similarity) while 76 additional OTUs (26%) could be identified to higher taxonomic levels. Decapods that have a mutualistic relationship with Pocillopora and are typically dominant among coral branches, represent a minor contribution of the predators’ diets. Instead, predators mainly consumed transient species including pelagic taxa such as copepods, chaetognaths and siphonophores suggesting non random feeding behavior. We also identified prey species known to have direct negative interactions with stony corals, such as Hapalocarcinus sp, a gall crab considered a coral parasite, as well as species of vermetid snails known for their deleterious effects on coral growth. Pocillopora DNA accounted for 20.8% and 20.1% of total number of sequences in the guts of the flame hawkfish and coral croucher but it was not detected in the guts of the arc-eye hawkfish. Comparison of diets among the three fishes demonstrates remarkable partitioning with nearly 80% of prey items consumed by only one predator. Overall, the taxonomic resolution provided by the metabarcoding approach highlights a highly complex interaction web and demonstrates that levels of trophic partitioning among coral reef fishes have likely been underestimated. Therefore, we strongly encourage further empirical approaches to dietary studies prior to making assumptions of trophic equivalency in food web reconstruction. creator: Matthieu Leray creator: Christopher P. Meyer creator: Suzanne C. Mills uri: https://doi.org/10.7717/peerj.1047 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Leray et al.