PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
items: Antityrosinase activity of Euphorbia characias extracts
items: Validation experiments on finite element models of an ostrich (Struthio camelus) cranium
items: Under which conditions can introverts achieve happiness? Mediation and moderation effects of the quality of social relationships and emotion regulation ability on happiness
items: Promoting an active form of learning out-of-class via answering online “study questions” leads to higher than expected exam scores in General Biology
items: Interdisciplinary, interinstitutional and international collaboration of family medicine researchers in Taiwan
items: Anvi’o: an advanced analysis and visualization platform for ‘omics data
items: Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria
items: Comments and corrections on 3D modeling studies of locomotor muscle moment arms in archosaurs
items: Competition from native hydrophytes reduces establishment and growth of invasive dense-flowered cordgrass (Spartina densiflora)

Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
type: item
type: AcademicArticle
description: Transient Receptor Potential cation channel, subfamily Melastatin, member 8 (TRPM8) is involved in detection of cold temperature, different noxious compounds and in execution of thermo- as well as chemo-sensitive responses at cellular levels. Here we explored the molecular evolution of TRPM8 by analyzing sequences from various species. We elucidate that several regions of TRPM8 had different levels of selection pressure but the 4th–5th transmembrane regions remain highly conserved. Analysis of synteny suggests that since vertebrate origin, TRPM8 gene is linked with SPP2, a bone morphogen. TRPM8, especially the N-terminal region of it, seems to be highly variable in human population. We found 16,656 TRPM8 variants in 1092 human genomes with top variations being SNPs, insertions and deletions. A total of 692 missense mutations are also mapped to human TRPM8 protein of which 509 seem to be delateroiours in nature as supported by Polyphen V2, SIFT and Grantham deviation score. Using a highly specific antibody, we demonstrate that TRPM8 is expressed endogenously in the testis of rat and sperm cells of different vertebrates ranging from fish to higher mammals. We hypothesize that TRPM8 had emerged during vertebrate evolution (ca 450 MYA). We propose that expression of TRPM8 in sperm cell and its role in regulating sperm function are important factors that have guided its molecular evolution, and that these understandings may have medical importance.
format: application/pdf
format: text/html
creator: Rakesh Kumar Majhi
creator: Somdatta Saha
creator: Ashutosh Kumar
creator: Arijit Ghosh
creator: Nirlipta Swain
creator: Luna Goswami
creator: Pratyush Mohapatra
creator: Apratim Maity
creator: Vivek Kumar Sahoo
creator: Abhishek Kumar
creator: Chandan Goswami
subject: Cell Biology
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Medical Genetics
description: doi:10.7717/peerj.1310
publisher: PeerJ Inc.
rights: © 2015 Majhi et al.
abstract: Transient Receptor Potential cation channel, subfamily Melastatin, member 8 (TRPM8) is involved in detection of cold temperature, different noxious compounds and in execution of thermo- as well as chemo-sensitive responses at cellular levels. Here we explored the molecular evolution of TRPM8 by analyzing sequences from various species. We elucidate that several regions of TRPM8 had different levels of selection pressure but the 4th–5th transmembrane regions remain highly conserved. Analysis of synteny suggests that since vertebrate origin, TRPM8 gene is linked with SPP2, a bone morphogen. TRPM8, especially the N-terminal region of it, seems to be highly variable in human population. We found 16,656 TRPM8 variants in 1092 human genomes with top variations being SNPs, insertions and deletions. A total of 692 missense mutations are also mapped to human TRPM8 protein of which 509 seem to be delateroiours in nature as supported by Polyphen V2, SIFT and Grantham deviation score. Using a highly specific antibody, we demonstrate that TRPM8 is expressed endogenously in the testis of rat and sperm cells of different vertebrates ranging from fish to higher mammals. We hypothesize that TRPM8 had emerged during vertebrate evolution (ca 450 MYA). We propose that expression of TRPM8 in sperm cell and its role in regulating sperm function are important factors that have guided its molecular evolution, and that these understandings may have medical importance.
bibliographic citation: Majhi et al. (2015) Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution. PeerJ 3:e1310 https://doi.org/10.7717/peerj.1310
date submitted: 2014-07-09
date accepted: 2015-09-19
issued: 2015-10-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Majhi
  given name: Rakesh Kumar
author list: Agent
  family name: Saha
  given name: Somdatta
author list: Agent
  family name: Kumar
  given name: Ashutosh
author list: Agent
  family name: Ghosh
  given name: Arijit
author list: Agent
  family name: Swain
  given name: Nirlipta
author list: Agent
  family name: Goswami
  given name: Luna
author list: Agent
  family name: Mohapatra
  given name: Pratyush
author list: Agent
  family name: Maity
  given name: Apratim
author list: Agent
  family name: Kumar Sahoo
  given name: Vivek
author list: Agent
  family name: Kumar
  given name: Abhishek
author list: Agent
  family name: Goswami
  given name: Chandan
doi: 10.7717/peerj.1310
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-13
copyright: © 2015 Majhi et al.
attribution name: Majhi et al.

Antityrosinase activity of Euphorbia characias extracts
type: item
type: AcademicArticle
description: Tyrosinase is a well-known key enzyme in melanin biosynthesis and its inhibitors have become increasingly important because of their potential use as hypopigmenting agents. In the present study, the anti-melanogenic effect of aqueous and ethanolic extracts from Euphorbia characias leaves, stems, and flowers in cell-free and cellular systems was examined. All the extracts showed inhibitory effects against mushroom tyrosinase with leaf extracts exhibiting the lowest IC50 values of 24 and 97 µg/mL for aqueous and ethanolic extracts respectively. Enzyme kinetic analysis indicated that leaf aqueous extract acts as a mixed type inhibitor, while ethanolic extract shows a competitive inhibition effect on mushroom tyrosinase using L-DOPA as substrate. In addition, the inhibitory effect of leaf extracts on tyrosinase activity and melanin production was examined in murine melanoma B16F10 cells. Cellular tyrosinase activity as well as levels of melanin synthesis are reduced in a dose-dependent manner by extracts in cells treated with α-melanocyte stimulating hormone (α-MSH). The effects are comparable, and sometimes even better, than that of kojic acid, a well known tyrosinase inhibitor used for reference. All these results suggest that E. characias could be a great source of the natural inhibitors from tyrosinase and has the potential to be used as a whitening agent in therapeutic fields.
format: application/pdf
format: text/html
creator: Francesca Pintus
creator: Delia Spanò
creator: Angela Corona
creator: Rosaria Medda
subject: Biochemistry
subject: Plant Science
subject: Dermatology
subject: Drugs and Devices
description: doi:10.7717/peerj.1305
publisher: PeerJ Inc.
rights: © 2015 Pintus et al.
abstract: Tyrosinase is a well-known key enzyme in melanin biosynthesis and its inhibitors have become increasingly important because of their potential use as hypopigmenting agents. In the present study, the anti-melanogenic effect of aqueous and ethanolic extracts from Euphorbia characias leaves, stems, and flowers in cell-free and cellular systems was examined. All the extracts showed inhibitory effects against mushroom tyrosinase with leaf extracts exhibiting the lowest IC50 values of 24 and 97 µg/mL for aqueous and ethanolic extracts respectively. Enzyme kinetic analysis indicated that leaf aqueous extract acts as a mixed type inhibitor, while ethanolic extract shows a competitive inhibition effect on mushroom tyrosinase using L-DOPA as substrate. In addition, the inhibitory effect of leaf extracts on tyrosinase activity and melanin production was examined in murine melanoma B16F10 cells. Cellular tyrosinase activity as well as levels of melanin synthesis are reduced in a dose-dependent manner by extracts in cells treated with α-melanocyte stimulating hormone (α-MSH). The effects are comparable, and sometimes even better, than that of kojic acid, a well known tyrosinase inhibitor used for reference. All these results suggest that E. characias could be a great source of the natural inhibitors from tyrosinase and has the potential to be used as a whitening agent in therapeutic fields.
bibliographic citation: Pintus et al. (2015) Antityrosinase activity of Euphorbia characias extracts. PeerJ 3:e1305 https://doi.org/10.7717/peerj.1305
date submitted: 2015-07-24
date accepted: 2015-09-17
issued: 2015-10-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pintus
  given name: Francesca
author list: Agent
  family name: Spanò
  given name: Delia
author list: Agent
  family name: Corona
  given name: Angela
author list: Agent
  family name: Medda
  given name: Rosaria
doi: 10.7717/peerj.1305
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-13
copyright: © 2015 Pintus et al.
attribution name: Pintus et al.

Validation experiments on finite element models of an ostrich (Struthio camelus) cranium
type: item
type: AcademicArticle
description: The first finite element (FE) validation of a complete avian cranium was performed on an extant palaeognath, the ostrich (Struthio camelus). Ex-vivo strains were collected from the cranial bone and rhamphotheca. These experimental strains were then compared to convergence tested, specimen-specific finite element (FE) models. The FE models contained segmented cortical and trabecular bone, sutures and the keratinous rhamphotheca as identified from micro-CT scan data. Each of these individual materials was assigned isotropic material properties either from the literature or from nanoindentation, and the FE models compared to the ex-vivo results. The FE models generally replicate the location of peak strains and reflect the correct mode of deformation in the rostral region. The models are too stiff in regions of experimentally recorded high strain and too elastic in regions of low experimentally recorded low strain. The mode of deformation in the low strain neurocranial region is not replicated by the FE models, and although the models replicate strain orientations to within 10° in some regions, in most regions the correlation is not strong. Cranial sutures, as has previously been found in other taxa, are important for modifying both strain magnitude and strain patterns across the entire skull, but especially between opposing the sutural junctions. Experimentally, we find that the strains on the surface of the rhamphotheca are much lower than those found on nearby bone. The FE models produce much higher principal strains despite similar strain ratios across the entirety of the rhamphotheca. This study emphasises the importance of attempting to validate FE models, modelling sutures and rhamphothecae in birds, and shows that whilst location of peak strain and patterns of deformation can be modelled, replicating experimental data in digital models of avian crania remains problematic.
format: application/pdf
format: text/html
creator: Andrew R. Cuff
creator: Jen A. Bright
creator: Emily J. Rayfield
subject: Bioengineering
subject: Anatomy and Physiology
description: doi:10.7717/peerj.1294
publisher: PeerJ Inc.
rights: © 2015 Cuff et al.
abstract: The first finite element (FE) validation of a complete avian cranium was performed on an extant palaeognath, the ostrich (Struthio camelus). Ex-vivo strains were collected from the cranial bone and rhamphotheca. These experimental strains were then compared to convergence tested, specimen-specific finite element (FE) models. The FE models contained segmented cortical and trabecular bone, sutures and the keratinous rhamphotheca as identified from micro-CT scan data. Each of these individual materials was assigned isotropic material properties either from the literature or from nanoindentation, and the FE models compared to the ex-vivo results. The FE models generally replicate the location of peak strains and reflect the correct mode of deformation in the rostral region. The models are too stiff in regions of experimentally recorded high strain and too elastic in regions of low experimentally recorded low strain. The mode of deformation in the low strain neurocranial region is not replicated by the FE models, and although the models replicate strain orientations to within 10° in some regions, in most regions the correlation is not strong. Cranial sutures, as has previously been found in other taxa, are important for modifying both strain magnitude and strain patterns across the entire skull, but especially between opposing the sutural junctions. Experimentally, we find that the strains on the surface of the rhamphotheca are much lower than those found on nearby bone. The FE models produce much higher principal strains despite similar strain ratios across the entirety of the rhamphotheca. This study emphasises the importance of attempting to validate FE models, modelling sutures and rhamphothecae in birds, and shows that whilst location of peak strain and patterns of deformation can be modelled, replicating experimental data in digital models of avian crania remains problematic.
bibliographic citation: Cuff et al. (2015) Validation experiments on finite element models of an ostrich (Struthio camelus) cranium. PeerJ 3:e1294 https://doi.org/10.7717/peerj.1294
date submitted: 2015-04-29
date accepted: 2015-09-15
issued: 2015-10-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cuff
  given name: Andrew R.
author list: Agent
  family name: Bright
  given name: Jen A.
author list: Agent
  family name: Rayfield
  given name: Emily J.
doi: 10.7717/peerj.1294
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-13
copyright: © 2015 Cuff et al.
attribution name: Cuff et al.

Under which conditions can introverts achieve happiness? Mediation and moderation effects of the quality of social relationships and emotion regulation ability on happiness
type: item
type: AcademicArticle
description: Personality traits have been directly associated with happiness. One consistent finding is a strong link between extraversion and happiness: extraverts are happier than introverts. Although happy introverts exist, it is currently unclear under what conditions they can achieve happiness. The present study analyzes, generally, how the quality of social relationships and emotion regulation ability influence happiness and, specifically, how these factors can lead introverts to be happy. In the present study, 1,006 participants aged 18–80 (42% males) completed measures of extraversion, neuroticism, quality of social relationships, emotion regulation ability, and happiness. We found that extraverts had significantly higher happiness, quality of social relationships and emotion regulation ability scores than introverts. In addition, people with high quality social relationships or high emotion regulation ability were happier. Serial mediation analyses indicated that greater levels of extraversion were associated with greater happiness, with small effect size, via two indirect mechanisms: (a) higher quality of social relationships, and (b) higher quality of social relationships followed serially by higher emotion regulation ability. We also found a moderating effect due to the three-way interaction of extraversion, quality of social relationships, and emotion regulation ability: introverts were happier when they had high scores for these two variables, though the effect size was small. These results suggest that the quality of social relationships and emotion regulation ability are relevant to our understanding of complex associations between extraversion and happiness.
format: application/pdf
format: text/html
creator: Rosario Cabello
creator: Pablo Fernandez-Berrocal
subject: Global Health
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.1300
publisher: PeerJ Inc.
rights: © 2015 Cabello and Fernandez-Berrocal
abstract: Personality traits have been directly associated with happiness. One consistent finding is a strong link between extraversion and happiness: extraverts are happier than introverts. Although happy introverts exist, it is currently unclear under what conditions they can achieve happiness. The present study analyzes, generally, how the quality of social relationships and emotion regulation ability influence happiness and, specifically, how these factors can lead introverts to be happy. In the present study, 1,006 participants aged 18–80 (42% males) completed measures of extraversion, neuroticism, quality of social relationships, emotion regulation ability, and happiness. We found that extraverts had significantly higher happiness, quality of social relationships and emotion regulation ability scores than introverts. In addition, people with high quality social relationships or high emotion regulation ability were happier. Serial mediation analyses indicated that greater levels of extraversion were associated with greater happiness, with small effect size, via two indirect mechanisms: (a) higher quality of social relationships, and (b) higher quality of social relationships followed serially by higher emotion regulation ability. We also found a moderating effect due to the three-way interaction of extraversion, quality of social relationships, and emotion regulation ability: introverts were happier when they had high scores for these two variables, though the effect size was small. These results suggest that the quality of social relationships and emotion regulation ability are relevant to our understanding of complex associations between extraversion and happiness.
bibliographic citation: Cabello et al. (2015) Under which conditions can introverts achieve happiness? Mediation and moderation effects of the quality of social relationships and emotion regulation ability on happiness. PeerJ 3:e1300 https://doi.org/10.7717/peerj.1300
date submitted: 2015-07-03
date accepted: 2015-09-16
issued: 2015-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cabello
  given name: Rosario
author list: Agent
  family name: Fernandez-Berrocal
  given name: Pablo
doi: 10.7717/peerj.1300
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-08
copyright: © 2015 Cabello and Fernandez-Berrocal
attribution name: Cabello and Fernandez-Berrocal

Promoting an active form of learning out-of-class via answering online “study questions” leads to higher than expected exam scores in General Biology
type: item
type: AcademicArticle
description: A rising need for workers in science, technology, engineering and mathematics (STEM) fields has fueled interest in improving teaching within STEM disciplines. Numerous studies have demonstrated the benefits of active learning approaches on student learning outcomes. However, many of these studies have been conducted in experimental, rather than real-life class, settings. In addition, most of these studies have focused on in-class active learning exercises. This study tested the effects of answering questions outside of class on exam performance for General Biology students at the University of Minnesota. An online database of 1,020 multiple-choice questions covering material from the first half of the course was generated. Students in seven course sections (with an average of ∼265 students per section) were given unlimited access to the online study questions. These students made extensive use of the online questions, with students answering an average of 1,323 questions covering material from the half of the semester for which the questions were available. After students answered a set of questions, they were shown the correct answers for those questions. More specific feedback describing how to arrive at the correct answer was provided for the 73% of the questions for which the correct answers were not deemed to be self-explanatory. The extent to which access to the online study questions improved student learning outcomes was assessed by comparing the performance on exam questions of students in the seven course sections with access to the online study questions with the performance of students in course sections without access to the online study questions. Student performance was analyzed for a total of 89 different exams questions that were not included in the study questions, but that covered the same material covered by the study questions. Each of these 89 questions was used on one to five exams given to students in course sections that had access to the on…
format: application/pdf
format: text/html
creator: Susan I. Gibson
subject: Science and Medical Education
description: doi:10.7717/peerj.1322
publisher: PeerJ Inc.
rights: © 2015 Gibson
abstract: A rising need for workers in science, technology, engineering and mathematics (STEM) fields has fueled interest in improving teaching within STEM disciplines. Numerous studies have demonstrated the benefits of active learning approaches on student learning outcomes. However, many of these studies have been conducted in experimental, rather than real-life class, settings. In addition, most of these studies have focused on in-class active learning exercises. This study tested the effects of answering questions outside of class on exam performance for General Biology students at the University of Minnesota. An online database of 1,020 multiple-choice questions covering material from the first half of the course was generated. Students in seven course sections (with an average of ∼265 students per section) were given unlimited access to the online study questions. These students made extensive use of the online questions, with students answering an average of 1,323 questions covering material from the half of the semester for which the questions were available. After students answered a set of questions, they were shown the correct answers for those questions. More specific feedback describing how to arrive at the correct answer was provided for the 73% of the questions for which the correct answers were not deemed to be self-explanatory. The extent to which access to the online study questions improved student learning outcomes was assessed by comparing the performance on exam questions of students in the seven course sections with access to the online study questions with the performance of students in course sections without access to the online study questions. Student performance was analyzed for a total of 89 different exams questions that were not included in the study questions, but that covered the same material covered by the study questions. Each of these 89 questions was used on one to five exams given to students in course sections that had access to the on…
bibliographic citation: Gibson (2015) Promoting an active form of learning out-of-class via answering online “study questions” leads to higher than expected exam scores in General Biology. PeerJ 3:e1322 https://doi.org/10.7717/peerj.1322
date submitted: 2015-07-09
date accepted: 2015-09-23
issued: 2015-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gibson
  given name: Susan I.
doi: 10.7717/peerj.1322
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-08
copyright: © 2015 Gibson
attribution name: Gibson

Interdisciplinary, interinstitutional and international collaboration of family medicine researchers in Taiwan
type: item
type: AcademicArticle
description: The family medicine researches flourished worldwide in the past decade. However, the collaborative patterns of family medicine publications had not been reported. Our study analyzed the collaborative activity of family medicine researchers in Taiwan. We focused on the types of collaboration among disciplines, institutions and countries. We searched “family medicine” AND “Taiwan” in address field from Web of Science and documented the disciplines, institutions and countries of all authors. We analyzed the collaborative patterns of family medicine researchers in Taiwan from 2010 to 2014. The journal’s impact factor of each article in the same publication year was also retrieved. Among 1,217 articles from 2010 to 2014, interdisciplinary collaboration existed in 1,185 (97.3%) articles, interinstitutional in 1,012 (83.2%) and international in 142 (11.7%). Public health was the most common collaborative discipline. All international researches were also interdisciplinary and interinstitutional. The United States (75 articles), the United Kingdom (21) and the People’s Republic of China (20) were the top three countries with which family medicine researchers in Taiwan had collaborated. We found a high degree of interdisciplinary and interinstitutional collaboration of family medicine researches in Taiwan. However, the collaboration of family medicine researchers in Taiwan with family medicine colleagues of other domestic or foreign institutions was insufficient. The future direction of family medicine studies could focus on the promotion of communication among family medicine researchers.
format: application/pdf
format: text/html
creator: Yi-Hsuan Lin
creator: Yen-Han Tseng
creator: Hsiao-Ting Chang
creator: Ming-Hwai Lin
creator: Yen-Chiang Tseng
creator: Tzeng-Ji Chen
creator: Shinn-Jang Hwang
subject: Science and Medical Education
subject: Science Policy
description: doi:10.7717/peerj.1321
publisher: PeerJ Inc.
rights: © 2015 Lin et al.
abstract: The family medicine researches flourished worldwide in the past decade. However, the collaborative patterns of family medicine publications had not been reported. Our study analyzed the collaborative activity of family medicine researchers in Taiwan. We focused on the types of collaboration among disciplines, institutions and countries. We searched “family medicine” AND “Taiwan” in address field from Web of Science and documented the disciplines, institutions and countries of all authors. We analyzed the collaborative patterns of family medicine researchers in Taiwan from 2010 to 2014. The journal’s impact factor of each article in the same publication year was also retrieved. Among 1,217 articles from 2010 to 2014, interdisciplinary collaboration existed in 1,185 (97.3%) articles, interinstitutional in 1,012 (83.2%) and international in 142 (11.7%). Public health was the most common collaborative discipline. All international researches were also interdisciplinary and interinstitutional. The United States (75 articles), the United Kingdom (21) and the People’s Republic of China (20) were the top three countries with which family medicine researchers in Taiwan had collaborated. We found a high degree of interdisciplinary and interinstitutional collaboration of family medicine researches in Taiwan. However, the collaboration of family medicine researchers in Taiwan with family medicine colleagues of other domestic or foreign institutions was insufficient. The future direction of family medicine studies could focus on the promotion of communication among family medicine researchers.
bibliographic citation: Lin et al. (2015) Interdisciplinary, interinstitutional and international collaboration of family medicine researchers in Taiwan. PeerJ 3:e1321 https://doi.org/10.7717/peerj.1321
date submitted: 2015-07-02
date accepted: 2015-09-23
issued: 2015-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Yi-Hsuan
author list: Agent
  family name: Tseng
  given name: Yen-Han
author list: Agent
  family name: Chang
  given name: Hsiao-Ting
author list: Agent
  family name: Lin
  given name: Ming-Hwai
author list: Agent
  family name: Tseng
  given name: Yen-Chiang
author list: Agent
  family name: Chen
  given name: Tzeng-Ji
author list: Agent
  family name: Hwang
  given name: Shinn-Jang
doi: 10.7717/peerj.1321
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-08
copyright: © 2015 Lin et al.
attribution name: Lin et al.

Anvi’o: an advanced analysis and visualization platform for ‘omics data
type: item
type: AcademicArticle
description: Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
format: application/pdf
format: text/html
creator: A. Murat Eren
creator: Özcan C. Esen
creator: Christopher Quince
creator: Joseph H. Vineis
creator: Hilary G. Morrison
creator: Mitchell L. Sogin
creator: Tom O. Delmont
subject: Bioinformatics
subject: Biotechnology
subject: Computational Biology
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.1319
publisher: PeerJ Inc.
rights: © 2015 Eren et al.
abstract: Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
bibliographic citation: Eren et al. (2015) Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3:e1319 https://doi.org/10.7717/peerj.1319
date submitted: 2015-08-18
date accepted: 2015-09-22
issued: 2015-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eren
  given name: A. Murat
author list: Agent
  family name: Esen
  given name: Özcan C.
author list: Agent
  family name: Quince
  given name: Christopher
author list: Agent
  family name: Vineis
  given name: Joseph H.
author list: Agent
  family name: Morrison
  given name: Hilary G.
author list: Agent
  family name: Sogin
  given name: Mitchell L.
author list: Agent
  family name: Delmont
  given name: Tom O.
doi: 10.7717/peerj.1319
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-08
copyright: © 2015 Eren et al.
attribution name: Eren et al.

Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria
type: item
type: AcademicArticle
description: Fertilizer application is a common anthropogenic alteration to terrestrial systems. Increased nutrient input can impact soil microbial diversity or function directly through altered soil environments, or indirectly through plant-microbe feedbacks, with potentially important effects on ecologically-important plant-associated mutualists. We investigated the impacts of plant fertilizer, containing all common macro and micronutrients on symbiotic nitrogen-fixing bacteria (rhizobia), a group of bacteria that are important for plant productivity and ecosystem function. We collected rhizobia nodule isolates from natural field soil that was treated with slow-release plant fertilizer over a single growing season and compared phenotypic traits related to free-living growth and host partner quality in these isolates to those of rhizobia from unfertilized soils. Through a series of single inoculation assays in controlled glasshouse conditions, we found that isolates from fertilized field soil provided legume hosts with higher mutualistic benefits. Through growth assays on media containing variable plant fertilizer concentrations, we found that plant fertilizer was generally beneficial for rhizobia growth. Rhizobia isolated from fertilized field soil had higher growth rates in the presence of plant fertilizer compared to isolates from unfertilized field soil, indicating that plant fertilizer application favoured rhizobia isolates with higher abilities to utilize fertilizer for free-living growth. We found a positive correlation between growth responses to fertilizer and mutualism benefits among isolates from fertilized field soil, demonstrating that variable plant fertilizer induces context-dependent genetic correlations, potentially changing the evolutionary trajectory of either trait through increased trait dependencies. Our study shows that short-term application is sufficient to alter the composition of rhizobia isolates in the population or community, either directly though…
format: application/pdf
format: text/html
creator: Anna K. Simonsen
creator: Shery Han
creator: Phil Rekret
creator: Christine S. Rentschler
creator: Katy D. Heath
creator: John R. Stinchcombe
subject: Ecology
subject: Evolutionary Studies
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.1291
publisher: PeerJ Inc.
rights: © 2015 Simonsen et al.
abstract: Fertilizer application is a common anthropogenic alteration to terrestrial systems. Increased nutrient input can impact soil microbial diversity or function directly through altered soil environments, or indirectly through plant-microbe feedbacks, with potentially important effects on ecologically-important plant-associated mutualists. We investigated the impacts of plant fertilizer, containing all common macro and micronutrients on symbiotic nitrogen-fixing bacteria (rhizobia), a group of bacteria that are important for plant productivity and ecosystem function. We collected rhizobia nodule isolates from natural field soil that was treated with slow-release plant fertilizer over a single growing season and compared phenotypic traits related to free-living growth and host partner quality in these isolates to those of rhizobia from unfertilized soils. Through a series of single inoculation assays in controlled glasshouse conditions, we found that isolates from fertilized field soil provided legume hosts with higher mutualistic benefits. Through growth assays on media containing variable plant fertilizer concentrations, we found that plant fertilizer was generally beneficial for rhizobia growth. Rhizobia isolated from fertilized field soil had higher growth rates in the presence of plant fertilizer compared to isolates from unfertilized field soil, indicating that plant fertilizer application favoured rhizobia isolates with higher abilities to utilize fertilizer for free-living growth. We found a positive correlation between growth responses to fertilizer and mutualism benefits among isolates from fertilized field soil, demonstrating that variable plant fertilizer induces context-dependent genetic correlations, potentially changing the evolutionary trajectory of either trait through increased trait dependencies. Our study shows that short-term application is sufficient to alter the composition of rhizobia isolates in the population or community, either directly though…
bibliographic citation: Simonsen et al. (2015) Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria. PeerJ 3:e1291 https://doi.org/10.7717/peerj.1291
date submitted: 2015-07-29
date accepted: 2015-09-14
issued: 2015-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simonsen
  given name: Anna K.
author list: Agent
  family name: Han
  given name: Shery
author list: Agent
  family name: Rekret
  given name: Phil
author list: Agent
  family name: Rentschler
  given name: Christine S.
author list: Agent
  family name: Heath
  given name: Katy D.
author list: Agent
  family name: Stinchcombe
  given name: John R.
doi: 10.7717/peerj.1291
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-08
copyright: © 2015 Simonsen et al.
attribution name: Simonsen et al.

Comments and corrections on 3D modeling studies of locomotor muscle moment arms in archosaurs
type: item
type: AcademicArticle
description: In a number of recent studies we used computer modeling to investigate the evolution of muscle leverage (moment arms) and function in extant and extinct archosaur lineages (crocodilians, dinosaurs including birds and pterosaurs). These studies sought to quantify the level of disparity and convergence in muscle moment arms during the evolution of bipedal and quadrupedal posture in various independent archosaur lineages, and in doing so further our understanding of changes in anatomy, locomotion and ecology during the group’s >250 million year evolutionary history. Subsequent work by others has led us to re-evaluate our models, which revealed a methodological error that impacted on the results obtained from the abduction–adduction and long-axis rotation moment arms in our published studies. In this paper we present corrected abduction–adduction and long axis rotation moment arms for all our models, and evaluate the impact of this new data on the conclusions of our previous studies. We find that, in general, our newly corrected data differed only slightly from that previously published, with very few qualitative changes in muscle moments (e.g., muscles originally identified as abductors remained abductors). As a result the majority of our previous conclusions regarding the functional evolution of key muscles in these archosaur groups are upheld.
format: application/pdf
format: text/html
creator: Karl Bates
creator: Susannah C.R. Maidment
creator: Emma R. Schachner
creator: Paul M. Barrett
subject: Bioengineering
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.1272
publisher: PeerJ Inc.
rights: © 2015 Bates et al.
abstract: In a number of recent studies we used computer modeling to investigate the evolution of muscle leverage (moment arms) and function in extant and extinct archosaur lineages (crocodilians, dinosaurs including birds and pterosaurs). These studies sought to quantify the level of disparity and convergence in muscle moment arms during the evolution of bipedal and quadrupedal posture in various independent archosaur lineages, and in doing so further our understanding of changes in anatomy, locomotion and ecology during the group’s >250 million year evolutionary history. Subsequent work by others has led us to re-evaluate our models, which revealed a methodological error that impacted on the results obtained from the abduction–adduction and long-axis rotation moment arms in our published studies. In this paper we present corrected abduction–adduction and long axis rotation moment arms for all our models, and evaluate the impact of this new data on the conclusions of our previous studies. We find that, in general, our newly corrected data differed only slightly from that previously published, with very few qualitative changes in muscle moments (e.g., muscles originally identified as abductors remained abductors). As a result the majority of our previous conclusions regarding the functional evolution of key muscles in these archosaur groups are upheld.
bibliographic citation: Bates et al. (2015) Comments and corrections on 3D modeling studies of locomotor muscle moment arms in archosaurs. PeerJ 3:e1272 https://doi.org/10.7717/peerj.1272
date submitted: 2015-06-02
date accepted: 2015-09-05
issued: 2015-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bates
  given name: Karl
author list: Agent
  family name: Maidment
  given name: Susannah C.R.
author list: Agent
  family name: Schachner
  given name: Emma R.
author list: Agent
  family name: Barrett
  given name: Paul M.
doi: 10.7717/peerj.1272
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-08
copyright: © 2015 Bates et al.
attribution name: Bates et al.

Competition from native hydrophytes reduces establishment and growth of invasive dense-flowered cordgrass (Spartina densiflora)
type: item
type: AcademicArticle
description: Experimental studies to determine the nature of ecological interactions between invasive and native species are necessary for conserving and restoring native species in impacted habitats. Theory predicts that species boundaries along environmental gradients are determined by physical factors in stressful environments and by competitive ability in benign environments, but little is known about the mechanisms by which hydrophytes exclude halophytes and the life history stage at which these mechanisms are able to operate. The ongoing invasion of the South American Spartina densiflora in European marshes is causing concern about potential impacts to native plants along the marsh salinity gradient, offering an opportunity to evaluate the mechanisms by which native hydrophytes may limit, or even prevent, the expansion of invasive halophytes. Our study compared S. densiflora seedling establishment with and without competition with Phragmites australis and Typha domingensis, two hydrophytes differing in clonal architecture. We hypothesized that seedlings of the stress tolerant S. densiflora would be out-competed by stands of P. australis and T. domingensis. Growth, survivorship, biomass patterns and foliar nutrient content were recorded in a common garden experiment to determine the effect of mature P. australis and T. domingensis on the growth and colonization of S. densiflora under fresh water conditions where invasion events are likely to occur. Mature P. australis stands prevented establishment of S. densiflora seedlings and T. domingensis reduced S. densiflora establishment by 38%. Seedlings grown with P. australis produced fewer than five short shoots and all plants died after ca. 2 yrs. Our results showed that direct competition, most likely for subterranean resources, was responsible for decreased growth rate and survivorship of S. densiflora. The presence of healthy stands of P. australis, and to some extent T. domingensis, along river channels and in brackish mars…
format: application/pdf
format: text/html
creator: Ahmed M. Abbas
creator: Adam M. Lambert
creator: Alfredo E. Rubio-Casal
creator: Alfonso De Cires
creator: Enrique M. Figueroa
creator: Jesús M. Castillo
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.1260
publisher: PeerJ Inc.
rights: © 2015 Abbas et al.
abstract: Experimental studies to determine the nature of ecological interactions between invasive and native species are necessary for conserving and restoring native species in impacted habitats. Theory predicts that species boundaries along environmental gradients are determined by physical factors in stressful environments and by competitive ability in benign environments, but little is known about the mechanisms by which hydrophytes exclude halophytes and the life history stage at which these mechanisms are able to operate. The ongoing invasion of the South American Spartina densiflora in European marshes is causing concern about potential impacts to native plants along the marsh salinity gradient, offering an opportunity to evaluate the mechanisms by which native hydrophytes may limit, or even prevent, the expansion of invasive halophytes. Our study compared S. densiflora seedling establishment with and without competition with Phragmites australis and Typha domingensis, two hydrophytes differing in clonal architecture. We hypothesized that seedlings of the stress tolerant S. densiflora would be out-competed by stands of P. australis and T. domingensis. Growth, survivorship, biomass patterns and foliar nutrient content were recorded in a common garden experiment to determine the effect of mature P. australis and T. domingensis on the growth and colonization of S. densiflora under fresh water conditions where invasion events are likely to occur. Mature P. australis stands prevented establishment of S. densiflora seedlings and T. domingensis reduced S. densiflora establishment by 38%. Seedlings grown with P. australis produced fewer than five short shoots and all plants died after ca. 2 yrs. Our results showed that direct competition, most likely for subterranean resources, was responsible for decreased growth rate and survivorship of S. densiflora. The presence of healthy stands of P. australis, and to some extent T. domingensis, along river channels and in brackish mars…
bibliographic citation: Abbas et al. (2015) Competition from native hydrophytes reduces establishment and growth of invasive dense-flowered cordgrass (Spartina densiflora). PeerJ 3:e1260 https://doi.org/10.7717/peerj.1260
date submitted: 2015-06-08
date accepted: 2015-09-02
issued: 2015-10-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abbas
  given name: Ahmed M.
author list: Agent
  family name: Lambert
  given name: Adam M.
author list: Agent
  family name: Rubio-Casal
  given name: Alfredo E.
author list: Agent
  family name: De Cires
  given name: Alfonso
author list: Agent
  family name: Figueroa
  given name: Enrique M.
author list: Agent
  family name: Castillo
  given name: Jesús M.
doi: 10.7717/peerj.1260
volume: 3
issn: 2167-8359
publication name: PeerJ
publication date: 2015-10-08
copyright: © 2015 Abbas et al.
attribution name: Abbas et al.

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