PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of common and experimental anti-tuberculosis treatments on Mycobacterium tuberculosis growing as biofilms
items: Pathogen reduction co-benefits of nutrient best management practices
items: Dominance relationships in a family pack of captive arctic wolves (Canis lupus arctos): the influence of competition for food, age and sex
items: Hypothesis on Serenoa repens (Bartram) small extract inhibition of prostatic 5α-reductase through an in silico approach on 5β-reductase x-ray structure
items: Detecting sedimentation impacts to coral reefs resulting from dredging the Port of Miami, Florida USA
items: Ficolin-2 inhibitors are present in sera after prolonged storage at −80 °C
items: Multiple, independent colonizations of the Hawaiian Archipelago by the family Dolichopodidae (Diptera)
items: Salinity modulates thermotolerance, energy metabolism and stress response in amphipods Gammarus lacustris
items: Ceratopogonidae (Diptera: Nematocera) of the piedmont of the Yungas forests of Tucumán: ecology and distribution
items: PDIA3 gene induces visceral hypersensitivity in rats with irritable bowel syndrome through the dendritic cell-mediated activation of T cells

Effect of common and experimental anti-tuberculosis treatments on Mycobacterium tuberculosis growing as biofilms
type: item
type: AcademicArticle
description: Much is known regarding the antibiotic susceptibility of planktonic cultures of Mycobacterium tuberculosis, the bacterium responsible for the lung disease tuberculosis (TB). As planktonically-grown M. tuberculosis are unlikely to be entirely representative of the bacterium during infection, we set out to determine how effective a range of anti-mycobacterial treatments were against M. tuberculosis growing as a biofilm, a bacterial phenotype known to be more resistant to antibiotic treatment. Light levels from bioluminescently-labelled M. tuberculosis H37Rv (strain BSG001) were used as a surrogate for bacterial viability, and were monitored before and after one week of treatment. After treatment, biofilms were disrupted, washed and inoculated into fresh broth and plated onto solid media to rescue any surviving bacteria. We found that in this phenotypic state M. tuberculosis was resistant to the majority of the compounds tested. Minimum inhibitory concentrations (MICs) increased by 20-fold to greater than 1,000-fold, underlying the potential of this phenotype to cause significant problems during treatment.
format: application/pdf
format: text/html
creator: James P. Dalton
creator: Benedict Uy
creator: Narisa Phummarin
creator: Brent R. Copp
creator: William A. Denny
creator: Simon Swift
creator: Siouxsie Wiles
subject: Microbiology
subject: Infectious Diseases
description: doi:10.7717/peerj.2717
publisher: PeerJ Inc.
rights: © 2016 Dalton et al.
abstract: Much is known regarding the antibiotic susceptibility of planktonic cultures of Mycobacterium tuberculosis, the bacterium responsible for the lung disease tuberculosis (TB). As planktonically-grown M. tuberculosis are unlikely to be entirely representative of the bacterium during infection, we set out to determine how effective a range of anti-mycobacterial treatments were against M. tuberculosis growing as a biofilm, a bacterial phenotype known to be more resistant to antibiotic treatment. Light levels from bioluminescently-labelled M. tuberculosis H37Rv (strain BSG001) were used as a surrogate for bacterial viability, and were monitored before and after one week of treatment. After treatment, biofilms were disrupted, washed and inoculated into fresh broth and plated onto solid media to rescue any surviving bacteria. We found that in this phenotypic state M. tuberculosis was resistant to the majority of the compounds tested. Minimum inhibitory concentrations (MICs) increased by 20-fold to greater than 1,000-fold, underlying the potential of this phenotype to cause significant problems during treatment.
bibliographic citation: Dalton et al. (2016) Effect of common and experimental anti-tuberculosis treatments on Mycobacterium tuberculosis growing as biofilms. PeerJ 4:e2717 https://doi.org/10.7717/peerj.2717
date submitted: 2014-11-24
date accepted: 2016-10-25
issued: 2016-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dalton
  given name: James P.
author list: Agent
  family name: Uy
  given name: Benedict
author list: Agent
  family name: Phummarin
  given name: Narisa
author list: Agent
  family name: Copp
  given name: Brent R.
author list: Agent
  family name: Denny
  given name: William A.
author list: Agent
  family name: Swift
  given name: Simon
author list: Agent
  family name: Wiles
  given name: Siouxsie
doi: 10.7717/peerj.2717
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-22
copyright: ©2016 Dalton et al.
attribution name: Dalton et al.

Pathogen reduction co-benefits of nutrient best management practices
type: item
type: AcademicArticle
description: Background Many of the practices currently underway to reduce nitrogen, phosphorus, and sediment loads entering the Chesapeake Bay have also been observed to support reduction of disease-causing pathogen loadings. We quantify how implementation of these practices, proposed to meet the nutrient and sediment caps prescribed by the Total Maximum Daily Load (TMDL), could reduce pathogen loadings and provide public health co-benefits within the Chesapeake Bay system. Methods We used published data on the pathogen reduction potential of management practices and baseline fecal coliform loadings estimated as part of prior modeling to estimate the reduction in pathogen loadings to the mainstem Potomac River and Chesapeake Bay attributable to practices implemented as part of the TMDL. We then compare the estimates with the baseline loadings of fecal coliform loadings to estimate the total pathogen reduction potential of the TMDL. Results We estimate that the TMDL practices have the potential to decrease disease-causing pathogen loads from all point and non-point sources to the mainstem Potomac River and the entire Chesapeake Bay watershed by 19% and 27%, respectively. These numbers are likely to be underestimates due to data limitations that forced us to omit some practices from analysis. Discussion Based on known impairments and disease incidence rates, we conclude that efforts to reduce nutrients may create substantial health co-benefits by improving the safety of water-contact recreation and seafood consumption.
format: application/pdf
format: text/html
creator: Jennifer Richkus
creator: Lisa A. Wainger
creator: Mary C. Barber
subject: Aquaculture, Fisheries and Fish Science
subject: Environmental Sciences
subject: Marine Biology
subject: Microbiology
subject: Coupled Natural and Human Systems
description: doi:10.7717/peerj.2713
publisher: PeerJ Inc.
rights: © 2016 Richkus et al.
abstract: Background Many of the practices currently underway to reduce nitrogen, phosphorus, and sediment loads entering the Chesapeake Bay have also been observed to support reduction of disease-causing pathogen loadings. We quantify how implementation of these practices, proposed to meet the nutrient and sediment caps prescribed by the Total Maximum Daily Load (TMDL), could reduce pathogen loadings and provide public health co-benefits within the Chesapeake Bay system. Methods We used published data on the pathogen reduction potential of management practices and baseline fecal coliform loadings estimated as part of prior modeling to estimate the reduction in pathogen loadings to the mainstem Potomac River and Chesapeake Bay attributable to practices implemented as part of the TMDL. We then compare the estimates with the baseline loadings of fecal coliform loadings to estimate the total pathogen reduction potential of the TMDL. Results We estimate that the TMDL practices have the potential to decrease disease-causing pathogen loads from all point and non-point sources to the mainstem Potomac River and the entire Chesapeake Bay watershed by 19% and 27%, respectively. These numbers are likely to be underestimates due to data limitations that forced us to omit some practices from analysis. Discussion Based on known impairments and disease incidence rates, we conclude that efforts to reduce nutrients may create substantial health co-benefits by improving the safety of water-contact recreation and seafood consumption.
bibliographic citation: Richkus et al. (2016) Pathogen reduction co-benefits of nutrient best management practices. PeerJ 4:e2713 https://doi.org/10.7717/peerj.2713
date submitted: 2016-06-15
date accepted: 2016-10-24
issued: 2016-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Richkus
  given name: Jennifer
author list: Agent
  family name: Wainger
  given name: Lisa A.
author list: Agent
  family name: Barber
  given name: Mary C.
doi: 10.7717/peerj.2713
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-22
copyright: © 2016 Richkus et al.
attribution name: Richkus et al.

Dominance relationships in a family pack of captive arctic wolves (Canis lupus arctos): the influence of competition for food, age and sex
type: item
type: AcademicArticle
description: Background Dominance is one of the most pervasive concepts in the study of wolf social behaviour but recently its validity has been questioned. For some authors, the bonds between members of wolf families are better described as parent-offspring relationships and the concept of dominance should be used just to evaluate the social dynamics of non-familial captive pack members (e.g., Mech & Cluff, 2010). However, there is a dearth of studies investigating dominance relationships and its correlates in wolf family packs. Methods Here, we applied a combination of the most commonly used quantitative methods to evaluate the dominance relationships in a captive family pack of 19 Arctic wolves. Results We found a significant linear and completely transitive hierarchy based on the direction of submissive behaviours and found that dominance relationships were not influenced by the competitive contexts (feeding vs. non-feeding context). A significant linear hierarchy also emerges amongst siblings once the breeding pair (the two top-ranking individuals) is removed from analyses. Furthermore, results suggest that wolves may use greeting behaviour as a formal signal of subordination. Whereas older wolves were mostly dominant over younger ones, no clear effect of sex was found. However, frequency of agonistic (submissive, dominant and aggressive) behaviours was higher between female–female and male–male dyads than female–male dyads and sex-separated linear hierarchies showed a stronger linearity than the mixed one. Furthermore, dominance status was conveyed through different behavioural categories during intra-sexual and inter-sexual interactions. Discussion Current results highlight the importance of applying a systematic methodology considering the individuals’ age and sex when evaluating the hierarchical structure of a social group. Moreover, they confirm the validity of the concept of dominance relationships in describing the social bonds within a family pack of captive wolves.
format: application/pdf
format: text/html
creator: Simona Cafazzo
creator: Martina Lazzaroni
creator: Sarah Marshall-Pescini
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.2707
publisher: PeerJ Inc.
rights: © 2016 Cafazzo et al.
abstract: Background Dominance is one of the most pervasive concepts in the study of wolf social behaviour but recently its validity has been questioned. For some authors, the bonds between members of wolf families are better described as parent-offspring relationships and the concept of dominance should be used just to evaluate the social dynamics of non-familial captive pack members (e.g., Mech & Cluff, 2010). However, there is a dearth of studies investigating dominance relationships and its correlates in wolf family packs. Methods Here, we applied a combination of the most commonly used quantitative methods to evaluate the dominance relationships in a captive family pack of 19 Arctic wolves. Results We found a significant linear and completely transitive hierarchy based on the direction of submissive behaviours and found that dominance relationships were not influenced by the competitive contexts (feeding vs. non-feeding context). A significant linear hierarchy also emerges amongst siblings once the breeding pair (the two top-ranking individuals) is removed from analyses. Furthermore, results suggest that wolves may use greeting behaviour as a formal signal of subordination. Whereas older wolves were mostly dominant over younger ones, no clear effect of sex was found. However, frequency of agonistic (submissive, dominant and aggressive) behaviours was higher between female–female and male–male dyads than female–male dyads and sex-separated linear hierarchies showed a stronger linearity than the mixed one. Furthermore, dominance status was conveyed through different behavioural categories during intra-sexual and inter-sexual interactions. Discussion Current results highlight the importance of applying a systematic methodology considering the individuals’ age and sex when evaluating the hierarchical structure of a social group. Moreover, they confirm the validity of the concept of dominance relationships in describing the social bonds within a family pack of captive wolves.
bibliographic citation: Cafazzo et al. (2016) Dominance relationships in a family pack of captive arctic wolves (Canis lupus arctos): the influence of competition for food, age and sex. PeerJ 4:e2707 https://doi.org/10.7717/peerj.2707
date submitted: 2016-07-11
date accepted: 2016-10-20
issued: 2016-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cafazzo
  given name: Simona
author list: Agent
  family name: Lazzaroni
  given name: Martina
author list: Agent
  family name: Marshall-Pescini
  given name: Sarah
doi: 10.7717/peerj.2707
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-22
copyright: ©2016 Cafazzo et al.
attribution name: Cafazzo et al.

Hypothesis on Serenoa repens (Bartram) small extract inhibition of prostatic 5α-reductase through an in silico approach on 5β-reductase x-ray structure
type: item
type: AcademicArticle
description: Benign prostatic hyperplasia is a common disease in men aged over 50 years old, with an incidence increasing to more than 80% over the age of 70, that is increasingly going to attract pharmaceutical interest. Within conventional therapies, such as α-adrenoreceptor antagonists and 5α-reductase inhibitor, there is a large requirement for treatments with less adverse events on, e.g., blood pressure and sexual function: phytotherapy may be the right way to fill this need. Serenoa repens standardized extract has been widely studied and its ability to reduce lower urinary tract symptoms related to benign prostatic hyperplasia is comprehensively described in literature. An innovative investigation on the mechanism of inhibition of 5α-reductase by Serenoa repens extract active principles is proposed in this work through computational methods, performing molecular docking simulations on the crystal structure of human liver 5β-reductase. The results confirm that both sterols and fatty acids can play a role in the inhibition of the enzyme, thus, suggesting a competitive mechanism of inhibition. This work proposes a further confirmation for the rational use of herbal products in the management of benign prostatic hyperplasia, and suggests computational methods as an innovative, low cost, and non-invasive process for the study of phytocomplex activity toward proteic targets.
format: application/pdf
format: text/html
creator: Paolo Governa
creator: Daniela Giachetti
creator: Marco Biagi
creator: Fabrizio Manetti
creator: Luca De Vico
subject: Computational Biology
subject: Pharmacology
description: doi:10.7717/peerj.2698
publisher: PeerJ Inc.
rights: © 2016 Governa et al.
abstract: Benign prostatic hyperplasia is a common disease in men aged over 50 years old, with an incidence increasing to more than 80% over the age of 70, that is increasingly going to attract pharmaceutical interest. Within conventional therapies, such as α-adrenoreceptor antagonists and 5α-reductase inhibitor, there is a large requirement for treatments with less adverse events on, e.g., blood pressure and sexual function: phytotherapy may be the right way to fill this need. Serenoa repens standardized extract has been widely studied and its ability to reduce lower urinary tract symptoms related to benign prostatic hyperplasia is comprehensively described in literature. An innovative investigation on the mechanism of inhibition of 5α-reductase by Serenoa repens extract active principles is proposed in this work through computational methods, performing molecular docking simulations on the crystal structure of human liver 5β-reductase. The results confirm that both sterols and fatty acids can play a role in the inhibition of the enzyme, thus, suggesting a competitive mechanism of inhibition. This work proposes a further confirmation for the rational use of herbal products in the management of benign prostatic hyperplasia, and suggests computational methods as an innovative, low cost, and non-invasive process for the study of phytocomplex activity toward proteic targets.
bibliographic citation: Governa et al. (2016) Hypothesis on Serenoa repens (Bartram) small extract inhibition of prostatic 5α-reductase through an in silico approach on 5β-reductase x-ray structure. PeerJ 4:e2698 https://doi.org/10.7717/peerj.2698
date submitted: 2016-04-29
date accepted: 2016-10-18
issued: 2016-11-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Governa
  given name: Paolo
author list: Agent
  family name: Giachetti
  given name: Daniela
author list: Agent
  family name: Biagi
  given name: Marco
author list: Agent
  family name: Manetti
  given name: Fabrizio
author list: Agent
  family name: De Vico
  given name: Luca
doi: 10.7717/peerj.2698
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-22
copyright: ©2016 Governa et al.
attribution name: Governa et al.

Detecting sedimentation impacts to coral reefs resulting from dredging the Port of Miami, Florida USA
type: item
type: AcademicArticle
description: The federal channel at Port of Miami, Florida, USA, was dredged between late 2013 and early 2015 to widen and deepen the channel. Due to the limited spatial extent of impact-assessment monitoring associated with the project, the extent of the dredging impacts on surrounding coral reefs has not been well quantified. Previously published remote sensing analyses, as well as agency and anecdotal reports suggest the most severe and largest area of sedimentation occurred on a coral reef feature referred to as the Inner Reef, particularly in the sector north of the channel. A confounding regional warm-water mass bleaching event followed by a coral disease outbreak during this same time frame made the assessment of dredging-related impacts to coral reefs adjacent to the federal channel difficult but still feasible. The current study sought to better understand the sedimentation impacts that occurred in the coral reef environment surrounding Port of Miami, to distinguish those impacts from other regional events or disturbances, and provide supplemental information on impact assessment that will inform discussions on compensatory mitigation requirements. To this end, in-water field assessments conducted after the completion of dredging and a time series analysis of tagged corals photographed pre-, during, and post-dredging, are used to discern dredging-related sedimentation impacts for the Inner Reef north. Results indicate increased sediment accumulation, severe in certain times and places, and an associated biological response (e.g., higher prevalence of partial mortality of corals) extended up to 700 m from the channel, whereas project-associated monitoring was limited to 50 m from the channel. These results can contribute to more realistic prediction of areas of indirect effect from dredging projects needed to accurately evaluate proposed projects and design appropriate compliance monitoring. Dredging projects near valuable and sensitive habitats subject to local and glob…
format: application/pdf
format: text/html
creator: Margaret W. Miller
creator: Jocelyn Karazsia
creator: Carolyn E. Groves
creator: Sean Griffin
creator: Tom Moore
creator: Pace Wilber
creator: Kurtis Gregg
subject: Biosphere Interactions
subject: Environmental Impacts
subject: Environmental Sciences
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.2711
publisher: PeerJ Inc.
rights: © 2016
abstract: The federal channel at Port of Miami, Florida, USA, was dredged between late 2013 and early 2015 to widen and deepen the channel. Due to the limited spatial extent of impact-assessment monitoring associated with the project, the extent of the dredging impacts on surrounding coral reefs has not been well quantified. Previously published remote sensing analyses, as well as agency and anecdotal reports suggest the most severe and largest area of sedimentation occurred on a coral reef feature referred to as the Inner Reef, particularly in the sector north of the channel. A confounding regional warm-water mass bleaching event followed by a coral disease outbreak during this same time frame made the assessment of dredging-related impacts to coral reefs adjacent to the federal channel difficult but still feasible. The current study sought to better understand the sedimentation impacts that occurred in the coral reef environment surrounding Port of Miami, to distinguish those impacts from other regional events or disturbances, and provide supplemental information on impact assessment that will inform discussions on compensatory mitigation requirements. To this end, in-water field assessments conducted after the completion of dredging and a time series analysis of tagged corals photographed pre-, during, and post-dredging, are used to discern dredging-related sedimentation impacts for the Inner Reef north. Results indicate increased sediment accumulation, severe in certain times and places, and an associated biological response (e.g., higher prevalence of partial mortality of corals) extended up to 700 m from the channel, whereas project-associated monitoring was limited to 50 m from the channel. These results can contribute to more realistic prediction of areas of indirect effect from dredging projects needed to accurately evaluate proposed projects and design appropriate compliance monitoring. Dredging projects near valuable and sensitive habitats subject to local and glob…
bibliographic citation: Miller et al. (2016) Detecting sedimentation impacts to coral reefs resulting from dredging the Port of Miami, Florida USA. PeerJ 4:e2711 https://doi.org/10.7717/peerj.2711
date submitted: 2016-06-21
date accepted: 2016-10-22
issued: 2016-11-17
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Miller
  given name: Margaret W.
author list: Agent
  family name: Karazsia
  given name: Jocelyn
author list: Agent
  family name: Groves
  given name: Carolyn E.
author list: Agent
  family name: Griffin
  given name: Sean
author list: Agent
  family name: Moore
  given name: Tom
author list: Agent
  family name: Wilber
  given name: Pace
author list: Agent
  family name: Gregg
  given name: Kurtis
doi: 10.7717/peerj.2711
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-17

Ficolin-2 inhibitors are present in sera after prolonged storage at −80 °C
type: item
type: AcademicArticle
description: Ficolins can activate the lectin pathway of the complement system that provides innate immune protection against pathogens, marks host cellular debris for clearance, and promotes inflammation. Baseline inflammation increases with aging in a phenomenon known as “inflammaging.” Although IL-6 and C-reactive protein are known to increase with age, contributions of many complement factors, including ficolins, to inflammaging have been little studied. Ficolin-2 is abundant in human serum and can recognize many target structures; therefore, ficolin-2 has potential to contribute to inflammaging. We hypothesized that inflammaging would alter ficolin-2 levels among older adults and examined 360 archived sera collected from older individuals. We found that these sera had apparently reduced ficolin-2 levels and that 84.2% of archived sera exhibited ficolin-2 inhibitors, which suppressed apparent amounts of ficolin-2 detected by enzyme-linked immunosorbent assay. Fresh serum samples were obtained from donors whose archived sera showed inhibitors, but the fresh sera did not have ficolin-2 inhibitors. Ficolin-2 inhibitors were present in other long-stored sera from younger persons. Furthermore, noninhibiting samples and fresh sera from older adults had apparently normal amounts of ficolin-2. Thus, ficolin-2 inhibitors may arise as an artifact of long-term storage of serum at −80 °C.
format: application/pdf
format: text/html
creator: Kimball Aaron Geno
creator: Richard E. Kennedy
creator: Patricia Sawyer
creator: Cynthia J. Brown
creator: Moon H. Nahm
subject: Immunology
subject: Translational Medicine
description: doi:10.7717/peerj.2705
publisher: PeerJ Inc.
rights: © 2016 Geno et al.
abstract: Ficolins can activate the lectin pathway of the complement system that provides innate immune protection against pathogens, marks host cellular debris for clearance, and promotes inflammation. Baseline inflammation increases with aging in a phenomenon known as “inflammaging.” Although IL-6 and C-reactive protein are known to increase with age, contributions of many complement factors, including ficolins, to inflammaging have been little studied. Ficolin-2 is abundant in human serum and can recognize many target structures; therefore, ficolin-2 has potential to contribute to inflammaging. We hypothesized that inflammaging would alter ficolin-2 levels among older adults and examined 360 archived sera collected from older individuals. We found that these sera had apparently reduced ficolin-2 levels and that 84.2% of archived sera exhibited ficolin-2 inhibitors, which suppressed apparent amounts of ficolin-2 detected by enzyme-linked immunosorbent assay. Fresh serum samples were obtained from donors whose archived sera showed inhibitors, but the fresh sera did not have ficolin-2 inhibitors. Ficolin-2 inhibitors were present in other long-stored sera from younger persons. Furthermore, noninhibiting samples and fresh sera from older adults had apparently normal amounts of ficolin-2. Thus, ficolin-2 inhibitors may arise as an artifact of long-term storage of serum at −80 °C.
bibliographic citation: Geno et al. (2016) Ficolin-2 inhibitors are present in sera after prolonged storage at −80 °C. PeerJ 4:e2705 https://doi.org/10.7717/peerj.2705
date submitted: 2016-07-08
date accepted: 2016-10-18
issued: 2016-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Geno
  given name: Kimball Aaron
author list: Agent
  family name: Kennedy
  given name: Richard E.
author list: Agent
  family name: Sawyer
  given name: Patricia
author list: Agent
  family name: Brown
  given name: Cynthia J.
author list: Agent
  family name: Nahm
  given name: Moon H.
doi: 10.7717/peerj.2705
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-17
copyright: ©2016 Geno et al.
attribution name: Geno et al.

Multiple, independent colonizations of the Hawaiian Archipelago by the family Dolichopodidae (Diptera)
type: item
type: AcademicArticle
description: The family Dolichopodidae forms two of the four largest evolutionary radiations in the Hawaiian Islands across all flies: Campsicnemus (183 spp) and the Eurynogaster complex (66 spp). They also include a small radiation of Conchopus (6 spp). A handful of other dolichopodid species are native to the islands in singleton lineages or small radiations. This study provides a phylogenetic perspective on the colonization history of the dolichopodid fauna in the islands. We generated a multi-gene data set including representatives from 11 of the 14 endemic Hawaiian dolichopodid genera to examine the history of colonization to the islands, and analyzed it using Bayesian and maximum likelihood phylogenetic methods. We used a subset of the data that included Conchopus and the eight genera comprising the Eurynogaster complex to estimate the first phylogenetic hypothesis for these endemic groups, then used Beast to estimate their age of arrival to the archipelago. The Eurynogaster complex, Campsicnemus and Conchopus are clearly the result of independent colonizations. The results strongly support the Eurynogaster complex as a monophyletic group, and also supports the monophyly of 4 of the 8 described genera within the complex (Adachia, Arciellia, Uropachys and Eurynogaster). Members of the family Dolichopodidae have been dispersing over vast distances to colonize the Hawaiian Archipelago for millions of years, leading to multiple independent evolutionary diversification events. The Eurynogaster complex arrived in the Hawaiian Archipelago 11.8 Ma, well before the arrival of Campsicnemus (4.5 Ma), and the even more recent Conchopus (1.8 Ma). Data presented here demonstrate that the Hawaiian Dolichopodidae both disperse and diversify easily, a rare combination that lays the groundwork for field studies on the reproductive isolating mechanisms and ecological partitioning of this group.
format: application/pdf
format: text/html
creator: Kari Roesch Goodman
creator: Neal Evenhuis
creator: Pavla Bartošová-Sojková
creator: Patrick Michael O’Grady
subject: Entomology
subject: Evolutionary Studies
description: doi:10.7717/peerj.2704
publisher: PeerJ Inc.
rights: © 2016 Goodman et al.
abstract: The family Dolichopodidae forms two of the four largest evolutionary radiations in the Hawaiian Islands across all flies: Campsicnemus (183 spp) and the Eurynogaster complex (66 spp). They also include a small radiation of Conchopus (6 spp). A handful of other dolichopodid species are native to the islands in singleton lineages or small radiations. This study provides a phylogenetic perspective on the colonization history of the dolichopodid fauna in the islands. We generated a multi-gene data set including representatives from 11 of the 14 endemic Hawaiian dolichopodid genera to examine the history of colonization to the islands, and analyzed it using Bayesian and maximum likelihood phylogenetic methods. We used a subset of the data that included Conchopus and the eight genera comprising the Eurynogaster complex to estimate the first phylogenetic hypothesis for these endemic groups, then used Beast to estimate their age of arrival to the archipelago. The Eurynogaster complex, Campsicnemus and Conchopus are clearly the result of independent colonizations. The results strongly support the Eurynogaster complex as a monophyletic group, and also supports the monophyly of 4 of the 8 described genera within the complex (Adachia, Arciellia, Uropachys and Eurynogaster). Members of the family Dolichopodidae have been dispersing over vast distances to colonize the Hawaiian Archipelago for millions of years, leading to multiple independent evolutionary diversification events. The Eurynogaster complex arrived in the Hawaiian Archipelago 11.8 Ma, well before the arrival of Campsicnemus (4.5 Ma), and the even more recent Conchopus (1.8 Ma). Data presented here demonstrate that the Hawaiian Dolichopodidae both disperse and diversify easily, a rare combination that lays the groundwork for field studies on the reproductive isolating mechanisms and ecological partitioning of this group.
bibliographic citation: Goodman et al. (2016) Multiple, independent colonizations of the Hawaiian Archipelago by the family Dolichopodidae (Diptera). PeerJ 4:e2704 https://doi.org/10.7717/peerj.2704
date submitted: 2016-07-15
date accepted: 2016-10-19
issued: 2016-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Goodman
  given name: Kari Roesch
author list: Agent
  family name: Evenhuis
  given name: Neal
author list: Agent
  family name: Bartošová-Sojková
  given name: Pavla
author list: Agent
  family name: O’Grady
  given name: Patrick Michael
doi: 10.7717/peerj.2704
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-17
copyright: ©2016 Goodman et al.
attribution name: Goodman et al.

Salinity modulates thermotolerance, energy metabolism and stress response in amphipods Gammarus lacustris
type: item
type: AcademicArticle
description: Temperature and salinity are important abiotic factors for aquatic invertebrates. We investigated the influence of different salinity regimes on thermotolerance, energy metabolism and cellular stress defense mechanisms in amphipods Gammarus lacustris Sars from two populations. We exposed amphipods to different thermal scenarios and determined their survival as well as activity of major antioxidant enzymes (peroxidase, catalase, glutathione S-transferase) and parameters of energy metabolism (content of glucose, glycogen, ATP, ADP, AMP and lactate). Amphipods from a freshwater population were more sensitive to the thermal challenge, showing higher mortality during acute and gradual temperature change compared to their counterparts from a saline lake. A more thermotolerant population from a saline lake had high activity of antioxidant enzymes. The energy limitations of the freshwater population (indicated by low baseline glucose levels, downward shift of the critical temperature of aerobic metabolism and inability to maintain steady-state ATP levels during warming) was observed, possibly reflecting a trade-off between the energy demands for osmoregulation under the hypo-osmotic condition of a freshwater environment and protection against temperature stress.
format: application/pdf
format: text/html
creator: Kseniya P. Vereshchagina
creator: Yulia A. Lubyaga
creator: Zhanna Shatilina
creator: Daria Bedulina
creator: Anton Gurkov
creator: Denis V. Axenov-Gribanov
creator: Boris Baduev
creator: Elizaveta S. Kondrateva
creator: Mikhail Gubanov
creator: Egor Zadereev
creator: Inna Sokolova
creator: Maxim Timofeyev
subject: Biochemistry
subject: Biological Oceanography
subject: Ecology
subject: Environmental Sciences
description: doi:10.7717/peerj.2657
publisher: PeerJ Inc.
rights: © 2016 Vereshchagina et al.
abstract: Temperature and salinity are important abiotic factors for aquatic invertebrates. We investigated the influence of different salinity regimes on thermotolerance, energy metabolism and cellular stress defense mechanisms in amphipods Gammarus lacustris Sars from two populations. We exposed amphipods to different thermal scenarios and determined their survival as well as activity of major antioxidant enzymes (peroxidase, catalase, glutathione S-transferase) and parameters of energy metabolism (content of glucose, glycogen, ATP, ADP, AMP and lactate). Amphipods from a freshwater population were more sensitive to the thermal challenge, showing higher mortality during acute and gradual temperature change compared to their counterparts from a saline lake. A more thermotolerant population from a saline lake had high activity of antioxidant enzymes. The energy limitations of the freshwater population (indicated by low baseline glucose levels, downward shift of the critical temperature of aerobic metabolism and inability to maintain steady-state ATP levels during warming) was observed, possibly reflecting a trade-off between the energy demands for osmoregulation under the hypo-osmotic condition of a freshwater environment and protection against temperature stress.
bibliographic citation: Vereshchagina et al. (2016) Salinity modulates thermotolerance, energy metabolism and stress response in amphipods Gammarus lacustris. PeerJ 4:e2657 https://doi.org/10.7717/peerj.2657
date submitted: 2016-07-26
date accepted: 2016-10-05
issued: 2016-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vereshchagina
  given name: Kseniya P.
author list: Agent
  family name: Lubyaga
  given name: Yulia A.
author list: Agent
  family name: Shatilina
  given name: Zhanna
author list: Agent
  family name: Bedulina
  given name: Daria
author list: Agent
  family name: Gurkov
  given name: Anton
author list: Agent
  family name: Axenov-Gribanov
  given name: Denis V.
author list: Agent
  family name: Baduev
  given name: Boris
author list: Agent
  family name: Kondrateva
  given name: Elizaveta S.
author list: Agent
  family name: Gubanov
  given name: Mikhail
author list: Agent
  family name: Zadereev
  given name: Egor
author list: Agent
  family name: Sokolova
  given name: Inna
author list: Agent
  family name: Timofeyev
  given name: Maxim
doi: 10.7717/peerj.2657
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-17
copyright: ©2016 Vereshchagina et al.
attribution name: Vereshchagina et al.

Ceratopogonidae (Diptera: Nematocera) of the piedmont of the Yungas forests of Tucumán: ecology and distribution
type: item
type: AcademicArticle
description: Within the Ceratopogonidae family, many genera transmit numerous diseases to humans and animals, while others are important pollinators of tropical crops. In the Yungas ecoregion of Argentina, previous systematic and ecological research on Ceratopogonidae focused on Culicoides, since they are the main transmitters of mansonelliasis in northwestern Argentina; however, few studies included the genera Forcipomyia, Dasyhelea, Atrichopogon, Alluaudomyia, Echinohelea, and Bezzia. Therefore, the objective of this study was to determine the presence and abundance of Ceratopogonidae in this region, their association with meteorological variables, and their variation in areas disturbed by human activity. Monthly collection of specimens was performed from July 2008 to July 2009 using CDC miniature light traps deployed for two consecutive days. A total of 360 specimens were collected, being the most abundant Dasyhelea genus (48.06%) followed by Forcipomyia (26.94%) and Atrichopogon (13.61%). Bivariate analyses showed significant differences in the abundance of the genera at different sampling sites and climatic conditions, with the summer season and El Corralito site showing the greatest abundance of specimens. Accumulated rainfall was the variable that related the most to the abundance of Culicoides (10.56%), while temperature was the most closely related variable to the abundance of Forcipomyia, Dasyhelea, and Atrichopogon.
format: application/pdf
format: text/html
creator: José Manuel Direni Mancini
creator: Cecilia Adriana Veggiani-Aybar
creator: Ana Denise Fuenzalida
creator: Mercedes Sara Lizarralde de Grosso
creator: María Gabriela Quintana
subject: Ecology
subject: Entomology
subject: Epidemiology
description: doi:10.7717/peerj.2655
publisher: PeerJ Inc.
rights: © 2016 Direni Mancini et al.
abstract: Within the Ceratopogonidae family, many genera transmit numerous diseases to humans and animals, while others are important pollinators of tropical crops. In the Yungas ecoregion of Argentina, previous systematic and ecological research on Ceratopogonidae focused on Culicoides, since they are the main transmitters of mansonelliasis in northwestern Argentina; however, few studies included the genera Forcipomyia, Dasyhelea, Atrichopogon, Alluaudomyia, Echinohelea, and Bezzia. Therefore, the objective of this study was to determine the presence and abundance of Ceratopogonidae in this region, their association with meteorological variables, and their variation in areas disturbed by human activity. Monthly collection of specimens was performed from July 2008 to July 2009 using CDC miniature light traps deployed for two consecutive days. A total of 360 specimens were collected, being the most abundant Dasyhelea genus (48.06%) followed by Forcipomyia (26.94%) and Atrichopogon (13.61%). Bivariate analyses showed significant differences in the abundance of the genera at different sampling sites and climatic conditions, with the summer season and El Corralito site showing the greatest abundance of specimens. Accumulated rainfall was the variable that related the most to the abundance of Culicoides (10.56%), while temperature was the most closely related variable to the abundance of Forcipomyia, Dasyhelea, and Atrichopogon.
bibliographic citation: Direni Mancini et al. (2016) Ceratopogonidae (Diptera: Nematocera) of the piedmont of the Yungas forests of Tucumán: ecology and distribution. PeerJ 4:e2655 https://doi.org/10.7717/peerj.2655
date submitted: 2016-07-15
date accepted: 2016-10-04
issued: 2016-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Direni Mancini
  given name: José Manuel
author list: Agent
  family name: Veggiani-Aybar
  given name: Cecilia Adriana
author list: Agent
  family name: Fuenzalida
  given name: Ana Denise
author list: Agent
  family name: Lizarralde de Grosso
  given name: Mercedes Sara
author list: Agent
  family name: Quintana
  given name: María Gabriela
doi: 10.7717/peerj.2655
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-17
copyright: © 2016 Direni Mancini et al.
attribution name: Direni Mancini et al.

PDIA3 gene induces visceral hypersensitivity in rats with irritable bowel syndrome through the dendritic cell-mediated activation of T cells
type: item
type: AcademicArticle
description: This study investigated the mechanism of protein disulfide-isomerase A3 (PDIA3)-induced visceral hypersensitivity in irritable bowel syndrome (IBS). Rats were treated with saline (control), acetic acid and restraint stress (IBS model), empty vector (RNAi control) and PDIA3-RNAi vector (PDIA3-RNAi). Mesenteric lymph node DCs (MLNDCs) and splenic CD4+/CD8+ T cells were isolated for co-cultivation. Compared with control, MLNDCs co-cultured with CD4+ or CD8+ T cells showed an increased ability to promote T cell proliferation and produced more IL-4 or IL-9 secretion. Compared with the RNAi control, MLNDCs from the PDIA3 knockdown models were less effective in promoting the proliferation of CD4+/CD8+ T cells. It is concluded that PDIA3 plays an important role in the development of IBS through the DC-mediated activation of T cells, resulting in degranulation of MCs and visceral hypersensitivity.
format: application/pdf
format: text/html
creator: Zhaomeng Zhuang
creator: Lu Zhang
creator: Xiaoteng Wang
creator: Liyuan Tao
creator: Bin Lv
subject: Allergy and Clinical Immunology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.2644
publisher: PeerJ Inc.
rights: © 2016 Zhuang et al.
abstract: This study investigated the mechanism of protein disulfide-isomerase A3 (PDIA3)-induced visceral hypersensitivity in irritable bowel syndrome (IBS). Rats were treated with saline (control), acetic acid and restraint stress (IBS model), empty vector (RNAi control) and PDIA3-RNAi vector (PDIA3-RNAi). Mesenteric lymph node DCs (MLNDCs) and splenic CD4+/CD8+ T cells were isolated for co-cultivation. Compared with control, MLNDCs co-cultured with CD4+ or CD8+ T cells showed an increased ability to promote T cell proliferation and produced more IL-4 or IL-9 secretion. Compared with the RNAi control, MLNDCs from the PDIA3 knockdown models were less effective in promoting the proliferation of CD4+/CD8+ T cells. It is concluded that PDIA3 plays an important role in the development of IBS through the DC-mediated activation of T cells, resulting in degranulation of MCs and visceral hypersensitivity.
bibliographic citation: Zhuang et al. (2016) PDIA3 gene induces visceral hypersensitivity in rats with irritable bowel syndrome through the dendritic cell-mediated activation of T cells. PeerJ 4:e2644 https://doi.org/10.7717/peerj.2644
date submitted: 2016-04-23
date accepted: 2016-10-02
issued: 2016-11-17
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhuang
  given name: Zhaomeng
author list: Agent
  family name: Zhang
  given name: Lu
author list: Agent
  family name: Wang
  given name: Xiaoteng
author list: Agent
  family name: Tao
  given name: Liyuan
author list: Agent
  family name: Lv
  given name: Bin
doi: 10.7717/peerj.2644
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-17
copyright: ©2016 Zhuang et al.
attribution name: Zhuang et al.

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