PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Weak population structure in the ant Formica fusca
items: Scraping marking behaviour of the largest Neotropical felids
items: Biological nitrification inhibition by root exudates of native species, Hibiscus splendens and Solanum echinatum
items: Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation
items: Comparative demography of commercially-harvested snappers and an emperor from American Samoa
items: Intein-mediated backbone cyclization of entolimod confers enhanced radioprotective activity in mouse models
items: Individual-based simulation of the spatial and temporal dynamics of macroinvertebrate functional groups provides insights into benthic community assembly mechanisms
items: Safe exposure distances for transcranial magnetic stimulation based on computer simulations
items: Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae)
items: Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case

Weak population structure in the ant Formica fusca
type: item
type: AcademicArticle
description: Dispersal is a fundamental trait of a species’ biology. High dispersal results in weakly structured or even panmictic populations over large areas, whereas weak dispersal enables population differentiation and strong spatial structuring. We report on the genetic population structure in the polygyne ant Formica fusca and the relative contribution of the dispersing males and females to this. We sampled 12 localities across a ∼35 km2 study area in Finland and generated mitochondrial DNA (mtDNA) haplotype data and microsatellite data. First, we assessed queen dispersal by estimating population differentiation from mtDNA haplotype data. Second, we analysed nuclear DNA microsatellite data to determine overall population genetic substructure in the study area with principal components analysis, Bayesian clustering, hierarchical F statistics and testing for evidence of isolation-by-distance. Third, we directly compared genetic differentiation estimates from maternally inherited mtDNA and bi-parentally inherited DNA microsatellites to test for sex-bias in dispersal. Our results showed no significant spatial structure or isolation by distance in neither mtDNA nor DNA microsatellite data, suggesting high dispersal of both sexes across the study area. However, mitochondrial differentiation was weaker (Fst-mt = 0.0047) than nuclear differentiation (Fst-nuc = 0.027), which translates into a sixfold larger female migration rate compared to that of males. We conclude that the weak population substructure reflects high dispersal in both sexes, and it is consistent with F. fusca as a pioneer species exploiting unstable habitats in successional boreal forests.
format: application/pdf
format: text/html
creator: Helena Johansson
creator: Perttu Seppä
creator: Heikki Helanterä
creator: Kalevi Trontti
creator: Liselotte Sundström
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
subject: Population Biology
description: doi:10.7717/peerj.5024
publisher: PeerJ Inc.
rights: © 2018 Johansson et al.
abstract: Dispersal is a fundamental trait of a species’ biology. High dispersal results in weakly structured or even panmictic populations over large areas, whereas weak dispersal enables population differentiation and strong spatial structuring. We report on the genetic population structure in the polygyne ant Formica fusca and the relative contribution of the dispersing males and females to this. We sampled 12 localities across a ∼35 km2 study area in Finland and generated mitochondrial DNA (mtDNA) haplotype data and microsatellite data. First, we assessed queen dispersal by estimating population differentiation from mtDNA haplotype data. Second, we analysed nuclear DNA microsatellite data to determine overall population genetic substructure in the study area with principal components analysis, Bayesian clustering, hierarchical F statistics and testing for evidence of isolation-by-distance. Third, we directly compared genetic differentiation estimates from maternally inherited mtDNA and bi-parentally inherited DNA microsatellites to test for sex-bias in dispersal. Our results showed no significant spatial structure or isolation by distance in neither mtDNA nor DNA microsatellite data, suggesting high dispersal of both sexes across the study area. However, mitochondrial differentiation was weaker (Fst-mt = 0.0047) than nuclear differentiation (Fst-nuc = 0.027), which translates into a sixfold larger female migration rate compared to that of males. We conclude that the weak population substructure reflects high dispersal in both sexes, and it is consistent with F. fusca as a pioneer species exploiting unstable habitats in successional boreal forests.
bibliographic citation: Johansson et al. (2018) Weak population structure in the ant Formica fusca. PeerJ 6:e5024 https://doi.org/10.7717/peerj.5024
date submitted: 2018-01-08
date accepted: 2018-05-26
issued: 2018-06-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johansson
  given name: Helena
author list: Agent
  family name: Seppä
  given name: Perttu
author list: Agent
  family name: Helanterä
  given name: Heikki
author list: Agent
  family name: Trontti
  given name: Kalevi
author list: Agent
  family name: Sundström
  given name: Liselotte
doi: 10.7717/peerj.5024
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-19
copyright: © 2018 Johansson et al.
attribution name: Johansson et al.

Scraping marking behaviour of the largest Neotropical felids
type: item
type: AcademicArticle
description: Background Details of how, why and in what conditions large felids make scrapes is unknown. Here, we examined the general hypothesis about the use of scrapes for marking proposals, as well as to communicate with other individuals to signalize particular points or areas of interest, by studying scrape-marking behaviour of jaguars and pumas. Methods We surveyed by scrapes between five days and two months mainly during dry season in five study areas from Mexico (El Edén and San Ignacio), Belize (Cockscomb) and Brazil (Angatuba and Serra das Almas), which differed in presence and/or abundance of jaguars and pumas. Paths were slowly walked while searching for scrapes by teams normally composed of two people and tracks were stored in GPS, distinguishing the type of path surveyed (unpaved track roads, trails and cross-country). Results We found a total of 269 felid scrapes along 467 km of paths surveyed, obtaining a finding rate of 0.576 scrapes per km. Most scrapes were found in car tracks (0.629 scrapes per km), followed by trails (0.581 scrapes per km), and rarely did we find scrapes in cross country (0.094 scrapes per km). In trails, scrapes were found in a similar frequency in the centre and edge, whereas in car tracks they were mainly found in the edge. There were also clear differences in the position of the scrapes between study areas that differed in presence and/or abundance of pumas and jaguars, with scrapes located mainly in the centre in areas only with pumas, in the centre and in the edge in areas with a similar number of jaguars and pumas, and in the edge in area mainly dominated by jaguars. The remarking rate tended to be higher in one of the areas with only pumas where natural vegetation was scarcer. Felids chose sites mainly covered by leaves and located in paths less wide, clean and rarely used. Discussion Scraping was a frequent behaviour in the largest felids of America, although in some areas, scraping behaviour was rare. Scrapes seem to be signalizin…
format: application/pdf
format: text/html
creator: Francisco Palomares
creator: Noa González-Borrajo
creator: Cuauhtémoc Chávez
creator: Yamel Rubio
creator: Luciano M. Verdade
creator: Rocio Monsa
creator: Bart Harmsen
creator: Begoña Adrados
creator: Marina Zanin
subject: Ecology
description: doi:10.7717/peerj.4983
publisher: PeerJ Inc.
rights: © 2018 Palomares et al.
abstract: Background Details of how, why and in what conditions large felids make scrapes is unknown. Here, we examined the general hypothesis about the use of scrapes for marking proposals, as well as to communicate with other individuals to signalize particular points or areas of interest, by studying scrape-marking behaviour of jaguars and pumas. Methods We surveyed by scrapes between five days and two months mainly during dry season in five study areas from Mexico (El Edén and San Ignacio), Belize (Cockscomb) and Brazil (Angatuba and Serra das Almas), which differed in presence and/or abundance of jaguars and pumas. Paths were slowly walked while searching for scrapes by teams normally composed of two people and tracks were stored in GPS, distinguishing the type of path surveyed (unpaved track roads, trails and cross-country). Results We found a total of 269 felid scrapes along 467 km of paths surveyed, obtaining a finding rate of 0.576 scrapes per km. Most scrapes were found in car tracks (0.629 scrapes per km), followed by trails (0.581 scrapes per km), and rarely did we find scrapes in cross country (0.094 scrapes per km). In trails, scrapes were found in a similar frequency in the centre and edge, whereas in car tracks they were mainly found in the edge. There were also clear differences in the position of the scrapes between study areas that differed in presence and/or abundance of pumas and jaguars, with scrapes located mainly in the centre in areas only with pumas, in the centre and in the edge in areas with a similar number of jaguars and pumas, and in the edge in area mainly dominated by jaguars. The remarking rate tended to be higher in one of the areas with only pumas where natural vegetation was scarcer. Felids chose sites mainly covered by leaves and located in paths less wide, clean and rarely used. Discussion Scraping was a frequent behaviour in the largest felids of America, although in some areas, scraping behaviour was rare. Scrapes seem to be signalizin…
bibliographic citation: Palomares et al. (2018) Scraping marking behaviour of the largest Neotropical felids. PeerJ 6:e4983 https://doi.org/10.7717/peerj.4983
date submitted: 2018-02-21
date accepted: 2018-05-25
issued: 2018-06-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palomares
  given name: Francisco
author list: Agent
  family name: González-Borrajo
  given name: Noa
author list: Agent
  family name: Chávez
  given name: Cuauhtémoc
author list: Agent
  family name: Rubio
  given name: Yamel
author list: Agent
  family name: Verdade
  given name: Luciano M.
author list: Agent
  family name: Monsa
  given name: Rocio
author list: Agent
  family name: Harmsen
  given name: Bart
author list: Agent
  family name: Adrados
  given name: Begoña
author list: Agent
  family name: Zanin
  given name: Marina
doi: 10.7717/peerj.4983
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-19
copyright: ©2018 Palomares et al.
attribution name: Palomares et al.

Biological nitrification inhibition by root exudates of native species, Hibiscus splendens and Solanum echinatum
type: item
type: AcademicArticle
description: Australian native species grow competitively in nutrient limited environments, particularly in nitrogen (N) limited soils; however, the mechanism that enables this is poorly understood. Biological nitrification inhibition (BNI), which is the release of root exudates into the plant rhizosphere to inhibit the nitrification process, is a hypothesized adaptive mechanism for maximizing N uptake. To date, few studies have investigated the temporal pattern and components of root exudates by Australian native plant species for BNI. This study examined root exudates from two Australian native species, Hibiscus splendens and Solanum echinatum, and contrasted with exudates of Sorghum bicolor, a plant widely demonstrated to exhibit BNI capacity. Root exudates were collected from plants at two, four, and six weeks after transplanting to solution culture. Root exudates contained three types of organic acids (OAs), oxalic, citric and succinic acids, regardless of the species. However, the two Australian natives species released larger amount of OAs in earlier development stages than S. bicolor. The total quantity of these OAs released per unit root dry mass was also seven-ten times greater for Australian native plant species compared to S. bicolor. The root exudates significantly inhibited nitrification activity over six weeks’ growth in a potential nitrification assay, with S. echinatum (ca. 81% inhibition) > S. bicolor (ca. 80% inhibition) > H. splendens (ca. 78% inhibition). The narrow range of BNI capacity in the study plants limited the determination of a relationship between OAs and BNI; however, a lack of correlation between individual OAs and inhibition of nitrification suggests OAs may not directly contribute to BNI. These results indicate that Australian native species generate a strongly N conserving environment within the rhizosphere up to six weeks after germination, establishing a competitive advantage in severely N limited environments.
format: application/pdf
format: text/html
creator: Chelsea K. Janke
creator: Laura A. Wendling
creator: Ryosuke Fujinuma
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Natural Resource Management
description: doi:10.7717/peerj.4960
publisher: PeerJ Inc.
rights: © 2018 Janke et al.
abstract: Australian native species grow competitively in nutrient limited environments, particularly in nitrogen (N) limited soils; however, the mechanism that enables this is poorly understood. Biological nitrification inhibition (BNI), which is the release of root exudates into the plant rhizosphere to inhibit the nitrification process, is a hypothesized adaptive mechanism for maximizing N uptake. To date, few studies have investigated the temporal pattern and components of root exudates by Australian native plant species for BNI. This study examined root exudates from two Australian native species, Hibiscus splendens and Solanum echinatum, and contrasted with exudates of Sorghum bicolor, a plant widely demonstrated to exhibit BNI capacity. Root exudates were collected from plants at two, four, and six weeks after transplanting to solution culture. Root exudates contained three types of organic acids (OAs), oxalic, citric and succinic acids, regardless of the species. However, the two Australian natives species released larger amount of OAs in earlier development stages than S. bicolor. The total quantity of these OAs released per unit root dry mass was also seven-ten times greater for Australian native plant species compared to S. bicolor. The root exudates significantly inhibited nitrification activity over six weeks’ growth in a potential nitrification assay, with S. echinatum (ca. 81% inhibition) > S. bicolor (ca. 80% inhibition) > H. splendens (ca. 78% inhibition). The narrow range of BNI capacity in the study plants limited the determination of a relationship between OAs and BNI; however, a lack of correlation between individual OAs and inhibition of nitrification suggests OAs may not directly contribute to BNI. These results indicate that Australian native species generate a strongly N conserving environment within the rhizosphere up to six weeks after germination, establishing a competitive advantage in severely N limited environments.
bibliographic citation: Janke et al. (2018) Biological nitrification inhibition by root exudates of native species, Hibiscus splendens and Solanum echinatum. PeerJ 6:e4960 https://doi.org/10.7717/peerj.4960
date submitted: 2018-02-01
date accepted: 2018-05-22
issued: 2018-06-19
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Janke
  given name: Chelsea K.
author list: Agent
  family name: Wendling
  given name: Laura A.
author list: Agent
  family name: Fujinuma
  given name: Ryosuke
doi: 10.7717/peerj.4960
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-19
copyright: ©2018 Janke et al.
attribution name: Janke et al.

Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation
type: item
type: AcademicArticle
description: Rhizoctonia solani AG1 IA is a soil-borne fungal phytopathogen that can significantly harm crops resulting in economic loss. This species overwinters in grass roots and diseased plants, and produces sclerotia that infect future crops. R. solani AG1 IA does not produce spores; therefore, understanding the molecular mechanism of sclerotia formation is important for crop disease control. To identify the genes involved in this process for the development of disease control targets, the transcriptomes of this species were determined at three important developmental stages (mycelium, sclerotial initiation, and sclerotial maturation) using an RNA-sequencing approach. A total of 5,016, 6,433, and 5,004 differentially expressed genes (DEGs) were identified in the sclerotial initiation vs. mycelial, sclerotial maturation vs. mycelial, and sclerotial maturation vs. sclerotial initiation stages, respectively. Moreover, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses showed that these DEGs were enriched in diverse categories, including oxidoreductase activity, carbohydrate metabolic process, and oxidation-reduction processes. A total of 12 DEGs were further verified using reverse transcription quantitative PCR. Among the genes examined, NADPH oxidase 1 (NOX1) and superoxide dismutase (SOD) were highly induced in the stages of sclerotial initiation and maturation. In addition, the highest reactive oxygen species (ROS) production levels were detected during sclerotial initiation, and enzyme activities of NOX1, SOD, and catalase (CAT) matched with the gene expression profiles. To further evaluate the role of ROS in sclerotial formation, R. solani AG1 IA was treated with the CAT inhibitor aminotriazole and H2O2, resulting in the early differentiation of sclerotia. Taken together, this study provides useful information toward understanding the molecular basis of R. solani AG1 IA sclerotial formation and maturation, and identified the important role of R…
format: application/pdf
format: text/html
creator: Bo Liu
creator: Haode Wang
creator: Zhoujie Ma
creator: Xiaotong Gai
creator: Yanqiu Sun
creator: Shidao He
creator: Xian Liu
creator: Yanfeng Wang
creator: Yuanhu Xuan
creator: Zenggui Gao
subject: Agricultural Science
subject: Microbiology
description: doi:10.7717/peerj.5103
publisher: PeerJ Inc.
rights: © 2018 Liu et al.
abstract: Rhizoctonia solani AG1 IA is a soil-borne fungal phytopathogen that can significantly harm crops resulting in economic loss. This species overwinters in grass roots and diseased plants, and produces sclerotia that infect future crops. R. solani AG1 IA does not produce spores; therefore, understanding the molecular mechanism of sclerotia formation is important for crop disease control. To identify the genes involved in this process for the development of disease control targets, the transcriptomes of this species were determined at three important developmental stages (mycelium, sclerotial initiation, and sclerotial maturation) using an RNA-sequencing approach. A total of 5,016, 6,433, and 5,004 differentially expressed genes (DEGs) were identified in the sclerotial initiation vs. mycelial, sclerotial maturation vs. mycelial, and sclerotial maturation vs. sclerotial initiation stages, respectively. Moreover, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses showed that these DEGs were enriched in diverse categories, including oxidoreductase activity, carbohydrate metabolic process, and oxidation-reduction processes. A total of 12 DEGs were further verified using reverse transcription quantitative PCR. Among the genes examined, NADPH oxidase 1 (NOX1) and superoxide dismutase (SOD) were highly induced in the stages of sclerotial initiation and maturation. In addition, the highest reactive oxygen species (ROS) production levels were detected during sclerotial initiation, and enzyme activities of NOX1, SOD, and catalase (CAT) matched with the gene expression profiles. To further evaluate the role of ROS in sclerotial formation, R. solani AG1 IA was treated with the CAT inhibitor aminotriazole and H2O2, resulting in the early differentiation of sclerotia. Taken together, this study provides useful information toward understanding the molecular basis of R. solani AG1 IA sclerotial formation and maturation, and identified the important role of R…
bibliographic citation: Liu et al. (2018) Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation. PeerJ 6:e5103 https://doi.org/10.7717/peerj.5103
date submitted: 2018-01-18
date accepted: 2018-06-06
issued: 2018-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Bo
author list: Agent
  family name: Wang
  given name: Haode
author list: Agent
  family name: Ma
  given name: Zhoujie
author list: Agent
  family name: Gai
  given name: Xiaotong
author list: Agent
  family name: Sun
  given name: Yanqiu
author list: Agent
  family name: He
  given name: Shidao
author list: Agent
  family name: Liu
  given name: Xian
author list: Agent
  family name: Wang
  given name: Yanfeng
author list: Agent
  family name: Xuan
  given name: Yuanhu
author list: Agent
  family name: Gao
  given name: Zenggui
doi: 10.7717/peerj.5103
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-18
copyright: © 2018 Liu et al.
attribution name: Liu et al.

Comparative demography of commercially-harvested snappers and an emperor from American Samoa
type: item
type: AcademicArticle
description: The age-based life history of two commercially-important species of snapper (Lutjanidae) and one emperor (Lethrinidae) were characterized from the nearshore fishery of Tutuila, American Samoa. Examination of sagittal otoliths across multiple months and years confirmed the annual deposition of increments and highlighted marked variation in life-history patterns among the three meso-predator species. The humpback red snapper Lutjanus gibbus is a medium-bodied gonochoristic species which exhibits striking sexual dimorphism in length-at-age and consequent growth trajectories and has a life span estimated to be at least 27 years. The yellow-lined snapper Lutjanus rufolineatus is a small-bodied gonochore with weak sexual dimorphism, early maturation, and a short life span of at least 12 years. The yellow-lip emperor Lethrinus xanthochilus is a large-bodied species with a moderate life span (estimated to be at least 19 years in this study), rapid initial growth, and a more complex sexual ontogeny likely involving pre- or post-maturational sex change, although this remains unresolved at present. Ratios of natural to fishing mortality indicate a low level of prevailing exploitation for all three species, which is supported by low proportions of immature female length classes captured by the fishery. However, considerable demographic variability among the three species highlights the value of detailed age-based information as a necessary component for informing monitoring efforts and future management decisions.
format: application/pdf
format: text/html
creator: Brett M. Taylor
creator: Zack S. Oyafuso
creator: Cassandra B. Pardee
creator: Domingo Ochavillo
creator: Stephen J. Newman
subject: Aquaculture
subject: Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.5069
publisher: PeerJ Inc.
rights: © 2018 Taylor et al.
abstract: The age-based life history of two commercially-important species of snapper (Lutjanidae) and one emperor (Lethrinidae) were characterized from the nearshore fishery of Tutuila, American Samoa. Examination of sagittal otoliths across multiple months and years confirmed the annual deposition of increments and highlighted marked variation in life-history patterns among the three meso-predator species. The humpback red snapper Lutjanus gibbus is a medium-bodied gonochoristic species which exhibits striking sexual dimorphism in length-at-age and consequent growth trajectories and has a life span estimated to be at least 27 years. The yellow-lined snapper Lutjanus rufolineatus is a small-bodied gonochore with weak sexual dimorphism, early maturation, and a short life span of at least 12 years. The yellow-lip emperor Lethrinus xanthochilus is a large-bodied species with a moderate life span (estimated to be at least 19 years in this study), rapid initial growth, and a more complex sexual ontogeny likely involving pre- or post-maturational sex change, although this remains unresolved at present. Ratios of natural to fishing mortality indicate a low level of prevailing exploitation for all three species, which is supported by low proportions of immature female length classes captured by the fishery. However, considerable demographic variability among the three species highlights the value of detailed age-based information as a necessary component for informing monitoring efforts and future management decisions.
bibliographic citation: Taylor et al. (2018) Comparative demography of commercially-harvested snappers and an emperor from American Samoa. PeerJ 6:e5069 https://doi.org/10.7717/peerj.5069
date submitted: 2018-04-02
date accepted: 2018-06-03
issued: 2018-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Taylor
  given name: Brett M.
author list: Agent
  family name: Oyafuso
  given name: Zack S.
author list: Agent
  family name: Pardee
  given name: Cassandra B.
author list: Agent
  family name: Ochavillo
  given name: Domingo
author list: Agent
  family name: Newman
  given name: Stephen J.
doi: 10.7717/peerj.5069
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-18
copyright: © 2018 Taylor et al.
attribution name: Taylor et al.

Intein-mediated backbone cyclization of entolimod confers enhanced radioprotective activity in mouse models
type: item
type: AcademicArticle
description: Background Entolimod is a Salmonella enterica flagellin derivate. Previous work has demonstrated that entolimod effectively protects mice and non-human primates from ionizing radiation. However, it caused a “flu-like” syndrome after radioprotective and anticancer clinical application, indicating some type of immunogenicity and toxicity. Cyclization is commonly used to improve the in vivo stability and activity of peptides and proteins. Methods We designed and constructed cyclic entolimod using split Nostoc punctiforme DnaE intein with almost 100% cyclization efficiency. We adopted different strategies to purify the linear and circular entolimod due to their different topologies. Both of linear and circular entolimod were first purified by Ni-chelating affinity chromatography, and then the linear and circular entolimod were purified by size-exclusion and ion-exchange chromatography, respectively. Results The circular entolimod showed significantly increased both the in vitro NF-κB signaling and in vivo radioprotective activity in mice. Conclusion Our data indicates that circular entolimod might be a good candidate for further clinical investigation.
format: application/pdf
format: text/html
creator: Bingyu Ye
creator: Wenlong Shen
creator: Minglei Shi
creator: Yan Zhang
creator: Cunshuan Xu
creator: Zhihu Zhao
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
description: doi:10.7717/peerj.5043
publisher: PeerJ Inc.
rights: © 2018 Ye et al.
abstract: Background Entolimod is a Salmonella enterica flagellin derivate. Previous work has demonstrated that entolimod effectively protects mice and non-human primates from ionizing radiation. However, it caused a “flu-like” syndrome after radioprotective and anticancer clinical application, indicating some type of immunogenicity and toxicity. Cyclization is commonly used to improve the in vivo stability and activity of peptides and proteins. Methods We designed and constructed cyclic entolimod using split Nostoc punctiforme DnaE intein with almost 100% cyclization efficiency. We adopted different strategies to purify the linear and circular entolimod due to their different topologies. Both of linear and circular entolimod were first purified by Ni-chelating affinity chromatography, and then the linear and circular entolimod were purified by size-exclusion and ion-exchange chromatography, respectively. Results The circular entolimod showed significantly increased both the in vitro NF-κB signaling and in vivo radioprotective activity in mice. Conclusion Our data indicates that circular entolimod might be a good candidate for further clinical investigation.
bibliographic citation: Ye et al. (2018) Intein-mediated backbone cyclization of entolimod confers enhanced radioprotective activity in mouse models. PeerJ 6:e5043 https://doi.org/10.7717/peerj.5043
date submitted: 2018-03-28
date accepted: 2018-05-31
issued: 2018-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ye
  given name: Bingyu
author list: Agent
  family name: Shen
  given name: Wenlong
author list: Agent
  family name: Shi
  given name: Minglei
author list: Agent
  family name: Zhang
  given name: Yan
author list: Agent
  family name: Xu
  given name: Cunshuan
author list: Agent
  family name: Zhao
  given name: Zhihu
doi: 10.7717/peerj.5043
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-18
copyright: © 2018 Ye et al.
attribution name: Ye et al.

Individual-based simulation of the spatial and temporal dynamics of macroinvertebrate functional groups provides insights into benthic community assembly mechanisms
type: item
type: AcademicArticle
description: The complexity and scales of the processes that shape communities of marine benthic macroinvertebrates has limited our understanding of their assembly mechanisms and the potential to make projections of their spatial and temporal dynamics. Individual-based models can shed light on community assembly mechanisms, by allowing observed spatiotemporal patterns to emerge from first principles about the modeled organisms. Previous work in the Rance estuary (Brittany, France) revealed the principal functional components of its benthic macroinvertebrate communities and derived a set of functional relationships between them. These elements were combined here for the development of a dynamic and spatially explicit model that operates at two spatial scales. At the fine scale, modeling each individual’s life cycle allowed the representation of recruitment, inter- and intra-group competition, biogenic habitat modification and predation mortality. Larval dispersal and environmental filtering due to the tidal characteristics of the Rance estuary were represented at the coarse scale. The two scales were dynamically linked and the model was parameterized on the basis of theoretical expectations and expert knowledge. The model was able to reproduce some patterns of α- and β-diversity that were observed in the Rance estuary in 1995. Model analysis demonstrated the role of local and regional processes, particularly early post-settlement mortality and spatially restricted dispersal, in shaping marine benthos. It also indicated biogenic habitat modification as a promising area for future research. The combination of this mechanism with different substrate types, along with the representation of physical disturbances and more trophic categories, could increase the model’s realism. The precise parameterization and validation of the model is expected to extend its scope from the exploration of community assembly mechanisms to the formulation of predictions about the responses of community st…
format: application/pdf
format: text/html
creator: Nikolaos Alexandridis
creator: Cédric Bacher
creator: Nicolas Desroy
creator: Fred Jean
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Biological Oceanography
subject: Population Biology
description: doi:10.7717/peerj.5038
publisher: PeerJ Inc.
rights: © 2018 Alexandridis et al.
abstract: The complexity and scales of the processes that shape communities of marine benthic macroinvertebrates has limited our understanding of their assembly mechanisms and the potential to make projections of their spatial and temporal dynamics. Individual-based models can shed light on community assembly mechanisms, by allowing observed spatiotemporal patterns to emerge from first principles about the modeled organisms. Previous work in the Rance estuary (Brittany, France) revealed the principal functional components of its benthic macroinvertebrate communities and derived a set of functional relationships between them. These elements were combined here for the development of a dynamic and spatially explicit model that operates at two spatial scales. At the fine scale, modeling each individual’s life cycle allowed the representation of recruitment, inter- and intra-group competition, biogenic habitat modification and predation mortality. Larval dispersal and environmental filtering due to the tidal characteristics of the Rance estuary were represented at the coarse scale. The two scales were dynamically linked and the model was parameterized on the basis of theoretical expectations and expert knowledge. The model was able to reproduce some patterns of α- and β-diversity that were observed in the Rance estuary in 1995. Model analysis demonstrated the role of local and regional processes, particularly early post-settlement mortality and spatially restricted dispersal, in shaping marine benthos. It also indicated biogenic habitat modification as a promising area for future research. The combination of this mechanism with different substrate types, along with the representation of physical disturbances and more trophic categories, could increase the model’s realism. The precise parameterization and validation of the model is expected to extend its scope from the exploration of community assembly mechanisms to the formulation of predictions about the responses of community st…
bibliographic citation: Alexandridis et al. (2018) Individual-based simulation of the spatial and temporal dynamics of macroinvertebrate functional groups provides insights into benthic community assembly mechanisms. PeerJ 6:e5038 https://doi.org/10.7717/peerj.5038
date submitted: 2017-11-26
date accepted: 2018-05-31
issued: 2018-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alexandridis
  given name: Nikolaos
author list: Agent
  family name: Bacher
  given name: Cédric
author list: Agent
  family name: Desroy
  given name: Nicolas
author list: Agent
  family name: Jean
  given name: Fred
doi: 10.7717/peerj.5038
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-18
copyright: © 2018 Alexandridis et al.
attribution name: Alexandridis et al.

Safe exposure distances for transcranial magnetic stimulation based on computer simulations
type: item
type: AcademicArticle
description: The results of a computer simulation examining the compliance of a given transcranial magnetic stimulation device to the 2010 International Commission on Non-Ionizing Radiation Protection (ICNIRP) guidelines are presented. The objective was to update the safe distance estimates with the most current safety guidelines, as well as comparing these to values reported in previous publications. The 3D data generated was compared against results available in the literature, regarding the MCB-70 coil by Medtronic. Regarding occupational exposure, safe distances of 1.46 m and 0.96 m are derived from the simulation according to the 2003 and 2010 ICNIRP guidelines, respectively. These values are then compared to safe distances previously reported in other studies.
format: application/pdf
format: text/html
creator: Iam Palatnik de Sousa
creator: Carlos R. H. Barbosa
creator: Elisabeth Costa Monteiro
subject: Bioengineering
subject: Neuroscience
subject: Public Health
description: doi:10.7717/peerj.5034
publisher: PeerJ Inc.
rights: © 2018 Palatnik de Sousa et al.
abstract: The results of a computer simulation examining the compliance of a given transcranial magnetic stimulation device to the 2010 International Commission on Non-Ionizing Radiation Protection (ICNIRP) guidelines are presented. The objective was to update the safe distance estimates with the most current safety guidelines, as well as comparing these to values reported in previous publications. The 3D data generated was compared against results available in the literature, regarding the MCB-70 coil by Medtronic. Regarding occupational exposure, safe distances of 1.46 m and 0.96 m are derived from the simulation according to the 2003 and 2010 ICNIRP guidelines, respectively. These values are then compared to safe distances previously reported in other studies.
bibliographic citation: Palatnik de Sousa et al. (2018) Safe exposure distances for transcranial magnetic stimulation based on computer simulations. PeerJ 6:e5034 https://doi.org/10.7717/peerj.5034
date submitted: 2018-04-19
date accepted: 2018-05-31
issued: 2018-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Palatnik de Sousa
  given name: Iam
author list: Agent
  family name: Barbosa
  given name: Carlos R. H.
author list: Agent
  family name: Costa Monteiro
  given name: Elisabeth
doi: 10.7717/peerj.5034
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-18
copyright: © 2018 Palatnik de Sousa et al.
attribution name: Palatnik de Sousa et al.

Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae)
type: item
type: AcademicArticle
description: Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic species T. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life.
format: application/pdf
format: text/html
creator: Xin Sun
creator: Anne Bedos
creator: Louis Deharveng
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.5021
publisher: PeerJ Inc.
rights: © 2018 Sun et al.
abstract: Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic species T. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life.
bibliographic citation: Sun et al. (2018) Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae). PeerJ 6:e5021 https://doi.org/10.7717/peerj.5021
date submitted: 2018-01-23
date accepted: 2018-05-29
issued: 2018-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Xin
author list: Agent
  family name: Bedos
  given name: Anne
author list: Agent
  family name: Deharveng
  given name: Louis
doi: 10.7717/peerj.5021
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-18
copyright: © 2018 Sun et al.
attribution name: Sun et al.

Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case
type: item
type: AcademicArticle
description: Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.
format: application/pdf
format: text/html
creator: Mami Tanaka
creator: Sayaka Mino
creator: Yoshitoshi Ogura
creator: Tetsuya Hayashi
creator: Tomoo Sawabe
subject: Genomics
subject: Taxonomy
description: doi:10.7717/peerj.5018
publisher: PeerJ Inc.
rights: © 2018 Tanaka et al.
abstract: Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.
bibliographic citation: Tanaka et al. (2018) Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case. PeerJ 6:e5018 https://doi.org/10.7717/peerj.5018
date submitted: 2018-04-24
date accepted: 2018-05-28
issued: 2018-06-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tanaka
  given name: Mami
author list: Agent
  family name: Mino
  given name: Sayaka
author list: Agent
  family name: Ogura
  given name: Yoshitoshi
author list: Agent
  family name: Hayashi
  given name: Tetsuya
author list: Agent
  family name: Sawabe
  given name: Tomoo
doi: 10.7717/peerj.5018
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-18
copyright: ©2018 Tanaka et al.
attribution name: Tanaka et al.

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