PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Fish species richness is associated with the availability of landscape components across seasons in the Amazonian floodplain
items: Initial response of phenology and yield components of wheat (Triticum durum L., CIRNO C2008) under experimental warming field conditions in the Yaqui Valley
items: aaquetzalli is required for epithelial cell polarity and neural tissue formation in Drosophila
items: Biodegradation of Crystal Violet dye by bacteria isolated from textile industry effluents
items: Effects of anthropogenic wildfire in low-elevation Pacific island vegetation communities in French Polynesia
items: Comparison of the toxic effects of different mycotoxins on porcine and mouse oocyte meiosis
items: Patients with chronic periodontitis present increased risk for primary Sjögren syndrome: a nationwide population-based cohort study
items: Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria
items: Plant-insect interactions patterns in three European paleoforests of the late-Neogene—early-Quaternary
items: How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities

Fish species richness is associated with the availability of landscape components across seasons in the Amazonian floodplain
type: item
type: AcademicArticle
description: Understanding environmental biodiversity drivers in freshwater systems continues to be a fundamental challenge in studies of their fish assemblages. The present study seeks to determine the degree to which landscape variables of Amazonian floodplain lakes influences fish assemblages in these environments. Fish species richness was estimated in 15 Amazonian floodplain lakes during the high and low-water phases and correlated with the areas of four inundated wetland classes: (i) open water, (ii) flooded herbaceous, (iii) flooded shrubs and (iv) flooded forest estimated in different radius circular areas around each sampling site. Data were analyzed using generalized linear models with fish species richness, total and guilds as the dependent variable and estimates of buffered landscape areas as explanatory variables. Our analysis identified the significance of landscape variables in determining the diversity of fish assemblages in Amazonian floodplain lakes. Spatial scale was also identified as a significant determinant of fish diversity as landscape effects were more evident at larger spatial scales. In particular, (1) total species richness was more sensitive to variations in the landscape areas than number of species within guilds and (2) the spatial extent of the wetland class of shrubs was consistently the more influential on fish species diversity.
format: application/pdf
format: text/html
creator: Carlos Edwar Carvalho Freitas
creator: Laurie Laurenson
creator: Kedma Cristine Yamamoto
creator: Bruce Rider Forsberg
creator: Miguel Petrere
creator: Caroline Arantes
creator: Flavia Kelly Siqueira-Souza
subject: Aquaculture, Fisheries and Fish Science
subject: Freshwater Biology
description: doi:10.7717/peerj.5080
publisher: PeerJ Inc.
rights: © 2018 Carvalho Freitas et al.
abstract: Understanding environmental biodiversity drivers in freshwater systems continues to be a fundamental challenge in studies of their fish assemblages. The present study seeks to determine the degree to which landscape variables of Amazonian floodplain lakes influences fish assemblages in these environments. Fish species richness was estimated in 15 Amazonian floodplain lakes during the high and low-water phases and correlated with the areas of four inundated wetland classes: (i) open water, (ii) flooded herbaceous, (iii) flooded shrubs and (iv) flooded forest estimated in different radius circular areas around each sampling site. Data were analyzed using generalized linear models with fish species richness, total and guilds as the dependent variable and estimates of buffered landscape areas as explanatory variables. Our analysis identified the significance of landscape variables in determining the diversity of fish assemblages in Amazonian floodplain lakes. Spatial scale was also identified as a significant determinant of fish diversity as landscape effects were more evident at larger spatial scales. In particular, (1) total species richness was more sensitive to variations in the landscape areas than number of species within guilds and (2) the spatial extent of the wetland class of shrubs was consistently the more influential on fish species diversity.
bibliographic citation: Carvalho Freitas et al. (2018) Fish species richness is associated with the availability of landscape components across seasons in the Amazonian floodplain. PeerJ 6:e5080 https://doi.org/10.7717/peerj.5080
date submitted: 2018-01-23
date accepted: 2018-06-04
issued: 2018-06-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carvalho Freitas
  given name: Carlos Edwar
author list: Agent
  family name: Laurenson
  given name: Laurie
author list: Agent
  family name: Yamamoto
  given name: Kedma Cristine
author list: Agent
  family name: Forsberg
  given name: Bruce Rider
author list: Agent
  family name: Petrere
  given name: Miguel
author list: Agent
  family name: Arantes
  given name: Caroline
author list: Agent
  family name: Siqueira-Souza
  given name: Flavia Kelly
doi: 10.7717/peerj.5080
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-21
copyright: © 2018 Carvalho Freitas et al.
attribution name: Carvalho Freitas et al.

Initial response of phenology and yield components of wheat (Triticum durum L., CIRNO C2008) under experimental warming field conditions in the Yaqui Valley
type: item
type: AcademicArticle
description: This work evaluates the experimental warming effects on phenology and grain yield components of wheat in the Yaqui Valley, Sonora, México, using CIRNO C2008 variety from Triticum durum L., as a model during the cropping cycle of 2016–2017 (December to April). Infrared radiators were deployed to induce experimental warming by 2 °C above ambient crop canopy temperature, in a temperature free-air controlled enhancement system. Temperature was controlled by infrared temperature sensors placed in eight plots which covered a circle of r = 1.5 m starting five days after germination until harvest. The warming treatment caused a reduction of phenophases occurrence starting at the stem extension phenophase. Such phenological responses generated a significant biological cycle reduction of 14 days. Despite this delay, CIRNO C2008 completed its biological cycle adequately. However, plant height under the warming treatment was reduced significantly and differences were particularly observed at the final phenophases of the vegetative cycle. Plant height correlated negatively with spikes length, spikes mass, and number of filled grains. Warming also reduced grain yield in 33%. The warming treatment caused a stress intensity (SI = 1-yield warming/yield control) of 39.4% and 33.2% in biomass and grain yield, respectively. The differences in stress intensities between biomass and grain yield were based on plant height reduction. Grain mass was not affected, demonstrating the crop capability for remobilization and adequate distribution of elaborated substances for the spikes under warming conditions.
format: application/pdf
format: text/html
creator: Jaime Garatuza-Payan
creator: Leandris Argentel-Martinez
creator: Enrico A. Yepez
creator: Tulio Arredondo
subject: Agricultural Science
subject: Plant Science
subject: Climate Change Biology
description: doi:10.7717/peerj.5064
publisher: PeerJ Inc.
rights: © 2018 Garatuza-Payan et al.
abstract: This work evaluates the experimental warming effects on phenology and grain yield components of wheat in the Yaqui Valley, Sonora, México, using CIRNO C2008 variety from Triticum durum L., as a model during the cropping cycle of 2016–2017 (December to April). Infrared radiators were deployed to induce experimental warming by 2 °C above ambient crop canopy temperature, in a temperature free-air controlled enhancement system. Temperature was controlled by infrared temperature sensors placed in eight plots which covered a circle of r = 1.5 m starting five days after germination until harvest. The warming treatment caused a reduction of phenophases occurrence starting at the stem extension phenophase. Such phenological responses generated a significant biological cycle reduction of 14 days. Despite this delay, CIRNO C2008 completed its biological cycle adequately. However, plant height under the warming treatment was reduced significantly and differences were particularly observed at the final phenophases of the vegetative cycle. Plant height correlated negatively with spikes length, spikes mass, and number of filled grains. Warming also reduced grain yield in 33%. The warming treatment caused a stress intensity (SI = 1-yield warming/yield control) of 39.4% and 33.2% in biomass and grain yield, respectively. The differences in stress intensities between biomass and grain yield were based on plant height reduction. Grain mass was not affected, demonstrating the crop capability for remobilization and adequate distribution of elaborated substances for the spikes under warming conditions.
bibliographic citation: Garatuza-Payan et al. (2018) Initial response of phenology and yield components of wheat (Triticum durum L., CIRNO C2008) under experimental warming field conditions in the Yaqui Valley. PeerJ 6:e5064 https://doi.org/10.7717/peerj.5064
date submitted: 2018-03-30
date accepted: 2018-06-04
issued: 2018-06-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garatuza-Payan
  given name: Jaime
author list: Agent
  family name: Argentel-Martinez
  given name: Leandris
author list: Agent
  family name: Yepez
  given name: Enrico A.
author list: Agent
  family name: Arredondo
  given name: Tulio
doi: 10.7717/peerj.5064
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-21
copyright: © 2018 Garatuza-Payan et al.
attribution name: Garatuza-Payan et al.

aaquetzalli is required for epithelial cell polarity and neural tissue formation in Drosophila
type: item
type: AcademicArticle
description: Morphogenetic movements during embryogenesis require dynamic changes in epithelial cell polarity and cytoskeletal reorganization. Such changes involve, among others, rearrangements of cell-cell contacts and protein traffic. In Drosophila melanogaster, neuroblast delamination during early neurogenesis is a well-characterized process requiring a polarized neuroepithelium, regulated by the Notch signaling pathway. Maintenance of epithelial cell polarity ensues proper Notch pathway activation during neurogenesis. We characterize here aaquetzalli (aqz), a gene whose mutations affect cell polarity and nervous system specification. The aqz locus encodes a protein that harbors a domain with significant homology to a proline-rich conserved domain of nuclear receptor co-activators. aqz expression occurs at all stages of the fly life cycle, and is dynamic. aqz mutants are lethal, showing a disruption of cell polarity during embryonic ventral neuroepithelium differentiation resulting in loss of epithelial integrity and mislocalization of membrane proteins (shown by mislocalization of Crumbs, DE-Cadherin, and Delta). As a consequence, aqz mutant embryos with compromised apical-basal cell polarity develop spotty changes of neuronal and epithelial numbers of cells.
format: application/pdf
format: text/html
creator: Miguel A. Mendoza-Ortíz
creator: Juan M. Murillo-Maldonado
creator: Juan R. Riesgo-Escovar
subject: Developmental Biology
subject: Genetics
description: doi:10.7717/peerj.5042
publisher: PeerJ Inc.
rights: © 2018 Mendoza-Ortíz et al.
abstract: Morphogenetic movements during embryogenesis require dynamic changes in epithelial cell polarity and cytoskeletal reorganization. Such changes involve, among others, rearrangements of cell-cell contacts and protein traffic. In Drosophila melanogaster, neuroblast delamination during early neurogenesis is a well-characterized process requiring a polarized neuroepithelium, regulated by the Notch signaling pathway. Maintenance of epithelial cell polarity ensues proper Notch pathway activation during neurogenesis. We characterize here aaquetzalli (aqz), a gene whose mutations affect cell polarity and nervous system specification. The aqz locus encodes a protein that harbors a domain with significant homology to a proline-rich conserved domain of nuclear receptor co-activators. aqz expression occurs at all stages of the fly life cycle, and is dynamic. aqz mutants are lethal, showing a disruption of cell polarity during embryonic ventral neuroepithelium differentiation resulting in loss of epithelial integrity and mislocalization of membrane proteins (shown by mislocalization of Crumbs, DE-Cadherin, and Delta). As a consequence, aqz mutant embryos with compromised apical-basal cell polarity develop spotty changes of neuronal and epithelial numbers of cells.
bibliographic citation: Mendoza-Ortíz et al. (2018) aaquetzalli is required for epithelial cell polarity and neural tissue formation in Drosophila. PeerJ 6:e5042 https://doi.org/10.7717/peerj.5042
date submitted: 2018-03-13
date accepted: 2018-05-31
issued: 2018-06-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza-Ortíz
  given name: Miguel A.
author list: Agent
  family name: Murillo-Maldonado
  given name: Juan M.
author list: Agent
  family name: Riesgo-Escovar
  given name: Juan R.
doi: 10.7717/peerj.5042
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-21
copyright: ©2018 Mendoza-Ortíz et al.
attribution name: Mendoza-Ortíz et al.

Biodegradation of Crystal Violet dye by bacteria isolated from textile industry effluents
type: item
type: AcademicArticle
description: Industrial effluent containing textile dyes is regarded as a major environmental concern in the present world. Crystal Violet is one of the vital textile dyes of the triphenylmethane group; it is widely used in textile industry and known for its mutagenic and mitotic poisoning nature. Bioremediation, especially through bacteria, is becoming an emerging and important sector in effluent treatment. This study aimed to isolate and identify Crystal Violet degrading bacteria from industrial effluents with potential use in bioremediation. The decolorizing activity of the bacteria was measured using a photo electric colorimeter after aerobic incubation in different time intervals of the isolates. Environmental parameters such as pH, temperature, initial dye concentration and inoculum size were optimized using mineral salt medium containing different concentration of Crystal Violet dye. Complete decolorizing efficiency was observed in a mineral salt medium containing up to 150 mg/l of Crystal Violet dye by 10% (v/v) inoculums of Enterobacter sp. CV–S1 tested under 72 h of shaking incubation at temperature 35 °C and pH 6.5. Newly identified bacteria Enterobacter sp. CV–S1, confirmed by 16S ribosomal RNA sequencing, was found as a potential bioremediation biocatalyst in the aerobic degradation/de-colorization of Crystal Violet dye. The efficiency of degrading triphenylmethane dye by this isolate, minus the supply of extra carbon or nitrogen sources in the media, highlights the significance of larger-scale treatment of textile effluent.
format: application/pdf
format: text/html
creator: Dipankar Chandra Roy
creator: Sudhangshu Kumar Biswas
creator: Ananda Kumar Saha
creator: Biswanath Sikdar
creator: Mizanur Rahman
creator: Apurba Kumar Roy
creator: Zakaria Hossain Prodhan
creator: Swee-Seong Tang
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
subject: Green Chemistry
description: doi:10.7717/peerj.5015
publisher: PeerJ Inc.
rights: © 2018 Roy et al.
abstract: Industrial effluent containing textile dyes is regarded as a major environmental concern in the present world. Crystal Violet is one of the vital textile dyes of the triphenylmethane group; it is widely used in textile industry and known for its mutagenic and mitotic poisoning nature. Bioremediation, especially through bacteria, is becoming an emerging and important sector in effluent treatment. This study aimed to isolate and identify Crystal Violet degrading bacteria from industrial effluents with potential use in bioremediation. The decolorizing activity of the bacteria was measured using a photo electric colorimeter after aerobic incubation in different time intervals of the isolates. Environmental parameters such as pH, temperature, initial dye concentration and inoculum size were optimized using mineral salt medium containing different concentration of Crystal Violet dye. Complete decolorizing efficiency was observed in a mineral salt medium containing up to 150 mg/l of Crystal Violet dye by 10% (v/v) inoculums of Enterobacter sp. CV–S1 tested under 72 h of shaking incubation at temperature 35 °C and pH 6.5. Newly identified bacteria Enterobacter sp. CV–S1, confirmed by 16S ribosomal RNA sequencing, was found as a potential bioremediation biocatalyst in the aerobic degradation/de-colorization of Crystal Violet dye. The efficiency of degrading triphenylmethane dye by this isolate, minus the supply of extra carbon or nitrogen sources in the media, highlights the significance of larger-scale treatment of textile effluent.
bibliographic citation: Roy et al. (2018) Biodegradation of Crystal Violet dye by bacteria isolated from textile industry effluents. PeerJ 6:e5015 https://doi.org/10.7717/peerj.5015
date submitted: 2018-01-29
date accepted: 2018-05-21
issued: 2018-06-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roy
  given name: Dipankar Chandra
author list: Agent
  family name: Biswas
  given name: Sudhangshu Kumar
author list: Agent
  family name: Saha
  given name: Ananda Kumar
author list: Agent
  family name: Sikdar
  given name: Biswanath
author list: Agent
  family name: Rahman
  given name: Mizanur
author list: Agent
  family name: Roy
  given name: Apurba Kumar
author list: Agent
  family name: Prodhan
  given name: Zakaria Hossain
author list: Agent
  family name: Tang
  given name: Swee-Seong
doi: 10.7717/peerj.5015
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-21
copyright: ©2018 Roy et al.
attribution name: Roy et al.

Effects of anthropogenic wildfire in low-elevation Pacific island vegetation communities in French Polynesia
type: item
type: AcademicArticle
description: Anthropogenic (or human-caused) wildfire is an increasingly important driver of ecological change on Pacific islands including southeastern Polynesia, but fire ecology studies are almost completely absent for this region. Where observations do exist, they mostly represent descriptions of fire effects on plant communities before the introduction of invasive species in the modern era. Understanding the effects of wildfire in southeastern Polynesian island vegetation communities can elucidate which species may become problematic invasives with continued wildfire activity. We investigate the effects of wildfire on vegetation in three low-elevation sites (45–379 m) on the island of Mo’orea in the Society Islands, French Polynesia, which are already heavily impacted by past human land use and invasive exotic plants, but retain some native flora. In six study areas (three burned and three unburned comparisons), we placed 30 transects across sites and collected species and abundance information at 390 points. We analyzed each local community of plants in three categories: natives, those introduced by Polynesians before European contact (1767 C.E.), and those introduced since European contact. Burned areas had the same or lower mean species richness than paired comparison sites. Although wildfire did not affect the proportions of native and introduced species, it may increase the abundance of introduced species on some sites. Non-metric multidimensional scaling indicates that (not recently modified) comparison plant communities are more distinct from one another than are those on burned sites. We discuss conservation concerns for particular native plants absent from burned sites, as well as invasive species (including Lantana camara and Paraserianthes falcataria) that may be promoted by fire in the Pacific.
format: application/pdf
format: text/html
creator: Erica A. Newman
creator: Carlea A. Winkler
creator: David H. Hembry
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Ecosystem Science
subject: Environmental Impacts
description: doi:10.7717/peerj.5114
publisher: PeerJ Inc.
rights: © 2018
abstract: Anthropogenic (or human-caused) wildfire is an increasingly important driver of ecological change on Pacific islands including southeastern Polynesia, but fire ecology studies are almost completely absent for this region. Where observations do exist, they mostly represent descriptions of fire effects on plant communities before the introduction of invasive species in the modern era. Understanding the effects of wildfire in southeastern Polynesian island vegetation communities can elucidate which species may become problematic invasives with continued wildfire activity. We investigate the effects of wildfire on vegetation in three low-elevation sites (45–379 m) on the island of Mo’orea in the Society Islands, French Polynesia, which are already heavily impacted by past human land use and invasive exotic plants, but retain some native flora. In six study areas (three burned and three unburned comparisons), we placed 30 transects across sites and collected species and abundance information at 390 points. We analyzed each local community of plants in three categories: natives, those introduced by Polynesians before European contact (1767 C.E.), and those introduced since European contact. Burned areas had the same or lower mean species richness than paired comparison sites. Although wildfire did not affect the proportions of native and introduced species, it may increase the abundance of introduced species on some sites. Non-metric multidimensional scaling indicates that (not recently modified) comparison plant communities are more distinct from one another than are those on burned sites. We discuss conservation concerns for particular native plants absent from burned sites, as well as invasive species (including Lantana camara and Paraserianthes falcataria) that may be promoted by fire in the Pacific.
bibliographic citation: Newman et al. (2018) Effects of anthropogenic wildfire in low-elevation Pacific island vegetation communities in French Polynesia. PeerJ 6:e5114 https://doi.org/10.7717/peerj.5114
date submitted: 2017-12-21
date accepted: 2018-06-07
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Newman
  given name: Erica A.
author list: Agent
  family name: Winkler
  given name: Carlea A.
author list: Agent
  family name: Hembry
  given name: David H.
doi: 10.7717/peerj.5114
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20

Comparison of the toxic effects of different mycotoxins on porcine and mouse oocyte meiosis
type: item
type: AcademicArticle
description: Background Aflatoxin B1 (AFB1), deoxynivalenol (DON), HT-2, ochratoxin A (OTA), zearalenone (ZEA) are the most common mycotoxins that are found in corn-based animal feed which have multiple toxic effects on animals and humans. Previous studies reported that these mycotoxins impaired mammalian oocyte quality. However, the effective concentrations of mycotoxins to animal oocytes were different. Methods In this study we aimed to compare the sensitivity of mouse and porcine oocytes to AFB1, DON, HT-2, OTA, and ZEA for mycotoxin research. We adopted the polar body extrusion rate of mouse and porcine oocyte as the standard for the effects of mycotoxins on oocyte maturation. Results and Discussion Our results showed that 10 μM AFB1 and 1 μM DON significantly affected porcine oocyte maturation compared with 50 μM AFB1 and 2 μM DON on mouse oocytes. However, 10 nM HT-2 significantly affected mouse oocyte maturation compared with 50 nM HT-2 on porcine oocytes. Moreover, 5 μM OTA and 10 μM ZEA significantly affected porcine oocyte maturation compared with 300 μM OTA and 50 μM ZEA on mouse oocytes. In summary, our results showed that porcine oocytes were more sensitive to AFB1, DON, OTA, and ZEA than mouse oocytes except HT-2 toxin.
format: application/pdf
format: text/html
creator: Yujie Lu
creator: Yue Zhang
creator: Jia-Qian Liu
creator: Peng Zou
creator: Lu Jia
creator: Yong-Teng Su
creator: Yu-Rong Sun
creator: Shao-Chen Sun
subject: Agricultural Science
subject: Cell Biology
subject: Developmental Biology
subject: Food Science and Technology
subject: Toxicology
description: doi:10.7717/peerj.5111
publisher: PeerJ Inc.
rights: © 2018 Lu et al.
abstract: Background Aflatoxin B1 (AFB1), deoxynivalenol (DON), HT-2, ochratoxin A (OTA), zearalenone (ZEA) are the most common mycotoxins that are found in corn-based animal feed which have multiple toxic effects on animals and humans. Previous studies reported that these mycotoxins impaired mammalian oocyte quality. However, the effective concentrations of mycotoxins to animal oocytes were different. Methods In this study we aimed to compare the sensitivity of mouse and porcine oocytes to AFB1, DON, HT-2, OTA, and ZEA for mycotoxin research. We adopted the polar body extrusion rate of mouse and porcine oocyte as the standard for the effects of mycotoxins on oocyte maturation. Results and Discussion Our results showed that 10 μM AFB1 and 1 μM DON significantly affected porcine oocyte maturation compared with 50 μM AFB1 and 2 μM DON on mouse oocytes. However, 10 nM HT-2 significantly affected mouse oocyte maturation compared with 50 nM HT-2 on porcine oocytes. Moreover, 5 μM OTA and 10 μM ZEA significantly affected porcine oocyte maturation compared with 300 μM OTA and 50 μM ZEA on mouse oocytes. In summary, our results showed that porcine oocytes were more sensitive to AFB1, DON, OTA, and ZEA than mouse oocytes except HT-2 toxin.
bibliographic citation: Lu et al. (2018) Comparison of the toxic effects of different mycotoxins on porcine and mouse oocyte meiosis. PeerJ 6:e5111 https://doi.org/10.7717/peerj.5111
date submitted: 2018-03-28
date accepted: 2018-06-06
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Yujie
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: Liu
  given name: Jia-Qian
author list: Agent
  family name: Zou
  given name: Peng
author list: Agent
  family name: Jia
  given name: Lu
author list: Agent
  family name: Su
  given name: Yong-Teng
author list: Agent
  family name: Sun
  given name: Yu-Rong
author list: Agent
  family name: Sun
  given name: Shao-Chen
doi: 10.7717/peerj.5111
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Lu et al.
attribution name: Lu et al.

Patients with chronic periodontitis present increased risk for primary Sjögren syndrome: a nationwide population-based cohort study
type: item
type: AcademicArticle
description: Many reports have mentioned the association between chronic periodontitis (CP) and primary Sjögren syndrome (pSS). However, no cohort study has been performed for the risk of pSS in patients with CP. In this study, we evaluated the risk of pSS from CP exposure in a nationwide population-based cohort study in Taiwan. We studied the claims data of Taiwanese population from 2001 to 2012. We identified 76,765 patients with CP from the National Health Insurance Database in Taiwan. We also selected 76,765 controls that were randomly frequency matched by age, sex, and index year from the general population. We analyzed the risk of pSS by using Cox proportional hazards regression models including sex, age, and comorbidities. In this study, 76,765 patients with CP (mean age: 40.8 years) and 76,765 controls (mean age: 41.0 years) were followed-up for 8.54 and 8.49 years, respectively. A total of 869 cases of pSS were identified in CP cohort and 483 cases in non-CP cohort. Multivariate Cox regression analysis indicated that the incidence rate of pSS was significantly higher in CP cohort than those who in non-CP cohort (adjusted HR: 1.79, 95% CI [1.60–2.00]). Taken together, this nationwide retrospective cohort study demonstrated that the risk of pSS was significantly higher in patients with CP than in the general population. The association between CP and pSS was significant in the female group.
format: application/pdf
format: text/html
creator: Tai-Chen Lin
creator: Chien-Fang Tseng
creator: Yu-Hsun Wang
creator: Hui-Chieh Yu
creator: Yu-Chao Chang
subject: Dentistry
subject: Epidemiology
subject: Immunology
subject: Public Health
subject: Rheumatology
description: doi:10.7717/peerj.5109
publisher: PeerJ Inc.
rights: © 2018 Lin et al.
abstract: Many reports have mentioned the association between chronic periodontitis (CP) and primary Sjögren syndrome (pSS). However, no cohort study has been performed for the risk of pSS in patients with CP. In this study, we evaluated the risk of pSS from CP exposure in a nationwide population-based cohort study in Taiwan. We studied the claims data of Taiwanese population from 2001 to 2012. We identified 76,765 patients with CP from the National Health Insurance Database in Taiwan. We also selected 76,765 controls that were randomly frequency matched by age, sex, and index year from the general population. We analyzed the risk of pSS by using Cox proportional hazards regression models including sex, age, and comorbidities. In this study, 76,765 patients with CP (mean age: 40.8 years) and 76,765 controls (mean age: 41.0 years) were followed-up for 8.54 and 8.49 years, respectively. A total of 869 cases of pSS were identified in CP cohort and 483 cases in non-CP cohort. Multivariate Cox regression analysis indicated that the incidence rate of pSS was significantly higher in CP cohort than those who in non-CP cohort (adjusted HR: 1.79, 95% CI [1.60–2.00]). Taken together, this nationwide retrospective cohort study demonstrated that the risk of pSS was significantly higher in patients with CP than in the general population. The association between CP and pSS was significant in the female group.
bibliographic citation: Lin et al. (2018) Patients with chronic periodontitis present increased risk for primary Sjögren syndrome: a nationwide population-based cohort study. PeerJ 6:e5109 https://doi.org/10.7717/peerj.5109
date submitted: 2018-03-29
date accepted: 2018-06-06
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Tai-Chen
author list: Agent
  family name: Tseng
  given name: Chien-Fang
author list: Agent
  family name: Wang
  given name: Yu-Hsun
author list: Agent
  family name: Yu
  given name: Hui-Chieh
author list: Agent
  family name: Chang
  given name: Yu-Chao
doi: 10.7717/peerj.5109
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Lin et al.
attribution name: Lin et al.

Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria
type: item
type: AcademicArticle
description: Honey bee colonies suffer from various pathogens, including honey bee viruses. About 24 viruses have been reported so far. However, six of them are considered to cause severe infection which inflicts heavy losses on beekeeping. The aim of this study was to investigate incidence of six honey bee viruses: deformed wing virus (DWV), acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV), sacbrood virus (SBV), kashmir bee virus (KBV), and black queen cell virus (BQCV) by a reverse transcription polymerase chain reaction (RT-PCR). A total of 250 adult honey bee samples were obtained from 50 colonies from eight apiaries situated in three different parts of the country (South, North and West Bulgaria). The results showed the highest prevalence of DWV followed by SBV and ABPV, and one case of BQCV. A comparison with homology sequences available in GenBank was performed by phylogenetic analysis, and phylogenetic relationships were discussed in the context of newly described genotypes in the uninvestigated South Eastern region of Europe. In conclusion, the present study has been the first to provide sequencing data and phylogenetics analyses of some honey bee viruses in Bulgaria.
format: application/pdf
format: text/html
creator: Rositsa Shumkova
creator: Boyko Neov
creator: Daniela Sirakova
creator: Ani Georgieva
creator: Dimitar Gadjev
creator: Denitsa Teofanova
creator: Georgi Radoslavov
creator: Maria Bouga
creator: Peter Hristov
subject: Biodiversity
subject: Entomology
subject: Genetics
subject: Virology
description: doi:10.7717/peerj.5077
publisher: PeerJ Inc.
rights: © 2018 Shumkova et al.
abstract: Honey bee colonies suffer from various pathogens, including honey bee viruses. About 24 viruses have been reported so far. However, six of them are considered to cause severe infection which inflicts heavy losses on beekeeping. The aim of this study was to investigate incidence of six honey bee viruses: deformed wing virus (DWV), acute bee paralysis virus (ABPV), chronic bee paralysis virus (CBPV), sacbrood virus (SBV), kashmir bee virus (KBV), and black queen cell virus (BQCV) by a reverse transcription polymerase chain reaction (RT-PCR). A total of 250 adult honey bee samples were obtained from 50 colonies from eight apiaries situated in three different parts of the country (South, North and West Bulgaria). The results showed the highest prevalence of DWV followed by SBV and ABPV, and one case of BQCV. A comparison with homology sequences available in GenBank was performed by phylogenetic analysis, and phylogenetic relationships were discussed in the context of newly described genotypes in the uninvestigated South Eastern region of Europe. In conclusion, the present study has been the first to provide sequencing data and phylogenetics analyses of some honey bee viruses in Bulgaria.
bibliographic citation: Shumkova et al. (2018) Molecular detection and phylogenetic assessment of six honeybee viruses in Apis mellifera L. colonies in Bulgaria. PeerJ 6:e5077 https://doi.org/10.7717/peerj.5077
date submitted: 2018-02-28
date accepted: 2018-06-04
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shumkova
  given name: Rositsa
author list: Agent
  family name: Neov
  given name: Boyko
author list: Agent
  family name: Sirakova
  given name: Daniela
author list: Agent
  family name: Georgieva
  given name: Ani
author list: Agent
  family name: Gadjev
  given name: Dimitar
author list: Agent
  family name: Teofanova
  given name: Denitsa
author list: Agent
  family name: Radoslavov
  given name: Georgi
author list: Agent
  family name: Bouga
  given name: Maria
author list: Agent
  family name: Hristov
  given name: Peter
doi: 10.7717/peerj.5077
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: ©2018 Shumkova et al.
attribution name: Shumkova et al.

Plant-insect interactions patterns in three European paleoforests of the late-Neogene—early-Quaternary
type: item
type: AcademicArticle
description: Plants and insects are constantly interacting in complex ways through forest communities since hundreds of millions of years. Those interactions are often related to variations in the climate. Climate change, due to human activities, may have disturbed these relationships in modern ecosystems. Fossil leaf assemblages are thus good opportunities to survey responses of plant–insect interactions to climate variations over the time. The goal of this study is to discuss the possible causes of the differences of plant–insect interactions’ patterns in European paleoforests from the Neogene–Quaternary transition. This was accomplished through three fossil leaf assemblages: Willershausen, Berga (both from the late Neogene of Germany) and Bernasso (from the early Quaternary of France). In Willershausen it has been measured that half of the leaves presented insect interactions, 35% of the fossil leaves were impacted by insects in Bernasso and only 25% in Berga. The largest proportion of these interactions in Bernasso were categorized as specialist (mainly due to galling) while in Willershausen and Berga those ones were significantly more generalist. Contrary to previous studies, this study did not support the hypothesis that the mean annual precipitation and temperature were the main factors that impacted the different plant–insect interactions’ patterns. However, for the first time, our results tend to support that the hydric seasonality and the mean temperature of the coolest months could be potential factors influencing fossil plant–insect interactions.
format: application/pdf
format: text/html
creator: Benjamin Adroit
creator: Vincent Girard
creator: Lutz Kunzmann
creator: Jean-Frédéric Terral
creator: Torsten Wappler
subject: Ecology
subject: Ecosystem Science
subject: Paleontology
subject: Plant Science
description: doi:10.7717/peerj.5075
publisher: PeerJ Inc.
rights: © 2018 Adroit et al.
abstract: Plants and insects are constantly interacting in complex ways through forest communities since hundreds of millions of years. Those interactions are often related to variations in the climate. Climate change, due to human activities, may have disturbed these relationships in modern ecosystems. Fossil leaf assemblages are thus good opportunities to survey responses of plant–insect interactions to climate variations over the time. The goal of this study is to discuss the possible causes of the differences of plant–insect interactions’ patterns in European paleoforests from the Neogene–Quaternary transition. This was accomplished through three fossil leaf assemblages: Willershausen, Berga (both from the late Neogene of Germany) and Bernasso (from the early Quaternary of France). In Willershausen it has been measured that half of the leaves presented insect interactions, 35% of the fossil leaves were impacted by insects in Bernasso and only 25% in Berga. The largest proportion of these interactions in Bernasso were categorized as specialist (mainly due to galling) while in Willershausen and Berga those ones were significantly more generalist. Contrary to previous studies, this study did not support the hypothesis that the mean annual precipitation and temperature were the main factors that impacted the different plant–insect interactions’ patterns. However, for the first time, our results tend to support that the hydric seasonality and the mean temperature of the coolest months could be potential factors influencing fossil plant–insect interactions.
bibliographic citation: Adroit et al. (2018) Plant-insect interactions patterns in three European paleoforests of the late-Neogene—early-Quaternary. PeerJ 6:e5075 https://doi.org/10.7717/peerj.5075
date submitted: 2017-11-29
date accepted: 2018-06-04
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adroit
  given name: Benjamin
author list: Agent
  family name: Girard
  given name: Vincent
author list: Agent
  family name: Kunzmann
  given name: Lutz
author list: Agent
  family name: Terral
  given name: Jean-Frédéric
author list: Agent
  family name: Wappler
  given name: Torsten
doi: 10.7717/peerj.5075
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Adroit et al.
attribution name: Adroit et al.

How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities
type: item
type: AcademicArticle
description: Background Underwater visual surveys (UVSs) for monitoring fish communities are preferred over fishing surveys in certain habitats, such as rocky or coral reefs and seagrass beds and are the standard monitoring tool in many cases, especially in protected areas. However, despite their wide application there are potential biases, mainly due to imperfect detectability and the behavioral responses of fish to the observers. Methods The performance of two methods of UVSs were compared to test whether they give similar results in terms of fish population density, occupancy, species richness, and community composition. Distance sampling (line transects) and plot sampling (strip transects) were conducted at 31 rocky reef sites in the Aegean Sea (Greece) using SCUBA diving. Results Line transects generated significantly higher values of occupancy, species richness, and total fish density compared to strip transects. For most species, density estimates differed significantly between the two sampling methods. For secretive species and species avoiding the observers, the line transect method yielded higher estimates, as it accounted for imperfect detectability and utilized a larger survey area compared to the strip transect method. On the other hand, large-scale spatial patterns of species composition were similar for both methods. Discussion Overall, both methods presented a number of advantages and limitations, which should be considered in survey design. Line transects appear to be more suitable for surveying secretive species, while strip transects should be preferred at high fish densities and for species of high mobility.
format: application/pdf
format: text/html
creator: Zoi Thanopoulou
creator: Maria Sini
creator: Konstantinos Vatikiotis
creator: Christos Katsoupis
creator: Panayiotis G. Dimitrakopoulos
creator: Stelios Katsanevakis
subject: Aquaculture
subject: Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.5066
publisher: PeerJ Inc.
rights: © 2018 Thanopoulou et al.
abstract: Background Underwater visual surveys (UVSs) for monitoring fish communities are preferred over fishing surveys in certain habitats, such as rocky or coral reefs and seagrass beds and are the standard monitoring tool in many cases, especially in protected areas. However, despite their wide application there are potential biases, mainly due to imperfect detectability and the behavioral responses of fish to the observers. Methods The performance of two methods of UVSs were compared to test whether they give similar results in terms of fish population density, occupancy, species richness, and community composition. Distance sampling (line transects) and plot sampling (strip transects) were conducted at 31 rocky reef sites in the Aegean Sea (Greece) using SCUBA diving. Results Line transects generated significantly higher values of occupancy, species richness, and total fish density compared to strip transects. For most species, density estimates differed significantly between the two sampling methods. For secretive species and species avoiding the observers, the line transect method yielded higher estimates, as it accounted for imperfect detectability and utilized a larger survey area compared to the strip transect method. On the other hand, large-scale spatial patterns of species composition were similar for both methods. Discussion Overall, both methods presented a number of advantages and limitations, which should be considered in survey design. Line transects appear to be more suitable for surveying secretive species, while strip transects should be preferred at high fish densities and for species of high mobility.
bibliographic citation: Thanopoulou et al. (2018) How many fish? Comparison of two underwater visual sampling methods for monitoring fish communities. PeerJ 6:e5066 https://doi.org/10.7717/peerj.5066
date submitted: 2018-01-23
date accepted: 2018-06-03
issued: 2018-06-20
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thanopoulou
  given name: Zoi
author list: Agent
  family name: Sini
  given name: Maria
author list: Agent
  family name: Vatikiotis
  given name: Konstantinos
author list: Agent
  family name: Katsoupis
  given name: Christos
author list: Agent
  family name: Dimitrakopoulos
  given name: Panayiotis G.
author list: Agent
  family name: Katsanevakis
  given name: Stelios
doi: 10.7717/peerj.5066
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-06-20
copyright: © 2018 Thanopoulou et al.
attribution name: Thanopoulou et al.

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