PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Assessing Mongolian gerbil emotional behavior: effects of two shock intensities and response-independent shocks during an extended inhibitory-avoidance task
items: Microbial agents in macroscopically healthy mammary gland tissues of small ruminants
items: Vegetation structure of plantain-based agrosystems determines numerical dominance in community of ground-dwelling ants
items: Overland movement in African clawed frogs (Xenopus laevis): empirical dispersal data from within their native range
items: Foliar microbiome transplants confer disease resistance in a critically-endangered plant
items: How can we reliably identify a taxon based on humeral morphology? Comparative morphology of desmostylian humeri
items: A unified approach to model peripheral nerves across different animal species
items: Anthropogenic water sources and the effects on Sonoran Desert small mammal communities
items: Preoperative cervical sagittal alignment parameters and their impacts on myelopathy in patients with cervical spondylotic myelopathy: a retrospective study
items: The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle

Assessing Mongolian gerbil emotional behavior: effects of two shock intensities and response-independent shocks during an extended inhibitory-avoidance task
type: item
type: AcademicArticle
description: Despite step-down inhibitory avoidance procedures that have been widely implemented in rats and mice to study learning and emotion phenomena, performance of other species in these tasks has received less attention. The case of the Mongolian gerbil is of relevance considering the discrepancies in the parameters of the step-down protocols implemented, especially the wide range of foot-shock intensities (i.e., 0.4–4.0 mA), and the lack of information on long-term performance, extinction effects, and behavioral patterning during these tasks. Experiment 1 aimed to (a) characterize gerbils’ acquisition, extinction, and steady-state performance during a multisession (i.e., extended) step-down protocol adapted for implementation in a commercially-available behavioral package (Video Fear Conditioning System—MED Associates Fairfax, VT, USA), and (b) compare gerbils’ performance in this task with two shock intensities – 0.5 vs. 1.0 mA—considered in the low-to-mid range. Results indicated that the 1.0 mA protocol produced more reliable and clear evidence of avoidance learning, extinction, and reacquisition in terms of increments in freezing and on-platform time as well as suppression of platform descent. Experiment 2 aimed to (a) assess whether an alternate protocol consisting of a random delivery of foot shocks could replicate the effects of Experiment 1 and (b) characterize gerbils’ exploratory behavior during the step-down task (jumping, digging, rearing, and probing). Random shocks did not reproduce the effects observed with the first protocol. The data also indicated that a change from random to response-dependent shocks affects (a) the length of each visit to the platform, but not the frequency of platform descends or freezing time, and (b) the patterns of exploratory behavior, namely, suppression of digging and rearing, as well as increments in probing and jumping. Overall, the study demonstrated the feasibility of the extended step-down protocol for studying steady perf…
format: application/pdf
format: text/html
creator: Camilo Hurtado-Parrado
creator: Camilo González-León
creator: Mónica A. Arias-Higuera
creator: Angelo Cardona
creator: Lucia G. Medina
creator: Laura García-Muñoz
creator: Christian Sánchez
creator: Julián Cifuentes
creator: Juan Carlos Forigua
creator: Andrea Ortiz
creator: Cesar A. Acevedo-Triana
creator: Javier L. Rico
subject: Animal Behavior
subject: Neuroscience
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.4009
publisher: PeerJ Inc.
rights: © 2017 Hurtado-Parrado et al.
abstract: Despite step-down inhibitory avoidance procedures that have been widely implemented in rats and mice to study learning and emotion phenomena, performance of other species in these tasks has received less attention. The case of the Mongolian gerbil is of relevance considering the discrepancies in the parameters of the step-down protocols implemented, especially the wide range of foot-shock intensities (i.e., 0.4–4.0 mA), and the lack of information on long-term performance, extinction effects, and behavioral patterning during these tasks. Experiment 1 aimed to (a) characterize gerbils’ acquisition, extinction, and steady-state performance during a multisession (i.e., extended) step-down protocol adapted for implementation in a commercially-available behavioral package (Video Fear Conditioning System—MED Associates Fairfax, VT, USA), and (b) compare gerbils’ performance in this task with two shock intensities – 0.5 vs. 1.0 mA—considered in the low-to-mid range. Results indicated that the 1.0 mA protocol produced more reliable and clear evidence of avoidance learning, extinction, and reacquisition in terms of increments in freezing and on-platform time as well as suppression of platform descent. Experiment 2 aimed to (a) assess whether an alternate protocol consisting of a random delivery of foot shocks could replicate the effects of Experiment 1 and (b) characterize gerbils’ exploratory behavior during the step-down task (jumping, digging, rearing, and probing). Random shocks did not reproduce the effects observed with the first protocol. The data also indicated that a change from random to response-dependent shocks affects (a) the length of each visit to the platform, but not the frequency of platform descends or freezing time, and (b) the patterns of exploratory behavior, namely, suppression of digging and rearing, as well as increments in probing and jumping. Overall, the study demonstrated the feasibility of the extended step-down protocol for studying steady perf…
bibliographic citation: Hurtado-Parrado et al. (2017) Assessing Mongolian gerbil emotional behavior: effects of two shock intensities and response-independent shocks during an extended inhibitory-avoidance task. PeerJ 5:e4009 https://doi.org/10.7717/peerj.4009
date submitted: 2017-07-24
date accepted: 2017-10-18
issued: 2017-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hurtado-Parrado
  given name: Camilo
author list: Agent
  family name: González-León
  given name: Camilo
author list: Agent
  family name: Arias-Higuera
  given name: Mónica A.
author list: Agent
  family name: Cardona
  given name: Angelo
author list: Agent
  family name: Medina
  given name: Lucia G.
author list: Agent
  family name: García-Muñoz
  given name: Laura
author list: Agent
  family name: Sánchez
  given name: Christian
author list: Agent
  family name: Cifuentes
  given name: Julián
author list: Agent
  family name: Forigua
  given name: Juan Carlos
author list: Agent
  family name: Ortiz
  given name: Andrea
author list: Agent
  family name: Acevedo-Triana
  given name: Cesar A.
author list: Agent
  family name: Rico
  given name: Javier L.
doi: 10.7717/peerj.4009
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-13
copyright: ©2017 Hurtado-Parrado et al.
attribution name: Hurtado-Parrado et al.

Microbial agents in macroscopically healthy mammary gland tissues of small ruminants
type: item
type: AcademicArticle
description: Background Health of mammary glands is fundamental for milk and dairy products hygiene and quality, with huge impacts on consumers welfare. Methods This study aims to investigate the microbial agents (bacteria, fungi and lentiviruses) isolated from 89 macroscopically healthy udders of regularly slaughtered small ruminants (41 sheep, 48 goats), also correlating their presence with the histological findings. Multinomial logistic regression was applied to evaluate the association between lesions and positivity for different microbial isolates, animal age and bacteria. Results Twenty-five samples were microbiologically negative; 138 different bacteria were isolated in 64 positive udders. Coagulase-negative staphylococci were the most prevalent bacteria isolated (46.42%), followed by environmental opportunists (34.76%), others (10.14%) and pathogens (8.68%). Most mammary glands showed coinfections (75%). Lentiviruses were detected in 39.3% of samples. Histologically, chronic non-suppurative mastitis was observed in 45/89 glands, followed by chronic mixed mastitis (12/89) and acute suppurative mastitis (4/89). Only 28 udders were normal. Histological lesions were significantly associated with the animal species and lentiviruses and coagulase-negative staphylococci infections. Goats had significantly higher risk to show chronic mixed mastitis compared to sheep. Goats showed a significantly lower risk (OR = 0.26; 95% CI [0.06–0.71]) of being infected by environmental opportunists compared to sheep, but higher risk (OR = 10.87; 95% CI [3.69–37.77]) of being infected with lentiviruses. Discussion The results of the present study suggest that macroscopically healthy glands of small ruminants could act as a reservoir of microbial agents for susceptible animals, representing a potential risk factor for the widespread of acute or chronic infection in the flock.
format: application/pdf
format: text/html
creator: Liliana Spuria
creator: Elena Biasibetti
creator: Donal Bisanzio
creator: Ilaria Biasato
creator: Daniele De Meneghi
creator: Patrizia Nebbia
creator: Patrizia Robino
creator: Paolo Bianco
creator: Michele Lamberti
creator: Claudio Caruso
creator: Alessia Di Blasio
creator: Simone Peletto
creator: Loretta Masoero
creator: Alessandro Dondo
creator: Maria Teresa Capucchio
subject: Microbiology
subject: Veterinary Medicine
subject: Histology
description: doi:10.7717/peerj.3994
publisher: PeerJ Inc.
rights: © 2017 Spuria et al.
abstract: Background Health of mammary glands is fundamental for milk and dairy products hygiene and quality, with huge impacts on consumers welfare. Methods This study aims to investigate the microbial agents (bacteria, fungi and lentiviruses) isolated from 89 macroscopically healthy udders of regularly slaughtered small ruminants (41 sheep, 48 goats), also correlating their presence with the histological findings. Multinomial logistic regression was applied to evaluate the association between lesions and positivity for different microbial isolates, animal age and bacteria. Results Twenty-five samples were microbiologically negative; 138 different bacteria were isolated in 64 positive udders. Coagulase-negative staphylococci were the most prevalent bacteria isolated (46.42%), followed by environmental opportunists (34.76%), others (10.14%) and pathogens (8.68%). Most mammary glands showed coinfections (75%). Lentiviruses were detected in 39.3% of samples. Histologically, chronic non-suppurative mastitis was observed in 45/89 glands, followed by chronic mixed mastitis (12/89) and acute suppurative mastitis (4/89). Only 28 udders were normal. Histological lesions were significantly associated with the animal species and lentiviruses and coagulase-negative staphylococci infections. Goats had significantly higher risk to show chronic mixed mastitis compared to sheep. Goats showed a significantly lower risk (OR = 0.26; 95% CI [0.06–0.71]) of being infected by environmental opportunists compared to sheep, but higher risk (OR = 10.87; 95% CI [3.69–37.77]) of being infected with lentiviruses. Discussion The results of the present study suggest that macroscopically healthy glands of small ruminants could act as a reservoir of microbial agents for susceptible animals, representing a potential risk factor for the widespread of acute or chronic infection in the flock.
bibliographic citation: Spuria et al. (2017) Microbial agents in macroscopically healthy mammary gland tissues of small ruminants. PeerJ 5:e3994 https://doi.org/10.7717/peerj.3994
date submitted: 2017-06-21
date accepted: 2017-10-16
issued: 2017-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spuria
  given name: Liliana
author list: Agent
  family name: Biasibetti
  given name: Elena
author list: Agent
  family name: Bisanzio
  given name: Donal
author list: Agent
  family name: Biasato
  given name: Ilaria
author list: Agent
  family name: De Meneghi
  given name: Daniele
author list: Agent
  family name: Nebbia
  given name: Patrizia
author list: Agent
  family name: Robino
  given name: Patrizia
author list: Agent
  family name: Bianco
  given name: Paolo
author list: Agent
  family name: Lamberti
  given name: Michele
author list: Agent
  family name: Caruso
  given name: Claudio
author list: Agent
  family name: Di Blasio
  given name: Alessia
author list: Agent
  family name: Peletto
  given name: Simone
author list: Agent
  family name: Masoero
  given name: Loretta
author list: Agent
  family name: Dondo
  given name: Alessandro
author list: Agent
  family name: Capucchio
  given name: Maria Teresa
doi: 10.7717/peerj.3994
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-13
copyright: ©2017 Spuria et al.
attribution name: Spuria et al.

Vegetation structure of plantain-based agrosystems determines numerical dominance in community of ground-dwelling ants
type: item
type: AcademicArticle
description: In tropics, ants can represent an important part of animal biomass and are known to be involved in ecosystem services, such as pest regulation. Understanding the mechanisms underlying the structuring of local ant communities is therefore important in agroecology. In the humid tropics of Africa, plantains are cropped in association with many other annual and perennial crops. Such agrosystems differ greatly in vegetation diversity and structure and are well-suited for studying how habitat-related factors affect the ant community. We analysed abundance data for the six numerically dominant ant taxa in 500 subplots located in 20 diversified, plantain-based fields. We found that the density of crops with foliage at intermediate and high canopy strata determined the numerical dominance of species. We found no relationship between the numerical dominance of each ant taxon with the crop diversity. Our results indicate that the manipulation of the densities of crops with leaves in the intermediate and high strata may help maintain the coexistence of ant species by providing different habitat patches. Further research in such agrosystems should be performed to assess if the effect of vegetation structure on ant abundance could result in efficient pest regulation.
format: application/pdf
format: text/html
creator: Anicet Gbéblonoudo Dassou
creator: Philippe Tixier
creator: Sylvain Dépigny
creator: Dominique Carval
subject: Agricultural Science
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.3917
publisher: PeerJ Inc.
rights: © 2017 Dassou et al.
abstract: In tropics, ants can represent an important part of animal biomass and are known to be involved in ecosystem services, such as pest regulation. Understanding the mechanisms underlying the structuring of local ant communities is therefore important in agroecology. In the humid tropics of Africa, plantains are cropped in association with many other annual and perennial crops. Such agrosystems differ greatly in vegetation diversity and structure and are well-suited for studying how habitat-related factors affect the ant community. We analysed abundance data for the six numerically dominant ant taxa in 500 subplots located in 20 diversified, plantain-based fields. We found that the density of crops with foliage at intermediate and high canopy strata determined the numerical dominance of species. We found no relationship between the numerical dominance of each ant taxon with the crop diversity. Our results indicate that the manipulation of the densities of crops with leaves in the intermediate and high strata may help maintain the coexistence of ant species by providing different habitat patches. Further research in such agrosystems should be performed to assess if the effect of vegetation structure on ant abundance could result in efficient pest regulation.
bibliographic citation: Dassou et al. (2017) Vegetation structure of plantain-based agrosystems determines numerical dominance in community of ground-dwelling ants. PeerJ 5:e3917 https://doi.org/10.7717/peerj.3917
date submitted: 2017-05-23
date accepted: 2017-09-22
issued: 2017-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dassou
  given name: Anicet Gbéblonoudo
author list: Agent
  family name: Tixier
  given name: Philippe
author list: Agent
  family name: Dépigny
  given name: Sylvain
author list: Agent
  family name: Carval
  given name: Dominique
doi: 10.7717/peerj.3917
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-13
copyright: ©2017 Dassou et al.
attribution name: Dassou et al.

Overland movement in African clawed frogs (Xenopus laevis): empirical dispersal data from within their native range
type: item
type: AcademicArticle
description: Dispersal forms are an important component of the ecology of many animals, and reach particular importance for predicting ranges of invasive species. African clawed frogs (Xenopus laevis) move overland between water bodies, but all empirical studies are from invasive populations with none from their native southern Africa. Here we report on incidents of overland movement found through a capture-recapture study carried out over a three year period in Overstrand, South Africa. The maximum distance moved was 2.4 km with most of the 91 animals, representing 5% of the population, moving ∼150 m. We found no differences in distances moved by males and females, despite the former being smaller. Fewer males moved overland, but this was no different from the sex bias found in the population. In laboratory performance trials, we found that males outperformed females, in both distance moved and time to exhaustion, when corrected for size. Overland movement occurred throughout the year, but reached peaks in spring and early summer when temporary water bodies were drying. Despite permanent impoundments being located within the study area, we found no evidence for migrations of animals between temporary and permanent water bodies. Our study provides the first dispersal kernel for X. laevis and suggests that it is similar to many non-pipid anurans with respect to dispersal.
format: application/pdf
format: text/html
creator: F. André De Villiers
creator: John Measey
subject: Animal Behavior
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.4039
publisher: PeerJ Inc.
rights: © 2017 De Villiers and Measey
abstract: Dispersal forms are an important component of the ecology of many animals, and reach particular importance for predicting ranges of invasive species. African clawed frogs (Xenopus laevis) move overland between water bodies, but all empirical studies are from invasive populations with none from their native southern Africa. Here we report on incidents of overland movement found through a capture-recapture study carried out over a three year period in Overstrand, South Africa. The maximum distance moved was 2.4 km with most of the 91 animals, representing 5% of the population, moving ∼150 m. We found no differences in distances moved by males and females, despite the former being smaller. Fewer males moved overland, but this was no different from the sex bias found in the population. In laboratory performance trials, we found that males outperformed females, in both distance moved and time to exhaustion, when corrected for size. Overland movement occurred throughout the year, but reached peaks in spring and early summer when temporary water bodies were drying. Despite permanent impoundments being located within the study area, we found no evidence for migrations of animals between temporary and permanent water bodies. Our study provides the first dispersal kernel for X. laevis and suggests that it is similar to many non-pipid anurans with respect to dispersal.
bibliographic citation: De Villiers et al. (2017) Overland movement in African clawed frogs (Xenopus laevis): empirical dispersal data from within their native range. PeerJ 5:e4039 https://doi.org/10.7717/peerj.4039
date submitted: 2017-09-04
date accepted: 2017-10-24
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Villiers
  given name: F. André
author list: Agent
  family name: Measey
  given name: John
doi: 10.7717/peerj.4039
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 De Villiers and Measey
attribution name: De Villiers and Measey

Foliar microbiome transplants confer disease resistance in a critically-endangered plant
type: item
type: AcademicArticle
description: There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped. Using the host/parasite system of Phyllostegia kaalaensis and Neoerysiphe galeopsidis, we conducted experiments to test total foliar microbiome transplants from healthy wild relatives onto fungicide-dependent endangered plants in an attempt to mitigate disease and reduce dependency on fungicides. Plants were treated with total microbiome transplants or cultured subsets of this community and monitored for disease severity. High-throughput DNA screening of fungal ITS1 rDNA was used to track the leaf-associated fungal communities and evaluate the effectiveness of transplantation methods. Individuals receiving traditionally isolated fungal treatments showed no improvement, but those receiving applications of a simple leaf slurry containing an uncultured fungal community showed significant disease reduction, to which we partially attribute an increase in the mycoparasitic Pseudozyma aphidis. These results were replicated in two independent experimental rounds. Treated plants have since been moved to a native habitat and, as of this writing, remain disease-free. Our results demonstrate the effectiveness of a simple low-tech method for transferring beneficial microbes from healthy wild plants to greenhouse-raised plants with reduced symbiotic microbiota. This technique was effective at reducing disease, and in conferring increased survival to an out-planted population of critically endangered plants. It was n…
format: application/pdf
format: text/html
creator: Geoffrey Zahn
creator: Anthony S. Amend
subject: Conservation Biology
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.4020
publisher: PeerJ Inc.
rights: © 2017 Zahn and Amend
abstract: There has been very little effort to incorporate foliar microbiomes into plant conservation efforts even though foliar endophytes are critically important to the fitness and function of hosts. Many critically endangered plants that have been extirpated from the wild are dependent on regular fungicidal applications in greenhouses that cannot be maintained for remote out-planted populations, which quickly perish. These fungicides negatively impact potentially beneficial fungal symbionts, which may reduce plant defenses to pathogens once fungicide treatments are stopped. Using the host/parasite system of Phyllostegia kaalaensis and Neoerysiphe galeopsidis, we conducted experiments to test total foliar microbiome transplants from healthy wild relatives onto fungicide-dependent endangered plants in an attempt to mitigate disease and reduce dependency on fungicides. Plants were treated with total microbiome transplants or cultured subsets of this community and monitored for disease severity. High-throughput DNA screening of fungal ITS1 rDNA was used to track the leaf-associated fungal communities and evaluate the effectiveness of transplantation methods. Individuals receiving traditionally isolated fungal treatments showed no improvement, but those receiving applications of a simple leaf slurry containing an uncultured fungal community showed significant disease reduction, to which we partially attribute an increase in the mycoparasitic Pseudozyma aphidis. These results were replicated in two independent experimental rounds. Treated plants have since been moved to a native habitat and, as of this writing, remain disease-free. Our results demonstrate the effectiveness of a simple low-tech method for transferring beneficial microbes from healthy wild plants to greenhouse-raised plants with reduced symbiotic microbiota. This technique was effective at reducing disease, and in conferring increased survival to an out-planted population of critically endangered plants. It was n…
bibliographic citation: Zahn et al. (2017) Foliar microbiome transplants confer disease resistance in a critically-endangered plant. PeerJ 5:e4020 https://doi.org/10.7717/peerj.4020
date submitted: 2017-09-05
date accepted: 2017-10-20
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zahn
  given name: Geoffrey
author list: Agent
  family name: Amend
  given name: Anthony S.
doi: 10.7717/peerj.4020
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 Zahn and Amend
attribution name: Zahn and Amend

How can we reliably identify a taxon based on humeral morphology? Comparative morphology of desmostylian humeri
type: item
type: AcademicArticle
description: Desmostylia is a clade of marine mammals belonging to either Tethytheria or Perissodactyla. Rich fossil records of Desmostylia were found in the Oligocene to Miocene strata of the Northern Pacific Rim, especially in the northwestern region, which includes the Japanese archipelago. Fossils in many shapes and forms, including whole or partial skeletons, skulls, teeth, and fragmentary bones have been discovered from this region. Despite the prevalent availability of fossil records, detailed taxonomic identification based on fragmentary postcranial materials has been difficult owing to to our limited knowledge of the postcranial diagnostic features of many desmostylian taxa. In this study, I propose the utilization of diagnostic characters found in the humerus to identify desmostylian genus. These characters can be used to identify isolated desmostylian humeri at the genus level, contributing to a better understanding of the stratigraphic and geographic distributions of each genus.
format: application/pdf
format: text/html
creator: Kumiko Matsui
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.4011
publisher: PeerJ Inc.
rights: © 2017 Matsui
abstract: Desmostylia is a clade of marine mammals belonging to either Tethytheria or Perissodactyla. Rich fossil records of Desmostylia were found in the Oligocene to Miocene strata of the Northern Pacific Rim, especially in the northwestern region, which includes the Japanese archipelago. Fossils in many shapes and forms, including whole or partial skeletons, skulls, teeth, and fragmentary bones have been discovered from this region. Despite the prevalent availability of fossil records, detailed taxonomic identification based on fragmentary postcranial materials has been difficult owing to to our limited knowledge of the postcranial diagnostic features of many desmostylian taxa. In this study, I propose the utilization of diagnostic characters found in the humerus to identify desmostylian genus. These characters can be used to identify isolated desmostylian humeri at the genus level, contributing to a better understanding of the stratigraphic and geographic distributions of each genus.
bibliographic citation: Matsui (2017) How can we reliably identify a taxon based on humeral morphology? Comparative morphology of desmostylian humeri. PeerJ 5:e4011 https://doi.org/10.7717/peerj.4011
date submitted: 2017-07-19
date accepted: 2017-10-19
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Matsui
  given name: Kumiko
doi: 10.7717/peerj.4011
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 Matsui
attribution name: Matsui

A unified approach to model peripheral nerves across different animal species
type: item
type: AcademicArticle
description: Peripheral nerves are extremely complex biological structures. The knowledge of their response to stretch is crucial to better understand physiological and pathological states (e.g., due to overstretch). Since their mechanical response is deterministically related to the nature of the external stimuli, theoretical and computational tools were used to investigate their behaviour. In this work, a Yeoh-like polynomial strain energy function was used to reproduce the response of in vitro porcine nerve. Moreover, this approach was applied to different nervous structures coming from different animal species (rabbit, lobster, Aplysia) and tested for different amount of stretch (up to extreme ones). Starting from this theoretical background, in silico models of both porcine nerves and cerebro-abdominal connective of Aplysia were built to reproduce experimental data (R2 > 0.9). Finally, bi-dimensional in silico models were provided to reduce computational time of more than 90% with respect to the performances of fully three-dimensional models.
format: application/pdf
format: text/html
creator: Elisabetta Giannessi
creator: Maria Rita Stornelli
creator: Pier Nicola Sergi
subject: Bioengineering
subject: Computational Biology
subject: Neurology
description: doi:10.7717/peerj.4005
publisher: PeerJ Inc.
rights: © 2017 Giannessi et al.
abstract: Peripheral nerves are extremely complex biological structures. The knowledge of their response to stretch is crucial to better understand physiological and pathological states (e.g., due to overstretch). Since their mechanical response is deterministically related to the nature of the external stimuli, theoretical and computational tools were used to investigate their behaviour. In this work, a Yeoh-like polynomial strain energy function was used to reproduce the response of in vitro porcine nerve. Moreover, this approach was applied to different nervous structures coming from different animal species (rabbit, lobster, Aplysia) and tested for different amount of stretch (up to extreme ones). Starting from this theoretical background, in silico models of both porcine nerves and cerebro-abdominal connective of Aplysia were built to reproduce experimental data (R2 > 0.9). Finally, bi-dimensional in silico models were provided to reduce computational time of more than 90% with respect to the performances of fully three-dimensional models.
bibliographic citation: Giannessi et al. (2017) A unified approach to model peripheral nerves across different animal species. PeerJ 5:e4005 https://doi.org/10.7717/peerj.4005
date submitted: 2016-04-15
date accepted: 2017-10-18
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giannessi
  given name: Elisabetta
author list: Agent
  family name: Stornelli
  given name: Maria Rita
author list: Agent
  family name: Sergi
  given name: Pier Nicola
doi: 10.7717/peerj.4005
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 Giannessi et al.
attribution name: Giannessi et al.

Anthropogenic water sources and the effects on Sonoran Desert small mammal communities
type: item
type: AcademicArticle
description: Anthropogenic water sources (AWS) are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012. A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse (Chaetodipus penicillatus) which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey’s pocket mouse (C. baileyi) and white-throated woodrat (Neotoma albigula), had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture.
format: application/pdf
format: text/html
creator: Aaron B. Switalski
creator: Heather L. Bateman
subject: Conservation Biology
subject: Ecohydrology
subject: Ecology
subject: Natural Resource Management
subject: Zoology
description: doi:10.7717/peerj.4003
publisher: PeerJ Inc.
rights: © 2017 Switalski and Bateman
abstract: Anthropogenic water sources (AWS) are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012. A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse (Chaetodipus penicillatus) which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey’s pocket mouse (C. baileyi) and white-throated woodrat (Neotoma albigula), had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture.
bibliographic citation: Switalski et al. (2017) Anthropogenic water sources and the effects on Sonoran Desert small mammal communities. PeerJ 5:e4003 https://doi.org/10.7717/peerj.4003
date submitted: 2017-06-15
date accepted: 2017-10-17
issued: 2017-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Switalski
  given name: Aaron B.
author list: Agent
  family name: Bateman
  given name: Heather L.
doi: 10.7717/peerj.4003
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-10
copyright: ©2017 Switalski and Bateman
attribution name: Switalski and Bateman

Preoperative cervical sagittal alignment parameters and their impacts on myelopathy in patients with cervical spondylotic myelopathy: a retrospective study
type: item
type: AcademicArticle
description: Background Cervical sagittal alignment plays an important role in the pathogenesis of cervical spondylotic myelopathy (CSM), but there are limited studies on the cervical sagittal parameters in CSM patients and their correlations with myelopathy. The aim of this study is to investigate the correlations among the preoperative cervical sagittal alignment parameters and their correlations with the development of myelopathy in patients with CSM. Methods We retrospectively collected 212 patients with CSM who underwent surgical interventions. Gender, age, modified Japanese Orthopedic Association score (mJOA), cervical lordosis (CL), C2–C7 sagittal vertical axis (C2–C7 SVA), T1 slope (T1S), neck tilt (NT) and thoracic inlet angle (TIA) were collected before operation. Interobserver and intraobserver reliability were calculated for all measurements (intraclass correlation coefficient, ICC). Data were analyzed with Pearson and Spearman correlation tests and multiple linear regression analysis. Results A total of 212 patients with CSM were included in this study (male: 136, female: 76) with an average age of 54.5 ± 10.1 years old. Intraobserver and interobserver reliability for all included radiographic parameters presented good to excellent agreement (ICC > 0.7). No significant differences in demographic and radiological parameters have been observed between males and females (P > 0.05). We found statistically significant correlations among the following parameters: age with CL (r = 0.135, P = 0.049), age with T1S (r = 0.222, P = 0.001), CL with T1S (r = 0.291, P < 0.001), CL with C2-C7 SVA (r = − 0.395, P < 0.001), mJOA with age (r = − 0.274, P < 0.001), mJOA with C2–C7 SVA (r = − 0.219, P < 0.001) and mJOA with T1S(r = − 0.171, p = 0.013). Linear regression analysis showed that C2–C7 SVA was the predictor of CL (adjusted R2 = 0.152, P < 0.001) and multiple linear regression showed that age combined with C2–C7 SVA was a sensitive predictor of mJOA (adjusted R2 = 0.106, P < …
format: application/pdf
format: text/html
creator: Wei Yuan
creator: Yue Zhu
creator: Haitao Zhu
creator: Cui Cui
creator: Lei Pei
creator: Zhuxi Huang
subject: Orthopedics
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.4027
publisher: PeerJ Inc.
rights: © 2017 Yuan et al.
abstract: Background Cervical sagittal alignment plays an important role in the pathogenesis of cervical spondylotic myelopathy (CSM), but there are limited studies on the cervical sagittal parameters in CSM patients and their correlations with myelopathy. The aim of this study is to investigate the correlations among the preoperative cervical sagittal alignment parameters and their correlations with the development of myelopathy in patients with CSM. Methods We retrospectively collected 212 patients with CSM who underwent surgical interventions. Gender, age, modified Japanese Orthopedic Association score (mJOA), cervical lordosis (CL), C2–C7 sagittal vertical axis (C2–C7 SVA), T1 slope (T1S), neck tilt (NT) and thoracic inlet angle (TIA) were collected before operation. Interobserver and intraobserver reliability were calculated for all measurements (intraclass correlation coefficient, ICC). Data were analyzed with Pearson and Spearman correlation tests and multiple linear regression analysis. Results A total of 212 patients with CSM were included in this study (male: 136, female: 76) with an average age of 54.5 ± 10.1 years old. Intraobserver and interobserver reliability for all included radiographic parameters presented good to excellent agreement (ICC > 0.7). No significant differences in demographic and radiological parameters have been observed between males and females (P > 0.05). We found statistically significant correlations among the following parameters: age with CL (r = 0.135, P = 0.049), age with T1S (r = 0.222, P = 0.001), CL with T1S (r = 0.291, P < 0.001), CL with C2-C7 SVA (r = − 0.395, P < 0.001), mJOA with age (r = − 0.274, P < 0.001), mJOA with C2–C7 SVA (r = − 0.219, P < 0.001) and mJOA with T1S(r = − 0.171, p = 0.013). Linear regression analysis showed that C2–C7 SVA was the predictor of CL (adjusted R2 = 0.152, P < 0.001) and multiple linear regression showed that age combined with C2–C7 SVA was a sensitive predictor of mJOA (adjusted R2 = 0.106, P < …
bibliographic citation: Yuan et al. (2017) Preoperative cervical sagittal alignment parameters and their impacts on myelopathy in patients with cervical spondylotic myelopathy: a retrospective study. PeerJ 5:e4027 https://doi.org/10.7717/peerj.4027
date submitted: 2017-07-17
date accepted: 2017-10-22
issued: 2017-11-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Wei
author list: Agent
  family name: Zhu
  given name: Yue
author list: Agent
  family name: Zhu
  given name: Haitao
author list: Agent
  family name: Cui
  given name: Cui
author list: Agent
  family name: Pei
  given name: Lei
author list: Agent
  family name: Huang
  given name: Zhuxi
doi: 10.7717/peerj.4027
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-09
copyright: ©2017 Yuan et al.
attribution name: Yuan et al.

The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle
type: item
type: AcademicArticle
description: The wood frog (Rana sylvatica) can endure freezing of up to 65% of total body water during winter. When frozen, wood frogs enter a dormant state characterized by a cessation of vital functions (i.e., no heartbeat, blood circulation, breathing, brain activity, or movement). Wood frogs utilize various behavioural and biochemical adaptations to survive extreme freezing and component anoxia and dehydration stresses, including a global suppression of metabolic functions and gene expression. The stress-responsive myocyte enhancer factor-2 (MEF2) transcription factor family regulates the selective expression of genes involved in glucose transport, protein quality control, and phosphagen homeostasis. This study examined the role of MEF2A and MEF2C proteins as well as select downstream targets (glucose transporter-4, calreticulin, and muscle and brain creatine kinase isozymes) in 40% dehydration and 24 h anoxia exposure at the transcriptional, translational, and post-translational levels using qRT-PCR, immunoblotting, and subcellular localization. Mef2a/c transcript levels remained constant during dehydration and anoxia. Total, cytoplasmic, and nuclear MEF2A/C and phospho-MEF2A/C protein levels remained constant during dehydration, whereas a decrease in total MEF2C levels was observed during rehydration. Total and phospho-MEF2A levels remained constant during anoxia, whereas total MEF2C levels decreased during 24 h anoxia and P-MEF2C levels increased during 4 h anoxia. In contrast, cytoplasmic MEF2A levels and nuclear phospho-MEF2A/C levels were upregulated during anoxia. MEF2 downstream targets remained constant during dehydration and anoxia, with the exception of glut4 which was upregulated during anoxia. These results suggest that the upregulated MEF2 response reported in wood frogs during freezing may in part stem from their cellular responses to surviving prolonged anoxia, rather than dehydration, leading to an increase in GLUT4 expression which may have an important ro…
format: application/pdf
format: text/html
creator: Myriam P. Hoyeck
creator: Hanane Hadj-Moussa
creator: Kenneth B. Storey
subject: Biochemistry
subject: Molecular Biology
description: doi:10.7717/peerj.4014
publisher: PeerJ Inc.
rights: © 2017 Hoyeck et al.
abstract: The wood frog (Rana sylvatica) can endure freezing of up to 65% of total body water during winter. When frozen, wood frogs enter a dormant state characterized by a cessation of vital functions (i.e., no heartbeat, blood circulation, breathing, brain activity, or movement). Wood frogs utilize various behavioural and biochemical adaptations to survive extreme freezing and component anoxia and dehydration stresses, including a global suppression of metabolic functions and gene expression. The stress-responsive myocyte enhancer factor-2 (MEF2) transcription factor family regulates the selective expression of genes involved in glucose transport, protein quality control, and phosphagen homeostasis. This study examined the role of MEF2A and MEF2C proteins as well as select downstream targets (glucose transporter-4, calreticulin, and muscle and brain creatine kinase isozymes) in 40% dehydration and 24 h anoxia exposure at the transcriptional, translational, and post-translational levels using qRT-PCR, immunoblotting, and subcellular localization. Mef2a/c transcript levels remained constant during dehydration and anoxia. Total, cytoplasmic, and nuclear MEF2A/C and phospho-MEF2A/C protein levels remained constant during dehydration, whereas a decrease in total MEF2C levels was observed during rehydration. Total and phospho-MEF2A levels remained constant during anoxia, whereas total MEF2C levels decreased during 24 h anoxia and P-MEF2C levels increased during 4 h anoxia. In contrast, cytoplasmic MEF2A levels and nuclear phospho-MEF2A/C levels were upregulated during anoxia. MEF2 downstream targets remained constant during dehydration and anoxia, with the exception of glut4 which was upregulated during anoxia. These results suggest that the upregulated MEF2 response reported in wood frogs during freezing may in part stem from their cellular responses to surviving prolonged anoxia, rather than dehydration, leading to an increase in GLUT4 expression which may have an important ro…
bibliographic citation: Hoyeck et al. (2017) The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle. PeerJ 5:e4014 https://doi.org/10.7717/peerj.4014
date submitted: 2017-09-07
date accepted: 2017-10-19
issued: 2017-11-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoyeck
  given name: Myriam P.
author list: Agent
  family name: Hadj-Moussa
  given name: Hanane
author list: Agent
  family name: Storey
  given name: Kenneth B.
doi: 10.7717/peerj.4014
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-11-09
copyright: ©2017 Hoyeck et al.
attribution name: Hoyeck et al.

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