PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Examining the stress-burnout relationship: the mediating role of negative thoughts
items: The first observations of Ischnochiton (Mollusca, Polyplacophora) movement behaviour, with comparison between habitats differing in complexity
items: Broad spectrum pesticide application alters natural enemy communities and may facilitate secondary pest outbreaks
items: Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise
items: Association between genetic polymorphisms of the IL28B gene and leukomonocyte in Chinese hepatitis B virus-infected individuals
items: Underrepresentation of women in the senior levels of Brazilian science
items: Simulations indicate that scores of lionfish (Pterois volitans) colonized the Atlantic Ocean
items: Structure and properties of slow-resorbing nanofibers obtained by (co-axial) electrospinning as tissue scaffolds in regenerative medicine
items: Three-dimensional variations in the lower limb caused by the windlass mechanism
items: Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.)

Examining the stress-burnout relationship: the mediating role of negative thoughts
type: item
type: AcademicArticle
description: Background Using Smith’s (1986) cognitive-affective model of athletic burnout as a guiding framework, the purpose of this study was to examine the relationships among athletes’ stress in life, negative thoughts, and the mediating role of negative thoughts on the stress-burnout relationship. Methods A total of 300 college student-athletes (males = 174; females = 126, Mage = 20.43 y, SD = 1.68) completed the College Student Athlete’s Life Stress Scale (CSALSS; Lu et al., 2012), the Automatic Thoughts Questionnaire (ATQ; Hollon & Kendall, 1980), and the Athlete Burnout Questionnaire (ABQ; Raedeke & Smith, 2001). Results Correlational analyses found that two types of life stress and four types of negative thoughts correlated with burnout. Additionally, hierarchical regression analyses found that four types of negative thoughts partially mediated the stress-burnout relationship. Discussion We concluded that an athlete’s negative thoughts play a pivotal role in predicting athletes’ stress-burnout relationship. Future study may examine how irrational cognition influences athletes’ motivation and psychological well-being.
format: application/pdf
format: text/html
creator: Ko-Hsin Chang
creator: Frank J.H. Lu
creator: Theresa Chyi
creator: Ya-Wen Hsu
creator: Shi-Wei Chan
creator: Erica T.W. Wang
subject: Kinesiology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.4181
publisher: PeerJ Inc.
rights: © 2017 Chang et al.
abstract: Background Using Smith’s (1986) cognitive-affective model of athletic burnout as a guiding framework, the purpose of this study was to examine the relationships among athletes’ stress in life, negative thoughts, and the mediating role of negative thoughts on the stress-burnout relationship. Methods A total of 300 college student-athletes (males = 174; females = 126, Mage = 20.43 y, SD = 1.68) completed the College Student Athlete’s Life Stress Scale (CSALSS; Lu et al., 2012), the Automatic Thoughts Questionnaire (ATQ; Hollon & Kendall, 1980), and the Athlete Burnout Questionnaire (ABQ; Raedeke & Smith, 2001). Results Correlational analyses found that two types of life stress and four types of negative thoughts correlated with burnout. Additionally, hierarchical regression analyses found that four types of negative thoughts partially mediated the stress-burnout relationship. Discussion We concluded that an athlete’s negative thoughts play a pivotal role in predicting athletes’ stress-burnout relationship. Future study may examine how irrational cognition influences athletes’ motivation and psychological well-being.
bibliographic citation: Chang et al. (2017) Examining the stress-burnout relationship: the mediating role of negative thoughts. PeerJ 5:e4181 https://doi.org/10.7717/peerj.4181
date submitted: 2017-09-14
date accepted: 2017-12-01
issued: 2017-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chang
  given name: Ko-Hsin
author list: Agent
  family name: Lu
  given name: Frank J.H.
author list: Agent
  family name: Chyi
  given name: Theresa
author list: Agent
  family name: Hsu
  given name: Ya-Wen
author list: Agent
  family name: Chan
  given name: Shi-Wei
author list: Agent
  family name: Wang
  given name: Erica T.W.
doi: 10.7717/peerj.4181
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-19
copyright: ©2017 Chang et al.
attribution name: Chang et al.

The first observations of Ischnochiton (Mollusca, Polyplacophora) movement behaviour, with comparison between habitats differing in complexity
type: item
type: AcademicArticle
description: Most species of Ischnochiton are habitat specialists and are almost always found underneath unstable marine hard-substrata such as boulders. The difficulty of experimenting on these chitons without causing disturbance means little is known about their ecology despite their importance as a group that often contributes greatly to coastal species diversity. In the present study we measured among-boulder distributional patterns of Ischnochiton smaragdinus, and used time-lapse photography to quantify movement behaviours within different habitat types (pebble substrata and rock-platform). In intertidal rock-pools in South Australia, I. smaragdinus were significantly overdispersed among boulders, as most boulders had few individuals but a small proportion harboured large populations. I. smaragdinus individuals emerge from underneath boulders during nocturnal low-tides and move amongst the inter-boulder matrix (pebbles or rock-platform). Seventy-two percent of chitons in the pebble matrix did not move from one pebble to another within the periods of observation (55–130 min) but a small proportion moved across as many as five pebbles per hour, indicating a capacity for adults to migrate among disconnected habitat patches. Chitons moved faster and movement paths were less tortuous across rock-platform compared to pebble substrata, which included more discontinuities among substratum patches. Overall, we show that patterns of distribution at the boulder-scale, such as the observed overdispersion, must be set largely by active dispersal of adults across the substratum, and that differing substratum-types may affect the degree of adult dispersal for this and possibly other under-boulder chiton species.
format: application/pdf
format: text/html
creator: Kiran Liversage
creator: Kirsten Benkendorff
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.4180
publisher: PeerJ Inc.
rights: © 2017 Liversage and Benkendorff
abstract: Most species of Ischnochiton are habitat specialists and are almost always found underneath unstable marine hard-substrata such as boulders. The difficulty of experimenting on these chitons without causing disturbance means little is known about their ecology despite their importance as a group that often contributes greatly to coastal species diversity. In the present study we measured among-boulder distributional patterns of Ischnochiton smaragdinus, and used time-lapse photography to quantify movement behaviours within different habitat types (pebble substrata and rock-platform). In intertidal rock-pools in South Australia, I. smaragdinus were significantly overdispersed among boulders, as most boulders had few individuals but a small proportion harboured large populations. I. smaragdinus individuals emerge from underneath boulders during nocturnal low-tides and move amongst the inter-boulder matrix (pebbles or rock-platform). Seventy-two percent of chitons in the pebble matrix did not move from one pebble to another within the periods of observation (55–130 min) but a small proportion moved across as many as five pebbles per hour, indicating a capacity for adults to migrate among disconnected habitat patches. Chitons moved faster and movement paths were less tortuous across rock-platform compared to pebble substrata, which included more discontinuities among substratum patches. Overall, we show that patterns of distribution at the boulder-scale, such as the observed overdispersion, must be set largely by active dispersal of adults across the substratum, and that differing substratum-types may affect the degree of adult dispersal for this and possibly other under-boulder chiton species.
bibliographic citation: Liversage et al. (2017) The first observations of Ischnochiton (Mollusca, Polyplacophora) movement behaviour, with comparison between habitats differing in complexity. PeerJ 5:e4180 https://doi.org/10.7717/peerj.4180
date submitted: 2017-10-03
date accepted: 2017-11-30
issued: 2017-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liversage
  given name: Kiran
author list: Agent
  family name: Benkendorff
  given name: Kirsten
doi: 10.7717/peerj.4180
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-19
copyright: © 2017 Liversage and Benkendorff
attribution name: Liversage and Benkendorff

Broad spectrum pesticide application alters natural enemy communities and may facilitate secondary pest outbreaks
type: item
type: AcademicArticle
description: Background Pesticide application is the dominant control method for arthropod pests in broad-acre arable systems. In Australia, organophosphate pesticides are often applied either prophylactically, or reactively, including at higher concentrations, to control crop establishment pests such as false wireworms and earth mite species. Organophosphates are reported to be disruptive to beneficial species, such as natural enemies, but this has not been widely assessed in Australian systems. Neither has the risk that secondary outbreaks may occur if the natural enemy community composition or function is altered. Methods We examine the abundance of ground-dwelling invertebrate communities in an arable field over successive seasons under rotation; barley, two years of wheat, then canola. Two organophosphates (chlorpyrifos and methidathion) were initially applied at recommended rates. After no discernible impact on target pest species, the rate for chlorpyrifos was doubled to elicit a definitive response to a level used at establishment when seedling damage is observed. Invertebrates were sampled using pitfalls and refuge traps throughout the experiments. We applied measures of community diversity, principal response curves and multiple generalised linear modelling techniques to understand the changes in pest and natural enemy communities. Results There was large variability due to seasonality and crop type. Nevertheless, both pest (e.g., mites and aphids) and natural enemy (e.g., predatory beetles) invertebrate communities were significantly affected by application of organophosphates. When the rate of chlorpyrifos was increased there was a reduction in the number of beetles that predate on slug populations. Slugs displayed opposite trends to many of the other target pests, and actually increased in numbers under the higher rates of chlorpyrifos in comparison to the other treatments. Slug numbers in the final rotation of canola resulted in significant yield loss regardless of…
format: application/pdf
format: text/html
creator: Matthew P. Hill
creator: Sarina Macfadyen
creator: Michael A. Nash
subject: Agricultural Science
subject: Ecosystem Science
subject: Entomology
subject: Ecotoxicology
subject: Environmental Impacts
description: doi:10.7717/peerj.4179
publisher: PeerJ Inc.
rights: © 2017 Hill et al.
abstract: Background Pesticide application is the dominant control method for arthropod pests in broad-acre arable systems. In Australia, organophosphate pesticides are often applied either prophylactically, or reactively, including at higher concentrations, to control crop establishment pests such as false wireworms and earth mite species. Organophosphates are reported to be disruptive to beneficial species, such as natural enemies, but this has not been widely assessed in Australian systems. Neither has the risk that secondary outbreaks may occur if the natural enemy community composition or function is altered. Methods We examine the abundance of ground-dwelling invertebrate communities in an arable field over successive seasons under rotation; barley, two years of wheat, then canola. Two organophosphates (chlorpyrifos and methidathion) were initially applied at recommended rates. After no discernible impact on target pest species, the rate for chlorpyrifos was doubled to elicit a definitive response to a level used at establishment when seedling damage is observed. Invertebrates were sampled using pitfalls and refuge traps throughout the experiments. We applied measures of community diversity, principal response curves and multiple generalised linear modelling techniques to understand the changes in pest and natural enemy communities. Results There was large variability due to seasonality and crop type. Nevertheless, both pest (e.g., mites and aphids) and natural enemy (e.g., predatory beetles) invertebrate communities were significantly affected by application of organophosphates. When the rate of chlorpyrifos was increased there was a reduction in the number of beetles that predate on slug populations. Slugs displayed opposite trends to many of the other target pests, and actually increased in numbers under the higher rates of chlorpyrifos in comparison to the other treatments. Slug numbers in the final rotation of canola resulted in significant yield loss regardless of…
bibliographic citation: Hill et al. (2017) Broad spectrum pesticide application alters natural enemy communities and may facilitate secondary pest outbreaks. PeerJ 5:e4179 https://doi.org/10.7717/peerj.4179
date submitted: 2017-08-06
date accepted: 2017-11-29
issued: 2017-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hill
  given name: Matthew P.
author list: Agent
  family name: Macfadyen
  given name: Sarina
author list: Agent
  family name: Nash
  given name: Michael A.
doi: 10.7717/peerj.4179
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-19
copyright: ©2017 Hill et al.
attribution name: Hill et al.

Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise
type: item
type: AcademicArticle
description: Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P < 0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.
format: application/pdf
format: text/html
creator: Taha Soliman
creator: Sung-Yin Yang
creator: Tomoko Yamazaki
creator: Holger Jenke-Kodama
subject: Genetics
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.4178
publisher: PeerJ Inc.
rights: © 2017 Soliman et al.
abstract: Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P < 0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.
bibliographic citation: Soliman et al. (2017) Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise. PeerJ 5:e4178 https://doi.org/10.7717/peerj.4178
date submitted: 2017-07-05
date accepted: 2017-11-29
issued: 2017-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soliman
  given name: Taha
author list: Agent
  family name: Yang
  given name: Sung-Yin
author list: Agent
  family name: Yamazaki
  given name: Tomoko
author list: Agent
  family name: Jenke-Kodama
  given name: Holger
doi: 10.7717/peerj.4178
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-19
copyright: ©2017 Soliman et al.
attribution name: Soliman et al.

Association between genetic polymorphisms of the IL28B gene and leukomonocyte in Chinese hepatitis B virus-infected individuals
type: item
type: AcademicArticle
description: Background Hepatitis B infection is one of the most severe hepatic diseases in China. Thus, understanding the genetic pathogenesis of hepatitis B virus (HBV)-infected individuals is important. Although no consistent result is obtained in different populations, HBV treatment effect is reportedly associated with the IL28B gene. Methods To investigate the role of the IL28B gene in HBV-infected individuals in Yunnan, China, we screened genotypes of three single nucleotide polymorphisms (SNPs, rs12979860, rs8099917, and rs12980275) in HBV-infected individuals and general controls by using SnapShot and sequencing. Results Results showed no significant difference was found in genotypes, alleles, and haplotypes frequency between the HBV-infected individuals and controls. After dividing the HBV-infected individuals into patients in acute infection, chronic HBV patients, and patients undergoing convalescence, the genotype GT (P = 0.033) and allele G (P = 0.038) of rs8099917 showed statistically higher frequency in the acutely infectious individuals than in the HBV patients undergoing convalescence. HBV viral load was higher in the acutely infectious patients than in the chronic infection group. Strikingly, we found that leukomonocyte (LYM) level was associated with SNPs in the IL28B gene. In addition, the LYM levels were lower in the HBV-infected individuals with genotype CC of rs12979860 and AA of rs12980275 than in the patients with other genotypes of these two SNPs. Conclusion Our results suggested genetic polymorphisms of the IL28B gene were associated with LYM level of HBV-infected individuals.
format: application/pdf
format: text/html
creator: Yuzhu Song
creator: Yunsong Shen
creator: Xueshan Xia
creator: A-Mei Zhang
subject: Genetics
subject: Infectious Diseases
description: doi:10.7717/peerj.4149
publisher: PeerJ Inc.
rights: © 2017 Song et al.
abstract: Background Hepatitis B infection is one of the most severe hepatic diseases in China. Thus, understanding the genetic pathogenesis of hepatitis B virus (HBV)-infected individuals is important. Although no consistent result is obtained in different populations, HBV treatment effect is reportedly associated with the IL28B gene. Methods To investigate the role of the IL28B gene in HBV-infected individuals in Yunnan, China, we screened genotypes of three single nucleotide polymorphisms (SNPs, rs12979860, rs8099917, and rs12980275) in HBV-infected individuals and general controls by using SnapShot and sequencing. Results Results showed no significant difference was found in genotypes, alleles, and haplotypes frequency between the HBV-infected individuals and controls. After dividing the HBV-infected individuals into patients in acute infection, chronic HBV patients, and patients undergoing convalescence, the genotype GT (P = 0.033) and allele G (P = 0.038) of rs8099917 showed statistically higher frequency in the acutely infectious individuals than in the HBV patients undergoing convalescence. HBV viral load was higher in the acutely infectious patients than in the chronic infection group. Strikingly, we found that leukomonocyte (LYM) level was associated with SNPs in the IL28B gene. In addition, the LYM levels were lower in the HBV-infected individuals with genotype CC of rs12979860 and AA of rs12980275 than in the patients with other genotypes of these two SNPs. Conclusion Our results suggested genetic polymorphisms of the IL28B gene were associated with LYM level of HBV-infected individuals.
bibliographic citation: Song et al. (2017) Association between genetic polymorphisms of the IL28B gene and leukomonocyte in Chinese hepatitis B virus-infected individuals. PeerJ 5:e4149 https://doi.org/10.7717/peerj.4149
date submitted: 2017-06-29
date accepted: 2017-11-13
issued: 2017-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Yuzhu
author list: Agent
  family name: Shen
  given name: Yunsong
author list: Agent
  family name: Xia
  given name: Xueshan
author list: Agent
  family name: Zhang
  given name: A-Mei
doi: 10.7717/peerj.4149
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-19
copyright: ©2017 Song et al.
attribution name: Song et al.

Underrepresentation of women in the senior levels of Brazilian science
type: item
type: AcademicArticle
description: Despite significant progress, there is still a gender gap in science all over the world, especially at senior levels. Some progressive countries are recognizing the need to address barriers to gender equality in order to retain their best scientists and innovators, and ensure research excellence and social and economic returns on the investment made by taxpayers each year on training women scientists. We investigated the gender distribution of: (i) the productivity scholarship (PS) holders of the Brazilian National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, N = 13,625), (ii) the members of the Brazilian Academy of Science (Academia Brasileira de Ciências, ABC, N = 899), and (iii) the amount of funding awarded for top quality research (“Universal” Call of CNPq, N = 3,836), between the years of 2013 and 2014. Our findings show evidence for gender imbalances in all the studied indicators of Brazilian science. We found that female scientists were more often represented among PS holders at the lower levels of the research ranking system (2). By contrast, male scientists were more often found at higher levels (1A and 1B) of PS holders, indicating the top scientific achievement, both in “Engineering, Exact Sciences, Earth Sciences”, and “Life Sciences”. This imbalance was not found in Humanities and Social Sciences. Only 14% of the ABC members were women. Humanities and Applied Social Sciences had a relatively low representation of women in the Academy (3.7%) compared to Engineering, Exact and Earth Sciences: 54.9% and Life Sciences: 41.4%. Finally, female scientists obtained significantly more funding at the lower level of the research ranking system (2), whereas male scientists obtained significantly more funding at the higher levels (1A and 1B). Our results show strong evidence of a gender imbalance in Brazilian science. We hope that our findings will be used to stimulate reforms that will r…
format: application/pdf
format: text/html
creator: Jaroslava V. Valentova
creator: Emma Otta
creator: Maria Luisa Silva
creator: Alan G. McElligott
subject: Ethical Issues
subject: Science Policy
description: doi:10.7717/peerj.4000
publisher: PeerJ Inc.
rights: © 2017 Valentova et al.
abstract: Despite significant progress, there is still a gender gap in science all over the world, especially at senior levels. Some progressive countries are recognizing the need to address barriers to gender equality in order to retain their best scientists and innovators, and ensure research excellence and social and economic returns on the investment made by taxpayers each year on training women scientists. We investigated the gender distribution of: (i) the productivity scholarship (PS) holders of the Brazilian National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, N = 13,625), (ii) the members of the Brazilian Academy of Science (Academia Brasileira de Ciências, ABC, N = 899), and (iii) the amount of funding awarded for top quality research (“Universal” Call of CNPq, N = 3,836), between the years of 2013 and 2014. Our findings show evidence for gender imbalances in all the studied indicators of Brazilian science. We found that female scientists were more often represented among PS holders at the lower levels of the research ranking system (2). By contrast, male scientists were more often found at higher levels (1A and 1B) of PS holders, indicating the top scientific achievement, both in “Engineering, Exact Sciences, Earth Sciences”, and “Life Sciences”. This imbalance was not found in Humanities and Social Sciences. Only 14% of the ABC members were women. Humanities and Applied Social Sciences had a relatively low representation of women in the Academy (3.7%) compared to Engineering, Exact and Earth Sciences: 54.9% and Life Sciences: 41.4%. Finally, female scientists obtained significantly more funding at the lower level of the research ranking system (2), whereas male scientists obtained significantly more funding at the higher levels (1A and 1B). Our results show strong evidence of a gender imbalance in Brazilian science. We hope that our findings will be used to stimulate reforms that will r…
bibliographic citation: Valentova et al. (2017) Underrepresentation of women in the senior levels of Brazilian science. PeerJ 5:e4000 https://doi.org/10.7717/peerj.4000
date submitted: 2016-06-05
date accepted: 2017-10-17
issued: 2017-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valentova
  given name: Jaroslava V.
author list: Agent
  family name: Otta
  given name: Emma
author list: Agent
  family name: Silva
  given name: Maria Luisa
author list: Agent
  family name: McElligott
  given name: Alan G.
doi: 10.7717/peerj.4000
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-19
copyright: ©2017 Valentova et al.
attribution name: Valentova et al.

Simulations indicate that scores of lionfish (Pterois volitans) colonized the Atlantic Ocean
type: item
type: AcademicArticle
description: The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish (Pterois volitans) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced probabilistic scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region. To rigorously estimate the number of lionfish that were introduced, we used a forward-time, Wright-Fisher, population genetic model in concert with a demographic, life-history model to simulate the invasion across a range of source population sizes and colonizing population fecundities. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was founded by 118 (54–514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22–328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Increasing the size, and therefore diversity, of the Indo-Pacific source population and fecundity of the founding population caused the number of colonists to decrease, but with rapidly diminishing returns. When the simulation was parameterized to minimize the number of colonists (high θ and relative fecundity), 96 (48–216, 95% HPD) colonists were most likely. In a more realistic scenario with Allee effects (e.g., 50% reduction in fecundity) plaguing the colonists, the most likely number of lionfish increased to 272 (106–950, 95% HPD). These results, in combination with other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. When building the model employed here, we made assumptions that minimize the number of colonists,…
format: application/pdf
format: text/html
creator: Jason D. Selwyn
creator: John E. Johnson
creator: Alan M. Downey-Wall
creator: Adam M. Bynum
creator: Rebecca M. Hamner
creator: J. Derek Hogan
creator: Christopher E. Bird
subject: Biogeography
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.3996
publisher: PeerJ Inc.
rights: © 2017 Selwyn et al.
abstract: The invasion of the western Atlantic Ocean by the Indo-Pacific red lionfish (Pterois volitans) has had devastating consequences for marine ecosystems. Estimating the number of colonizing lionfish can be useful in identifying the introduction pathway and can inform policy decisions aimed at preventing similar invasions. It is well-established that at least ten lionfish were initially introduced. However, that estimate has not faced probabilistic scrutiny and is based solely on the number of haplotypes in the maternally-inherited mitochondrial control region. To rigorously estimate the number of lionfish that were introduced, we used a forward-time, Wright-Fisher, population genetic model in concert with a demographic, life-history model to simulate the invasion across a range of source population sizes and colonizing population fecundities. Assuming a balanced sex ratio and no Allee effects, the simulations indicate that the Atlantic population was founded by 118 (54–514, 95% HPD) lionfish from the Indo-Pacific, the Caribbean by 84 (22–328, 95% HPD) lionfish from the Atlantic, and the Gulf of Mexico by at least 114 (no upper bound on 95% HPD) lionfish from the Caribbean. Increasing the size, and therefore diversity, of the Indo-Pacific source population and fecundity of the founding population caused the number of colonists to decrease, but with rapidly diminishing returns. When the simulation was parameterized to minimize the number of colonists (high θ and relative fecundity), 96 (48–216, 95% HPD) colonists were most likely. In a more realistic scenario with Allee effects (e.g., 50% reduction in fecundity) plaguing the colonists, the most likely number of lionfish increased to 272 (106–950, 95% HPD). These results, in combination with other published data, support the hypothesis that lionfish were introduced to the Atlantic via the aquarium trade, rather than shipping. When building the model employed here, we made assumptions that minimize the number of colonists,…
bibliographic citation: Selwyn et al. (2017) Simulations indicate that scores of lionfish (Pterois volitans) colonized the Atlantic Ocean. PeerJ 5:e3996 https://doi.org/10.7717/peerj.3996
date submitted: 2017-06-19
date accepted: 2017-10-13
issued: 2017-12-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Selwyn
  given name: Jason D.
author list: Agent
  family name: Johnson
  given name: John E.
author list: Agent
  family name: Downey-Wall
  given name: Alan M.
author list: Agent
  family name: Bynum
  given name: Adam M.
author list: Agent
  family name: Hamner
  given name: Rebecca M.
author list: Agent
  family name: Hogan
  given name: J. Derek
author list: Agent
  family name: Bird
  given name: Christopher E.
doi: 10.7717/peerj.3996
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-19
copyright: ©2017 Selwyn et al.
attribution name: Selwyn et al.

Structure and properties of slow-resorbing nanofibers obtained by (co-axial) electrospinning as tissue scaffolds in regenerative medicine
type: item
type: AcademicArticle
description: With the rapid advancement of regenerative medicine technologies, there is an urgent need for the development of new, cell-friendly techniques for obtaining nanofibers—the raw material for an artificial extracellular matrix production. We investigated the structure and properties of PCL10 nanofibers, PCL5/PCL10 core-shell type nanofibers, as well as PCL5/PCLAg nanofibres prepared by electrospinning. For the production of the fiber variants, a 5–10% solution of polycaprolactone (PCL) (Mw = 70,000–90,000), dissolved in a mixture of formic acid and acetic acid at a ratio of 70:30 m/m was used. In order to obtain fibers containing PCLAg 1% of silver nanoparticles was added. The electrospin was conducted using the above-described solutions at the electrostatic field. The subsequent bio-analysis shows that synthesis of core-shell nanofibers PCL5/PCL10, and the silver-doped variant nanofiber core shell PCL5/PCLAg, by using organic acids as solvents, is a robust technique. Furthermore, the incorporation of silver nanoparticles into PCL5/PCLAg makes such nanofibers toxic to model microbes without compromising its biocompatibility. Nanofibers obtained such way may then be used in regenerative medicine, for the preparation of extracellular scaffolds: (i) for controlled bone regeneration due to the long decay time of the PCL, (ii) as bioscaffolds for generation of other types of artificial tissues, (iii) and as carriers of nanocapsules for local drug delivery. Furthermore, the used solvents are significantly less toxic than the solvents for polycaprolactone currently commonly used in electrospin, like for example chloroform (CHCl3), methanol (CH3OH), dimethylformamide (C3H7NO) or tetrahydrofuran (C4H8O), hence the presented here electrospin technique may allow for the production of multilayer nanofibres more suitable for the use in medical field.
format: application/pdf
format: text/html
creator: Andrzej Hudecki
creator: Joanna Gola
creator: Saeid Ghavami
creator: Magdalena Skonieczna
creator: Jarosław Markowski
creator: Wirginia Likus
creator: Magdalena Lewandowska
creator: Wojciech Maziarz
creator: Marek J. Los
subject: Bioengineering
subject: Biotechnology
subject: Synthetic Biology
description: doi:10.7717/peerj.4125
publisher: PeerJ Inc.
rights: © 2017 Hudecki et al.
abstract: With the rapid advancement of regenerative medicine technologies, there is an urgent need for the development of new, cell-friendly techniques for obtaining nanofibers—the raw material for an artificial extracellular matrix production. We investigated the structure and properties of PCL10 nanofibers, PCL5/PCL10 core-shell type nanofibers, as well as PCL5/PCLAg nanofibres prepared by electrospinning. For the production of the fiber variants, a 5–10% solution of polycaprolactone (PCL) (Mw = 70,000–90,000), dissolved in a mixture of formic acid and acetic acid at a ratio of 70:30 m/m was used. In order to obtain fibers containing PCLAg 1% of silver nanoparticles was added. The electrospin was conducted using the above-described solutions at the electrostatic field. The subsequent bio-analysis shows that synthesis of core-shell nanofibers PCL5/PCL10, and the silver-doped variant nanofiber core shell PCL5/PCLAg, by using organic acids as solvents, is a robust technique. Furthermore, the incorporation of silver nanoparticles into PCL5/PCLAg makes such nanofibers toxic to model microbes without compromising its biocompatibility. Nanofibers obtained such way may then be used in regenerative medicine, for the preparation of extracellular scaffolds: (i) for controlled bone regeneration due to the long decay time of the PCL, (ii) as bioscaffolds for generation of other types of artificial tissues, (iii) and as carriers of nanocapsules for local drug delivery. Furthermore, the used solvents are significantly less toxic than the solvents for polycaprolactone currently commonly used in electrospin, like for example chloroform (CHCl3), methanol (CH3OH), dimethylformamide (C3H7NO) or tetrahydrofuran (C4H8O), hence the presented here electrospin technique may allow for the production of multilayer nanofibres more suitable for the use in medical field.
bibliographic citation: Hudecki et al. (2017) Structure and properties of slow-resorbing nanofibers obtained by (co-axial) electrospinning as tissue scaffolds in regenerative medicine. PeerJ 5:e4125 https://doi.org/10.7717/peerj.4125
date submitted: 2017-06-26
date accepted: 2017-11-13
issued: 2017-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hudecki
  given name: Andrzej
author list: Agent
  family name: Gola
  given name: Joanna
author list: Agent
  family name: Ghavami
  given name: Saeid
author list: Agent
  family name: Skonieczna
  given name: Magdalena
author list: Agent
  family name: Markowski
  given name: Jarosław
author list: Agent
  family name: Likus
  given name: Wirginia
author list: Agent
  family name: Lewandowska
  given name: Magdalena
author list: Agent
  family name: Maziarz
  given name: Wojciech
author list: Agent
  family name: Los
  given name: Marek J.
doi: 10.7717/peerj.4125
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-18
copyright: ©2017 Hudecki et al.
attribution name: Hudecki et al.

Three-dimensional variations in the lower limb caused by the windlass mechanism
type: item
type: AcademicArticle
description: Background The windlass mechanism was described as the effect caused by the extension of the first metatarsalphalangeal joint (1st MTPJ). Quantify the degrees of movement produced in the leg by means of the Bioval® sensor system, after performing two measurements in the 1st MTPJ, 45° extension and maximum extension. Methods Tests-post-test study with just one intervention group, performed in the Clinical Podiatry Area of the Faculty of Nursing, Physiotherapy and Podiatry of the University of Seville. Subjects were included as of age 20, with a value from 0° to 3° valgus, Helbing line, a value from 0° to +5° for the foot postural index, and a localisation axis for the normalised subtalar joint. Subjects with surgical operations of the first ray, fractures and surgical operations in the leg, pathologies in the first ray and rheumatic diseases were excluded. Measurement was performed with the Bioval® system by means of inserting four sensors in the bone structures involved in the windlass mechanism. Results With the 45° wedge we observed a direct correlation among the variables extension–plantar flexion 1st MTPJ and rotation of the femur. With maximal extension of the 1st MTPJ we obtained a direct relationship between the variable extension of the 1st MTPJ and the variables plantar flexion and prono-supination of the 1st metatarsal as well as with the variables tibia rotation and femur rotation. Conclusion Kinematic analysis suggested that the higher the degree of extension the more movement will be generated. This reduces the level of impact the more distal the structure with respect to the 1st MTPJ, which has an impact on the entire leg. Because of the kinematic system used wasn’t suitable, its impact wasn’t exactly quantified.
format: application/pdf
format: text/html
creator: María José Manfredi-Márquez
creator: Natalia Tovaruela-Carrión
creator: Priscila Távara-Vidalón
creator: Gabriel Domínguez-Maldonado
creator: Lourdes María Fernández-Seguín
creator: Javier Ramos-Ortega
subject: Kinesiology
subject: Orthopedics
subject: Public Health
description: doi:10.7717/peerj.4103
publisher: PeerJ Inc.
rights: © 2017 Manfredi-Márquez et al.
abstract: Background The windlass mechanism was described as the effect caused by the extension of the first metatarsalphalangeal joint (1st MTPJ). Quantify the degrees of movement produced in the leg by means of the Bioval® sensor system, after performing two measurements in the 1st MTPJ, 45° extension and maximum extension. Methods Tests-post-test study with just one intervention group, performed in the Clinical Podiatry Area of the Faculty of Nursing, Physiotherapy and Podiatry of the University of Seville. Subjects were included as of age 20, with a value from 0° to 3° valgus, Helbing line, a value from 0° to +5° for the foot postural index, and a localisation axis for the normalised subtalar joint. Subjects with surgical operations of the first ray, fractures and surgical operations in the leg, pathologies in the first ray and rheumatic diseases were excluded. Measurement was performed with the Bioval® system by means of inserting four sensors in the bone structures involved in the windlass mechanism. Results With the 45° wedge we observed a direct correlation among the variables extension–plantar flexion 1st MTPJ and rotation of the femur. With maximal extension of the 1st MTPJ we obtained a direct relationship between the variable extension of the 1st MTPJ and the variables plantar flexion and prono-supination of the 1st metatarsal as well as with the variables tibia rotation and femur rotation. Conclusion Kinematic analysis suggested that the higher the degree of extension the more movement will be generated. This reduces the level of impact the more distal the structure with respect to the 1st MTPJ, which has an impact on the entire leg. Because of the kinematic system used wasn’t suitable, its impact wasn’t exactly quantified.
bibliographic citation: Manfredi-Márquez et al. (2017) Three-dimensional variations in the lower limb caused by the windlass mechanism. PeerJ 5:e4103 https://doi.org/10.7717/peerj.4103
date submitted: 2017-08-12
date accepted: 2017-11-07
issued: 2017-12-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manfredi-Márquez
  given name: María José
author list: Agent
  family name: Tovaruela-Carrión
  given name: Natalia
author list: Agent
  family name: Távara-Vidalón
  given name: Priscila
author list: Agent
  family name: Domínguez-Maldonado
  given name: Gabriel
author list: Agent
  family name: Fernández-Seguín
  given name: Lourdes María
author list: Agent
  family name: Ramos-Ortega
  given name: Javier
doi: 10.7717/peerj.4103
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-18
copyright: © 2017 Manfredi-Márquez et al.
attribution name: Manfredi-Márquez et al.

Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.)
type: item
type: AcademicArticle
description: NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.
format: application/pdf
format: text/html
creator: Bernard Kinuthia Karanja
creator: Liang Xu
creator: Yan Wang
creator: Everlyne M’mbone Muleke
creator: Bashir Mohammed Jabir
creator: Yang Xie
creator: Xianwen Zhu
creator: Wanwan Cheng
creator: Liwang Liu
subject: Bioinformatics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.4172
publisher: PeerJ Inc.
rights: © 2017 Karanja et al.
abstract: NAC (NAM, no apical meristem; ATAF, Arabidopsis transcription activation factor and CUC, cup-shaped cotyledon) proteins are among the largest transcription factor (TF) families playing fundamental biological processes, including cell expansion and differentiation, and hormone signaling in response to biotic and abiotic stresses. In this study, 172 RsNACs comprising 17 membrane-bound members were identified from the whole radish genome. In total, 98 RsNAC genes were non-uniformly distributed across the nine radish chromosomes. In silico analysis revealed that expression patterns of several NAC genes were tissue-specific such as a preferential expression in roots and leaves. In addition, 21 representative NAC genes were selected to investigate their responses to heavy metals (HMs), salt, heat, drought and abscisic acid (ABA) stresses using real-time polymerase chain reaction (RT-qPCR). As a result, differential expressions among these genes were identified where RsNAC023 and RsNAC080 genes responded positively to all stresses except ABA, while RsNAC145 responded more actively to salt, heat and drought stresses compared with other genes. The results provides more valuable information and robust candidate genes for future functional analysis for improving abiotic stress tolerances in radish.
bibliographic citation: Karanja et al. (2017) Genome-wide characterization and expression profiling of NAC transcription factor genes under abiotic stresses in radish (Raphanus sativus L.). PeerJ 5:e4172 https://doi.org/10.7717/peerj.4172
date submitted: 2017-06-23
date accepted: 2017-11-28
issued: 2017-12-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karanja
  given name: Bernard Kinuthia
author list: Agent
  family name: Xu
  given name: Liang
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Muleke
  given name: Everlyne M’mbone
author list: Agent
  family name: Jabir
  given name: Bashir Mohammed
author list: Agent
  family name: Xie
  given name: Yang
author list: Agent
  family name: Zhu
  given name: Xianwen
author list: Agent
  family name: Cheng
  given name: Wanwan
author list: Agent
  family name: Liu
  given name: Liwang
doi: 10.7717/peerj.4172
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-12-15
copyright: ©2017 Karanja et al.
attribution name: Karanja et al.

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