PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: New Cernotina caddisflies from the Ecuadorian Amazon (Trichoptera: Polycentropodidae)
items: Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits
items: Inferring microevolution from museum collections and resampling: lessons learned from Cepaea
items: Augmented cartilage regeneration by implantation of cellular versus acellular implants after bone marrow stimulation: a systematic review and meta-analysis of animal studies
items: Novel mesostructured inclusions in the epidermal lining of Artemia franciscana ovisacs show optical activity
items: Comparative demography of two common scleractinian corals: Orbicella annularis and Porites astreoides
items: Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops
items: Ancient divergence time estimates in Eutropis rugifera support the existence of Pleistocene barriers on the exposed Sunda Shelf
items: Inorganic, organic, and encapsulated minerals in vegetable meal based diets for Sparus aurata (Linnaeus, 1758)
items: Work-related stress, associated comorbidities and stress causes in French community pharmacies: a nationwide cross-sectional study

New Cernotina caddisflies from the Ecuadorian Amazon (Trichoptera: Polycentropodidae)
type: item
type: AcademicArticle
description: Two new species of the caddisfly genus Cernotina Ross, 1938 (Polycentropodidae) are described from the lowland Amazon basin of Ecuador, Cernotina tiputini, new species, and Cernotina waorani, new species. These represent the first new species described from this region. We also record from Ecuador for the first time Cernotina hastilis Flint, previously known from Tobago, and present new Ecuadorian locality records for C. cygnea Flint, and C. lobisomem Santos & Nessimian. The homology of the intermediate appendage of the male genitalia of this genus is established. The region surveyed is under severe environmental threat from logging, mining, and crude oil extraction, making the description of the biodiversity of the region imperative.
format: application/pdf
format: text/html
creator: Lucas M. Camargos
creator: Blanca Ríos-Touma
creator: Ralph W. Holzenthal
subject: Biodiversity
subject: Entomology
subject: Taxonomy
description: doi:10.7717/peerj.3960
publisher: PeerJ Inc.
rights: © 2017 Camargos et al.
abstract: Two new species of the caddisfly genus Cernotina Ross, 1938 (Polycentropodidae) are described from the lowland Amazon basin of Ecuador, Cernotina tiputini, new species, and Cernotina waorani, new species. These represent the first new species described from this region. We also record from Ecuador for the first time Cernotina hastilis Flint, previously known from Tobago, and present new Ecuadorian locality records for C. cygnea Flint, and C. lobisomem Santos & Nessimian. The homology of the intermediate appendage of the male genitalia of this genus is established. The region surveyed is under severe environmental threat from logging, mining, and crude oil extraction, making the description of the biodiversity of the region imperative.
bibliographic citation: Camargos et al. (2017) New Cernotina caddisflies from the Ecuadorian Amazon (Trichoptera: Polycentropodidae). PeerJ 5:e3960 https://doi.org/10.7717/peerj.3960
date submitted: 2017-08-29
date accepted: 2017-10-05
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Camargos
  given name: Lucas M.
author list: Agent
  family name: Ríos-Touma
  given name: Blanca
author list: Agent
  family name: Holzenthal
  given name: Ralph W.
doi: 10.7717/peerj.3960
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Camargos et al.
attribution name: Camargos et al.

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits
type: item
type: AcademicArticle
description: Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.
format: application/pdf
format: text/html
creator: Ara S. Winter
creator: Jennifer J.M. Hathaway
creator: Jason C. Kimble
creator: Debbie C. Buecher
creator: Ernest W. Valdez
creator: Andrea Porras-Alfaro
creator: Jesse M. Young
creator: Kaitlyn J.H. Read
creator: Diana E. Northup
subject: Biogeography
subject: Bioinformatics
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.3944
publisher: PeerJ Inc.
rights: © 2017
abstract: Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.
bibliographic citation: Winter et al. (2017) Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits. PeerJ 5:e3944 https://doi.org/10.7717/peerj.3944
date submitted: 2016-10-10
date accepted: 2017-09-28
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Winter
  given name: Ara S.
author list: Agent
  family name: Hathaway
  given name: Jennifer J.M.
author list: Agent
  family name: Kimble
  given name: Jason C.
author list: Agent
  family name: Buecher
  given name: Debbie C.
author list: Agent
  family name: Valdez
  given name: Ernest W.
author list: Agent
  family name: Porras-Alfaro
  given name: Andrea
author list: Agent
  family name: Young
  given name: Jesse M.
author list: Agent
  family name: Read
  given name: Kaitlyn J.H.
author list: Agent
  family name: Northup
  given name: Diana E.
doi: 10.7717/peerj.3944
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27

Inferring microevolution from museum collections and resampling: lessons learned from Cepaea
type: item
type: AcademicArticle
description: Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.
format: application/pdf
format: text/html
creator: Małgorzata Ożgo
creator: Thor-Seng Liew
creator: Nicole B. Webster
creator: Menno Schilthuizen
subject: Environmental Impacts
subject: Environmental Sciences
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.3938
publisher: PeerJ Inc.
rights: © 2017 Ożgo et al.
abstract: Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.
bibliographic citation: Ożgo et al. (2017) Inferring microevolution from museum collections and resampling: lessons learned from Cepaea. PeerJ 5:e3938 https://doi.org/10.7717/peerj.3938
date submitted: 2016-07-19
date accepted: 2017-09-26
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ożgo
  given name: Małgorzata
author list: Agent
  family name: Liew
  given name: Thor-Seng
author list: Agent
  family name: Webster
  given name: Nicole B.
author list: Agent
  family name: Schilthuizen
  given name: Menno
doi: 10.7717/peerj.3938
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Ożgo et al.
attribution name: Ożgo et al.

Augmented cartilage regeneration by implantation of cellular versus acellular implants after bone marrow stimulation: a systematic review and meta-analysis of animal studies
type: item
type: AcademicArticle
description: Bone marrow stimulation may be applied to regenerate focal cartilage defects, but generally results in transient clinical improvement and formation of fibrocartilage rather than hyaline cartilage. Tissue engineering and regenerative medicine strive to develop new solutions to regenerate hyaline cartilage tissue. This systematic review and meta-analysis provides a comprehensive overview of current literature and assesses the efficacy of articular cartilage regeneration by implantation of cell-laden versus cell-free biomaterials in the knee and ankle joint in animals after bone marrow stimulation. PubMed and EMBASE (via OvidSP) were systematically searched using tissue engineering, cartilage and animals search strategies. Included were primary studies in which cellular and acellular biomaterials were implanted after applying bone marrow stimulation in the knee or ankle joint in healthy animals. Study characteristics were tabulated and outcome data were collected for meta-analysis for studies applying semi-quantitative histology as outcome measure (117 studies). Cartilage regeneration was expressed on an absolute 0–100% scale and random effects meta-analyses were performed. Implantation of cellular biomaterials significantly improved cartilage regeneration by 18.6% compared to acellular biomaterials. No significant differences were found between biomaterials loaded with stem cells and those loaded with somatic cells. Culture conditions of cells did not affect cartilage regeneration. Cartilage formation was reduced with adipose-derived stem cells compared to other cell types, but still improved compared to acellular scaffolds. Assessment of the risk of bias was impaired due to incomplete reporting for most studies. Implantation of cellular biomaterials improves cartilage regeneration compared to acellular biomaterials.
format: application/pdf
format: text/html
creator: Michiel W. Pot
creator: Toin H. van Kuppevelt
creator: Veronica K. Gonzales
creator: Pieter Buma
creator: Joanna IntHout
creator: Rob B.M. de Vries
creator: Willeke F. Daamen
subject: Bioengineering
subject: Evidence Based Medicine
subject: Orthopedics
subject: Rheumatology
subject: Translational Medicine
description: doi:10.7717/peerj.3927
publisher: PeerJ Inc.
rights: © 2017 Pot et al.
abstract: Bone marrow stimulation may be applied to regenerate focal cartilage defects, but generally results in transient clinical improvement and formation of fibrocartilage rather than hyaline cartilage. Tissue engineering and regenerative medicine strive to develop new solutions to regenerate hyaline cartilage tissue. This systematic review and meta-analysis provides a comprehensive overview of current literature and assesses the efficacy of articular cartilage regeneration by implantation of cell-laden versus cell-free biomaterials in the knee and ankle joint in animals after bone marrow stimulation. PubMed and EMBASE (via OvidSP) were systematically searched using tissue engineering, cartilage and animals search strategies. Included were primary studies in which cellular and acellular biomaterials were implanted after applying bone marrow stimulation in the knee or ankle joint in healthy animals. Study characteristics were tabulated and outcome data were collected for meta-analysis for studies applying semi-quantitative histology as outcome measure (117 studies). Cartilage regeneration was expressed on an absolute 0–100% scale and random effects meta-analyses were performed. Implantation of cellular biomaterials significantly improved cartilage regeneration by 18.6% compared to acellular biomaterials. No significant differences were found between biomaterials loaded with stem cells and those loaded with somatic cells. Culture conditions of cells did not affect cartilage regeneration. Cartilage formation was reduced with adipose-derived stem cells compared to other cell types, but still improved compared to acellular scaffolds. Assessment of the risk of bias was impaired due to incomplete reporting for most studies. Implantation of cellular biomaterials improves cartilage regeneration compared to acellular biomaterials.
bibliographic citation: Pot et al. (2017) Augmented cartilage regeneration by implantation of cellular versus acellular implants after bone marrow stimulation: a systematic review and meta-analysis of animal studies. PeerJ 5:e3927 https://doi.org/10.7717/peerj.3927
date submitted: 2017-06-23
date accepted: 2017-09-25
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pot
  given name: Michiel W.
author list: Agent
  family name: van Kuppevelt
  given name: Toin H.
author list: Agent
  family name: Gonzales
  given name: Veronica K.
author list: Agent
  family name: Buma
  given name: Pieter
author list: Agent
  family name: IntHout
  given name: Joanna
author list: Agent
  family name: de Vries
  given name: Rob B.M.
author list: Agent
  family name: Daamen
  given name: Willeke F.
doi: 10.7717/peerj.3927
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Pot et al.
attribution name: Pot et al.

Novel mesostructured inclusions in the epidermal lining of Artemia franciscana ovisacs show optical activity
type: item
type: AcademicArticle
description: Background Biomineralization, e.g., in sea urchins or mollusks, includes the assembly of mesoscopic superstructures from inorganic crystalline components and biopolymers. The resulting mesocrystals inspire biophysicists and material scientists alike, because of their extraordinary physical properties. Current efforts to replicate mesocrystal synthesis in vitro require understanding the principles of their self-assembly in vivo. One question, not addressed so far, is whether intracellular crystals of proteins can assemble with biopolymers into functional mesocrystal-like structures. During our electron microscopy studies into Artemia franciscana (Crustacea: Branchiopoda), we found initial evidence of such proteinaceous mesostructures. Results EM preparations with high-pressure freezing and accelerated freeze substitution revealed an extraordinary intracellular source of mesostructured inclusions in both the cyto-and nucleoplasm of the epidermal lining of ovisacs of A. franciscana. Confocal reflection microscopy not only confirmed our finding; it also revealed reflective, light dispersing activity of these flake-like structures, their positioning and orientation with respect to the ovisac inside. Both the striation of alternating electron dense and electron-lucent components and the sharp edges of the flakes indicate self-assembly of material of yet unknown origin under supposed participation of crystallization. However, selected area electron diffraction could not verify the status of crystallization. Energy dispersive X-ray analysis measured a marked increase in nitrogen within the flake-like inclusion, and the almost complete absence of elements that are typically involved in inorganic crystallization. This rise in nitrogen could possibility be related to higher package density of proteins, achieved by mesostructure assembly. Conclusions The ovisac lining of A. franciscana is endowed with numerous mesostructured inclusions that have not been previously reported. We…
format: application/pdf
format: text/html
creator: Elena Hollergschwandtner
creator: Thomas Schwaha
creator: Josef Neumüller
creator: Ulrich Kaindl
creator: Daniela Gruber
creator: Margret Eckhard
creator: Michael Stöger-Pollach
creator: Siegfried Reipert
subject: Aquaculture, Fisheries and Fish Science
subject: Cell Biology
subject: Marine Biology
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.3923
publisher: PeerJ Inc.
rights: © 2017 Hollergschwandtner et al.
abstract: Background Biomineralization, e.g., in sea urchins or mollusks, includes the assembly of mesoscopic superstructures from inorganic crystalline components and biopolymers. The resulting mesocrystals inspire biophysicists and material scientists alike, because of their extraordinary physical properties. Current efforts to replicate mesocrystal synthesis in vitro require understanding the principles of their self-assembly in vivo. One question, not addressed so far, is whether intracellular crystals of proteins can assemble with biopolymers into functional mesocrystal-like structures. During our electron microscopy studies into Artemia franciscana (Crustacea: Branchiopoda), we found initial evidence of such proteinaceous mesostructures. Results EM preparations with high-pressure freezing and accelerated freeze substitution revealed an extraordinary intracellular source of mesostructured inclusions in both the cyto-and nucleoplasm of the epidermal lining of ovisacs of A. franciscana. Confocal reflection microscopy not only confirmed our finding; it also revealed reflective, light dispersing activity of these flake-like structures, their positioning and orientation with respect to the ovisac inside. Both the striation of alternating electron dense and electron-lucent components and the sharp edges of the flakes indicate self-assembly of material of yet unknown origin under supposed participation of crystallization. However, selected area electron diffraction could not verify the status of crystallization. Energy dispersive X-ray analysis measured a marked increase in nitrogen within the flake-like inclusion, and the almost complete absence of elements that are typically involved in inorganic crystallization. This rise in nitrogen could possibility be related to higher package density of proteins, achieved by mesostructure assembly. Conclusions The ovisac lining of A. franciscana is endowed with numerous mesostructured inclusions that have not been previously reported. We…
bibliographic citation: Hollergschwandtner et al. (2017) Novel mesostructured inclusions in the epidermal lining of Artemia franciscana ovisacs show optical activity. PeerJ 5:e3923 https://doi.org/10.7717/peerj.3923
date submitted: 2017-04-25
date accepted: 2017-09-23
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hollergschwandtner
  given name: Elena
author list: Agent
  family name: Schwaha
  given name: Thomas
author list: Agent
  family name: Neumüller
  given name: Josef
author list: Agent
  family name: Kaindl
  given name: Ulrich
author list: Agent
  family name: Gruber
  given name: Daniela
author list: Agent
  family name: Eckhard
  given name: Margret
author list: Agent
  family name: Stöger-Pollach
  given name: Michael
author list: Agent
  family name: Reipert
  given name: Siegfried
doi: 10.7717/peerj.3923
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Hollergschwandtner et al.
attribution name: Hollergschwandtner et al.

Comparative demography of two common scleractinian corals: Orbicella annularis and Porites astreoides
type: item
type: AcademicArticle
description: Background Studies directed at understanding the demography and population dynamics of corals are relatively scarce. This limits our understanding of both the dynamics of coral populations and our capacity to develop management and conservation initiatives directed at conserving such ecosystems. Methods From 2012 to 2014, we collected data on the growth, survival, and recruitment rates of two common Caribbean coral species, the stress-tolerant Orbicella annularis and the weedy Porites astreoides. A set of size-based population matrix model was developed for two localities in Northeastern Puerto Rico and used to estimate population growth rates (λ) and determine the life cycle transition(s) that contribute the most to spatiotemporal differences in λs. The model was parameterized by following the fate of 100 colonies of each species at the two sites for two years. Results Our data indicate that spatial variability in vital rates of both species was higher than temporal variability. During the first year, populations of O. annularis exhibited λs below equilibrium at Carlos Rosario (0.817) and Palomino (0.694), followed by a considerable decline at both sites during the second year (0.700 and 0.667). Populations of P. astreoides showed higher λs than O. annularis during the first census period at Carlos Rosario (0.898) and Palomino (0.894) with a decline at one of the sites (0.681 and 0.893) during the second census period. Colony fate in both species exhibited a significant interaction with respect to location but not to time (G2 = 20.96; df = 3 for O. annularis and G2 = 9.55; df = 3 for P. astreoides). Discussion The similar variability of λs as well as the similar survival rates for both species during the two-year census period (2012–2014) show similar variability on demographic patterns in space and time. Our results suggest that location rather than time is important for the resiliency in coral colonies. Also, P. astreoides will show higher resistance to disturban…
format: application/pdf
format: text/html
creator: Francisco J. Soto-Santiago
creator: Alex Mercado-Molina
creator: Koralis Reyes-Maldonado
creator: Yaileen Vélez
creator: Claudia P. Ruiz-Díaz
creator: Alberto Sabat
subject: Ecology
subject: Ecosystem Science
subject: Environmental Sciences
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.3906
publisher: PeerJ Inc.
rights: © 2017 Soto-Santiago et al.
abstract: Background Studies directed at understanding the demography and population dynamics of corals are relatively scarce. This limits our understanding of both the dynamics of coral populations and our capacity to develop management and conservation initiatives directed at conserving such ecosystems. Methods From 2012 to 2014, we collected data on the growth, survival, and recruitment rates of two common Caribbean coral species, the stress-tolerant Orbicella annularis and the weedy Porites astreoides. A set of size-based population matrix model was developed for two localities in Northeastern Puerto Rico and used to estimate population growth rates (λ) and determine the life cycle transition(s) that contribute the most to spatiotemporal differences in λs. The model was parameterized by following the fate of 100 colonies of each species at the two sites for two years. Results Our data indicate that spatial variability in vital rates of both species was higher than temporal variability. During the first year, populations of O. annularis exhibited λs below equilibrium at Carlos Rosario (0.817) and Palomino (0.694), followed by a considerable decline at both sites during the second year (0.700 and 0.667). Populations of P. astreoides showed higher λs than O. annularis during the first census period at Carlos Rosario (0.898) and Palomino (0.894) with a decline at one of the sites (0.681 and 0.893) during the second census period. Colony fate in both species exhibited a significant interaction with respect to location but not to time (G2 = 20.96; df = 3 for O. annularis and G2 = 9.55; df = 3 for P. astreoides). Discussion The similar variability of λs as well as the similar survival rates for both species during the two-year census period (2012–2014) show similar variability on demographic patterns in space and time. Our results suggest that location rather than time is important for the resiliency in coral colonies. Also, P. astreoides will show higher resistance to disturban…
bibliographic citation: Soto-Santiago et al. (2017) Comparative demography of two common scleractinian corals: Orbicella annularis and Porites astreoides. PeerJ 5:e3906 https://doi.org/10.7717/peerj.3906
date submitted: 2017-06-29
date accepted: 2017-09-19
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soto-Santiago
  given name: Francisco J.
author list: Agent
  family name: Mercado-Molina
  given name: Alex
author list: Agent
  family name: Reyes-Maldonado
  given name: Koralis
author list: Agent
  family name: Vélez
  given name: Yaileen
author list: Agent
  family name: Ruiz-Díaz
  given name: Claudia P.
author list: Agent
  family name: Sabat
  given name: Alberto
doi: 10.7717/peerj.3906
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: © 2017 Soto-Santiago et al.
attribution name: Soto-Santiago et al.

Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops
type: item
type: AcademicArticle
description: Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H)—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies.
format: application/pdf
format: text/html
creator: Hafiz Sohaib Ahmed Saqib
creator: Minsheng You
creator: Geoff M. Gurr
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
description: doi:10.7717/peerj.3795
publisher: PeerJ Inc.
rights: © 2017 Saqib et al.
abstract: Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H)—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies.
bibliographic citation: Saqib et al. (2017) Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops. PeerJ 5:e3795 https://doi.org/10.7717/peerj.3795
date submitted: 2017-06-02
date accepted: 2017-08-18
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saqib
  given name: Hafiz Sohaib Ahmed
author list: Agent
  family name: You
  given name: Minsheng
author list: Agent
  family name: Gurr
  given name: Geoff M.
doi: 10.7717/peerj.3795
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Saqib et al.
attribution name: Saqib et al.

Ancient divergence time estimates in Eutropis rugifera support the existence of Pleistocene barriers on the exposed Sunda Shelf
type: item
type: AcademicArticle
description: Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. Eutropis rugifera is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1, BRCA2, RAG1, and MC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations of E. rugifera occurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find that E. rugifera shows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence within E. rugifera separates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the Pleistocene E. rugifera still faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes.
format: application/pdf
format: text/html
creator: Benjamin R. Karin
creator: Indraneil Das
creator: Todd R. Jackman
creator: Aaron M. Bauer
subject: Biogeography
subject: Evolutionary Studies
description: doi:10.7717/peerj.3762
publisher: PeerJ Inc.
rights: © 2017 Karin et al.
abstract: Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. Eutropis rugifera is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf. In this study, we sequenced one mitochondrial (ND2) and four nuclear (BRCA1, BRCA2, RAG1, and MC1R) markers and generated a time-calibrated phylogeny in BEAST to test whether divergence times between Sundaic populations of E. rugifera occurred during Pleistocene sea-level changes, or if they predate the Pleistocene. We find that E. rugifera shows pre-Pleistocene divergences between populations on different Sundaic land-masses. The earliest divergence within E. rugifera separates the Philippine samples from the Sundaic samples approximately 16 Ma; the Philippine populations thus cannot be considered conspecific with Sundaic congeners. Sundaic populations diverged approximately 6 Ma, and populations within Borneo from Sabah and Sarawak separated approximately 4.5 Ma in the early Pliocene, followed by further cladogenesis in Sarawak through the Pleistocene. Divergence of peninsular Malaysian populations from the Mentawai Archipelago occurred approximately 5 Ma. Separation among island populations from the Mentawai Archipelago likely dates to the Pliocene/Pleistocene boundary approximately 3.5 Ma, and our samples from peninsular Malaysia appear to coalesce in the middle Pleistocene, about 1 Ma. Coupled with the monophyly of these populations, these divergence times suggest that despite consistent land-connections between these regions throughout the Pleistocene E. rugifera still faced barriers to dispersal, which may be a result of environmental shifts that accompanied the sea-level changes.
bibliographic citation: Karin et al. (2017) Ancient divergence time estimates in Eutropis rugifera support the existence of Pleistocene barriers on the exposed Sunda Shelf. PeerJ 5:e3762 https://doi.org/10.7717/peerj.3762
date submitted: 2017-07-10
date accepted: 2017-08-15
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Karin
  given name: Benjamin R.
author list: Agent
  family name: Das
  given name: Indraneil
author list: Agent
  family name: Jackman
  given name: Todd R.
author list: Agent
  family name: Bauer
  given name: Aaron M.
doi: 10.7717/peerj.3762
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Karin et al.
attribution name: Karin et al.

Inorganic, organic, and encapsulated minerals in vegetable meal based diets for Sparus aurata (Linnaeus, 1758)
type: item
type: AcademicArticle
description: Substituting fishmeal (FM) with vegetable meal (VM) can markedly affect the mineral composition of feeds, and may require additional mineral supplementation. Their bioavailability and optimal supplementation levels depend also on the form of delivery of minerals. The aim of the study was to determine the effect of different delivery forms of three major trace elements (Zn, Mn and Se) in a marine teleost. Gilthead sea bream juveniles of 22.5 g were fed a VM-based diet for 12 weeks that was either not supplemented with these minerals or supplemented with inorganic, organic, or encapsulated inorganic forms of minerals in triplicate and compared to a FM-based diet. Our results showed that mineral delivery form significantly affected the biochemical composition and morphology of posterior vertebrae. Supplementation of VM-based diets with inorganic forms of the target minerals significantly promoted growth, increased the vertebral weight and content of ash and Zn, enhanced bone mineralization and affected the vertebral shape. Conversely, encapsulation of inorganic minerals reduced fish growth and vertebral mineral content, whereas supplementation of organic minerals, enhanced bone osteogenesis by upregulating bone morphogenetic protein 2 (bmp2) gene and produced vertebrae with a larger length in relation to height. Furthermore, organic mineral forms of delivery downregulated the expression of oxidative stress related genes, such as Cu/Zn superoxide dismutase (Cu/Zn sod) and glutathione peroxidase 1 (gpx-1), suggesting thus that dietary minerals supplemented in the organic form could be reasonably considered more effective than the inorganic and encapsulated forms of supply.
format: application/pdf
format: text/html
creator: David Domínguez
creator: Simona Rimoldi
creator: Lidia E. Robaina
creator: Silvia Torrecillas
creator: Genciana Terova
creator: María J. Zamorano
creator: Vasileios Karalazos
creator: Kristin Hamre
creator: Marisol Izquierdo
subject: Aquaculture, Fisheries and Fish Science
subject: Nutrition
description: doi:10.7717/peerj.3710
publisher: PeerJ Inc.
rights: © 2017 Domínguez et al.
abstract: Substituting fishmeal (FM) with vegetable meal (VM) can markedly affect the mineral composition of feeds, and may require additional mineral supplementation. Their bioavailability and optimal supplementation levels depend also on the form of delivery of minerals. The aim of the study was to determine the effect of different delivery forms of three major trace elements (Zn, Mn and Se) in a marine teleost. Gilthead sea bream juveniles of 22.5 g were fed a VM-based diet for 12 weeks that was either not supplemented with these minerals or supplemented with inorganic, organic, or encapsulated inorganic forms of minerals in triplicate and compared to a FM-based diet. Our results showed that mineral delivery form significantly affected the biochemical composition and morphology of posterior vertebrae. Supplementation of VM-based diets with inorganic forms of the target minerals significantly promoted growth, increased the vertebral weight and content of ash and Zn, enhanced bone mineralization and affected the vertebral shape. Conversely, encapsulation of inorganic minerals reduced fish growth and vertebral mineral content, whereas supplementation of organic minerals, enhanced bone osteogenesis by upregulating bone morphogenetic protein 2 (bmp2) gene and produced vertebrae with a larger length in relation to height. Furthermore, organic mineral forms of delivery downregulated the expression of oxidative stress related genes, such as Cu/Zn superoxide dismutase (Cu/Zn sod) and glutathione peroxidase 1 (gpx-1), suggesting thus that dietary minerals supplemented in the organic form could be reasonably considered more effective than the inorganic and encapsulated forms of supply.
bibliographic citation: Domínguez et al. (2017) Inorganic, organic, and encapsulated minerals in vegetable meal based diets for Sparus aurata (Linnaeus, 1758). PeerJ 5:e3710 https://doi.org/10.7717/peerj.3710
date submitted: 2016-12-05
date accepted: 2017-07-28
issued: 2017-10-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Domínguez
  given name: David
author list: Agent
  family name: Rimoldi
  given name: Simona
author list: Agent
  family name: Robaina
  given name: Lidia E.
author list: Agent
  family name: Torrecillas
  given name: Silvia
author list: Agent
  family name: Terova
  given name: Genciana
author list: Agent
  family name: Zamorano
  given name: María J.
author list: Agent
  family name: Karalazos
  given name: Vasileios
author list: Agent
  family name: Hamre
  given name: Kristin
author list: Agent
  family name: Izquierdo
  given name: Marisol
doi: 10.7717/peerj.3710
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-27
copyright: ©2017 Domínguez et al.
attribution name: Domínguez et al.

Work-related stress, associated comorbidities and stress causes in French community pharmacies: a nationwide cross-sectional study
type: item
type: AcademicArticle
description: Background Like other health professionals, community pharmacists are exposed to stress factors (being efficient, avoiding mistakes and bearing emotional load), but they are also under the pressure of entrepreneurial responsibilities. The main objective was to assess the level of work-related stress in French community pharmacies. The other objectives of the study were to assess the associated comorbidities and causes of work-related stress. Methods This observational cross-sectional study was sent to all French community pharmacies by email. The survey was anonymous and designed to collect the following items: socio-demographic factors, professional status, characteristics of community pharmacy, work-related stress (visual analogic scale—VAS), fatigue (VAS), sleep disturbances (questions), anxiety and depression symptoms (hospital anxiety and depression scale), medical consultation for work-related stress, medication use for work related stress, psychoactive drug-use and causes of work-related stress. Participants were included in the survey if they were pharmacists (owner or assistant) or pharmacy technicians working in a community pharmacy at the time of the survey. Exclusion criteria were defined as follows: pharmacy students or other professionals involved in a community pharmacy (e.g. dietician, beautician) and lack of professional status information. There was no age limitation. Results After three months of data collection, 1,339 participants answered the survey and 1,272 participants were included in conformity with the inclusion and exclusion criteria, and to avoid missing data on the primary endpoint. Work-related stress was detected in 32.8% (417/1,272) of individuals (scores ≥70/100). Men were significantly more affected than women and there was no difference between professional statuses and no relation with the age of the participants. Work-related stress was significantly associated with anxiety, depression, fatigue, sleep disturbances, medical consu…
format: application/pdf
format: text/html
creator: David Balayssac
creator: Bruno Pereira
creator: Julie Virot
creator: Céline Lambert
creator: Aurore Collin
creator: David Alapini
creator: Jean-Marc Gagnaire
creator: Nicolas Authier
creator: Damien Cuny
creator: Brigitte Vennat
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.3973
publisher: PeerJ Inc.
rights: © 2017 Balayssac et al.
abstract: Background Like other health professionals, community pharmacists are exposed to stress factors (being efficient, avoiding mistakes and bearing emotional load), but they are also under the pressure of entrepreneurial responsibilities. The main objective was to assess the level of work-related stress in French community pharmacies. The other objectives of the study were to assess the associated comorbidities and causes of work-related stress. Methods This observational cross-sectional study was sent to all French community pharmacies by email. The survey was anonymous and designed to collect the following items: socio-demographic factors, professional status, characteristics of community pharmacy, work-related stress (visual analogic scale—VAS), fatigue (VAS), sleep disturbances (questions), anxiety and depression symptoms (hospital anxiety and depression scale), medical consultation for work-related stress, medication use for work related stress, psychoactive drug-use and causes of work-related stress. Participants were included in the survey if they were pharmacists (owner or assistant) or pharmacy technicians working in a community pharmacy at the time of the survey. Exclusion criteria were defined as follows: pharmacy students or other professionals involved in a community pharmacy (e.g. dietician, beautician) and lack of professional status information. There was no age limitation. Results After three months of data collection, 1,339 participants answered the survey and 1,272 participants were included in conformity with the inclusion and exclusion criteria, and to avoid missing data on the primary endpoint. Work-related stress was detected in 32.8% (417/1,272) of individuals (scores ≥70/100). Men were significantly more affected than women and there was no difference between professional statuses and no relation with the age of the participants. Work-related stress was significantly associated with anxiety, depression, fatigue, sleep disturbances, medical consu…
bibliographic citation: Balayssac et al. (2017) Work-related stress, associated comorbidities and stress causes in French community pharmacies: a nationwide cross-sectional study. PeerJ 5:e3973 https://doi.org/10.7717/peerj.3973
date submitted: 2017-06-12
date accepted: 2017-10-08
issued: 2017-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Balayssac
  given name: David
author list: Agent
  family name: Pereira
  given name: Bruno
author list: Agent
  family name: Virot
  given name: Julie
author list: Agent
  family name: Lambert
  given name: Céline
author list: Agent
  family name: Collin
  given name: Aurore
author list: Agent
  family name: Alapini
  given name: David
author list: Agent
  family name: Gagnaire
  given name: Jean-Marc
author list: Agent
  family name: Authier
  given name: Nicolas
author list: Agent
  family name: Cuny
  given name: Damien
author list: Agent
  family name: Vennat
  given name: Brigitte
doi: 10.7717/peerj.3973
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-10-26
copyright: ©2017 Balayssac et al.
attribution name: Balayssac et al.

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