PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A non-invasive method to assess environmental contamination with avian pathogens: beak and feather disease virus (BFDV) detection in nest boxes
items: Expression and clinical significance of HSP27 and its phosphorylation in lower extremity arteriosclerosis obliterans
items: Adsorption and bonding strength of chromium species by ferrihydrite from acidic aqueous solutions
items: Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia
items: No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment
items: Consumer perceptions and reported wild and domestic meat and fish consumption behavior during the Ebola epidemic in Guinea, West Africa
items: Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.)
items: In silico and in vitro identification of secoisolariciresinol as a re-sensitizer of P-glycoprotein-dependent doxorubicin-resistance NCI/ADR-RES cancer cells
items: Fire severity effects on resprouting of subtropical dune thicket of the Cape Floristic Region
items: Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis)

A non-invasive method to assess environmental contamination with avian pathogens: beak and feather disease virus (BFDV) detection in nest boxes
type: item
type: AcademicArticle
description: Indirect transmission of pathogens can pose major risks to wildlife, yet the presence and persistence of wildlife pathogens in the environment has been little studied. Beak and feather disease virus (BFDV) is of global conservation concern: it can infect all members of the Psittaciformes, one of the most threatened bird orders, with infection often being lethal. Indirect transmission of BFDV through contaminated nest hollows has been proposed as a major infection source. However, data on whether and for how long nest sites in the wild remain contaminated have been absent. We determined the BFDV status of birds (parents and nestlings) for 82 nests of Crimson Rosellas, Platycercus elegans and Eastern Rosellas, Platycercus eximius. In 11 of these nests (13.4%, 95% confidence interval 6.9–22.7), we found an infected parent or nestling. Using nest swabs, we then compared BFDV presence at three points in time (before, during and after breeding) in three groups of nest boxes. These were nest boxes occupied by infected birds, and two control groups (nest boxes occupied by uninfected birds, and unoccupied nest boxes). Detection of BFDV on nest swabs was strongly associated with the infection status of parents in each nest box and with the timing of breeding. During breeding, boxes occupied by BFDV-positive birds were significantly more likely to have BFDV-positive nest swabs than boxes occupied by BFDV-negative birds; nest swabs tested BFDV-positive in 80% (28.4–99.5) of nests with parental antigen excretion, 66.7% (9.4–99.2) of nests occupied by parents with BFDV-positive cloacal swabs and 66.7% (22.3–95.7) of nests occupied by parents with BFDV–positive blood. 0% (0–52.2) of nests with BFDV–positive nestlings had BFDV–positive nest swabs. Across all boxes occupied by BFDV-positive birds (parents or nestlings), no nest swabs were BFDV–positive before breeding, 36.4% (95% CI 10.9–69.2) were positive during breeding and 9.1% (0.2–41.3) remained positive after breeding. BFDV w…
format: application/pdf
format: text/html
creator: Johanne M. Martens
creator: Helena S. Stokes
creator: Mathew L. Berg
creator: Ken Walder
creator: Shane R. Raidal
creator: Michael J.L. Magrath
creator: Andrew T.D. Bennett
subject: Conservation Biology
subject: Ecology
subject: Virology
subject: Zoology
description: doi:10.7717/peerj.9211
publisher: PeerJ Inc.
rights: © 2020 Martens et al.
abstract: Indirect transmission of pathogens can pose major risks to wildlife, yet the presence and persistence of wildlife pathogens in the environment has been little studied. Beak and feather disease virus (BFDV) is of global conservation concern: it can infect all members of the Psittaciformes, one of the most threatened bird orders, with infection often being lethal. Indirect transmission of BFDV through contaminated nest hollows has been proposed as a major infection source. However, data on whether and for how long nest sites in the wild remain contaminated have been absent. We determined the BFDV status of birds (parents and nestlings) for 82 nests of Crimson Rosellas, Platycercus elegans and Eastern Rosellas, Platycercus eximius. In 11 of these nests (13.4%, 95% confidence interval 6.9–22.7), we found an infected parent or nestling. Using nest swabs, we then compared BFDV presence at three points in time (before, during and after breeding) in three groups of nest boxes. These were nest boxes occupied by infected birds, and two control groups (nest boxes occupied by uninfected birds, and unoccupied nest boxes). Detection of BFDV on nest swabs was strongly associated with the infection status of parents in each nest box and with the timing of breeding. During breeding, boxes occupied by BFDV-positive birds were significantly more likely to have BFDV-positive nest swabs than boxes occupied by BFDV-negative birds; nest swabs tested BFDV-positive in 80% (28.4–99.5) of nests with parental antigen excretion, 66.7% (9.4–99.2) of nests occupied by parents with BFDV-positive cloacal swabs and 66.7% (22.3–95.7) of nests occupied by parents with BFDV–positive blood. 0% (0–52.2) of nests with BFDV–positive nestlings had BFDV–positive nest swabs. Across all boxes occupied by BFDV-positive birds (parents or nestlings), no nest swabs were BFDV–positive before breeding, 36.4% (95% CI 10.9–69.2) were positive during breeding and 9.1% (0.2–41.3) remained positive after breeding. BFDV w…
bibliographic citation: Martens et al. (2020) A non-invasive method to assess environmental contamination with avian pathogens: beak and feather disease virus (BFDV) detection in nest boxes. PeerJ 8:e9211 https://doi.org/10.7717/peerj.9211
date submitted: 2020-02-27
date accepted: 2020-04-27
issued: 2020-06-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martens
  given name: Johanne M.
author list: Agent
  family name: Stokes
  given name: Helena S.
author list: Agent
  family name: Berg
  given name: Mathew L.
author list: Agent
  family name: Walder
  given name: Ken
author list: Agent
  family name: Raidal
  given name: Shane R.
author list: Agent
  family name: Magrath
  given name: Michael J.L.
author list: Agent
  family name: Bennett
  given name: Andrew T.D.
doi: 10.7717/peerj.9211
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-11
copyright: ©2020 Martens et al.
attribution name: Martens et al.

Expression and clinical significance of HSP27 and its phosphorylation in lower extremity arteriosclerosis obliterans
type: item
type: AcademicArticle
description: Objectives This study set out to analyze the difference of heat shock protein 27 (HSP27) and its phosphorylation in patients with lower extremity arteriosclerosis obliterans (LEASO) at different stages. This research also examined their clinical significance in this disease. Methods Blood samples from 60 patients with LEASO were collected and divided into two groups according to ankle-brachial index (ABI): group A (ABI ≤ 0.43) and group B (ABI > 0.43). The expression of HSP27 in each stage of Fontaine was measured by ELISA, and the difference of HSP27 concentration and ABI between the two groups was analyzed. Meanwhile, three normal femoral artery specimens (normal group) and three atherosclerotic femoral artery specimens (lesion group) were collected, and HSP27 and its Phospho-HSP27 (Ser15), Phospho-HSP27 (Ser78) and Phospho-HSP27 (Ser82) were detected by western blotting. The data of the protein level between the normal group and the lesion group was made a statistical analysis. Results HSP27 concentration in group A was (40.73 ± 15.99) ng/ml, and ABI was 0.26 ± 0.20. HSP27 concentration in group B was (66.30 ± 24.70) ng/ml, and ABI was 0.64 ± 0.20. The protein expression of HSP27 and its phosphorylation in the normal group was 0.82 ± 0.13, 0.66 ± 0.12, 0.91 ± 0.24 and 0.90 ± 0.16, respectively; the protein expression of the lesion group was 0.45 ± 0.08, 0.42 ± 0.09, 0.39 ± 0.12 and 0.58 ± 0.11. Conclusion Patients with higher LEASO Fontaine stage and lower ABI had a lower HSP27 concentration. Serum HSP27 concentration was negatively correlated with the severity of LEASO, while HSP27 concentration was positively correlated with ABI value. The content of HSP27 and its phosphorylation of lesion group is significantly lower than that of normal group, which may be closely related to the occurrence and development of atherosclerosis.
format: application/pdf
format: text/html
creator: Junqing Bai
creator: Fule Wang
creator: Xuguang Wang
creator: Eerde Mutu
creator: Chen Duan
creator: Yili Qi
creator: Liqiang Hu
creator: Zhanfeng Gao
subject: Molecular Biology
subject: Cardiology
description: doi:10.7717/peerj.9305
publisher: PeerJ Inc.
rights: © 2020 Bai et al.
abstract: Objectives This study set out to analyze the difference of heat shock protein 27 (HSP27) and its phosphorylation in patients with lower extremity arteriosclerosis obliterans (LEASO) at different stages. This research also examined their clinical significance in this disease. Methods Blood samples from 60 patients with LEASO were collected and divided into two groups according to ankle-brachial index (ABI): group A (ABI ≤ 0.43) and group B (ABI > 0.43). The expression of HSP27 in each stage of Fontaine was measured by ELISA, and the difference of HSP27 concentration and ABI between the two groups was analyzed. Meanwhile, three normal femoral artery specimens (normal group) and three atherosclerotic femoral artery specimens (lesion group) were collected, and HSP27 and its Phospho-HSP27 (Ser15), Phospho-HSP27 (Ser78) and Phospho-HSP27 (Ser82) were detected by western blotting. The data of the protein level between the normal group and the lesion group was made a statistical analysis. Results HSP27 concentration in group A was (40.73 ± 15.99) ng/ml, and ABI was 0.26 ± 0.20. HSP27 concentration in group B was (66.30 ± 24.70) ng/ml, and ABI was 0.64 ± 0.20. The protein expression of HSP27 and its phosphorylation in the normal group was 0.82 ± 0.13, 0.66 ± 0.12, 0.91 ± 0.24 and 0.90 ± 0.16, respectively; the protein expression of the lesion group was 0.45 ± 0.08, 0.42 ± 0.09, 0.39 ± 0.12 and 0.58 ± 0.11. Conclusion Patients with higher LEASO Fontaine stage and lower ABI had a lower HSP27 concentration. Serum HSP27 concentration was negatively correlated with the severity of LEASO, while HSP27 concentration was positively correlated with ABI value. The content of HSP27 and its phosphorylation of lesion group is significantly lower than that of normal group, which may be closely related to the occurrence and development of atherosclerosis.
bibliographic citation: Bai et al. (2020) Expression and clinical significance of HSP27 and its phosphorylation in lower extremity arteriosclerosis obliterans. PeerJ 8:e9305 https://doi.org/10.7717/peerj.9305
date submitted: 2020-01-20
date accepted: 2020-05-16
issued: 2020-06-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Junqing
author list: Agent
  family name: Wang
  given name: Fule
author list: Agent
  family name: Wang
  given name: Xuguang
author list: Agent
  family name: Mutu
  given name: Eerde
author list: Agent
  family name: Duan
  given name: Chen
author list: Agent
  family name: Qi
  given name: Yili
author list: Agent
  family name: Hu
  given name: Liqiang
author list: Agent
  family name: Gao
  given name: Zhanfeng
doi: 10.7717/peerj.9305
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-11
copyright: ©2020 Bai et al.
attribution name: Bai et al.

Adsorption and bonding strength of chromium species by ferrihydrite from acidic aqueous solutions
type: item
type: AcademicArticle
description: The adsorption behavior of Cr(III) and Cr(VI) ions onto laboratory-synthesized 2-line ferrihydrite was investigated under a batch method as a function of initial chromium concentration (0.1–1000 mg L−1) and pH (3.0 and 5.0). Moreover, the effect of the type of anion (chloride and sulfate) on Cr(III) adsorption was studied. The affinity of Cr(III) ions for the ferrihydrite surface depended on both the type of anion and pH of the solution and the maximum adsorption capacities decreased as follows: q (SO42−, pH 5.0) > q (SO42−, pH 3.0) > q (Cl−, pH 5.0) > q (Cl−, pH 3.0), and were found to be 86.06 mg g−1, 83.59 mg g−1, 61.51 mg g−1 and 40.67 mg g−1, respectively. Cr(VI) ions were bound to ferrihydrite in higher amounts then Cr(III) ions and the maximum adsorption capacity increased as the pH of the solution decreased and was 53.14 mg g−1 at pH 5.0 and 83.73 mg g−1 at pH 3.0. The adsorption process of Cr species was pH dependent, and the ions were bound to the surface of ferrihydrite by surface complexation. The Sips isotherm was the best-fit model to the results obtained from among the four isotherm models used, i.e., Freundlich, Langmuir, Dubinin-Radushkevich and Sips, indicating different adsorption centers participate in Cr uptake. In order to assess the bonding strength of the adsorbed chromium ions the modified BCR procedure, dedicated to the samples with a high iron content, was used. The results of the sequential extraction showed that Cr(III) ions were bound mainly in the immobile residual fraction and Cr(VI) ions were bound in the reducible fraction. The presence of Fe (oxyhydr)oxides in soil and sediments increases their adsorption capacity for Cr, in particular for hexavalent Cr in an acid environment due to their properties (high pHPZC).
format: application/pdf
format: text/html
creator: Agnieszka Dzieniszewska
creator: Joanna Kyziol-Komosinska
creator: Magdalena Pająk
subject: Soil Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.9324
publisher: PeerJ Inc.
rights: © 2020 Dzieniszewska et al.
abstract: The adsorption behavior of Cr(III) and Cr(VI) ions onto laboratory-synthesized 2-line ferrihydrite was investigated under a batch method as a function of initial chromium concentration (0.1–1000 mg L−1) and pH (3.0 and 5.0). Moreover, the effect of the type of anion (chloride and sulfate) on Cr(III) adsorption was studied. The affinity of Cr(III) ions for the ferrihydrite surface depended on both the type of anion and pH of the solution and the maximum adsorption capacities decreased as follows: q (SO42−, pH 5.0) > q (SO42−, pH 3.0) > q (Cl−, pH 5.0) > q (Cl−, pH 3.0), and were found to be 86.06 mg g−1, 83.59 mg g−1, 61.51 mg g−1 and 40.67 mg g−1, respectively. Cr(VI) ions were bound to ferrihydrite in higher amounts then Cr(III) ions and the maximum adsorption capacity increased as the pH of the solution decreased and was 53.14 mg g−1 at pH 5.0 and 83.73 mg g−1 at pH 3.0. The adsorption process of Cr species was pH dependent, and the ions were bound to the surface of ferrihydrite by surface complexation. The Sips isotherm was the best-fit model to the results obtained from among the four isotherm models used, i.e., Freundlich, Langmuir, Dubinin-Radushkevich and Sips, indicating different adsorption centers participate in Cr uptake. In order to assess the bonding strength of the adsorbed chromium ions the modified BCR procedure, dedicated to the samples with a high iron content, was used. The results of the sequential extraction showed that Cr(III) ions were bound mainly in the immobile residual fraction and Cr(VI) ions were bound in the reducible fraction. The presence of Fe (oxyhydr)oxides in soil and sediments increases their adsorption capacity for Cr, in particular for hexavalent Cr in an acid environment due to their properties (high pHPZC).
bibliographic citation: Dzieniszewska et al. (2020) Adsorption and bonding strength of chromium species by ferrihydrite from acidic aqueous solutions. PeerJ 8:e9324 https://doi.org/10.7717/peerj.9324
date submitted: 2019-12-21
date accepted: 2020-05-18
issued: 2020-06-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dzieniszewska
  given name: Agnieszka
author list: Agent
  family name: Kyziol-Komosinska
  given name: Joanna
author list: Agent
  family name: Pająk
  given name: Magdalena
doi: 10.7717/peerj.9324
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-11
copyright: ©2020 Dzieniszewska et al.
attribution name: Dzieniszewska et al.

Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia
type: item
type: AcademicArticle
description: Transcription factors regulate gene expression in response to various external and internal cues by activating or suppressing downstream genes. Significant progress has been made in identifying and characterizing the Cysteine3Histidine (C3H) gene family in several dicots and monocots. They are characterized by their signature motif of three cysteine and one histidine residues, and reportedly play important roles in regulation of plant growth, developmental processes and environmental responses. In this study, we performed genome-wide and deep analysis of putative C3H genes, and a total of 117 PbeC3H members, were identified in P. betulaefolia and classified into 12 groups. Results were supported by the gene structural characteristics and phylogenetic analysis. These genes were unevenly distributed on 17 chromosomes. The gene structures of the C3H genes were relatively complex but conserved in each group. The C3H genes experienced a WGD event that occurred in the ancestor genome of P. betulaefolia and apple before their divergence based on the synonymous substitutions (Ks) values. There were 35 and 37 pairs of paralogous genes in the P. betulaefolia and apple genome, respectively, and 87 pairs of orthologous genes between P. betulaefolia and apple were identified. Except for one orthologous pairs PbeC3H66 and MD05G1311700 which had undergone positive selection, the other C3H genes had undergone purifying selection. Expression profiles showed that high salinity stress could influence the expression level of C3H genes in P. betulaefolia. Four members were responsive to salt stress in roots, nine were responsive to salt stress in leaves and eight showed inhibited expression in leaves. Results suggested important roles of PbeC3H genes in response to salt stress and will be useful for better understanding the complex functions of the C3H genes, and will provide excellent candidates for salt-tolerance improvement.
format: application/pdf
format: text/html
creator: Chunxiao Liu
creator: Xiaoyang Xu
creator: Jialiang Kan
creator: Zong ming Cheng
creator: Youhong Chang
creator: Jing Lin
creator: Hui Li
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9328
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Transcription factors regulate gene expression in response to various external and internal cues by activating or suppressing downstream genes. Significant progress has been made in identifying and characterizing the Cysteine3Histidine (C3H) gene family in several dicots and monocots. They are characterized by their signature motif of three cysteine and one histidine residues, and reportedly play important roles in regulation of plant growth, developmental processes and environmental responses. In this study, we performed genome-wide and deep analysis of putative C3H genes, and a total of 117 PbeC3H members, were identified in P. betulaefolia and classified into 12 groups. Results were supported by the gene structural characteristics and phylogenetic analysis. These genes were unevenly distributed on 17 chromosomes. The gene structures of the C3H genes were relatively complex but conserved in each group. The C3H genes experienced a WGD event that occurred in the ancestor genome of P. betulaefolia and apple before their divergence based on the synonymous substitutions (Ks) values. There were 35 and 37 pairs of paralogous genes in the P. betulaefolia and apple genome, respectively, and 87 pairs of orthologous genes between P. betulaefolia and apple were identified. Except for one orthologous pairs PbeC3H66 and MD05G1311700 which had undergone positive selection, the other C3H genes had undergone purifying selection. Expression profiles showed that high salinity stress could influence the expression level of C3H genes in P. betulaefolia. Four members were responsive to salt stress in roots, nine were responsive to salt stress in leaves and eight showed inhibited expression in leaves. Results suggested important roles of PbeC3H genes in response to salt stress and will be useful for better understanding the complex functions of the C3H genes, and will provide excellent candidates for salt-tolerance improvement.
bibliographic citation: Liu et al. (2020) Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia. PeerJ 8:e9328 https://doi.org/10.7717/peerj.9328
date submitted: 2019-08-16
date accepted: 2020-05-18
issued: 2020-06-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Chunxiao
author list: Agent
  family name: Xu
  given name: Xiaoyang
author list: Agent
  family name: Kan
  given name: Jialiang
author list: Agent
  family name: Cheng
  given name: Zong ming
author list: Agent
  family name: Chang
  given name: Youhong
author list: Agent
  family name: Lin
  given name: Jing
author list: Agent
  family name: Li
  given name: Hui
doi: 10.7717/peerj.9328
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-11
copyright: ©2020 Liu et al.
attribution name: Liu et al.

No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment
type: item
type: AcademicArticle
description: Environmental DNA (eDNA) is an emerging tool for monitoring invasive and imperiled species, particularly at low densities. However, the factors that control eDNA production, transport, and persistence in aquatic systems remain poorly understood. For example, the extent to which carcasses produce detectable eDNA is unknown. If positive detections are associated with dead organisms, this could confound monitoring for imperiled or invasive species. Here, we present results from one of the first studies to examine carcass eDNA in situ by deploying carcasses of the invasive red swamp crayfish (Procambarus clarkii) in a stream enclosure experiment for 28 days. We predicted that carcasses would initially produce eDNA that would decline over time as carcasses decayed. Unsurprisingly, crayfish carcasses lost biomass over time, but at the conclusion of our experiment much of the carapace and chelae remained. However, no eDNA of P. clarkii was detected in any of our samples at the crayfish density (15 P. clarkii carcasses at ∼615 g of biomass initially), stream flow (520–20,319 L/s), or temperature (∼14–25 °C) at our site. Subsequent analyses demonstrated that these results were not the consequence of PCR inhibition in our field samples, poor performance of the eDNA assay for intraspecific genetic diversity within P. clarkii, or due to the preservation and extraction procedure used. Therefore, our results suggest that when crayfish are relatively rare, such as in cases of new invasive populations or endangered species, carcasses may not produce detectable eDNA. In such scenarios, positive detections from field studies may be more confidently attributed to the presence of live organisms. We recommend that future studies should explore how biomass, flow, and differences in system (lentic vs. lotic) influence the ability to detect eDNA from carcasses.
format: application/pdf
format: text/html
creator: Amanda N. Curtis
creator: Eric R. Larson
subject: Molecular Biology
subject: Freshwater Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.9333
publisher: PeerJ Inc.
rights: © 2020 Curtis and Larson
abstract: Environmental DNA (eDNA) is an emerging tool for monitoring invasive and imperiled species, particularly at low densities. However, the factors that control eDNA production, transport, and persistence in aquatic systems remain poorly understood. For example, the extent to which carcasses produce detectable eDNA is unknown. If positive detections are associated with dead organisms, this could confound monitoring for imperiled or invasive species. Here, we present results from one of the first studies to examine carcass eDNA in situ by deploying carcasses of the invasive red swamp crayfish (Procambarus clarkii) in a stream enclosure experiment for 28 days. We predicted that carcasses would initially produce eDNA that would decline over time as carcasses decayed. Unsurprisingly, crayfish carcasses lost biomass over time, but at the conclusion of our experiment much of the carapace and chelae remained. However, no eDNA of P. clarkii was detected in any of our samples at the crayfish density (15 P. clarkii carcasses at ∼615 g of biomass initially), stream flow (520–20,319 L/s), or temperature (∼14–25 °C) at our site. Subsequent analyses demonstrated that these results were not the consequence of PCR inhibition in our field samples, poor performance of the eDNA assay for intraspecific genetic diversity within P. clarkii, or due to the preservation and extraction procedure used. Therefore, our results suggest that when crayfish are relatively rare, such as in cases of new invasive populations or endangered species, carcasses may not produce detectable eDNA. In such scenarios, positive detections from field studies may be more confidently attributed to the presence of live organisms. We recommend that future studies should explore how biomass, flow, and differences in system (lentic vs. lotic) influence the ability to detect eDNA from carcasses.
bibliographic citation: Curtis et al. (2020) No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment. PeerJ 8:e9333 https://doi.org/10.7717/peerj.9333
date submitted: 2020-01-21
date accepted: 2020-05-19
issued: 2020-06-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Curtis
  given name: Amanda N.
author list: Agent
  family name: Larson
  given name: Eric R.
doi: 10.7717/peerj.9333
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-11
copyright: ©2020 Curtis and Larson
attribution name: Curtis and Larson

Consumer perceptions and reported wild and domestic meat and fish consumption behavior during the Ebola epidemic in Guinea, West Africa
type: item
type: AcademicArticle
description: The handling, capturing, butchering, and transportation of wildmeat can increase the risk of zoonoses, including the Ebola virus disease (EVD). Guinea, West Africa, experienced a catastrophic outbreak of EVD between 2013 and 2016. This study aimed to understand local people’s sources of information concerning EVD, their perceptions of potential wildlife carriers of EVD and their meat and fish consumption behavior during this period. A semi-structured questionnaire was administered to 332 participants in two urban centers (N = 209) and three villages (N = 123) between January 3 and March 30, 2015 in the prefecture of Lola in southeastern Guinea. Chi-square analyses revealed that, in rural areas, awareness missions represented the main source of information about EVD (94.3%), whereas in urban settings such missions (36.1%), as well as newspapers (31.6%) and radio (32.3%) were equally mentioned. Bats (30.1% and 79.4%), chimpanzees (16.3% and 48.8%) and monkeys (13.0% and 53.1%) were the most commonly cited potential agents of EVD in both rural and urban areas respectively, while the warthog (2.3% rural and 6.5% urban), crested porcupine (1.7% rural and 10.7% urban), duiker (1.19% rural and 2.6% urban) and the greater cane rat (1.1% rural and 9.5% urban) were also cited but to a lesser extent. However, 66.7% of rural respondents compared to only 17.2% in the urban area did not consider any of these species as potential carriers of the Ebola virus. Nonetheless, a fifth of our respondents reported not consuming any of these species altogether during the EVD outbreak. Among all seven faunal groups mentioned, a significant reduction in reported consumption during the Ebola outbreak was only noted for bats (before: 78.3% and during: 31.9%) and chimpanzees (before: 31.6% and during: 13.5%). Automatic Chi-Square Interaction Detection (CHAID) analysis revealed that the belief that bats or chimpanzees were associated with EVD or not had a significant effect respectively on their…
format: application/pdf
format: text/html
creator: Lucie Duonamou
creator: Alexandre Konate
creator: Sylvie Djègo Djossou
creator: Guy Apollinaire Mensah
creator: Jiliang Xu
creator: Tatyana Humle
subject: Conservation Biology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.9229
publisher: PeerJ Inc.
rights: © 2020 Duonamou et al.
abstract: The handling, capturing, butchering, and transportation of wildmeat can increase the risk of zoonoses, including the Ebola virus disease (EVD). Guinea, West Africa, experienced a catastrophic outbreak of EVD between 2013 and 2016. This study aimed to understand local people’s sources of information concerning EVD, their perceptions of potential wildlife carriers of EVD and their meat and fish consumption behavior during this period. A semi-structured questionnaire was administered to 332 participants in two urban centers (N = 209) and three villages (N = 123) between January 3 and March 30, 2015 in the prefecture of Lola in southeastern Guinea. Chi-square analyses revealed that, in rural areas, awareness missions represented the main source of information about EVD (94.3%), whereas in urban settings such missions (36.1%), as well as newspapers (31.6%) and radio (32.3%) were equally mentioned. Bats (30.1% and 79.4%), chimpanzees (16.3% and 48.8%) and monkeys (13.0% and 53.1%) were the most commonly cited potential agents of EVD in both rural and urban areas respectively, while the warthog (2.3% rural and 6.5% urban), crested porcupine (1.7% rural and 10.7% urban), duiker (1.19% rural and 2.6% urban) and the greater cane rat (1.1% rural and 9.5% urban) were also cited but to a lesser extent. However, 66.7% of rural respondents compared to only 17.2% in the urban area did not consider any of these species as potential carriers of the Ebola virus. Nonetheless, a fifth of our respondents reported not consuming any of these species altogether during the EVD outbreak. Among all seven faunal groups mentioned, a significant reduction in reported consumption during the Ebola outbreak was only noted for bats (before: 78.3% and during: 31.9%) and chimpanzees (before: 31.6% and during: 13.5%). Automatic Chi-Square Interaction Detection (CHAID) analysis revealed that the belief that bats or chimpanzees were associated with EVD or not had a significant effect respectively on their…
bibliographic citation: Duonamou et al. (2020) Consumer perceptions and reported wild and domestic meat and fish consumption behavior during the Ebola epidemic in Guinea, West Africa. PeerJ 8:e9229 https://doi.org/10.7717/peerj.9229
date submitted: 2019-12-22
date accepted: 2020-04-30
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Duonamou
  given name: Lucie
author list: Agent
  family name: Konate
  given name: Alexandre
author list: Agent
  family name: Djègo Djossou
  given name: Sylvie
author list: Agent
  family name: Mensah
  given name: Guy Apollinaire
author list: Agent
  family name: Xu
  given name: Jiliang
author list: Agent
  family name: Humle
  given name: Tatyana
doi: 10.7717/peerj.9229
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: ©2020 Duonamou et al.
attribution name: Duonamou et al.

Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.)
type: item
type: AcademicArticle
description: Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis.
format: application/pdf
format: text/html
creator: Weina Zhang
creator: Zhongjian Chen
creator: Yichen Kang
creator: Yanling Fan
creator: Yuhui Liu
creator: Xinyu Yang
creator: Mingfu Shi
creator: Kai Yao
creator: Shuhao Qin
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.9310
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis.
bibliographic citation: Zhang et al. (2020) Genome-wide analysis of lectin receptor-like kinases family from potato (Solanum tuberosum L.). PeerJ 8:e9310 https://doi.org/10.7717/peerj.9310
date submitted: 2019-10-07
date accepted: 2020-05-17
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Weina
author list: Agent
  family name: Chen
  given name: Zhongjian
author list: Agent
  family name: Kang
  given name: Yichen
author list: Agent
  family name: Fan
  given name: Yanling
author list: Agent
  family name: Liu
  given name: Yuhui
author list: Agent
  family name: Yang
  given name: Xinyu
author list: Agent
  family name: Shi
  given name: Mingfu
author list: Agent
  family name: Yao
  given name: Kai
author list: Agent
  family name: Qin
  given name: Shuhao
doi: 10.7717/peerj.9310
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Zhang et al.
attribution name: Zhang et al.

In silico and in vitro identification of secoisolariciresinol as a re-sensitizer of P-glycoprotein-dependent doxorubicin-resistance NCI/ADR-RES cancer cells
type: item
type: AcademicArticle
description: P-glycoprotein (P-gp) is one of the highly expressed cancer cell efflux transporters that cause the failure of chemotherapy. To reverse P-gp induced multidrug resistance, we employed a flaxseed-derived lignan; secoisolariciresinol (SECO) that acts as an inhibitor of breast cancer resistance protein; another efflux transporter that shares some substrate/inhibitor specificity with P-gp. Molecular dynamics (MD) simulation identified SECO as a possible P-gp inhibitor. Comparing root mean square deviation (RMSD) of P-gp bound with SECO with that bound to its standard inhibitor verapamil showed that fluctuations in RMSD were lower in P-gp bound to SECO demonstrating higher stability of the complex of P-gp with SECO. In addition, the superimposition of P-gp structures after MD simulation showed that the nucleotide-binding domains of P-gp bound to SECO undertook a more central closer position compared with that bound to verapamil. Using rhodamine efflux assay on NCI/ADR-RES cancer cells, SECO was confirmed as a P-gp inhibitor, where cells treated with 25 or 50 µM of SECO showed significantly higher fluorescence intensity compared to control. Using MTT assay, SECO alone showed dose-dependent cytotoxicity, where 25 or 50 µM of SECO caused significantly less NCI/ADR-RES cellular viability compared to control. Furthermore, when 50 µM of SECO was added to doxorubicin (DOX), an anticancer drug, SECO significantly enhanced DOX-induced cytotoxicity compared to DOX alone. The combination index calculated by CompuSyn software indicated synergism between DOX and SECO. Our results suggest SECO as a novel P-gp inhibitor that can re-sensitize cancer cells during DOX chemotherapy.
format: application/pdf
format: text/html
creator: Mohamed A. Morsy
creator: Azza A.K. El-Sheikh
creator: Ahmed R.N. Ibrahim
creator: Katharigatta N. Venugopala
creator: Mahmoud Kandeel
subject: Bioinformatics
subject: Pharmacology
description: doi:10.7717/peerj.9163
publisher: PeerJ Inc.
rights: © 2020 Morsy et al.
abstract: P-glycoprotein (P-gp) is one of the highly expressed cancer cell efflux transporters that cause the failure of chemotherapy. To reverse P-gp induced multidrug resistance, we employed a flaxseed-derived lignan; secoisolariciresinol (SECO) that acts as an inhibitor of breast cancer resistance protein; another efflux transporter that shares some substrate/inhibitor specificity with P-gp. Molecular dynamics (MD) simulation identified SECO as a possible P-gp inhibitor. Comparing root mean square deviation (RMSD) of P-gp bound with SECO with that bound to its standard inhibitor verapamil showed that fluctuations in RMSD were lower in P-gp bound to SECO demonstrating higher stability of the complex of P-gp with SECO. In addition, the superimposition of P-gp structures after MD simulation showed that the nucleotide-binding domains of P-gp bound to SECO undertook a more central closer position compared with that bound to verapamil. Using rhodamine efflux assay on NCI/ADR-RES cancer cells, SECO was confirmed as a P-gp inhibitor, where cells treated with 25 or 50 µM of SECO showed significantly higher fluorescence intensity compared to control. Using MTT assay, SECO alone showed dose-dependent cytotoxicity, where 25 or 50 µM of SECO caused significantly less NCI/ADR-RES cellular viability compared to control. Furthermore, when 50 µM of SECO was added to doxorubicin (DOX), an anticancer drug, SECO significantly enhanced DOX-induced cytotoxicity compared to DOX alone. The combination index calculated by CompuSyn software indicated synergism between DOX and SECO. Our results suggest SECO as a novel P-gp inhibitor that can re-sensitize cancer cells during DOX chemotherapy.
bibliographic citation: Morsy et al. (2020) In silico and in vitro identification of secoisolariciresinol as a re-sensitizer of P-glycoprotein-dependent doxorubicin-resistance NCI/ADR-RES cancer cells. PeerJ 8:e9163 https://doi.org/10.7717/peerj.9163
date submitted: 2020-01-23
date accepted: 2020-04-18
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Morsy
  given name: Mohamed A.
author list: Agent
  family name: El-Sheikh
  given name: Azza A.K.
author list: Agent
  family name: Ibrahim
  given name: Ahmed R.N.
author list: Agent
  family name: Venugopala
  given name: Katharigatta N.
author list: Agent
  family name: Kandeel
  given name: Mahmoud
doi: 10.7717/peerj.9163
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Morsy et al.
attribution name: Morsy et al.

Fire severity effects on resprouting of subtropical dune thicket of the Cape Floristic Region
type: item
type: AcademicArticle
description: It has been hypothesised that high-intensity fires prevent fire-dependent fynbos from being replaced by fire-avoiding subtropical thicket on dune landscapes of the Cape Floristic Region (CFR). Recent extensive fires provided an opportunity to test this hypothesis. We posit that (1) fire-related thicket shrub mortality would be size dependent, with smaller individuals suffering higher mortality than larger ones; and (2) that survival and resprouting vigour of thicket shrubs would be negatively correlated with fire severity. We assessed survival and resprouting vigour post-fire in relation to fire severity and pre-fire shrub size at two dune landscapes in the CFR. Fire severity was scored at the base of the shrub and categorised into four levels. Pre-fire size was quantified as an index of lignotuber diameter and stem count of each shrub. Resprouting vigour consisted of two variables; resprouting shoot count and resprouting canopy volume. A total of 29 species were surveyed. Post-fire survival of thicket was high (83–85%). We found that smaller shrubs did have a lower probability of post-fire survival than larger individuals but could detect no consistent relationship between shrub mortality and fire severity. Fire severity had a positive effect on resprouting shoot count but a variable effect on resprouting volume. Pre-fire size was positively related to survival and both measures of resprouting vigour. We conclude that thicket is resilient to high-severity fires but may be vulnerable to frequent fires. Prescribed high-intensity fires in dune landscapes are unlikely to reduce the extent of thicket and promote fynbos expansion.
format: application/pdf
format: text/html
creator: Tiaan Strydom
creator: Tineke Kraaij
creator: Mark Difford
creator: Richard M. Cowling
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
description: doi:10.7717/peerj.9240
publisher: PeerJ Inc.
rights: © 2020 Strydom et al.
abstract: It has been hypothesised that high-intensity fires prevent fire-dependent fynbos from being replaced by fire-avoiding subtropical thicket on dune landscapes of the Cape Floristic Region (CFR). Recent extensive fires provided an opportunity to test this hypothesis. We posit that (1) fire-related thicket shrub mortality would be size dependent, with smaller individuals suffering higher mortality than larger ones; and (2) that survival and resprouting vigour of thicket shrubs would be negatively correlated with fire severity. We assessed survival and resprouting vigour post-fire in relation to fire severity and pre-fire shrub size at two dune landscapes in the CFR. Fire severity was scored at the base of the shrub and categorised into four levels. Pre-fire size was quantified as an index of lignotuber diameter and stem count of each shrub. Resprouting vigour consisted of two variables; resprouting shoot count and resprouting canopy volume. A total of 29 species were surveyed. Post-fire survival of thicket was high (83–85%). We found that smaller shrubs did have a lower probability of post-fire survival than larger individuals but could detect no consistent relationship between shrub mortality and fire severity. Fire severity had a positive effect on resprouting shoot count but a variable effect on resprouting volume. Pre-fire size was positively related to survival and both measures of resprouting vigour. We conclude that thicket is resilient to high-severity fires but may be vulnerable to frequent fires. Prescribed high-intensity fires in dune landscapes are unlikely to reduce the extent of thicket and promote fynbos expansion.
bibliographic citation: Strydom et al. (2020) Fire severity effects on resprouting of subtropical dune thicket of the Cape Floristic Region. PeerJ 8:e9240 https://doi.org/10.7717/peerj.9240
date submitted: 2020-01-23
date accepted: 2020-05-05
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Strydom
  given name: Tiaan
author list: Agent
  family name: Kraaij
  given name: Tineke
author list: Agent
  family name: Difford
  given name: Mark
author list: Agent
  family name: Cowling
  given name: Richard M.
doi: 10.7717/peerj.9240
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: © 2020 Strydom et al.
attribution name: Strydom et al.

Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis)
type: item
type: AcademicArticle
description: Background DNA-binding one zinc finger (Dof) proteins are plant-specific transcription factors important for seed development, hormone regulation, and defense against abiotic stress. Although drought stress is a key determinant of plant physiology and metabolic homeostasis, the role of Dof genes in different degrees of PEG6000-induced drought stress has received little attention. Methods Tea plants (Camellia sinensis) were exposed to mild, moderate and severe drought stress. The Tea Genome and Plant TFDB databases were used to identify Dof gene family members in the tea plant. Clustal W2.1, MEGA6.0, ScanProsite, SMART, ExPASy, GSDS, MEME and STRING were used to build a phylogenetic tree, predict the molecular masses and isoelectric points of the Dof proteins, and construct a predicted protein-protein interaction network between the CsDof TFs and proteins in the A. thaliana database. The expression patterns of Dof genes in different tissues were analyzed, and qRT-PCR was used to measure the expression of Dof genes under different degrees of drought stress in tea. Results We identified 16 Dof genes in tea (C. sinensis cv. Huangjinya) using whole-genome analysis. Through comparative analysis of tea and Arabidopsis thaliana, we divided the Dof genes into four families (A, B, C, and D). We identified 15 motifs in the amino acid sequences of the CsDof proteins. Gene sequences and motif structures were highly conserved among families, especially in the B1 and C2 subfamilies. The protein-protein interaction network indicated that multiple CsDof proteins may be involved in the response to drought stress. Real-time PCR was used to examine the tissue-specific expression patterns of the CsDof genes and to measure their responses to different levels of PEG6000-induced drought stress in mature leaves. Most CsDof genes responded to drought stress. These results provide information on the Dof gene family in tea, offer new insights into the function of CsDof genes in a perennial spe…
format: application/pdf
format: text/html
creator: Qian Yu
creator: Chen Li
creator: Jiucheng Zhang
creator: Yueyue Tian
creator: Hanyue Wang
creator: Yue Zhang
creator: Zhengqun Zhang
creator: Qinzeng Xiang
creator: Xiaoyang Han
creator: Lixia Zhang
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.9269
publisher: PeerJ Inc.
rights: © 2020 Yu et al.
abstract: Background DNA-binding one zinc finger (Dof) proteins are plant-specific transcription factors important for seed development, hormone regulation, and defense against abiotic stress. Although drought stress is a key determinant of plant physiology and metabolic homeostasis, the role of Dof genes in different degrees of PEG6000-induced drought stress has received little attention. Methods Tea plants (Camellia sinensis) were exposed to mild, moderate and severe drought stress. The Tea Genome and Plant TFDB databases were used to identify Dof gene family members in the tea plant. Clustal W2.1, MEGA6.0, ScanProsite, SMART, ExPASy, GSDS, MEME and STRING were used to build a phylogenetic tree, predict the molecular masses and isoelectric points of the Dof proteins, and construct a predicted protein-protein interaction network between the CsDof TFs and proteins in the A. thaliana database. The expression patterns of Dof genes in different tissues were analyzed, and qRT-PCR was used to measure the expression of Dof genes under different degrees of drought stress in tea. Results We identified 16 Dof genes in tea (C. sinensis cv. Huangjinya) using whole-genome analysis. Through comparative analysis of tea and Arabidopsis thaliana, we divided the Dof genes into four families (A, B, C, and D). We identified 15 motifs in the amino acid sequences of the CsDof proteins. Gene sequences and motif structures were highly conserved among families, especially in the B1 and C2 subfamilies. The protein-protein interaction network indicated that multiple CsDof proteins may be involved in the response to drought stress. Real-time PCR was used to examine the tissue-specific expression patterns of the CsDof genes and to measure their responses to different levels of PEG6000-induced drought stress in mature leaves. Most CsDof genes responded to drought stress. These results provide information on the Dof gene family in tea, offer new insights into the function of CsDof genes in a perennial spe…
bibliographic citation: Yu et al. (2020) Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea (Camellia sinensis). PeerJ 8:e9269 https://doi.org/10.7717/peerj.9269
date submitted: 2020-01-08
date accepted: 2020-05-10
issued: 2020-06-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Qian
author list: Agent
  family name: Li
  given name: Chen
author list: Agent
  family name: Zhang
  given name: Jiucheng
author list: Agent
  family name: Tian
  given name: Yueyue
author list: Agent
  family name: Wang
  given name: Hanyue
author list: Agent
  family name: Zhang
  given name: Yue
author list: Agent
  family name: Zhang
  given name: Zhengqun
author list: Agent
  family name: Xiang
  given name: Qinzeng
author list: Agent
  family name: Han
  given name: Xiaoyang
author list: Agent
  family name: Zhang
  given name: Lixia
doi: 10.7717/peerj.9269
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-10
copyright: ©2020 Yu et al.
attribution name: Yu et al.

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