PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Chrysophyllum cainito stem bark extract induces apoptosis in Human hepatocarcinoma HepG2 cells through ROS-mediated mitochondrial pathway
items: Testing the short-and long-term effects of elevated prenatal exposure to different forms of thyroid hormones
items: Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
items: The fungal community in non-rhizosphere soil of Panax ginseng are driven by different cultivation modes and increased cultivation periods
items: Molecular epidemiology and clinical characteristics of herpangina children in Beijing, China: a surveillance study
items: Injuries among children and adolescents in a rapidly growing urban African metropolis: a cross-sectional survey of 1,968 households in Dar es Salaam, Tanzania
items: Multiple factors influence local perceptions of snow leopards and Himalayan wolves in the central Himalayas, Nepal
items: Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)
items: Colonization of novel algal habitats by juveniles of a marine tube-dwelling amphipod
items: Physical inactivity as a risk factor to mortality by ischemic heart disease during economic and political crisis in Brazil

Chrysophyllum cainito stem bark extract induces apoptosis in Human hepatocarcinoma HepG2 cells through ROS-mediated mitochondrial pathway
type: item
type: AcademicArticle
description: Hepatocellular carcinoma is the most common type of primary liver cancer in humans. This study aimed to demonstrate anticancer properties of an aqueous extract from Chrysophyllum cainito stem bark (CE) and its underlying mechanisms. Our MTT assay results showed that CE significantly reduced human hepatocellular carcinoma (HepG2) cell viability with the IC50of 100 µg/mL, while human dermal primary fibroblast (HDFa) cells showed less susceptibility in every concentration tested. Determined by Annexin V staining, the proportion of apoptotic HepG2 cells increased in a dose-dependent fashion after 24 hour-exposure of CE. The results from Western blot analysis confirmed that CE reduced procaspase-3, suggesting apoptosis by activating caspase-3 cleavage. Using the DCFH-DA and DiOC6 fluorescent probes, it was found that CE significantly stimulated the generation of reactive oxygen species (ROS) and reduced mitochondrial membrane potential (Δψ m), respectively. According to cell cycle analysis, CE (100 µg/mL) profoundly increased the percentage of cells in the sub-G1 phase, indicating cell apoptosis. These data suggest that CE induces apoptosis and cell death in human hepatocellular carcinoma via generation of intracellular ROS and disruption of Δψm. This is the first demonstration of the anticancer activity with proposed underlying mechanism of CE in liver cancer cells.
format: application/pdf
format: text/html
creator: Hau V. Doan
creator: Pishyaporn Sritangos
creator: Roongtip Iyara
creator: Nuannoi Chudapongse
subject: Toxicology
subject: Evidence Based Medicine
subject: Pharmacology
subject: Translational Medicine
description: doi:10.7717/peerj.10168
publisher: PeerJ Inc.
rights: © 2020 Doan et al.
abstract: Hepatocellular carcinoma is the most common type of primary liver cancer in humans. This study aimed to demonstrate anticancer properties of an aqueous extract from Chrysophyllum cainito stem bark (CE) and its underlying mechanisms. Our MTT assay results showed that CE significantly reduced human hepatocellular carcinoma (HepG2) cell viability with the IC50of 100 µg/mL, while human dermal primary fibroblast (HDFa) cells showed less susceptibility in every concentration tested. Determined by Annexin V staining, the proportion of apoptotic HepG2 cells increased in a dose-dependent fashion after 24 hour-exposure of CE. The results from Western blot analysis confirmed that CE reduced procaspase-3, suggesting apoptosis by activating caspase-3 cleavage. Using the DCFH-DA and DiOC6 fluorescent probes, it was found that CE significantly stimulated the generation of reactive oxygen species (ROS) and reduced mitochondrial membrane potential (Δψ m), respectively. According to cell cycle analysis, CE (100 µg/mL) profoundly increased the percentage of cells in the sub-G1 phase, indicating cell apoptosis. These data suggest that CE induces apoptosis and cell death in human hepatocellular carcinoma via generation of intracellular ROS and disruption of Δψm. This is the first demonstration of the anticancer activity with proposed underlying mechanism of CE in liver cancer cells.
bibliographic citation: Doan et al. (2020) Chrysophyllum cainito stem bark extract induces apoptosis in Human hepatocarcinoma HepG2 cells through ROS-mediated mitochondrial pathway. PeerJ 8:e10168 https://doi.org/10.7717/peerj.10168
date submitted: 2019-09-24
date accepted: 2020-09-22
issued: 2020-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doan
  given name: Hau V.
author list: Agent
  family name: Sritangos
  given name: Pishyaporn
author list: Agent
  family name: Iyara
  given name: Roongtip
author list: Agent
  family name: Chudapongse
  given name: Nuannoi
doi: 10.7717/peerj.10168
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-16
copyright: ©2020 Doan et al.
attribution name: Doan et al.

Testing the short-and long-term effects of elevated prenatal exposure to different forms of thyroid hormones
type: item
type: AcademicArticle
description: Maternal thyroid hormones (THs) are known to be crucial in embryonic development in humans, but their influence on other, especially wild, animals remains poorly understood. So far, the studies that experimentally investigated the consequences of maternal THs focused on short-term effects, while early organisational effects with long-term consequences, as shown for other prenatal hormones, could also be expected. In this study, we aimed at investigating both the short- and long-term effects of prenatal THs in a bird species, the Japanese quail Coturnix japonica. We experimentally elevated yolk TH content (the prohormone T4, and its active metabolite T3, as well as a combination of both hormones). We analysed hatching success, embryonic development, offspring growth and oxidative stress as well as their potential organisational effects on reproduction, moult and oxidative stress in adulthood. We found that eggs injected with T4 had a higher hatching success compared with control eggs, suggesting conversion of T4 into T3 by the embryo. We detected no evidence for other short-term or long-term effects of yolk THs. These results suggest that yolk THs are important in the embryonic stage of precocial birds, but other short- and long-term consequences remain unclear. Research on maternal THs will greatly benefit from studies investigating how embryos use and respond to this maternal signalling. Long-term studies on prenatal THs in other taxa in the wild are needed for a better understanding of this hormone-mediated maternal pathway.
format: application/pdf
format: text/html
creator: Tom Sarraude
creator: Bin-Yan Hsu
creator: Ton Groothuis
creator: Suvi Ruuskanen
subject: Developmental Biology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.10175
publisher: PeerJ Inc.
rights: © 2020 Sarraude et al.
abstract: Maternal thyroid hormones (THs) are known to be crucial in embryonic development in humans, but their influence on other, especially wild, animals remains poorly understood. So far, the studies that experimentally investigated the consequences of maternal THs focused on short-term effects, while early organisational effects with long-term consequences, as shown for other prenatal hormones, could also be expected. In this study, we aimed at investigating both the short- and long-term effects of prenatal THs in a bird species, the Japanese quail Coturnix japonica. We experimentally elevated yolk TH content (the prohormone T4, and its active metabolite T3, as well as a combination of both hormones). We analysed hatching success, embryonic development, offspring growth and oxidative stress as well as their potential organisational effects on reproduction, moult and oxidative stress in adulthood. We found that eggs injected with T4 had a higher hatching success compared with control eggs, suggesting conversion of T4 into T3 by the embryo. We detected no evidence for other short-term or long-term effects of yolk THs. These results suggest that yolk THs are important in the embryonic stage of precocial birds, but other short- and long-term consequences remain unclear. Research on maternal THs will greatly benefit from studies investigating how embryos use and respond to this maternal signalling. Long-term studies on prenatal THs in other taxa in the wild are needed for a better understanding of this hormone-mediated maternal pathway.
bibliographic citation: Sarraude et al. (2020) Testing the short-and long-term effects of elevated prenatal exposure to different forms of thyroid hormones. PeerJ 8:e10175 https://doi.org/10.7717/peerj.10175
date submitted: 2020-04-13
date accepted: 2020-09-22
issued: 2020-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sarraude
  given name: Tom
author list: Agent
  family name: Hsu
  given name: Bin-Yan
author list: Agent
  family name: Groothuis
  given name: Ton
author list: Agent
  family name: Ruuskanen
  given name: Suvi
doi: 10.7717/peerj.10175
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-16
copyright: © 2020 Sarraude et al.
attribution name: Sarraude et al.

Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function
type: item
type: AcademicArticle
description: Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Methods Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. Results We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.
format: application/pdf
format: text/html
creator: Alejandro Berrio
creator: Valerie Gartner
creator: Gregory A. Wray
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Virology
description: doi:10.7717/peerj.10234
publisher: PeerJ Inc.
rights: © 2020 Berrio et al.
abstract: Background The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Methods Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. Results We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.
bibliographic citation: Berrio et al. (2020) Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function. PeerJ 8:e10234 https://doi.org/10.7717/peerj.10234
date submitted: 2020-09-15
date accepted: 2020-10-04
issued: 2020-10-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berrio
  given name: Alejandro
author list: Agent
  family name: Gartner
  given name: Valerie
author list: Agent
  family name: Wray
  given name: Gregory A.
doi: 10.7717/peerj.10234
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-16
copyright: © 2020 Berrio et al.
attribution name: Berrio et al.

The fungal community in non-rhizosphere soil of Panax ginseng are driven by different cultivation modes and increased cultivation periods
type: item
type: AcademicArticle
description: Continuous cropping obstacles severely hindered the sustained development of the ginseng industry. Among the obstacles, an imbalance of soil microbiome community was considered one of the major culprits. The fungal community is an essential part of the soil microbiome community. Extensive characterization of the fungal community composition and variation during ginseng cultivation will help us understand the mechanism underlying continuous cropping obstacles. By using a high-throughput amplicon sequencing method, the non-rhizospheric fungal community of farmland cultivated ginseng of 2 years old (C2) and 5 years old (C5), understory wild ginseng of 15 years old (W15) and 35 years old (W35), fallow fields which have been abandoned for 10 (F10) years were characterized. Farmland cultivated ginseng and understory wild ginseng harbored distinct non-rhizospheric fungal communities, and extension of cultivation periods enlarged the fungal community difference between two cultivation modes. Extended cultivation periods significantly decreased the OTU richness and PD whole tree indices, and OTU number and cultivation periods were negatively correlated. Extension of cultivation periods led to an increased abundance of pathotrophs. Still, the increased abundance of pathotrophs may not be the leading cause of severe continuous cropping obstacles in farmland cultivated ginseng. Compared with understory wild ginseng, farmland cultivated ginseng had a lower abundance of symbiotrophs and a higher abundance of saprotrophs. This changed symbiotrophs/saprotrophs ratio may have some correlation with the severe continuous cropping obstacles that occurred in farmland cultivated ginseng. Fallowing on the fungal community of the non-rhizosphere soil was generally opposite of that of extension of ginseng cultivation periods. The impacts of farmland cultivation on the fungal community of the non-rhizosphere soil can last for decades, even if the following is practiced.
format: application/pdf
format: text/html
creator: Yu Bao
creator: Bao Qi
creator: Wei Huang
creator: Bao Liu
creator: Yu Li
subject: Agricultural Science
subject: Biodiversity
subject: Microbiology
subject: Mycology
subject: Soil Science
description: doi:10.7717/peerj.9930
publisher: PeerJ Inc.
rights: © 2020 Bao et al.
abstract: Continuous cropping obstacles severely hindered the sustained development of the ginseng industry. Among the obstacles, an imbalance of soil microbiome community was considered one of the major culprits. The fungal community is an essential part of the soil microbiome community. Extensive characterization of the fungal community composition and variation during ginseng cultivation will help us understand the mechanism underlying continuous cropping obstacles. By using a high-throughput amplicon sequencing method, the non-rhizospheric fungal community of farmland cultivated ginseng of 2 years old (C2) and 5 years old (C5), understory wild ginseng of 15 years old (W15) and 35 years old (W35), fallow fields which have been abandoned for 10 (F10) years were characterized. Farmland cultivated ginseng and understory wild ginseng harbored distinct non-rhizospheric fungal communities, and extension of cultivation periods enlarged the fungal community difference between two cultivation modes. Extended cultivation periods significantly decreased the OTU richness and PD whole tree indices, and OTU number and cultivation periods were negatively correlated. Extension of cultivation periods led to an increased abundance of pathotrophs. Still, the increased abundance of pathotrophs may not be the leading cause of severe continuous cropping obstacles in farmland cultivated ginseng. Compared with understory wild ginseng, farmland cultivated ginseng had a lower abundance of symbiotrophs and a higher abundance of saprotrophs. This changed symbiotrophs/saprotrophs ratio may have some correlation with the severe continuous cropping obstacles that occurred in farmland cultivated ginseng. Fallowing on the fungal community of the non-rhizosphere soil was generally opposite of that of extension of ginseng cultivation periods. The impacts of farmland cultivation on the fungal community of the non-rhizosphere soil can last for decades, even if the following is practiced.
bibliographic citation: Bao et al. (2020) The fungal community in non-rhizosphere soil of Panax ginseng are driven by different cultivation modes and increased cultivation periods. PeerJ 8:e9930 https://doi.org/10.7717/peerj.9930
date submitted: 2019-06-05
date accepted: 2020-08-21
issued: 2020-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bao
  given name: Yu
author list: Agent
  family name: Qi
  given name: Bao
author list: Agent
  family name: Huang
  given name: Wei
author list: Agent
  family name: Liu
  given name: Bao
author list: Agent
  family name: Li
  given name: Yu
doi: 10.7717/peerj.9930
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-15
copyright: ©2020 Bao et al.
attribution name: Bao et al.

Molecular epidemiology and clinical characteristics of herpangina children in Beijing, China: a surveillance study
type: item
type: AcademicArticle
description: Background Herpangina is a highly infectious disease, which is usually prevalent in preschool children. Methods This study analyzed the clinical and pathogenic characteristics of herpangina children to demonstrate the epidemiology of herpangina. Clinical manifestations, laboratory indicators and pharyngeal swabs were collected from children with herpangina who were monitored by Tongzhou Center for Disease Control and Prevention in Beijing, 2008. Utilizing pharyngeal swabs, virus extraction and amplification were performed for nucleotide identification and sequencing. The phylogenetic analysis was conducted based on all sequences amplified in this study and strains retrieved from GenBank. Results Among 190 children with herpangina, 69.0% (131/190) were positive for enterovirus. Eight genotypes were identified, mainly including CV-A6 (39/131), CV-A4 (25/131), CV-A10 (24/131). The phylogenetic analysis showed one CV-A6 strain of Tongzhou was imported from Japan. CV-A10 strains were clustered into five groups (A-E). The dominant cluster of CV-A10 was Group E6 between 2009 and 2013, and converted to Group E5 after 2013. CV-A6 was the predominant pathogen causing herpangina in Tongzhou in 2018, followed by CV-A4 and CV-A10. Conclusions The circulation of coxsackievirus had spatiotemporal cluster. In controlling the transmission of herpangina, the surveillance and reporting system should be enhanced.
format: application/pdf
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creator: Tian-Shuo Zhao
creator: Juan Du
creator: Hong-Jun Li
creator: Yan Cui
creator: Yaqiong Liu
creator: Yanna Yang
creator: Fuqiang Cui
creator: Qing-Bin Lu
subject: Virology
subject: Dentistry
subject: Epidemiology
subject: Infectious Diseases
subject: Pediatrics
description: doi:10.7717/peerj.9991
publisher: PeerJ Inc.
rights: © 2020 Zhao et al.
abstract: Background Herpangina is a highly infectious disease, which is usually prevalent in preschool children. Methods This study analyzed the clinical and pathogenic characteristics of herpangina children to demonstrate the epidemiology of herpangina. Clinical manifestations, laboratory indicators and pharyngeal swabs were collected from children with herpangina who were monitored by Tongzhou Center for Disease Control and Prevention in Beijing, 2008. Utilizing pharyngeal swabs, virus extraction and amplification were performed for nucleotide identification and sequencing. The phylogenetic analysis was conducted based on all sequences amplified in this study and strains retrieved from GenBank. Results Among 190 children with herpangina, 69.0% (131/190) were positive for enterovirus. Eight genotypes were identified, mainly including CV-A6 (39/131), CV-A4 (25/131), CV-A10 (24/131). The phylogenetic analysis showed one CV-A6 strain of Tongzhou was imported from Japan. CV-A10 strains were clustered into five groups (A-E). The dominant cluster of CV-A10 was Group E6 between 2009 and 2013, and converted to Group E5 after 2013. CV-A6 was the predominant pathogen causing herpangina in Tongzhou in 2018, followed by CV-A4 and CV-A10. Conclusions The circulation of coxsackievirus had spatiotemporal cluster. In controlling the transmission of herpangina, the surveillance and reporting system should be enhanced.
bibliographic citation: Zhao et al. (2020) Molecular epidemiology and clinical characteristics of herpangina children in Beijing, China: a surveillance study. PeerJ 8:e9991 https://doi.org/10.7717/peerj.9991
date submitted: 2020-05-06
date accepted: 2020-08-28
issued: 2020-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Tian-Shuo
author list: Agent
  family name: Du
  given name: Juan
author list: Agent
  family name: Li
  given name: Hong-Jun
author list: Agent
  family name: Cui
  given name: Yan
author list: Agent
  family name: Liu
  given name: Yaqiong
author list: Agent
  family name: Yang
  given name: Yanna
author list: Agent
  family name: Cui
  given name: Fuqiang
author list: Agent
  family name: Lu
  given name: Qing-Bin
doi: 10.7717/peerj.9991
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-15
copyright: ©2020 Zhao et al.
attribution name: Zhao et al.

Injuries among children and adolescents in a rapidly growing urban African metropolis: a cross-sectional survey of 1,968 households in Dar es Salaam, Tanzania
type: item
type: AcademicArticle
description: Objectives To assess the patterns and incidence of child and adolescent injury and explore associations with household deprivation and child characteristics in a low-income urban setting. Study Design Cross-sectional household survey in Dar es Salaam, Tanzania. Methods Data collection took place during July 2009. Injuries requiring medical attention were recorded with a one month period of recall. A total of 1,968 households representing 3,927 children and adolescents were visited by health workers. Gender-, age-, and type-specific injury incidence was compiled. Odds ratios were calculated to measure associations with child injury, perceived deprivation, household characteristics and child characteristics. Results One household in five reported injuries. The estimated incidence was 3.2 per 10,000 child-years. The most common identifiable injuries were falls (41%), cuts (22%) and burns (16%). Male and younger children aged 1–4 years were at higher risk (respectively OR = 1.36; p = 0.004; OR = 1.47; p ≤ 0.001). Conclusions In Dar e Salaam injuries are common. Future investigations should take into account both subjective and objective measurements of relative household deprivation and a clear criteria for the assessment of injury severity in community-based survey contexts.
format: application/pdf
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creator: Mónica Alejandra Pérez Méndez
creator: Hamisi A. Kigwangalla
creator: Till Bärnighausen
creator: Michael Lowery Wilson
subject: Epidemiology
subject: Global Health
subject: Nursing
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.10048
publisher: PeerJ Inc.
rights: © 2020 Pérez Méndez et al.
abstract: Objectives To assess the patterns and incidence of child and adolescent injury and explore associations with household deprivation and child characteristics in a low-income urban setting. Study Design Cross-sectional household survey in Dar es Salaam, Tanzania. Methods Data collection took place during July 2009. Injuries requiring medical attention were recorded with a one month period of recall. A total of 1,968 households representing 3,927 children and adolescents were visited by health workers. Gender-, age-, and type-specific injury incidence was compiled. Odds ratios were calculated to measure associations with child injury, perceived deprivation, household characteristics and child characteristics. Results One household in five reported injuries. The estimated incidence was 3.2 per 10,000 child-years. The most common identifiable injuries were falls (41%), cuts (22%) and burns (16%). Male and younger children aged 1–4 years were at higher risk (respectively OR = 1.36; p = 0.004; OR = 1.47; p ≤ 0.001). Conclusions In Dar e Salaam injuries are common. Future investigations should take into account both subjective and objective measurements of relative household deprivation and a clear criteria for the assessment of injury severity in community-based survey contexts.
bibliographic citation: Pérez Méndez et al. (2020) Injuries among children and adolescents in a rapidly growing urban African metropolis: a cross-sectional survey of 1,968 households in Dar es Salaam, Tanzania. PeerJ 8:e10048 https://doi.org/10.7717/peerj.10048
date submitted: 2020-03-02
date accepted: 2020-09-05
issued: 2020-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pérez Méndez
  given name: Mónica Alejandra
author list: Agent
  family name: Kigwangalla
  given name: Hamisi A.
author list: Agent
  family name: Bärnighausen
  given name: Till
author list: Agent
  family name: Lowery Wilson
  given name: Michael
doi: 10.7717/peerj.10048
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-15
copyright: ©2020 Pérez Méndez et al.
attribution name: Pérez Méndez et al.

Multiple factors influence local perceptions of snow leopards and Himalayan wolves in the central Himalayas, Nepal
type: item
type: AcademicArticle
description: An understanding of local perceptions of carnivores is important for conservation and management planning. In the central Himalayas, Nepal, we interviewed 428 individuals from 85 settlements using a semi-structured questionnaire to quantitatively assess local perceptions and tolerance of snow leopards and wolves. We used generalized linear mixed effect models to assess influential factors, and found that tolerance of snow leopards was much higher than of wolves. Interestingly, having experienced livestock losses had a minor impact on perceptions of the carnivores. Occupation of the respondents had a strong effect on perceptions of snow leopards but not of wolves. Literacy and age had weak impacts on snow leopard perceptions, but the interaction among these terms showed a marked effect, that is, being illiterate had a more marked negative impact among older respondents. Among the various factors affecting perceptions of wolves, numbers of livestock owned and gender were the most important predictors. People with larger livestock herds were more negative towards wolves. In terms of gender, males were more positive to wolves than females, but no such pattern was observed for snow leopards. People’s negative perceptions towards wolves were also related to the remoteness of the villages. Factors affecting people’s perceptions could not be generalized for the two species, and thus need to be addressed separately. We suggest future conservation projects and programs should prioritize remote settlements.
format: application/pdf
format: text/html
creator: Madhu Chetri
creator: Morten Odden
creator: Olivier Devineau
creator: Thomas McCarthy
creator: Per Wegge
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.10108
publisher: PeerJ Inc.
rights: © 2020 Chetri et al.
abstract: An understanding of local perceptions of carnivores is important for conservation and management planning. In the central Himalayas, Nepal, we interviewed 428 individuals from 85 settlements using a semi-structured questionnaire to quantitatively assess local perceptions and tolerance of snow leopards and wolves. We used generalized linear mixed effect models to assess influential factors, and found that tolerance of snow leopards was much higher than of wolves. Interestingly, having experienced livestock losses had a minor impact on perceptions of the carnivores. Occupation of the respondents had a strong effect on perceptions of snow leopards but not of wolves. Literacy and age had weak impacts on snow leopard perceptions, but the interaction among these terms showed a marked effect, that is, being illiterate had a more marked negative impact among older respondents. Among the various factors affecting perceptions of wolves, numbers of livestock owned and gender were the most important predictors. People with larger livestock herds were more negative towards wolves. In terms of gender, males were more positive to wolves than females, but no such pattern was observed for snow leopards. People’s negative perceptions towards wolves were also related to the remoteness of the villages. Factors affecting people’s perceptions could not be generalized for the two species, and thus need to be addressed separately. We suggest future conservation projects and programs should prioritize remote settlements.
bibliographic citation: Chetri et al. (2020) Multiple factors influence local perceptions of snow leopards and Himalayan wolves in the central Himalayas, Nepal. PeerJ 8:e10108 https://doi.org/10.7717/peerj.10108
date submitted: 2020-05-05
date accepted: 2020-09-15
issued: 2020-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chetri
  given name: Madhu
author list: Agent
  family name: Odden
  given name: Morten
author list: Agent
  family name: Devineau
  given name: Olivier
author list: Agent
  family name: McCarthy
  given name: Thomas
author list: Agent
  family name: Wegge
  given name: Per
doi: 10.7717/peerj.10108
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-15
copyright: © 2020 Chetri et al.
attribution name: Chetri et al.

Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae)
type: item
type: AcademicArticle
description: Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.
format: application/pdf
format: text/html
creator: Tian-Wen Xiao
creator: Yong Xu
creator: Lu Jin
creator: Tong-Jian Liu
creator: Hai-Fei Yan
creator: Xue-Jun Ge
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.10155
publisher: PeerJ Inc.
rights: © 2020 Xiao et al.
abstract: Background Gene tree discordance is common in phylogenetic analyses. Many phylogenetic studies have excluded non-coding regions of the plastome without evaluating their impact on tree topology. In general, plastid loci have often been treated as a single unit, and tree discordance among these loci has seldom been examined. Using samples of Laureae (Lauraceae) plastomes, we explored plastome variation among the tribe, examined the influence of non-coding regions on tree topology, and quantified intra-plastome conflict. Results We found that the plastomes of Laureae have low inter-specific variation and are highly similar in structure, size, and gene content. Laureae was divided into three groups, subclades I, II and III. The inclusion of non-coding regions changed the phylogenetic relationship among the three subclades. Topologies based on coding and non-coding regions were largely congruent except for the relationship among subclades I, II and III. By measuring the distribution of phylogenetic signal across loci that supported different topologies, we found that nine loci (two coding regions, two introns and five intergenic spacers) played a critical role at the contentious node. Conclusions Our results suggest that subclade III and subclade II are successively sister to subclade I. Conflicting phylogenetic signals exist between coding and non-coding regions of Laureae plastomes. Our study highlights the importance of evaluating the influence of non-coding regions on tree topology and emphasizes the necessity of examining discordance among different plastid loci in phylogenetic studies.
bibliographic citation: Xiao et al. (2020) Conflicting phylogenetic signals in plastomes of the tribe Laureae (Lauraceae). PeerJ 8:e10155 https://doi.org/10.7717/peerj.10155
date submitted: 2020-06-10
date accepted: 2020-09-21
issued: 2020-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Tian-Wen
author list: Agent
  family name: Xu
  given name: Yong
author list: Agent
  family name: Jin
  given name: Lu
author list: Agent
  family name: Liu
  given name: Tong-Jian
author list: Agent
  family name: Yan
  given name: Hai-Fei
author list: Agent
  family name: Ge
  given name: Xue-Jun
doi: 10.7717/peerj.10155
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-15
copyright: ©2020 Xiao et al.
attribution name: Xiao et al.

Colonization of novel algal habitats by juveniles of a marine tube-dwelling amphipod
type: item
type: AcademicArticle
description: Background Dispersal is an important process affecting population dynamics and connectivity. For marine direct developers, both adults and juveniles may disperse. Although the distribution of juveniles can be initially constrained by their mothers’ choice, they may be able to leave the parental habitat and colonize other habitats. We investigated the effect of habitat quality, patch size and presence of conspecific adults on the colonization of novel habitats by juveniles of the tube-dwelling amphipod Cymadusa filosa associated with the macroalgal host Sargassum filipendula. Methods We tested the factors listed above on the colonization of juveniles by manipulating natural and artificial plants in both the field and laboratory. Results In the laboratory, juveniles selected high-quality habitats (i.e., natural alga), where both food and shelter are provided, when low-quality resources (i.e., artificial alga) were also available. In contrast, habitat quality and algal patch size did not affect the colonization by juveniles in the field. Finally, the presence of conspecific adults did not affect the colonization of juveniles under laboratory condition but had a weak effect in the field experiment. Our results suggest that C. filosa juveniles can select and colonize novel habitats, and that such process can be partially affected by habitat quality, but not by patch size. Also, the presence of conspecifics may affect the colonization by juveniles. Successful colonization by this specific developmental stage under different scenarios indicates that juveniles may act as a dispersal agent in this species.
format: application/pdf
format: text/html
creator: Marilia Bueno
creator: Glauco B.O. Machado
creator: Fosca P.P. Leite
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.10188
publisher: PeerJ Inc.
rights: © 2020 Bueno et al.
abstract: Background Dispersal is an important process affecting population dynamics and connectivity. For marine direct developers, both adults and juveniles may disperse. Although the distribution of juveniles can be initially constrained by their mothers’ choice, they may be able to leave the parental habitat and colonize other habitats. We investigated the effect of habitat quality, patch size and presence of conspecific adults on the colonization of novel habitats by juveniles of the tube-dwelling amphipod Cymadusa filosa associated with the macroalgal host Sargassum filipendula. Methods We tested the factors listed above on the colonization of juveniles by manipulating natural and artificial plants in both the field and laboratory. Results In the laboratory, juveniles selected high-quality habitats (i.e., natural alga), where both food and shelter are provided, when low-quality resources (i.e., artificial alga) were also available. In contrast, habitat quality and algal patch size did not affect the colonization by juveniles in the field. Finally, the presence of conspecific adults did not affect the colonization of juveniles under laboratory condition but had a weak effect in the field experiment. Our results suggest that C. filosa juveniles can select and colonize novel habitats, and that such process can be partially affected by habitat quality, but not by patch size. Also, the presence of conspecifics may affect the colonization by juveniles. Successful colonization by this specific developmental stage under different scenarios indicates that juveniles may act as a dispersal agent in this species.
bibliographic citation: Bueno et al. (2020) Colonization of novel algal habitats by juveniles of a marine tube-dwelling amphipod. PeerJ 8:e10188 https://doi.org/10.7717/peerj.10188
date submitted: 2020-08-06
date accepted: 2020-09-24
issued: 2020-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bueno
  given name: Marilia
author list: Agent
  family name: Machado
  given name: Glauco B.O.
author list: Agent
  family name: Leite
  given name: Fosca P.P.
doi: 10.7717/peerj.10188
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-15
copyright: © 2020 Bueno et al.
attribution name: Bueno et al.

Physical inactivity as a risk factor to mortality by ischemic heart disease during economic and political crisis in Brazil
type: item
type: AcademicArticle
description: Background To investigate the burden of mortality due to ischemic heart disease (IHD) attributable to low levels of physical activity in the Brazilian population (aged ≥ 25 years) before, during and after economic and political crises (2007–2017). Methods This study was focused on IHD as a cause of death. The International Statistical Classification of Diseases (10th revision) codes related to IHD have been mapped. The data used for the physical activity estimates of the present study refer to surveys with random sampling carried out in the Brazilian territory that considers all domains of physical activity. The contribution of physical activity for mortality due to IHD was estimated using a comparative risk assessment approach. In addition, we verified the association between mortality due to IHD attributable to low levels of physical activity according to the Socio-demographic Index of the Brazilian states. Results For males it was estimated that in 2007 and 2017 there were, respectively, 9,585 and 11,821 deaths due to IHD as a result low physical activity. For females there were 8,689 deaths in 2007 and 10,779 deaths in 2017 due to IHD attributable to low physical activity. From 2007 to 2017, there was 12.0% (for males) and 16.0% (for females) of reduction in age-adjusted mortality rate due to IHD attributable to low physical activity. This reduction was not observed in the Northern and Northeastern regions of Brazil for the male population. Brazilian states with better socioeconomic conditions showed greater reductions in age-adjusted mortality rate due to IHD attributable to low physical activity (male: ρ = −0.74; female: ρ = −0.54) Conclusion The fiscal austerity policies implemented and the lower investment in social programs in the period of economic and political crisis highlighted the social inequalities between Brazilian geographic regions for the burden of mortality due to IHD attributable to low levels of physical activity.
format: application/pdf
format: text/html
creator: Diego Augusto Santos Silva
subject: Cardiology
subject: Epidemiology
subject: Global Health
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.10192
publisher: PeerJ Inc.
rights: © 2020 Silva
abstract: Background To investigate the burden of mortality due to ischemic heart disease (IHD) attributable to low levels of physical activity in the Brazilian population (aged ≥ 25 years) before, during and after economic and political crises (2007–2017). Methods This study was focused on IHD as a cause of death. The International Statistical Classification of Diseases (10th revision) codes related to IHD have been mapped. The data used for the physical activity estimates of the present study refer to surveys with random sampling carried out in the Brazilian territory that considers all domains of physical activity. The contribution of physical activity for mortality due to IHD was estimated using a comparative risk assessment approach. In addition, we verified the association between mortality due to IHD attributable to low levels of physical activity according to the Socio-demographic Index of the Brazilian states. Results For males it was estimated that in 2007 and 2017 there were, respectively, 9,585 and 11,821 deaths due to IHD as a result low physical activity. For females there were 8,689 deaths in 2007 and 10,779 deaths in 2017 due to IHD attributable to low physical activity. From 2007 to 2017, there was 12.0% (for males) and 16.0% (for females) of reduction in age-adjusted mortality rate due to IHD attributable to low physical activity. This reduction was not observed in the Northern and Northeastern regions of Brazil for the male population. Brazilian states with better socioeconomic conditions showed greater reductions in age-adjusted mortality rate due to IHD attributable to low physical activity (male: ρ = −0.74; female: ρ = −0.54) Conclusion The fiscal austerity policies implemented and the lower investment in social programs in the period of economic and political crisis highlighted the social inequalities between Brazilian geographic regions for the burden of mortality due to IHD attributable to low levels of physical activity.
bibliographic citation: Silva (2020) Physical inactivity as a risk factor to mortality by ischemic heart disease during economic and political crisis in Brazil. PeerJ 8:e10192 https://doi.org/10.7717/peerj.10192
date submitted: 2020-07-26
date accepted: 2020-09-24
issued: 2020-10-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Diego Augusto Santos
doi: 10.7717/peerj.10192
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-10-15
copyright: © 2020 Silva
attribution name: Silva

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