PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: In vitro evaluation of osteoprotegerin in chitosan for potential bone defect applications
items: Microendemicity in the northern Hajar Mountains of Oman and the United Arab Emirates with the description of two new species of geckos of the genus Asaccus (Squamata: Phyllodactylidae)
items: Agricultural land-use change in a Mexican oligotrophic desert depletes ecosystem stability
items: Evaluation of outbreak response immunization in the control of pertussis using agent-based modeling
items: Population genetic structure between Yap and Palau for the coral Acropora hyacinthus
items: A resource-based game theoretical approach for the paradox of the plankton
items: Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice
items: Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines
items: Microbe-ID: an open source toolbox for microbial genotyping and species identification
items: Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals

In vitro evaluation of osteoprotegerin in chitosan for potential bone defect applications
type: item
type: AcademicArticle
description: Background The receptor activator of nuclear factor kappa-B (RANK)/RANK ligand/osteoprotegerin (OPG) system plays a critical role in bone remodelling by regulating osteoclast formation and activity. OPG has been used systemically in the treatment of bone diseases. In searching for more effective and safer treatment for bone diseases, we investigated newly formulated OPG-chitosan complexes, which is prepared as a local application for its osteogenic potential to remediate bone defects. Methods We examined high, medium and low molecular weights of chitosan combined with OPG. The cytotoxicity of OPG in chitosan and its proliferation in vitro was evaluated using normal, human periodontal ligament (NHPL) fibroblasts in 2D and 3D cell culture. The cytotoxicity of these combinations was compared by measuring cell survival with a tetrazolium salt reduction (MTT) assay and AlamarBlue assay. The cellular morphological changes were observed under an inverted microscope. A propidium iodide and acridine orange double-staining assay was used to evaluate the morphology and quantify the viable and nonviable cells. The expression level of osteopontin and osteocalcin protein in treated normal human osteoblast cells was evaluated by using Western blot. Results The results demonstrated that OPG in combination with chitosan was non-toxic, and OPG combined with low molecular weight chitosan has the most significant effect on NHPL fibroblasts and stimulates proliferation of cells over the period of treatment.
format: application/pdf
format: text/html
creator: Soher Nagi Jayash
creator: Najihah M. Hashim
creator: Misni Misran
creator: NA Baharuddin
subject: Bioengineering
subject: Orthopedics
subject: Pharmacology
subject: Rheumatology
description: doi:10.7717/peerj.2229
publisher: PeerJ Inc.
rights: © 2016 Jayash et al.
abstract: Background The receptor activator of nuclear factor kappa-B (RANK)/RANK ligand/osteoprotegerin (OPG) system plays a critical role in bone remodelling by regulating osteoclast formation and activity. OPG has been used systemically in the treatment of bone diseases. In searching for more effective and safer treatment for bone diseases, we investigated newly formulated OPG-chitosan complexes, which is prepared as a local application for its osteogenic potential to remediate bone defects. Methods We examined high, medium and low molecular weights of chitosan combined with OPG. The cytotoxicity of OPG in chitosan and its proliferation in vitro was evaluated using normal, human periodontal ligament (NHPL) fibroblasts in 2D and 3D cell culture. The cytotoxicity of these combinations was compared by measuring cell survival with a tetrazolium salt reduction (MTT) assay and AlamarBlue assay. The cellular morphological changes were observed under an inverted microscope. A propidium iodide and acridine orange double-staining assay was used to evaluate the morphology and quantify the viable and nonviable cells. The expression level of osteopontin and osteocalcin protein in treated normal human osteoblast cells was evaluated by using Western blot. Results The results demonstrated that OPG in combination with chitosan was non-toxic, and OPG combined with low molecular weight chitosan has the most significant effect on NHPL fibroblasts and stimulates proliferation of cells over the period of treatment.
bibliographic citation: Jayash et al. (2016) In vitro evaluation of osteoprotegerin in chitosan for potential bone defect applications. PeerJ 4:e2229 https://doi.org/10.7717/peerj.2229
date submitted: 2016-04-19
date accepted: 2016-06-16
issued: 2016-08-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jayash
  given name: Soher Nagi
author list: Agent
  family name: Hashim
  given name: Najihah M.
author list: Agent
  family name: Misran
  given name: Misni
author list: Agent
  family name: Baharuddin
  given name: NA
doi: 10.7717/peerj.2229
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-23
copyright: ©2016 Jayash et al.
attribution name: Jayash et al.

Microendemicity in the northern Hajar Mountains of Oman and the United Arab Emirates with the description of two new species of geckos of the genus Asaccus (Squamata: Phyllodactylidae)
type: item
type: AcademicArticle
description: Background The Hajar Mountains of Oman and the United Arab Emirates (UAE) is the highest mountain range in Eastern Arabia. As a result of their old geological origin, geographical isolation, complex topography and local climate, these mountains provide an important refuge for endemic and relict species of plants and animals with strong Indo-Iranian affinities. Among vertebrates, the rock climbing nocturnal geckos of the genus Asaccus represent the genus with the highest number of endemic species in the Hajar Mountains. Recent taxonomic studies on the Zagros populations of Asaccus have shown that this genus is much richer than it was previously thought and preliminary morphological and molecular data suggest that its diversity in Arabia may also be underestimated. Methods A total of 83 specimens originally classified as Asaccus caudivolvulus (including specimens of the two new species described herein), six other Asaccus species from the Hajar and the Zagros Mountains and two representatives of the genus Haemodracon were sequenced for up to 2,311 base pairs including the mitochondrial 12S and cytb and the nuclear c-mos, MC1R and ACM4 genes. Phylogenetic relationships were inferred using both Bayesian and maximum-likelihood approaches and the former method was also used to calibrate the phylogenetic tree. Haplotype networks and phylogenetic trees were inferred from the phased nuclear genes only. Sixty-one alcohol-preserved adult specimens originally classified as Asaccus caudivolvulus from the northern Hajar Mountains were examined for 13 morphometric and the five meristic variables using multivariate methods and were also used to diagnose and describe the two new species. Results The results of the molecular and morphological analyses indicate that the species originally classified as Asaccus caudivolvulus is, in fact, an assemblage of three different species that started diversifying during the Mid-Miocene. The molecular phylogenies consistently recovered the Hajar …
format: application/pdf
format: text/html
creator: Salvador Carranza
creator: Marc Simó-Riudalbas
creator: Sithum Jayasinghe
creator: Thomas Wilms
creator: Johannes Els
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2371
publisher: PeerJ Inc.
rights: © 2016 Carranza et al.
abstract: Background The Hajar Mountains of Oman and the United Arab Emirates (UAE) is the highest mountain range in Eastern Arabia. As a result of their old geological origin, geographical isolation, complex topography and local climate, these mountains provide an important refuge for endemic and relict species of plants and animals with strong Indo-Iranian affinities. Among vertebrates, the rock climbing nocturnal geckos of the genus Asaccus represent the genus with the highest number of endemic species in the Hajar Mountains. Recent taxonomic studies on the Zagros populations of Asaccus have shown that this genus is much richer than it was previously thought and preliminary morphological and molecular data suggest that its diversity in Arabia may also be underestimated. Methods A total of 83 specimens originally classified as Asaccus caudivolvulus (including specimens of the two new species described herein), six other Asaccus species from the Hajar and the Zagros Mountains and two representatives of the genus Haemodracon were sequenced for up to 2,311 base pairs including the mitochondrial 12S and cytb and the nuclear c-mos, MC1R and ACM4 genes. Phylogenetic relationships were inferred using both Bayesian and maximum-likelihood approaches and the former method was also used to calibrate the phylogenetic tree. Haplotype networks and phylogenetic trees were inferred from the phased nuclear genes only. Sixty-one alcohol-preserved adult specimens originally classified as Asaccus caudivolvulus from the northern Hajar Mountains were examined for 13 morphometric and the five meristic variables using multivariate methods and were also used to diagnose and describe the two new species. Results The results of the molecular and morphological analyses indicate that the species originally classified as Asaccus caudivolvulus is, in fact, an assemblage of three different species that started diversifying during the Mid-Miocene. The molecular phylogenies consistently recovered the Hajar …
bibliographic citation: Carranza et al. (2016) Microendemicity in the northern Hajar Mountains of Oman and the United Arab Emirates with the description of two new species of geckos of the genus Asaccus (Squamata: Phyllodactylidae). PeerJ 4:e2371 https://doi.org/10.7717/peerj.2371
date submitted: 2016-06-09
date accepted: 2016-07-26
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carranza
  given name: Salvador
author list: Agent
  family name: Simó-Riudalbas
  given name: Marc
author list: Agent
  family name: Jayasinghe
  given name: Sithum
author list: Agent
  family name: Wilms
  given name: Thomas
author list: Agent
  family name: Els
  given name: Johannes
doi: 10.7717/peerj.2371
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Carranza et al.
attribution name: Carranza et al.

Agricultural land-use change in a Mexican oligotrophic desert depletes ecosystem stability
type: item
type: AcademicArticle
description: Background Global demand for food has led to increased land-use change, particularly in dry land ecosystems, which has caused several environmental problems due to the soil degradation. In the Cuatro Cienegas Basin (CCB), alfalfa production irrigated by flooding impacts strongly on the soil. Methods In order to analyze the effect of such agricultural land-use change on soil nutrient dynamics and soil bacterial community composition, this work examined an agricultural gradient within the CCB which was comprised of a native desert grassland, a plot currently cultivated with alfalfa and a former agricultural field that had been abandoned for over 30 years. For each site, we analyzed C, N and P dynamic fractions, the activity of the enzyme phosphatase and the bacterial composition obtained using 16S rRNA clone libraries. Results The results showed that the cultivated site presented a greater availability of water and dissolved organic carbon, these conditions promoted mineralization processes mediated by heterotrophic microorganisms, while the abandoned land was limited by water and dissolved organic nitrogen. The low amount of dissolved organic matter promoted nitrification, which is mediated by autotrophic microorganisms. The microbial N immobilization process and specific phosphatase activity were both favored in the native grassland. As expected, differences in bacterial taxonomical composition were observed among sites. The abandoned site exhibited similar compositions than native grassland, while the cultivated site differed. Discussion The results suggest that the transformation of native grassland into agricultural land induces drastic changes in soil nutrient dynamics as well as in the bacterial community. However, with the absence of agricultural practices, some of the soil characteristics analyzed slowly recovers their natural state.
format: application/pdf
format: text/html
creator: Natali Hernández-Becerra
creator: Yunuen Tapia-Torres
creator: Ofelia Beltrán-Paz
creator: Jazmín Blaz
creator: Valeria Souza
creator: Felipe García-Oliva
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
subject: Soil Science
description: doi:10.7717/peerj.2365
publisher: PeerJ Inc.
rights: © 2016 Hernández-Becerra et al.
abstract: Background Global demand for food has led to increased land-use change, particularly in dry land ecosystems, which has caused several environmental problems due to the soil degradation. In the Cuatro Cienegas Basin (CCB), alfalfa production irrigated by flooding impacts strongly on the soil. Methods In order to analyze the effect of such agricultural land-use change on soil nutrient dynamics and soil bacterial community composition, this work examined an agricultural gradient within the CCB which was comprised of a native desert grassland, a plot currently cultivated with alfalfa and a former agricultural field that had been abandoned for over 30 years. For each site, we analyzed C, N and P dynamic fractions, the activity of the enzyme phosphatase and the bacterial composition obtained using 16S rRNA clone libraries. Results The results showed that the cultivated site presented a greater availability of water and dissolved organic carbon, these conditions promoted mineralization processes mediated by heterotrophic microorganisms, while the abandoned land was limited by water and dissolved organic nitrogen. The low amount of dissolved organic matter promoted nitrification, which is mediated by autotrophic microorganisms. The microbial N immobilization process and specific phosphatase activity were both favored in the native grassland. As expected, differences in bacterial taxonomical composition were observed among sites. The abandoned site exhibited similar compositions than native grassland, while the cultivated site differed. Discussion The results suggest that the transformation of native grassland into agricultural land induces drastic changes in soil nutrient dynamics as well as in the bacterial community. However, with the absence of agricultural practices, some of the soil characteristics analyzed slowly recovers their natural state.
bibliographic citation: Hernández-Becerra et al. (2016) Agricultural land-use change in a Mexican oligotrophic desert depletes ecosystem stability. PeerJ 4:e2365 https://doi.org/10.7717/peerj.2365
date submitted: 2016-05-09
date accepted: 2016-07-25
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Becerra
  given name: Natali
author list: Agent
  family name: Tapia-Torres
  given name: Yunuen
author list: Agent
  family name: Beltrán-Paz
  given name: Ofelia
author list: Agent
  family name: Blaz
  given name: Jazmín
author list: Agent
  family name: Souza
  given name: Valeria
author list: Agent
  family name: García-Oliva
  given name: Felipe
doi: 10.7717/peerj.2365
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Hernández-Becerra et al.
attribution name: Hernández-Becerra et al.

Evaluation of outbreak response immunization in the control of pertussis using agent-based modeling
type: item
type: AcademicArticle
description: Background Pertussis control remains a challenge due to recently observed effects of waning immunity to acellular vaccine and suboptimal vaccine coverage. Multiple outbreaks have been reported in different ages worldwide. For certain outbreaks, public health authorities can launch an outbreak response immunization (ORI) campaign to control pertussis spread. We investigated effects of an outbreak response immunization targeting young adolescents in averting pertussis cases. Methods We developed an agent-based model for pertussis transmission representing disease mechanism, waning immunity, vaccination schedule and pathogen transmission in a spatially-explicit 500,000-person contact network representing a typical Canadian Public Health district. Parameters were derived from literature and calibration. We used published cumulative incidence and dose-specific vaccine coverage to calibrate the model’s epidemiological curves. We endogenized outbreak response by defining thresholds to trigger simulated immunization campaigns in the 10–14 age group offering 80% coverage. We ran paired simulations with and without outbreak response immunization and included those resulting in a single ORI within a 10-year span. We calculated the number of cases averted attributable to outbreak immunization campaign in all ages, in the 10–14 age group and in infants. The count of cases averted were tested using Mann–Whitney U test to determine statistical significance. Numbers needed to vaccinate during immunization campaign to prevent a single case in respective age groups were derived from the model. We varied adult vaccine coverage, waning immunity parameters, immunization campaign eligibility and tested stronger vaccination boosting effect in sensitivity analyses. Results 189 qualified paired-runs were analyzed. On average, ORI was triggered every 26 years. On a per-run basis, there were an average of 124, 243 and 429 pertussis cases averted across all age groups within 1, 3 and 10 years …
format: application/pdf
format: text/html
creator: Alexander Doroshenko
creator: Weicheng Qian
creator: Nathaniel D. Osgood
subject: Computational Biology
subject: Mathematical Biology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.2337
publisher: PeerJ Inc.
rights: © 2016 Doroshenko et al.
abstract: Background Pertussis control remains a challenge due to recently observed effects of waning immunity to acellular vaccine and suboptimal vaccine coverage. Multiple outbreaks have been reported in different ages worldwide. For certain outbreaks, public health authorities can launch an outbreak response immunization (ORI) campaign to control pertussis spread. We investigated effects of an outbreak response immunization targeting young adolescents in averting pertussis cases. Methods We developed an agent-based model for pertussis transmission representing disease mechanism, waning immunity, vaccination schedule and pathogen transmission in a spatially-explicit 500,000-person contact network representing a typical Canadian Public Health district. Parameters were derived from literature and calibration. We used published cumulative incidence and dose-specific vaccine coverage to calibrate the model’s epidemiological curves. We endogenized outbreak response by defining thresholds to trigger simulated immunization campaigns in the 10–14 age group offering 80% coverage. We ran paired simulations with and without outbreak response immunization and included those resulting in a single ORI within a 10-year span. We calculated the number of cases averted attributable to outbreak immunization campaign in all ages, in the 10–14 age group and in infants. The count of cases averted were tested using Mann–Whitney U test to determine statistical significance. Numbers needed to vaccinate during immunization campaign to prevent a single case in respective age groups were derived from the model. We varied adult vaccine coverage, waning immunity parameters, immunization campaign eligibility and tested stronger vaccination boosting effect in sensitivity analyses. Results 189 qualified paired-runs were analyzed. On average, ORI was triggered every 26 years. On a per-run basis, there were an average of 124, 243 and 429 pertussis cases averted across all age groups within 1, 3 and 10 years …
bibliographic citation: Doroshenko et al. (2016) Evaluation of outbreak response immunization in the control of pertussis using agent-based modeling. PeerJ 4:e2337 https://doi.org/10.7717/peerj.2337
date submitted: 2016-02-16
date accepted: 2016-07-17
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doroshenko
  given name: Alexander
author list: Agent
  family name: Qian
  given name: Weicheng
author list: Agent
  family name: Osgood
  given name: Nathaniel D.
doi: 10.7717/peerj.2337
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Doroshenko et al.
attribution name: Doroshenko et al.

Population genetic structure between Yap and Palau for the coral Acropora hyacinthus
type: item
type: AcademicArticle
description: Information on connectivity is becoming increasingly in demand as marine protected areas are being designed as an integral part of a network to protect marine resources at the ecosystem level. Larval dispersal and population structure, however, remain very difficult to assess. Here, we tested the predictions of a detailed oceanographic connectivity model of larval dispersal and coral recruitment within Palau and between Palau and Yap, which was developed to support the review of the existing network of marine protected areas in Palau. We used high throughput microsatellite genotyping of the coral Acropora hyacinthus to characterize population genetic structure. Pairwise F′ST values between Palau and Yap (0.10), Palau and Ngulu (0.09) and Yap and Ngulu (0.09) were all significant and similar to pairwise F′ST values of sites within Palau (0.02–0.12) and within Yap (0.02–0.09) highlighting structure at island scale and indicating that recruitment may be even more localized than previously anticipated. A bottleneck test did not reveal any signs of a founder effect between Yap and Palau. Overall, the data supports the idea that recovery of A. hyacinthus in Palau did not come exclusively from a single source but most likely came from a combination of areas, including sites within Palau. In light of these results there seems to be very little connectivity around the barrier reef and management recommendation would be to increase the number or the size of MPAs within Palau.
format: application/pdf
format: text/html
creator: Annick Cros
creator: Robert J. Toonen
creator: Sarah W. Davies
creator: Stephen A. Karl
subject: Genetics
subject: Marine Biology
description: doi:10.7717/peerj.2330
publisher: PeerJ Inc.
rights: © 2016 Cros et al.
abstract: Information on connectivity is becoming increasingly in demand as marine protected areas are being designed as an integral part of a network to protect marine resources at the ecosystem level. Larval dispersal and population structure, however, remain very difficult to assess. Here, we tested the predictions of a detailed oceanographic connectivity model of larval dispersal and coral recruitment within Palau and between Palau and Yap, which was developed to support the review of the existing network of marine protected areas in Palau. We used high throughput microsatellite genotyping of the coral Acropora hyacinthus to characterize population genetic structure. Pairwise F′ST values between Palau and Yap (0.10), Palau and Ngulu (0.09) and Yap and Ngulu (0.09) were all significant and similar to pairwise F′ST values of sites within Palau (0.02–0.12) and within Yap (0.02–0.09) highlighting structure at island scale and indicating that recruitment may be even more localized than previously anticipated. A bottleneck test did not reveal any signs of a founder effect between Yap and Palau. Overall, the data supports the idea that recovery of A. hyacinthus in Palau did not come exclusively from a single source but most likely came from a combination of areas, including sites within Palau. In light of these results there seems to be very little connectivity around the barrier reef and management recommendation would be to increase the number or the size of MPAs within Palau.
bibliographic citation: Cros et al. (2016) Population genetic structure between Yap and Palau for the coral Acropora hyacinthus. PeerJ 4:e2330 https://doi.org/10.7717/peerj.2330
date submitted: 2016-04-27
date accepted: 2016-07-14
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cros
  given name: Annick
author list: Agent
  family name: Toonen
  given name: Robert J.
author list: Agent
  family name: Davies
  given name: Sarah W.
author list: Agent
  family name: Karl
  given name: Stephen A.
doi: 10.7717/peerj.2330
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Cros et al.
attribution name: Cros et al.

A resource-based game theoretical approach for the paradox of the plankton
type: item
type: AcademicArticle
description: The maintenance of species diversity is a central focus in ecology. It is not rare to observe more species than the number of limiting resources, especially in plankton communities. However, such high species diversity is hard to achieve in theory under the competitive exclusion principles, known as the plankton paradox. Previous studies often focus on the coexistence of predefined species and ignore the fact that species can evolve. We model multi-resource competitions using evolutionary games, where the number of species fluctuates under extinction and the appearance of new species. The interspecific and intraspecific competitions are captured by a dynamical payoff matrix, which has a size of the number of species. The competition strength (payoff entries) is obtained from comparing the capability of species in consuming resources, which can change over time. This allows for the robust coexistence of a large number of species, providing a possible solution to the plankton paradox.
format: application/pdf
format: text/html
creator: Weini Huang
creator: Paulo Roberto de Araujo Campos
creator: Viviane Moraes de Oliveira
creator: Fernando Fagundes Ferrreira
subject: Computational Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.2329
publisher: PeerJ Inc.
rights: © 2016 Huang et al.
abstract: The maintenance of species diversity is a central focus in ecology. It is not rare to observe more species than the number of limiting resources, especially in plankton communities. However, such high species diversity is hard to achieve in theory under the competitive exclusion principles, known as the plankton paradox. Previous studies often focus on the coexistence of predefined species and ignore the fact that species can evolve. We model multi-resource competitions using evolutionary games, where the number of species fluctuates under extinction and the appearance of new species. The interspecific and intraspecific competitions are captured by a dynamical payoff matrix, which has a size of the number of species. The competition strength (payoff entries) is obtained from comparing the capability of species in consuming resources, which can change over time. This allows for the robust coexistence of a large number of species, providing a possible solution to the plankton paradox.
bibliographic citation: Huang et al. (2016) A resource-based game theoretical approach for the paradox of the plankton. PeerJ 4:e2329 https://doi.org/10.7717/peerj.2329
date submitted: 2016-05-18
date accepted: 2016-07-14
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Weini
author list: Agent
  family name: de Araujo Campos
  given name: Paulo Roberto
author list: Agent
  family name: Moraes de Oliveira
  given name: Viviane
author list: Agent
  family name: Fagundes Ferrreira
  given name: Fernando
doi: 10.7717/peerj.2329
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Huang et al.
attribution name: Huang et al.

Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice
type: item
type: AcademicArticle
description: It has been reported that social isolation stress could be a key factor that leads to cognitive deficit for both humans and rodent models. However, detailed mechanisms are not yet clear. ADAR1 (Adenosine deaminase acting on RNA) is an enzyme involved in RNA editing that has a close relation to cognitive function. We have hypothesized that social isolation stress may impact the expression of ADAR1 in the brain of mice with cognitive deficit. To test our hypothesis, we evaluated the cognition ability of mice isolated for different durations (2, 4, and 8 weeks) using object recognition and object location tests; we also measured ADAR1 expression in hippocampus and cortex using immunohistochemistry and western blot. Our study showed that social isolation stress induced spatial and non-spatial cognition deficits of the tested mice. In addition, social isolation significantly increased both the immunoreactivity and protein expression of ADAR1 (p110) in the hippocampus and frontal cortex. Furthermore, re-socialization could not only recover the cognition deficits, but also bring ADAR1 (p110) immunoreactivity of hippocampus and frontal cortex, as well as ADAR1 (p110) protein expression of hippocampus back to the normal level for the isolated mice in adolescence. In conclusion, social isolation stress significantly increases ADAR1 (p110) expression in the hippocampus and frontal cortex of the mice with cognitive deficit. This finding may open a window to better understand the reasons (e.g., epigenetic change) that are responsible for social isolation-induced cognitive deficit and help the development of novel therapies for the resulted diseases.
format: application/pdf
format: text/html
creator: Wei Chen
creator: Dong An
creator: Hong Xu
creator: Xiaoxin Cheng
creator: Shiwei Wang
creator: Weizhi Yu
creator: Deqin Yu
creator: Dan Zhao
creator: Yiping Sun
creator: Wuguo Deng
creator: Yiyuan Tang
creator: Shengming Yin
subject: Animal Behavior
subject: Biochemistry
subject: Neuroscience
subject: Toxicology
subject: Pharmacology
description: doi:10.7717/peerj.2306
publisher: PeerJ Inc.
rights: © 2016 Chen et al.
abstract: It has been reported that social isolation stress could be a key factor that leads to cognitive deficit for both humans and rodent models. However, detailed mechanisms are not yet clear. ADAR1 (Adenosine deaminase acting on RNA) is an enzyme involved in RNA editing that has a close relation to cognitive function. We have hypothesized that social isolation stress may impact the expression of ADAR1 in the brain of mice with cognitive deficit. To test our hypothesis, we evaluated the cognition ability of mice isolated for different durations (2, 4, and 8 weeks) using object recognition and object location tests; we also measured ADAR1 expression in hippocampus and cortex using immunohistochemistry and western blot. Our study showed that social isolation stress induced spatial and non-spatial cognition deficits of the tested mice. In addition, social isolation significantly increased both the immunoreactivity and protein expression of ADAR1 (p110) in the hippocampus and frontal cortex. Furthermore, re-socialization could not only recover the cognition deficits, but also bring ADAR1 (p110) immunoreactivity of hippocampus and frontal cortex, as well as ADAR1 (p110) protein expression of hippocampus back to the normal level for the isolated mice in adolescence. In conclusion, social isolation stress significantly increases ADAR1 (p110) expression in the hippocampus and frontal cortex of the mice with cognitive deficit. This finding may open a window to better understand the reasons (e.g., epigenetic change) that are responsible for social isolation-induced cognitive deficit and help the development of novel therapies for the resulted diseases.
bibliographic citation: Chen et al. (2016) Effects of social isolation and re-socialization on cognition and ADAR1 (p110) expression in mice. PeerJ 4:e2306 https://doi.org/10.7717/peerj.2306
date submitted: 2016-04-24
date accepted: 2016-07-09
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Wei
author list: Agent
  family name: An
  given name: Dong
author list: Agent
  family name: Xu
  given name: Hong
author list: Agent
  family name: Cheng
  given name: Xiaoxin
author list: Agent
  family name: Wang
  given name: Shiwei
author list: Agent
  family name: Yu
  given name: Weizhi
author list: Agent
  family name: Yu
  given name: Deqin
author list: Agent
  family name: Zhao
  given name: Dan
author list: Agent
  family name: Sun
  given name: Yiping
author list: Agent
  family name: Deng
  given name: Wuguo
author list: Agent
  family name: Tang
  given name: Yiyuan
author list: Agent
  family name: Yin
  given name: Shengming
doi: 10.7717/peerj.2306
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Chen et al.
attribution name: Chen et al.

Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines
type: item
type: AcademicArticle
description: The vertebrate fauna of the Philippines, known for its diversity and high proportion of endemic species, comprises mainly small- to medium-sized forms with a few large exceptions. As with other tropical ecosystems, the major threats to wildlife are habitat loss, hunting and invasive species, of which the feral cat (Felis catus) is considered the most damaging. Our camera-trapping study focused on a terrestrial vertebrate species inventory on Bohol Island and tempo-spatial co-occurrences of feral cats with their prey and competitors. The survey took place in the Rajah Sikatuna Protected Landscape, and we examined the primary rainforest, its border with agricultural land, and rural areas in the vicinity of villages. Altogether, over 2,885 trap days we captured 30 species of vertebrates–10 mammals (including Sus philippensis), 19 birds and one reptile, Varanus cumingi. We trapped 81.8% of expected vertebrates. Based on the number of events, the most frequent native species was the barred rail (Gallirallus torquatus). The highest overlap in diel activity between cats and potential prey was recorded with rodents in rural areas (Δ = 0.62); the lowest was in the same habitat with ground-dwelling birds (Δ = 0.40). Cat activity was not recorded inside the rainforest; in other habitats their diel activity pattern differed. The cats’ activity declined in daylight in the proximity of humans, while it peaked at the transition zone between rainforest and fields. Both rodents and ground-dwelling birds exhibited a shift in activity levels between sites where cats were present or absent. Rodents tend to become active by day in cat-free habitats. No cats’ temporal response to co-occurrences of civets (Paradoxurus hermaphroditus and Viverra tangalunga) was found but cats in diel activity avoided domestic dogs (Canis lupus familiaris). Our first insight into the ecology of this invasive predator in the Philippines revealed an avoidance of homogeneous primary rainforest and a tendency t…
format: application/pdf
format: text/html
creator: Vlastimil Bogdan
creator: Tomáš Jůnek
creator: Pavla Jůnková Vymyslická
subject: Biodiversity
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
description: doi:10.7717/peerj.2288
publisher: PeerJ Inc.
rights: © 2016 Bogdan et al.
abstract: The vertebrate fauna of the Philippines, known for its diversity and high proportion of endemic species, comprises mainly small- to medium-sized forms with a few large exceptions. As with other tropical ecosystems, the major threats to wildlife are habitat loss, hunting and invasive species, of which the feral cat (Felis catus) is considered the most damaging. Our camera-trapping study focused on a terrestrial vertebrate species inventory on Bohol Island and tempo-spatial co-occurrences of feral cats with their prey and competitors. The survey took place in the Rajah Sikatuna Protected Landscape, and we examined the primary rainforest, its border with agricultural land, and rural areas in the vicinity of villages. Altogether, over 2,885 trap days we captured 30 species of vertebrates–10 mammals (including Sus philippensis), 19 birds and one reptile, Varanus cumingi. We trapped 81.8% of expected vertebrates. Based on the number of events, the most frequent native species was the barred rail (Gallirallus torquatus). The highest overlap in diel activity between cats and potential prey was recorded with rodents in rural areas (Δ = 0.62); the lowest was in the same habitat with ground-dwelling birds (Δ = 0.40). Cat activity was not recorded inside the rainforest; in other habitats their diel activity pattern differed. The cats’ activity declined in daylight in the proximity of humans, while it peaked at the transition zone between rainforest and fields. Both rodents and ground-dwelling birds exhibited a shift in activity levels between sites where cats were present or absent. Rodents tend to become active by day in cat-free habitats. No cats’ temporal response to co-occurrences of civets (Paradoxurus hermaphroditus and Viverra tangalunga) was found but cats in diel activity avoided domestic dogs (Canis lupus familiaris). Our first insight into the ecology of this invasive predator in the Philippines revealed an avoidance of homogeneous primary rainforest and a tendency t…
bibliographic citation: Bogdan et al. (2016) Temporal overlaps of feral cats with prey and competitors in primary and human-altered habitats on Bohol Island, Philippines. PeerJ 4:e2288 https://doi.org/10.7717/peerj.2288
date submitted: 2016-02-20
date accepted: 2016-07-05
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bogdan
  given name: Vlastimil
author list: Agent
  family name: Jůnek
  given name: Tomáš
author list: Agent
  family name: Jůnková Vymyslická
  given name: Pavla
doi: 10.7717/peerj.2288
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Bogdan et al.
attribution name: Bogdan et al.

Microbe-ID: an open source toolbox for microbial genotyping and species identification
type: item
type: AcademicArticle
description: Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.
format: application/pdf
format: text/html
creator: Javier F. Tabima
creator: Sydney E. Everhart
creator: Meredith M. Larsen
creator: Alexandra J. Weisberg
creator: Zhian N. Kamvar
creator: Matthew A. Tancos
creator: Christine D. Smart
creator: Jeff H. Chang
creator: Niklaus J. Grünwald
subject: Agricultural Science
subject: Bioinformatics
subject: Microbiology
subject: Mycology
subject: Taxonomy
description: doi:10.7717/peerj.2279
publisher: PeerJ Inc.
rights: © 2016 Tabima et al.
abstract: Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.
bibliographic citation: Tabima et al. (2016) Microbe-ID: an open source toolbox for microbial genotyping and species identification. PeerJ 4:e2279 https://doi.org/10.7717/peerj.2279
date submitted: 2016-04-29
date accepted: 2016-07-02
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tabima
  given name: Javier F.
author list: Agent
  family name: Everhart
  given name: Sydney E.
author list: Agent
  family name: Larsen
  given name: Meredith M.
author list: Agent
  family name: Weisberg
  given name: Alexandra J.
author list: Agent
  family name: Kamvar
  given name: Zhian N.
author list: Agent
  family name: Tancos
  given name: Matthew A.
author list: Agent
  family name: Smart
  given name: Christine D.
author list: Agent
  family name: Chang
  given name: Jeff H.
author list: Agent
  family name: Grünwald
  given name: Niklaus J.
doi: 10.7717/peerj.2279
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: ©2016 Tabima et al.
attribution name: Tabima et al.

Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals
type: item
type: AcademicArticle
description: Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.
format: application/pdf
format: text/html
creator: Jean-Baptiste Raina
creator: Dianne Tapiolas
creator: Cherie A. Motti
creator: Sylvain Foret
creator: Torsten Seemann
creator: Jan Tebben
creator: Bette L. Willis
creator: David G. Bourne
subject: Marine Biology
subject: Microbiology
description: doi:10.7717/peerj.2275
publisher: PeerJ Inc.
rights: © 2016 Raina et al.
abstract: Bacterial communities associated with healthy corals produce antimicrobial compounds that inhibit the colonization and growth of invasive microbes and potential pathogens. To date, however, bacteria-derived antimicrobial molecules have not been identified in reef-building corals. Here, we report the isolation of an antimicrobial compound produced by Pseudovibrio sp. P12, a common and abundant coral-associated bacterium. This strain was capable of metabolizing dimethylsulfoniopropionate (DMSP), a sulfur molecule produced in high concentrations by reef-building corals and playing a role in structuring their bacterial communities. Bioassay-guided fractionation coupled with nuclear magnetic resonance (NMR) and mass spectrometry (MS), identified the antimicrobial as tropodithietic acid (TDA), a sulfur-containing compound likely derived from DMSP catabolism. TDA was produced in large quantities by Pseudovibrio sp., and prevented the growth of two previously identified coral pathogens, Vibrio coralliilyticus and V. owensii, at very low concentrations (0.5 μg/mL) in agar diffusion assays. Genome sequencing of Pseudovibrio sp. P12 identified gene homologs likely involved in the metabolism of DMSP and production of TDA. These results provide additional evidence for the integral role of DMSP in structuring coral-associated bacterial communities and underline the potential of these DMSP-metabolizing microbes to contribute to coral disease prevention.
bibliographic citation: Raina et al. (2016) Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals. PeerJ 4:e2275 https://doi.org/10.7717/peerj.2275
date submitted: 2016-05-15
date accepted: 2016-07-19
issued: 2016-08-18
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Raina
  given name: Jean-Baptiste
author list: Agent
  family name: Tapiolas
  given name: Dianne
author list: Agent
  family name: Motti
  given name: Cherie A.
author list: Agent
  family name: Foret
  given name: Sylvain
author list: Agent
  family name: Seemann
  given name: Torsten
author list: Agent
  family name: Tebben
  given name: Jan
author list: Agent
  family name: Willis
  given name: Bette L.
author list: Agent
  family name: Bourne
  given name: David G.
doi: 10.7717/peerj.2275
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-18
copyright: © 2016 Raina et al.
attribution name: Raina et al.

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