PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion
items: Antimicrobial consumption on Austrian dairy farms: an observational study of udder disease treatments based on veterinary medication records
items: HRV-derived data similarity and distribution index based on ensemble neural network for measuring depth of anaesthesia
items: Increased risk of periodontitis in patients with psoriatic disease: a nationwide population-based retrospective cohort study
items: Adult zebra finches rehearse highly variable song patterns during sleep
items: Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans”
items: 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro
items: Sediment tolerance mechanisms identified in sponges using advanced imaging techniques
items: Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts
items: Lowland extirpation of anuran populations on a tropical mountain

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion
type: item
type: AcademicArticle
description: The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attributable to dietary specialization. Several populations discriminated between the koala and wombat fecal communities, most notably S24-7 and Synergistaceae in the koala, and Christensenellaceae and RF39 in the wombat. As expected for herbivores, both communities contained the genes necessary for lignocellulose degradation and urea recycling partitioned and redundantly encoded across multiple populations. Secondary metabolism was overrepresented in the koala fecal samples, consistent with the need to process Eucalyptus secondary metabolites. The Synergistaceae population encodes multiple pathways potentially relevant to Eucalyptus compound metabolism, and is predicted to be a key player in detoxification of the koala’s diet. Notably, characterized microbial isolates from the koala gut appear to be minor constituents of this habitat, and the metagenomes provide the opportunity for genome-directed isolation of more representative populations. Metagenomic analysis of other obligate and facultative Eucalyptus folivores will reveal whether putatively detoxifying bacteria identified in the koala are shared across these marsupials.
format: application/pdf
format: text/html
creator: Miriam E. Shiffman
creator: Rochelle M. Soo
creator: Paul G. Dennis
creator: Mark Morrison
creator: Gene W. Tyson
creator: Philip Hugenholtz
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.4075
publisher: PeerJ Inc.
rights: © 2017 Shiffman et al.
abstract: The koala has evolved to become a specialist Eucalyptus herbivore since diverging from its closest relative, the wombat, a generalist herbivore. This niche adaptation involves, in part, changes in the gut microbiota. The goal of this study was to compare koala and wombat fecal microbiomes using metagenomics to identify potential differences attributable to dietary specialization. Several populations discriminated between the koala and wombat fecal communities, most notably S24-7 and Synergistaceae in the koala, and Christensenellaceae and RF39 in the wombat. As expected for herbivores, both communities contained the genes necessary for lignocellulose degradation and urea recycling partitioned and redundantly encoded across multiple populations. Secondary metabolism was overrepresented in the koala fecal samples, consistent with the need to process Eucalyptus secondary metabolites. The Synergistaceae population encodes multiple pathways potentially relevant to Eucalyptus compound metabolism, and is predicted to be a key player in detoxification of the koala’s diet. Notably, characterized microbial isolates from the koala gut appear to be minor constituents of this habitat, and the metagenomes provide the opportunity for genome-directed isolation of more representative populations. Metagenomic analysis of other obligate and facultative Eucalyptus folivores will reveal whether putatively detoxifying bacteria identified in the koala are shared across these marsupials.
bibliographic citation: Shiffman et al. (2017) Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ 5:e4075 https://doi.org/10.7717/peerj.4075
date submitted: 2017-07-31
date accepted: 2017-10-31
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shiffman
  given name: Miriam E.
author list: Agent
  family name: Soo
  given name: Rochelle M.
author list: Agent
  family name: Dennis
  given name: Paul G.
author list: Agent
  family name: Morrison
  given name: Mark
author list: Agent
  family name: Tyson
  given name: Gene W.
author list: Agent
  family name: Hugenholtz
  given name: Philip
doi: 10.7717/peerj.4075
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Shiffman et al.
attribution name: Shiffman et al.

Antimicrobial consumption on Austrian dairy farms: an observational study of udder disease treatments based on veterinary medication records
type: item
type: AcademicArticle
description: Background Antimicrobial use in livestock production is an important contemporary issue, which is of public interest worldwide. Antimicrobials are not freely available to Austrian farmers and can only be administered to livestock by veterinarians, or by farmers who are trained members of the Animal Health Service. Since 2015, veterinarians have been required by law to report antimicrobials dispensed to farmers for use in food-producing animals. The study presented here went further than the statutory framework, and collected data on antimicrobials dispensed to farmers and those administered by veterinarians. Methods Seventeen veterinary practices were enrolled in the study via convenience sampling. These veterinarians were asked to contact interested dairy farmers regarding participation in the study (respondent-driven sampling). Data were collected from veterinary practice software between 1st October 2015 and 30th September 2016. Electronic data (89.4%) were transferred via an online interface and paper records (10.6%) were entered by the authors. Antimicrobial treatments with respect to udder disease were analysed by number of defined daily doses per cow and year (nDDDvet/cow/year), based on the European Medicines Agency technical unit, Defined Daily Dose for animals (DDDvet). Descriptive statistics and the Wilcoxon rank sum test were used to analyse the results. Results Antimicrobial use data from a total of 248 dairy farms were collected during the study, 232 of these farms treated cows with antibiotics; dry cow therapy was excluded from the current analysis. The mean number of DDDvet/cow/year for the antimicrobial treatment of all udder disease was 1.33 DDDvet/cow/year. Of these treatments, 0.73 DDDvet/cow/year were classed as highest priority critically important antimicrobials (HPCIAs), according to the World Health Organization (WHO) definition. The Wilcoxon rank sum test determined a statistically significant difference between the median number of DDDvet/…
format: application/pdf
format: text/html
creator: Clair L. Firth
creator: Annemarie Käsbohrer
creator: Corina Schleicher
creator: Klemens Fuchs
creator: Christa Egger-Danner
creator: Martin Mayerhofer
creator: Hermann Schobesberger
creator: Josef Köfer
creator: Walter Obritzhauser
subject: Agricultural Science
subject: Veterinary Medicine
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.4072
publisher: PeerJ Inc.
rights: © 2017 Firth et al.
abstract: Background Antimicrobial use in livestock production is an important contemporary issue, which is of public interest worldwide. Antimicrobials are not freely available to Austrian farmers and can only be administered to livestock by veterinarians, or by farmers who are trained members of the Animal Health Service. Since 2015, veterinarians have been required by law to report antimicrobials dispensed to farmers for use in food-producing animals. The study presented here went further than the statutory framework, and collected data on antimicrobials dispensed to farmers and those administered by veterinarians. Methods Seventeen veterinary practices were enrolled in the study via convenience sampling. These veterinarians were asked to contact interested dairy farmers regarding participation in the study (respondent-driven sampling). Data were collected from veterinary practice software between 1st October 2015 and 30th September 2016. Electronic data (89.4%) were transferred via an online interface and paper records (10.6%) were entered by the authors. Antimicrobial treatments with respect to udder disease were analysed by number of defined daily doses per cow and year (nDDDvet/cow/year), based on the European Medicines Agency technical unit, Defined Daily Dose for animals (DDDvet). Descriptive statistics and the Wilcoxon rank sum test were used to analyse the results. Results Antimicrobial use data from a total of 248 dairy farms were collected during the study, 232 of these farms treated cows with antibiotics; dry cow therapy was excluded from the current analysis. The mean number of DDDvet/cow/year for the antimicrobial treatment of all udder disease was 1.33 DDDvet/cow/year. Of these treatments, 0.73 DDDvet/cow/year were classed as highest priority critically important antimicrobials (HPCIAs), according to the World Health Organization (WHO) definition. The Wilcoxon rank sum test determined a statistically significant difference between the median number of DDDvet/…
bibliographic citation: Firth et al. (2017) Antimicrobial consumption on Austrian dairy farms: an observational study of udder disease treatments based on veterinary medication records. PeerJ 5:e4072 https://doi.org/10.7717/peerj.4072
date submitted: 2017-08-29
date accepted: 2017-10-30
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Firth
  given name: Clair L.
author list: Agent
  family name: Käsbohrer
  given name: Annemarie
author list: Agent
  family name: Schleicher
  given name: Corina
author list: Agent
  family name: Fuchs
  given name: Klemens
author list: Agent
  family name: Egger-Danner
  given name: Christa
author list: Agent
  family name: Mayerhofer
  given name: Martin
author list: Agent
  family name: Schobesberger
  given name: Hermann
author list: Agent
  family name: Köfer
  given name: Josef
author list: Agent
  family name: Obritzhauser
  given name: Walter
doi: 10.7717/peerj.4072
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Firth et al.
attribution name: Firth et al.

HRV-derived data similarity and distribution index based on ensemble neural network for measuring depth of anaesthesia
type: item
type: AcademicArticle
description: Evaluation of depth of anaesthesia (DoA) is critical in clinical surgery. Indices derived from electroencephalogram (EEG) are currently widely used to quantify DoA. However, there are known to be inaccurate under certain conditions; therefore, experienced anaesthesiologists rely on the monitoring of vital signs such as body temperature, pulse rate, respiration rate, and blood pressure to control the procedure. Because of the lack of an ideal approach for quantifying level of consciousness, studies have been conducted to develop improved methods of measuring DoA. In this study, a short-term index known as the similarity and distribution index (SDI) is proposed. The SDI is generated using heart rate variability (HRV) in the time domain and is based on observations of data distribution differences between two consecutive 32 s HRV data segments. A comparison between SDI results and expert assessments of consciousness level revealed that the SDI has strong correlation with anaesthetic depth. To optimise the effect, artificial neural network (ANN) models were constructed to fit the SDI, and ANN blind cross-validation was conducted to overcome random errors and overfitting problems. An ensemble ANN was then employed and was discovered to provide favourable DoA assessment in comparison with commonly used Bispectral Index. This study demonstrated the effectiveness of this method of DoA assessment, and the results imply that it is feasible and meaningful to use the SDI to measure DoA with the additional use of other measurement methods, if appropriate.
format: application/pdf
format: text/html
creator: Quan Liu
creator: Li Ma
creator: Ren-Chun Chiu
creator: Shou-Zen Fan
creator: Maysam F. Abbod
creator: Jiann-Shing Shieh
subject: Anesthesiology and Pain Management
subject: Computational Science
subject: Statistics
description: doi:10.7717/peerj.4067
publisher: PeerJ Inc.
rights: © 2017 Liu et al.
abstract: Evaluation of depth of anaesthesia (DoA) is critical in clinical surgery. Indices derived from electroencephalogram (EEG) are currently widely used to quantify DoA. However, there are known to be inaccurate under certain conditions; therefore, experienced anaesthesiologists rely on the monitoring of vital signs such as body temperature, pulse rate, respiration rate, and blood pressure to control the procedure. Because of the lack of an ideal approach for quantifying level of consciousness, studies have been conducted to develop improved methods of measuring DoA. In this study, a short-term index known as the similarity and distribution index (SDI) is proposed. The SDI is generated using heart rate variability (HRV) in the time domain and is based on observations of data distribution differences between two consecutive 32 s HRV data segments. A comparison between SDI results and expert assessments of consciousness level revealed that the SDI has strong correlation with anaesthetic depth. To optimise the effect, artificial neural network (ANN) models were constructed to fit the SDI, and ANN blind cross-validation was conducted to overcome random errors and overfitting problems. An ensemble ANN was then employed and was discovered to provide favourable DoA assessment in comparison with commonly used Bispectral Index. This study demonstrated the effectiveness of this method of DoA assessment, and the results imply that it is feasible and meaningful to use the SDI to measure DoA with the additional use of other measurement methods, if appropriate.
bibliographic citation: Liu et al. (2017) HRV-derived data similarity and distribution index based on ensemble neural network for measuring depth of anaesthesia. PeerJ 5:e4067 https://doi.org/10.7717/peerj.4067
date submitted: 2017-07-31
date accepted: 2017-10-29
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Quan
author list: Agent
  family name: Ma
  given name: Li
author list: Agent
  family name: Chiu
  given name: Ren-Chun
author list: Agent
  family name: Fan
  given name: Shou-Zen
author list: Agent
  family name: Abbod
  given name: Maysam F.
author list: Agent
  family name: Shieh
  given name: Jiann-Shing
doi: 10.7717/peerj.4067
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Liu et al.
attribution name: Liu et al.

Increased risk of periodontitis in patients with psoriatic disease: a nationwide population-based retrospective cohort study
type: item
type: AcademicArticle
description: Aims Periodontitis and psoriatic disease, including psoriasis (PS) and psoriatic arthritis (PsA), share the common risk factors and co-morbidities. However, the risk of periodontitis in patients with psoriatic disease still needs further investigation. This study was a nationwide population-based retrospective cohort study assessing the risk of periodontitis from psoriatic disease exposure. Materials and Methods Patients with newly diagnosed psoriatic disease from 2003 to 2012 were identified from the Taiwanese National Health Insurance Research Database. The 1:4 ratio propensity score matched controls were selected from no psoriatic disease participations. The subsequent risk of periodontitis was evaluated in exposure and comparison groups. Multiple Cox proportional hazard models were used for the estimation. Results A total of 3,487 psoriatic disease patients and 13,948 controls were identified. Incidence rate of periodontitis was higher in patients with PsA. The adjusted hazard ratio (aHRs) for moderate/severe periodontitis were 0.85 (95% CI [0.65–1.11]) in PS group and 1.66 (95% CI [0.99–2.78]) in PsA group. The aHRs of PsA were increased over time, aHRs was changed from 0.65 (0–11 months from index date) to 1.34 (≥12 months from index date) in all types of periodontitis and from 1.09 to 1.79 in moderate/severe periodontitis group, respectively. Conclusions The increased risk of periodontitis was observed, especially the association between PsA and moderate/severe periodontitis. The patients with psoriatic disease should receive regular periodontal evaluation.
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format: text/html
creator: Ni-Yu Su
creator: Jing-Yang Huang
creator: Chien-Jen Hu
creator: Hui-Chieh Yu
creator: Yu-Chao Chang
subject: Dentistry
subject: Dermatology
subject: Epidemiology
subject: Public Health
subject: Rheumatology
description: doi:10.7717/peerj.4064
publisher: PeerJ Inc.
rights: © 2017 Su et al.
abstract: Aims Periodontitis and psoriatic disease, including psoriasis (PS) and psoriatic arthritis (PsA), share the common risk factors and co-morbidities. However, the risk of periodontitis in patients with psoriatic disease still needs further investigation. This study was a nationwide population-based retrospective cohort study assessing the risk of periodontitis from psoriatic disease exposure. Materials and Methods Patients with newly diagnosed psoriatic disease from 2003 to 2012 were identified from the Taiwanese National Health Insurance Research Database. The 1:4 ratio propensity score matched controls were selected from no psoriatic disease participations. The subsequent risk of periodontitis was evaluated in exposure and comparison groups. Multiple Cox proportional hazard models were used for the estimation. Results A total of 3,487 psoriatic disease patients and 13,948 controls were identified. Incidence rate of periodontitis was higher in patients with PsA. The adjusted hazard ratio (aHRs) for moderate/severe periodontitis were 0.85 (95% CI [0.65–1.11]) in PS group and 1.66 (95% CI [0.99–2.78]) in PsA group. The aHRs of PsA were increased over time, aHRs was changed from 0.65 (0–11 months from index date) to 1.34 (≥12 months from index date) in all types of periodontitis and from 1.09 to 1.79 in moderate/severe periodontitis group, respectively. Conclusions The increased risk of periodontitis was observed, especially the association between PsA and moderate/severe periodontitis. The patients with psoriatic disease should receive regular periodontal evaluation.
bibliographic citation: Su et al. (2017) Increased risk of periodontitis in patients with psoriatic disease: a nationwide population-based retrospective cohort study. PeerJ 5:e4064 https://doi.org/10.7717/peerj.4064
date submitted: 2017-08-24
date accepted: 2017-10-29
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Ni-Yu
author list: Agent
  family name: Huang
  given name: Jing-Yang
author list: Agent
  family name: Hu
  given name: Chien-Jen
author list: Agent
  family name: Yu
  given name: Hui-Chieh
author list: Agent
  family name: Chang
  given name: Yu-Chao
doi: 10.7717/peerj.4064
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Su et al.
attribution name: Su et al.

Adult zebra finches rehearse highly variable song patterns during sleep
type: item
type: AcademicArticle
description: Brain activity during sleep is fairly ubiquitous and the best studied possible function is a role in memory consolidation, including motor memory. One suggested mechanism of how neural activity effects these benefits is through reactivation of neurons in patterns resembling those of the preceding experience. The specific patterns of motor activation replayed during sleep are largely unknown for any system. Brain areas devoted to song production in the songbird brain exhibit spontaneous song-like activity during sleep, but single cell neural recordings did not permit detection of the specific song patterns. We have now discovered that this sleep activation can be detected in the muscles of the vocal organ, thus providing a unique window into song-related brain activity at night. We show that male zebra finches (Taeniopygia guttata) frequently exhibit spontaneous song-like activity during the night, but that the fictive song patterns are highly variable and uncoordinated compared to the highly stereotyped day-time song production. This substantial variability is not consistent with the idea that night-time activity replays day-time experiences for consolidation. Although the function of this frequent activation is unknown, it may represent a mechanism for exploring motor space or serve to generate internal error signals that help maintain the high stereotypy of day-time song. In any case, the described activity supports the emerging insight that brain activity during sleep may serve a variety of functions.
format: application/pdf
format: text/html
creator: Brent K. Young
creator: Gabriel B. Mindlin
creator: Ezequiel Arneodo
creator: Franz Goller
subject: Animal Behavior
subject: Neuroscience
subject: Computational Science
description: doi:10.7717/peerj.4052
publisher: PeerJ Inc.
rights: © 2017 Young et al.
abstract: Brain activity during sleep is fairly ubiquitous and the best studied possible function is a role in memory consolidation, including motor memory. One suggested mechanism of how neural activity effects these benefits is through reactivation of neurons in patterns resembling those of the preceding experience. The specific patterns of motor activation replayed during sleep are largely unknown for any system. Brain areas devoted to song production in the songbird brain exhibit spontaneous song-like activity during sleep, but single cell neural recordings did not permit detection of the specific song patterns. We have now discovered that this sleep activation can be detected in the muscles of the vocal organ, thus providing a unique window into song-related brain activity at night. We show that male zebra finches (Taeniopygia guttata) frequently exhibit spontaneous song-like activity during the night, but that the fictive song patterns are highly variable and uncoordinated compared to the highly stereotyped day-time song production. This substantial variability is not consistent with the idea that night-time activity replays day-time experiences for consolidation. Although the function of this frequent activation is unknown, it may represent a mechanism for exploring motor space or serve to generate internal error signals that help maintain the high stereotypy of day-time song. In any case, the described activity supports the emerging insight that brain activity during sleep may serve a variety of functions.
bibliographic citation: Young et al. (2017) Adult zebra finches rehearse highly variable song patterns during sleep. PeerJ 5:e4052 https://doi.org/10.7717/peerj.4052
date submitted: 2017-09-15
date accepted: 2017-10-27
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Young
  given name: Brent K.
author list: Agent
  family name: Mindlin
  given name: Gabriel B.
author list: Agent
  family name: Arneodo
  given name: Ezequiel
author list: Agent
  family name: Goller
  given name: Franz
doi: 10.7717/peerj.4052
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Young et al.
attribution name: Young et al.

Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans”
type: item
type: AcademicArticle
description: Hörnig, Haug & Haug (2017) published a description of a new specimen of Santanmantis axelrodi MB.I.2068, an extinct species of praying mantis from the Crato Formation of Brazil. According to Hörnig, Haug & Haug (2017), the discovery of this new specimen brought with it implications for praying mantis character evolution and predatory behavior; it is with these lines of reasoning that we find fault. More specifically, we point to four flawed assumptions in their study that led to their unsubstantiated conclusion that S. axelrodi employed their mesothoracic legs in prey capture.
format: application/pdf
format: text/html
creator: Sydney K. Brannoch
creator: Gavin J. Svenson
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.4046
publisher: PeerJ Inc.
rights: © 2017 Brannoch and Svenson
abstract: Hörnig, Haug & Haug (2017) published a description of a new specimen of Santanmantis axelrodi MB.I.2068, an extinct species of praying mantis from the Crato Formation of Brazil. According to Hörnig, Haug & Haug (2017), the discovery of this new specimen brought with it implications for praying mantis character evolution and predatory behavior; it is with these lines of reasoning that we find fault. More specifically, we point to four flawed assumptions in their study that led to their unsubstantiated conclusion that S. axelrodi employed their mesothoracic legs in prey capture.
bibliographic citation: Brannoch et al. (2017) Response to “An exceptionally preserved 110 million years old praying mantis provides new insights into the predatory behaviour of early mantodeans”. PeerJ 5:e4046 https://doi.org/10.7717/peerj.4046
date submitted: 2017-08-21
date accepted: 2017-10-25
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brannoch
  given name: Sydney K.
author list: Agent
  family name: Svenson
  given name: Gavin J.
doi: 10.7717/peerj.4046
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Brannoch and Svenson
attribution name: Brannoch and Svenson

5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro
type: item
type: AcademicArticle
description: Gastrointestinal mucositis is a debilitating side effect of chemotherapy treatment, with currently no treatment available. As changes in microbial composition have been reported upon chemotherapy treatment in vivo, it is thought that gut microbiota dysbiosis contribute to the mucositis etiology. Yet it is not known whether chemotherapeutics directly cause microbial dysbiosis, thereby increasing mucositis risk, or whether the chemotherapeutic subjected host environment disturbs the microbiome thereby aggravating the disease. To address this question, we used the M-SHIME®, an in vitro mucosal simulator of the human intestinal microbial ecosystem, as an experimental setup that excludes the host factor. The direct impact of two chemotherapeutics, 5-fluorouracil (5-FU) and SN-38 (active metabolite of irinotecan), on the luminal and mucosal gut microbiota from several human donors was investigated through monitoring fermentation activity and next generation sequencing. At a dose of 10 µM in the mucosal environment, 5-FU impacted the functionality and composition of the colon microbiota to a minor extent. Similarly, a daily dose of 10 µM SN-38 in the luminal environment did not cause significant changes in the functionality or microbiome composition. As our mucosal model does not include a host-compartment, our findings strongly indicate that a putative microbial contribution to mucositis is initially triggered by an altered host environment upon chemotherapy.
format: application/pdf
format: text/html
creator: Eline Vanlancker
creator: Barbara Vanhoecke
creator: Andrea Stringer
creator: Tom Van de Wiele
subject: Microbiology
subject: Oncology
description: doi:10.7717/peerj.4017
publisher: PeerJ Inc.
rights: © 2017 Vanlancker et al.
abstract: Gastrointestinal mucositis is a debilitating side effect of chemotherapy treatment, with currently no treatment available. As changes in microbial composition have been reported upon chemotherapy treatment in vivo, it is thought that gut microbiota dysbiosis contribute to the mucositis etiology. Yet it is not known whether chemotherapeutics directly cause microbial dysbiosis, thereby increasing mucositis risk, or whether the chemotherapeutic subjected host environment disturbs the microbiome thereby aggravating the disease. To address this question, we used the M-SHIME®, an in vitro mucosal simulator of the human intestinal microbial ecosystem, as an experimental setup that excludes the host factor. The direct impact of two chemotherapeutics, 5-fluorouracil (5-FU) and SN-38 (active metabolite of irinotecan), on the luminal and mucosal gut microbiota from several human donors was investigated through monitoring fermentation activity and next generation sequencing. At a dose of 10 µM in the mucosal environment, 5-FU impacted the functionality and composition of the colon microbiota to a minor extent. Similarly, a daily dose of 10 µM SN-38 in the luminal environment did not cause significant changes in the functionality or microbiome composition. As our mucosal model does not include a host-compartment, our findings strongly indicate that a putative microbial contribution to mucositis is initially triggered by an altered host environment upon chemotherapy.
bibliographic citation: Vanlancker et al. (2017) 5-Fluorouracil and irinotecan (SN-38) have limited impact on colon microbial functionality and composition in vitro. PeerJ 5:e4017 https://doi.org/10.7717/peerj.4017
date submitted: 2017-07-13
date accepted: 2017-10-20
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vanlancker
  given name: Eline
author list: Agent
  family name: Vanhoecke
  given name: Barbara
author list: Agent
  family name: Stringer
  given name: Andrea
author list: Agent
  family name: Van de Wiele
  given name: Tom
doi: 10.7717/peerj.4017
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Vanlancker et al.
attribution name: Vanlancker et al.

Sediment tolerance mechanisms identified in sponges using advanced imaging techniques
type: item
type: AcademicArticle
description: Terrestrial runoff, resuspension events and dredging can affect filter-feeding sponges by elevating the concentration of suspended sediments, reducing light intensity, and smothering sponges with sediments. To investigate how sponges respond to pressures associated with increased sediment loads, the abundant and widely distributed Indo-Pacific species Ianthella basta was exposed to elevated suspended sediment concentrations, sediment deposition, and light attenuation for 48 h (acute exposure) and 4 weeks (chronic exposure). In order to visualise the response mechanisms, sponge tissue was examined by 3D X-ray microscopy and scanning electron microscopy (SEM). Acute exposures resulted in sediment rapidly accumulating in the aquiferous system of I. basta, although this sediment was fully removed within three days. Sediment removal took longer (>2 weeks) following chronic exposures, and I. basta also exhibited tissue regression and a smaller aquiferous system. The application of advanced imaging approaches revealed that I. basta employs a multilevel system for sediment rejection and elimination, containing both active and passive components. Sponges responded to sediment stress through (i) mucus production, (ii) exclusion of particles by incurrent pores, (iii) closure of oscula and pumping cessation, (iv) expulsion of particles from the aquiferous system, and (v) tissue regression to reduce the volume of the aquiferous system, thereby entering a dormant state. These mechanisms would result in tolerance and resilience to exposure to variable and high sediment loads associated with both anthropogenic impacts like dredging programs and natural pressures like flood events.
format: application/pdf
format: text/html
creator: Brian W. Strehlow
creator: Mari-Carmen Pineda
creator: Alan Duckworth
creator: Gary A. Kendrick
creator: Michael Renton
creator: Muhammad Azmi Abdul Wahab
creator: Nicole S. Webster
creator: Peta L. Clode
subject: Ecology
subject: Marine Biology
subject: Biosphere Interactions
description: doi:10.7717/peerj.3904
publisher: PeerJ Inc.
rights: © 2017 Strehlow et al.
abstract: Terrestrial runoff, resuspension events and dredging can affect filter-feeding sponges by elevating the concentration of suspended sediments, reducing light intensity, and smothering sponges with sediments. To investigate how sponges respond to pressures associated with increased sediment loads, the abundant and widely distributed Indo-Pacific species Ianthella basta was exposed to elevated suspended sediment concentrations, sediment deposition, and light attenuation for 48 h (acute exposure) and 4 weeks (chronic exposure). In order to visualise the response mechanisms, sponge tissue was examined by 3D X-ray microscopy and scanning electron microscopy (SEM). Acute exposures resulted in sediment rapidly accumulating in the aquiferous system of I. basta, although this sediment was fully removed within three days. Sediment removal took longer (>2 weeks) following chronic exposures, and I. basta also exhibited tissue regression and a smaller aquiferous system. The application of advanced imaging approaches revealed that I. basta employs a multilevel system for sediment rejection and elimination, containing both active and passive components. Sponges responded to sediment stress through (i) mucus production, (ii) exclusion of particles by incurrent pores, (iii) closure of oscula and pumping cessation, (iv) expulsion of particles from the aquiferous system, and (v) tissue regression to reduce the volume of the aquiferous system, thereby entering a dormant state. These mechanisms would result in tolerance and resilience to exposure to variable and high sediment loads associated with both anthropogenic impacts like dredging programs and natural pressures like flood events.
bibliographic citation: Strehlow et al. (2017) Sediment tolerance mechanisms identified in sponges using advanced imaging techniques. PeerJ 5:e3904 https://doi.org/10.7717/peerj.3904
date submitted: 2017-06-08
date accepted: 2017-09-18
issued: 2017-11-16
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strehlow
  given name: Brian W.
author list: Agent
  family name: Pineda
  given name: Mari-Carmen
author list: Agent
  family name: Duckworth
  given name: Alan
author list: Agent
  family name: Kendrick
  given name: Gary A.
author list: Agent
  family name: Renton
  given name: Michael
author list: Agent
  family name: Abdul Wahab
  given name: Muhammad Azmi
author list: Agent
  family name: Webster
  given name: Nicole S.
author list: Agent
  family name: Clode
  given name: Peta L.
doi: 10.7717/peerj.3904
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-16
copyright: ©2017 Strehlow et al.
attribution name: Strehlow et al.

Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts
type: item
type: AcademicArticle
description: Specific regulation and activation of focal adhesion kinase (FAK) are thought to be important for focal adhesion formation, and activation of Rho-kinase has been suggested to play a role in determining the effects of FAK on the formation of stress fibers and focal adhesions. To clarify the role of FAK in stress fiber formation and focal adhesion organization, the author examined the formation of new stress fibers and focal adhesions by activation of Rho-kinase in FAK knockout (FAK–/–) fibroblasts. FAK–/– cells were elliptical in shape, and showed reduced numbers of stress fibers and focal adhesions in the central part of the cells along with large focal adhesions in the peripheral regions. Activation of Rho-kinase in FAK–/– cells transiently increased the actin filaments in the cell center, but these did not form typical thick stress fibers. Moreover, only plaque-like structures as the origins of newly formed focal adhesions were observed in the center of the cell. Furthermore, introduction of an exogenous GFP-labeled FAK gene into FAK–/– cells resulted in increased numbers of stress fibers and focal adhesions in the center of the cells, which showed typical fibroblast morphology. These results indicated that FAK plays an important role in the formation of stress fibers and focal adhesions as well as in regulation of cell shape and morphology with the activation of Rho-kinase.
format: application/pdf
format: text/html
creator: Kazuo Katoh
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.4063
publisher: PeerJ Inc.
rights: © 2017 Katoh
abstract: Specific regulation and activation of focal adhesion kinase (FAK) are thought to be important for focal adhesion formation, and activation of Rho-kinase has been suggested to play a role in determining the effects of FAK on the formation of stress fibers and focal adhesions. To clarify the role of FAK in stress fiber formation and focal adhesion organization, the author examined the formation of new stress fibers and focal adhesions by activation of Rho-kinase in FAK knockout (FAK–/–) fibroblasts. FAK–/– cells were elliptical in shape, and showed reduced numbers of stress fibers and focal adhesions in the central part of the cells along with large focal adhesions in the peripheral regions. Activation of Rho-kinase in FAK–/– cells transiently increased the actin filaments in the cell center, but these did not form typical thick stress fibers. Moreover, only plaque-like structures as the origins of newly formed focal adhesions were observed in the center of the cell. Furthermore, introduction of an exogenous GFP-labeled FAK gene into FAK–/– cells resulted in increased numbers of stress fibers and focal adhesions in the center of the cells, which showed typical fibroblast morphology. These results indicated that FAK plays an important role in the formation of stress fibers and focal adhesions as well as in regulation of cell shape and morphology with the activation of Rho-kinase.
bibliographic citation: Katoh (2017) Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts. PeerJ 5:e4063 https://doi.org/10.7717/peerj.4063
date submitted: 2017-09-28
date accepted: 2017-10-29
issued: 2017-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Katoh
  given name: Kazuo
doi: 10.7717/peerj.4063
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-15
copyright: ©2017 Katoh
attribution name: Katoh

Lowland extirpation of anuran populations on a tropical mountain
type: item
type: AcademicArticle
description: Background Climate change and infectious diseases threaten animal and plant species, even in natural and protected areas. To cope with these changes, species may acclimate, adapt, move or decline. Here, we test for shifts in anuran distributions in the Luquillo Mountains (LM), a tropical montane forest in Puerto Rico by comparing species distributions from historical (1931–1989)and current data (2015/2016). Methods Historical data, which included different methodologies, were gathered through the Global Biodiversity Information Facility (GBIF) and published literature, and the current data were collected using acoustic recorders along three elevational transects. Results In the recordings, we detected the 12 native frog species known to occur in LM. Over a span of ∼25 years, two species have become extinct and four species suffered extirpation in lowland areas. As a consequence, low elevation areas in the LM (<300 m) have lost at least six anuran species. Discussion We hypothesize that these extirpations are due to the effects of climate change and infectious diseases, which are restricting many species to higher elevations and a much smaller area. Land use change is not responsible for these changes because LM has been a protected reserve for the past 80 years. However, previous studies indicate that (1) climate change has increased temperatures in Puerto Rico, and (2) Batrachochytrium dendrobatidis (Bd) was found in 10 native species and early detection of Bd coincides with anurans declines in the LM. Our study confirms the general impressions of amphibian population extirpations at low elevations, and corroborates the levels of threat assigned by IUCN.
format: application/pdf
format: text/html
creator: Marconi Campos-Cerqueira
creator: T. Mitchell Aide
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Climate Change Biology
description: doi:10.7717/peerj.4059
publisher: PeerJ Inc.
rights: © 2017 Campos-Cerqueira and Aide
abstract: Background Climate change and infectious diseases threaten animal and plant species, even in natural and protected areas. To cope with these changes, species may acclimate, adapt, move or decline. Here, we test for shifts in anuran distributions in the Luquillo Mountains (LM), a tropical montane forest in Puerto Rico by comparing species distributions from historical (1931–1989)and current data (2015/2016). Methods Historical data, which included different methodologies, were gathered through the Global Biodiversity Information Facility (GBIF) and published literature, and the current data were collected using acoustic recorders along three elevational transects. Results In the recordings, we detected the 12 native frog species known to occur in LM. Over a span of ∼25 years, two species have become extinct and four species suffered extirpation in lowland areas. As a consequence, low elevation areas in the LM (<300 m) have lost at least six anuran species. Discussion We hypothesize that these extirpations are due to the effects of climate change and infectious diseases, which are restricting many species to higher elevations and a much smaller area. Land use change is not responsible for these changes because LM has been a protected reserve for the past 80 years. However, previous studies indicate that (1) climate change has increased temperatures in Puerto Rico, and (2) Batrachochytrium dendrobatidis (Bd) was found in 10 native species and early detection of Bd coincides with anurans declines in the LM. Our study confirms the general impressions of amphibian population extirpations at low elevations, and corroborates the levels of threat assigned by IUCN.
bibliographic citation: Campos-Cerqueira et al. (2017) Lowland extirpation of anuran populations on a tropical mountain. PeerJ 5:e4059 https://doi.org/10.7717/peerj.4059
date submitted: 2017-08-04
date accepted: 2017-10-28
issued: 2017-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Campos-Cerqueira
  given name: Marconi
author list: Agent
  family name: Aide
  given name: T. Mitchell
doi: 10.7717/peerj.4059
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-15
copyright: ©2017 Campos-Cerqueira and Aide
attribution name: Campos-Cerqueira and Aide

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