PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Influence of rimonabant treatment on peripheral blood mononuclear cells; flow cytometry analysis and gene expression profiling
items: Comprehensive comparison of large-scale tissue expression datasets
items: US adolescents’ friendship networks and health risk behaviors: a systematic review of studies using social network analysis and Add Health data
items: Attitudes of medical students in Lahore, Pakistan towards the doctor–patient relationship
items: Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids
items: Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas
items: HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors
items: Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet
items: FDAAA legislation is working, but methodological flaws undermine the reliability of clinical trials: a cross-sectional study
items: Imbalance in the blood antioxidant system in growth hormone-deficient children before and after 1 year of recombinant growth hormone therapy

Influence of rimonabant treatment on peripheral blood mononuclear cells; flow cytometry analysis and gene expression profiling
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
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
subject: Cell Biology
subject: Neuroscience
subject: Hematology
subject: Immunology
subject: Metabolic Sciences
description: doi:10.7717/peerj.1056
publisher: PeerJ Inc.
rights: © 2015 Almestrand et al.
abstract: 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.
bibliographic citation: Almestrand et al. (2015) Influence of rimonabant treatment on peripheral blood mononuclear cells; flow cytometry analysis and gene expression profiling. PeerJ 3:e1056 https://doi.org/10.7717/peerj.1056
date submitted: 2015-02-23
date accepted: 2015-06-05
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Almestrand
  given name: Stefan
author list: Agent
  family name: Wang
  given name: Xiao
author list: Agent
  family name: Jeppsson-Ahlberg
  given name: Åsa
author list: Agent
  family name: Nordgren
  given name: Marcus
author list: Agent
  family name: Flygare
  given name: Jenny
author list: Agent
  family name: Christensson
  given name: Birger
author list: Agent
  family name: Rössner
  given name: Stephan
author list: Agent
  family name: Sander
  given name: Birgitta
doi: 10.7717/peerj.1056
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Almestrand et al.
attribution name: Almestrand et al.

Comprehensive comparison of large-scale tissue expression datasets
type: item
type: AcademicArticle
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.
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creator: Alberto Santos
creator: Kalliopi Tsafou
creator: Christian Stolte
creator: Sune Pletscher-Frankild
creator: Seán I. O’Donoghue
creator: Lars Juhl Jensen
subject: Computational Biology
subject: Genomics
description: doi:10.7717/peerj.1054
publisher: PeerJ Inc.
rights: © 2015 Santos et al.
abstract: 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.
bibliographic citation: Santos et al. (2015) Comprehensive comparison of large-scale tissue expression datasets. PeerJ 3:e1054 https://doi.org/10.7717/peerj.1054
date submitted: 2015-02-16
date accepted: 2015-06-04
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Santos
  given name: Alberto
author list: Agent
  family name: Tsafou
  given name: Kalliopi
author list: Agent
  family name: Stolte
  given name: Christian
author list: Agent
  family name: Pletscher-Frankild
  given name: Sune
author list: Agent
  family name: O’Donoghue
  given name: Seán I.
author list: Agent
  family name: Jensen
  given name: Lars Juhl
doi: 10.7717/peerj.1054
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Santos et al.
attribution name: Santos et al.

US adolescents’ friendship networks and health risk behaviors: a systematic review of studies using social network analysis and Add Health data
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Kwon Chan Jeon
creator: Patricia Goodson
subject: Global Health
subject: Public Health
description: doi:10.7717/peerj.1052
publisher: PeerJ Inc.
rights: © 2015 Jeon and Goodson
abstract: 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.
bibliographic citation: Jeon et al. (2015) US adolescents’ friendship networks and health risk behaviors: a systematic review of studies using social network analysis and Add Health data. PeerJ 3:e1052 https://doi.org/10.7717/peerj.1052
date submitted: 2015-04-14
date accepted: 2015-06-03
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jeon
  given name: Kwon Chan
author list: Agent
  family name: Goodson
  given name: Patricia
doi: 10.7717/peerj.1052
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Jeon and Goodson
attribution name: Jeon and Goodson

Attitudes of medical students in Lahore, Pakistan towards the doctor–patient relationship
type: item
type: AcademicArticle
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 de…
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creator: Waqas Ahmad
creator: Edward Krupat
creator: Yumna Asma
creator: Noor-E- Fatima
creator: Rayan Attique
creator: Umar Mahmood
creator: Ahmed Waqas
subject: Evidence Based Medicine
subject: Psychiatry and Psychology
subject: Ethical Issues
subject: Science and Medical Education
description: doi:10.7717/peerj.1050
publisher: PeerJ Inc.
rights: © 2015 Ahmad et al.
abstract: 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 de…
bibliographic citation: Ahmad et al. (2015) Attitudes of medical students in Lahore, Pakistan towards the doctor–patient relationship. PeerJ 3:e1050 https://doi.org/10.7717/peerj.1050
date submitted: 2015-04-20
date accepted: 2015-06-03
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmad
  given name: Waqas
author list: Agent
  family name: Krupat
  given name: Edward
author list: Agent
  family name: Asma
  given name: Yumna
author list: Agent
  family name: Fatima
  given name: Noor-E-
author list: Agent
  family name: Attique
  given name: Rayan
author list: Agent
  family name: Mahmood
  given name: Umar
author list: Agent
  family name: Waqas
  given name: Ahmed
doi: 10.7717/peerj.1050
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Ahmad et al.
attribution name: Ahmad et al.

Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids
type: item
type: AcademicArticle
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.
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creator: Tyler J. Ford
creator: Jeffrey C. Way
subject: Biochemistry
subject: Bioengineering
description: doi:10.7717/peerj.1040
publisher: PeerJ Inc.
rights: © 2015 Ford and Way
abstract: 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.
bibliographic citation: Ford et al. (2015) Enhancement of E. coli acyl-CoA synthetase FadD activity on medium chain fatty acids. PeerJ 3:e1040 https://doi.org/10.7717/peerj.1040
date submitted: 2015-04-22
date accepted: 2015-05-31
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ford
  given name: Tyler J.
author list: Agent
  family name: Way
  given name: Jeffrey C.
doi: 10.7717/peerj.1040
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Ford and Way
attribution name: Ford and Way

Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas
type: item
type: AcademicArticle
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.
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creator: Howard R. Lasker
creator: Isabel Porto-Hannes
subject: Biogeography
subject: Ecology
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.1019
publisher: PeerJ Inc.
rights: © 2015 Lasker and Porto-Hannes
abstract: 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.
bibliographic citation: Lasker et al. (2015) Population structure among octocoral adults and recruits identifies scale dependent patterns of population isolation in The Bahamas. PeerJ 3:e1019 https://doi.org/10.7717/peerj.1019
date submitted: 2015-03-20
date accepted: 2015-05-24
issued: 2015-06-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lasker
  given name: Howard R.
author list: Agent
  family name: Porto-Hannes
  given name: Isabel
doi: 10.7717/peerj.1019
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-30
copyright: © 2015 Lasker and Porto-Hannes
attribution name: Lasker and Porto-Hannes

HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors
type: item
type: AcademicArticle
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.
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format: text/html
creator: Changye Sun
creator: Yong Li
creator: Sarah E. Taylor
creator: Xianqing Mao
creator: Mark C. Wilkinson
creator: David G. Fernig
subject: Biochemistry
description: doi:10.7717/peerj.1060
publisher: PeerJ Inc.
rights: © 2015 Sun et al.
abstract: 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.
bibliographic citation: Sun et al. (2015) HaloTag is an effective expression and solubilisation fusion partner for a range of fibroblast growth factors. PeerJ 3:e1060 https://doi.org/10.7717/peerj.1060
date submitted: 2014-12-23
date accepted: 2015-06-08
issued: 2015-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Changye
author list: Agent
  family name: Li
  given name: Yong
author list: Agent
  family name: Taylor
  given name: Sarah E.
author list: Agent
  family name: Mao
  given name: Xianqing
author list: Agent
  family name: Wilkinson
  given name: Mark C.
author list: Agent
  family name: Fernig
  given name: David G.
doi: 10.7717/peerj.1060
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-25
copyright: © 2015 Sun et al.
attribution name: Sun et al.

Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet
type: item
type: AcademicArticle
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 highli…
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creator: Matthieu Leray
creator: Christopher P. Meyer
creator: Suzanne C. Mills
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.1047
publisher: PeerJ Inc.
rights: © 2015 Leray et al.
abstract: 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 highli…
bibliographic citation: Leray et al. (2015) Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3:e1047 https://doi.org/10.7717/peerj.1047
date submitted: 2015-04-07
date accepted: 2015-06-02
issued: 2015-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Leray
  given name: Matthieu
author list: Agent
  family name: Meyer
  given name: Christopher P.
author list: Agent
  family name: Mills
  given name: Suzanne C.
doi: 10.7717/peerj.1047
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-25
copyright: © 2015 Leray et al.
attribution name: Leray et al.

FDAAA legislation is working, but methodological flaws undermine the reliability of clinical trials: a cross-sectional study
type: item
type: AcademicArticle
description: The relationship between clinical research and the pharmaceutical industry has placed clinical trials in jeopardy. According to the medical literature, more than 70% of clinical trials are industry-funded. Many of these trials remain unpublished or have methodological flaws that distort their results. In 2007, it was signed into law the Food and Drug Administration Amendments Act (FDAAA), aiming to provide publicly access to a broad range of biomedical information to be made available on the platform ClinicalTrials (available at https://www.clinicaltrials.gov). We accessed ClinicalTrials.gov and evaluated the compliance of researchers and sponsors with the FDAAA. Our sample comprised 243 protocols of clinical trials of biological monoclonal antibodies (mAb) adalimumab, bevacizumab, infliximab, rituximab, and trastuzumab. We demonstrate that the new legislation has positively affected transparency patterns in clinical research, through a significant increase in publication and online reporting rates after the enactment of the law. Poorly designed trials, however, remain a challenge to be overcome, due to a high prevalence of methodological flaws. These flaws affect the quality of clinical information available, breaching ethical duties of sponsors and researchers, as well as the human right to health.
format: application/pdf
format: text/html
creator: Douglas H. Marin dos Santos
creator: Álvaro N. Atallah
subject: Clinical Trials
subject: Global Health
subject: Public Health
subject: Ethical Issues
subject: Legal Issues
description: doi:10.7717/peerj.1015
publisher: PeerJ Inc.
rights: © 2015 Marin dos Santos and Atallah
abstract: The relationship between clinical research and the pharmaceutical industry has placed clinical trials in jeopardy. According to the medical literature, more than 70% of clinical trials are industry-funded. Many of these trials remain unpublished or have methodological flaws that distort their results. In 2007, it was signed into law the Food and Drug Administration Amendments Act (FDAAA), aiming to provide publicly access to a broad range of biomedical information to be made available on the platform ClinicalTrials (available at https://www.clinicaltrials.gov). We accessed ClinicalTrials.gov and evaluated the compliance of researchers and sponsors with the FDAAA. Our sample comprised 243 protocols of clinical trials of biological monoclonal antibodies (mAb) adalimumab, bevacizumab, infliximab, rituximab, and trastuzumab. We demonstrate that the new legislation has positively affected transparency patterns in clinical research, through a significant increase in publication and online reporting rates after the enactment of the law. Poorly designed trials, however, remain a challenge to be overcome, due to a high prevalence of methodological flaws. These flaws affect the quality of clinical information available, breaching ethical duties of sponsors and researchers, as well as the human right to health.
bibliographic citation: Marin dos Santos et al. (2015) FDAAA legislation is working, but methodological flaws undermine the reliability of clinical trials: a cross-sectional study. PeerJ 3:e1015 https://doi.org/10.7717/peerj.1015
date submitted: 2015-02-25
date accepted: 2015-05-21
issued: 2015-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/3.0/
author list: Agent
  family name: Marin dos Santos
  given name: Douglas H.
author list: Agent
  family name: Atallah
  given name: Álvaro N.
doi: 10.7717/peerj.1015
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-25
copyright: © 2015 Marin dos Santos and Atallah
attribution name: Marin dos Santos and Atallah

Imbalance in the blood antioxidant system in growth hormone-deficient children before and after 1 year of recombinant growth hormone therapy
type: item
type: AcademicArticle
description: The aim of our study was to examine the effects of 12-month therapy with recombinant growth hormone (rGH) on the blood antioxidant system in children with growth hormone deficiency (GHD). Total antioxidant capacity (TAC) of plasma was measured by FRAP (ferric reducing antioxidant power or ferric reducing ability of plasma); activities of superoxide dismutase (SOD) and catalase (CAT) in erythrocytes were assessed; non-protein thiols (NT) and ceruloplasmin (CP) levels were also measured. These parameters were determined before and after 12 month of rGH treatment. Eleven treatment-naive prepubertal children with growth hormone deficiency were included in the study. Another 11 prepubertal children comprised a control group. Before rGH treatment, TAC of plasma and NT level in the control group were significantly lower (726 ± 196 vs. 525 ± 166 µmol/L, P = 0.0182 and 0.92 ± 0.18 vs. 0.70 ± 0.22 µmol/ml, P = 0.0319, before and after the therapy, respectively). The only parameter that significantly (19.6 ± 4.7 vs. 14.5 ± 3.4 Units/g Hb, P = 0.0396) exceeded the same in the control group after rGH therapy was SOD activity. However, none of the measured parameters of antioxidant system in GHD children, except for TAC (525 ± 166 vs. 658 ± 115 µmol/L, P = 0.0205), exhibited significant improvement toward the end of the 12-month treatment period, although non-significant changes in CAT activity and CP level were also observed. This work has demonstrated that some parameters of the blood antioxidant system are out of balance and even impaired in GHD children. A 12-month treatment with rGH resulted in a partial improvement of the antioxidant system.
format: application/pdf
format: text/html
creator: Maria S. Pankratova
creator: Adil A. Baizhumanov
creator: Alexander I. Yusipovich
creator: Maria Faassen
creator: Tatyana Yu. Shiryaeva
creator: Valentina A. Peterkova
creator: Svetlana S. Kovalenko
creator: Tatiana A. Kazakova
creator: Georgy V. Maksimov
subject: Diabetes and Endocrinology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.1055
publisher: PeerJ Inc.
rights: © 2015 Pankratova et al.
abstract: The aim of our study was to examine the effects of 12-month therapy with recombinant growth hormone (rGH) on the blood antioxidant system in children with growth hormone deficiency (GHD). Total antioxidant capacity (TAC) of plasma was measured by FRAP (ferric reducing antioxidant power or ferric reducing ability of plasma); activities of superoxide dismutase (SOD) and catalase (CAT) in erythrocytes were assessed; non-protein thiols (NT) and ceruloplasmin (CP) levels were also measured. These parameters were determined before and after 12 month of rGH treatment. Eleven treatment-naive prepubertal children with growth hormone deficiency were included in the study. Another 11 prepubertal children comprised a control group. Before rGH treatment, TAC of plasma and NT level in the control group were significantly lower (726 ± 196 vs. 525 ± 166 µmol/L, P = 0.0182 and 0.92 ± 0.18 vs. 0.70 ± 0.22 µmol/ml, P = 0.0319, before and after the therapy, respectively). The only parameter that significantly (19.6 ± 4.7 vs. 14.5 ± 3.4 Units/g Hb, P = 0.0396) exceeded the same in the control group after rGH therapy was SOD activity. However, none of the measured parameters of antioxidant system in GHD children, except for TAC (525 ± 166 vs. 658 ± 115 µmol/L, P = 0.0205), exhibited significant improvement toward the end of the 12-month treatment period, although non-significant changes in CAT activity and CP level were also observed. This work has demonstrated that some parameters of the blood antioxidant system are out of balance and even impaired in GHD children. A 12-month treatment with rGH resulted in a partial improvement of the antioxidant system.
bibliographic citation: Pankratova et al. (2015) Imbalance in the blood antioxidant system in growth hormone-deficient children before and after 1 year of recombinant growth hormone therapy. PeerJ 3:e1055 https://doi.org/10.7717/peerj.1055
date submitted: 2015-02-13
date accepted: 2015-06-05
issued: 2015-06-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pankratova
  given name: Maria S.
author list: Agent
  family name: Baizhumanov
  given name: Adil A.
author list: Agent
  family name: Yusipovich
  given name: Alexander I.
author list: Agent
  family name: Faassen
  given name: Maria
author list: Agent
  family name: Shiryaeva
  given name: Tatyana Yu.
author list: Agent
  family name: Peterkova
  given name: Valentina A.
author list: Agent
  family name: Kovalenko
  given name: Svetlana S.
author list: Agent
  family name: Kazakova
  given name: Tatiana A.
author list: Agent
  family name: Maksimov
  given name: Georgy V.
doi: 10.7717/peerj.1055
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-06-25
copyright: © 2015 Pankratova et al.
attribution name: Pankratova et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359