PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A putative effector UvHrip1 inhibits BAX-triggered cell death in Nicotiana benthamiana, and infection of Ustilaginoidea virens suppresses defense-related genes expression
items: The reproductive inhibitory effects of levonorgestrel, quinestrol, and EP-1 in Brandt’s vole (Lasiopodomys brandtii)
items: GISA: using Gauss Integrals to identify rare conformations in protein structures
items: Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment
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

A putative effector UvHrip1 inhibits BAX-triggered cell death in Nicotiana benthamiana, and infection of Ustilaginoidea virens suppresses defense-related genes expression
type: item
type: AcademicArticle
description: Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most detrimental rice fungal diseases and pose a severe threat to rice production and quality. Effectors in U. virens often act as a set of essential virulence factors that play crucial roles in the interaction between host and the pathogen. Thus, the functions of each effector in U. virens need to be further explored. Here, we performed multiple alignment analysis and demonstrated a small secreted hypersensitive response-inducing protein (hrip), named UvHrip1, was highly conserved in fungi. The predicted SP of UvHrip1 was functional, which guided SUC secreted from yeast and was recognized by plant cells. The localization of UvHrip1 was mainly in the nucleus and cytoplasm monitored through the GFP fusion protein in Nicotiana benthamiana cells. uvhrip1 was drastically up-regulated in the susceptible cultivar LYP9 of rice during the pathogen infection, while did not in the resistant cultivar IR28. We also proved that UvHrip1 suppressed the mammalian BAX-induced necrosis-like defense symptoms in N. benthamiana. Furthermore, patterns of expression of defense-related genes, OsPR1#012 and OsPR10b, were regulated over U. virens infection in rice. Collectively, our data demonstrated that infection of U. virens suppresses defense-related genes expression and UvHrip1 was most likely a core effector in regulating plant immunity.
format: application/pdf
format: text/html
creator: Yingling Wang
creator: Jing Li
creator: Shibo Xiang
creator: Jianming Zhou
creator: Xunwen Peng
creator: Yingfan Hai
creator: Yan Wang
creator: Shuai Li
creator: Songhong Wei
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.9354
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most detrimental rice fungal diseases and pose a severe threat to rice production and quality. Effectors in U. virens often act as a set of essential virulence factors that play crucial roles in the interaction between host and the pathogen. Thus, the functions of each effector in U. virens need to be further explored. Here, we performed multiple alignment analysis and demonstrated a small secreted hypersensitive response-inducing protein (hrip), named UvHrip1, was highly conserved in fungi. The predicted SP of UvHrip1 was functional, which guided SUC secreted from yeast and was recognized by plant cells. The localization of UvHrip1 was mainly in the nucleus and cytoplasm monitored through the GFP fusion protein in Nicotiana benthamiana cells. uvhrip1 was drastically up-regulated in the susceptible cultivar LYP9 of rice during the pathogen infection, while did not in the resistant cultivar IR28. We also proved that UvHrip1 suppressed the mammalian BAX-induced necrosis-like defense symptoms in N. benthamiana. Furthermore, patterns of expression of defense-related genes, OsPR1#012 and OsPR10b, were regulated over U. virens infection in rice. Collectively, our data demonstrated that infection of U. virens suppresses defense-related genes expression and UvHrip1 was most likely a core effector in regulating plant immunity.
bibliographic citation: Wang et al. (2020) A putative effector UvHrip1 inhibits BAX-triggered cell death in Nicotiana benthamiana, and infection of Ustilaginoidea virens suppresses defense-related genes expression. PeerJ 8:e9354 https://doi.org/10.7717/peerj.9354
date submitted: 2020-03-13
date accepted: 2020-05-23
issued: 2020-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yingling
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Xiang
  given name: Shibo
author list: Agent
  family name: Zhou
  given name: Jianming
author list: Agent
  family name: Peng
  given name: Xunwen
author list: Agent
  family name: Hai
  given name: Yingfan
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Li
  given name: Shuai
author list: Agent
  family name: Wei
  given name: Songhong
doi: 10.7717/peerj.9354
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: ©2020 Wang et al.
attribution name: Wang et al.

The reproductive inhibitory effects of levonorgestrel, quinestrol, and EP-1 in Brandt’s vole (Lasiopodomys brandtii)
type: item
type: AcademicArticle
description: Background Rodent pests can inflict devastating impacts on agriculture and the environment, leading to significant economic damage associated with their high species diversity, reproductive rates and adaptability. Fertility control methods could indirectly control rodent pest populations as well as limit ecological consequences and environmental concerns caused by lethal chemical poisons. Brandt’s voles, which are common rodent pests found in the grasslands of middle-eastern Inner Mongolia, eastern regions of Mongolia, and some regions of southern Russia, were assessed in the present study. Methods We evaluated the effects of a 2-mg/kg dose of levonorgestrel and quinestrol and a 1:1 mixture of the two (EP-1) on reproductive behavior as well as changes in the reproductive system, reproductive hormone levels, and toxicity in Brandt’s voles. Results Our results revealed that all three fertility control agents can cause reproductive inhibition at a dosage of 2 mg/kg. However, quinestrol caused a greater degree of toxicity, as determined by visible liver damage and reduced expression of the detoxifying molecule CYP1A2. Of the remaining two fertility control agents, EP-1 was superior to levonorgestrel in inhibiting the secretion of follicle-stimulating hormone and causing reproductive inhibition. We believe that these findings could help promote the use of these fertility control agents and, in turn, reduce the use of chemical poisons and limit their detrimental ecological and environmental impacts.
format: application/pdf
format: text/html
creator: Luye Shi
creator: Xiujuan Li
creator: Zhihong Ji
creator: Zishi Wang
creator: Yuhua Shi
creator: Xiangyu Tian
creator: Zhenlong Wang
subject: Agricultural Science
subject: Ecology
subject: Veterinary Medicine
subject: Zoology
subject: Population Biology
description: doi:10.7717/peerj.9140
publisher: PeerJ Inc.
rights: © 2020 Shi et al.
abstract: Background Rodent pests can inflict devastating impacts on agriculture and the environment, leading to significant economic damage associated with their high species diversity, reproductive rates and adaptability. Fertility control methods could indirectly control rodent pest populations as well as limit ecological consequences and environmental concerns caused by lethal chemical poisons. Brandt’s voles, which are common rodent pests found in the grasslands of middle-eastern Inner Mongolia, eastern regions of Mongolia, and some regions of southern Russia, were assessed in the present study. Methods We evaluated the effects of a 2-mg/kg dose of levonorgestrel and quinestrol and a 1:1 mixture of the two (EP-1) on reproductive behavior as well as changes in the reproductive system, reproductive hormone levels, and toxicity in Brandt’s voles. Results Our results revealed that all three fertility control agents can cause reproductive inhibition at a dosage of 2 mg/kg. However, quinestrol caused a greater degree of toxicity, as determined by visible liver damage and reduced expression of the detoxifying molecule CYP1A2. Of the remaining two fertility control agents, EP-1 was superior to levonorgestrel in inhibiting the secretion of follicle-stimulating hormone and causing reproductive inhibition. We believe that these findings could help promote the use of these fertility control agents and, in turn, reduce the use of chemical poisons and limit their detrimental ecological and environmental impacts.
bibliographic citation: Shi et al. (2020) The reproductive inhibitory effects of levonorgestrel, quinestrol, and EP-1 in Brandt’s vole (Lasiopodomys brandtii). PeerJ 8:e9140 https://doi.org/10.7717/peerj.9140
date submitted: 2019-10-28
date accepted: 2020-04-16
issued: 2020-06-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Luye
author list: Agent
  family name: Li
  given name: Xiujuan
author list: Agent
  family name: Ji
  given name: Zhihong
author list: Agent
  family name: Wang
  given name: Zishi
author list: Agent
  family name: Shi
  given name: Yuhua
author list: Agent
  family name: Tian
  given name: Xiangyu
author list: Agent
  family name: Wang
  given name: Zhenlong
doi: 10.7717/peerj.9140
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-11
copyright: © 2020 Shi et al.
attribution name: Shi et al.

GISA: using Gauss Integrals to identify rare conformations in protein structures
type: item
type: AcademicArticle
description: The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a ”fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general. To achieve this our new algorithm, GISA, as a key novelty produces the descriptors, so called Gauss integrals, not only for the full chains of a protein but for all its sub-chains. This allows fingerprinting on any scale from local to global. The Gauss integrals are known to be effective descriptors of global protein folds. Applying GISA to sets of several thousand high resolution structures, we first show how the most basic Gauss integral, the writhe, enables swift identification of pre-defined geometries such as pokes and links. We then apply GISA with no restrictions on geometry, to show how it allows identifying rare conformations by finding rare invariant values only. In this unrestricted search, pokes and links are still found, but also knotted conformations, as well as more highly entangled configurations not previously described. Thus, an application of the basic scan method in GISA’s tool-box revealed 10 known cases of knots as the top positive writhe cases, while placing at the top of the negative writhe 14 cases in cis-trans isomerases sharing a spatial motif of little secondary structure content, which possibly has gone unnoticed. Possible general applicat…
format: application/pdf
format: text/html
creator: Christian Grønbæk
creator: Thomas Hamelryck
creator: Peter Røgen
subject: Bioinformatics
subject: Computational Biology
subject: Mathematical Biology
description: doi:10.7717/peerj.9159
publisher: PeerJ Inc.
rights: © 2020 Grønbæk et al.
abstract: The native structure of a protein is important for its function, and therefore methods for exploring protein structures have attracted much research. However, rather few methods are sensitive to topologic-geometric features, the examples being knots, slipknots, lassos, links, and pokes, and with each method aimed only for a specific set of such configurations. We here propose a general method which transforms a structure into a ”fingerprint of topological-geometric values” consisting in a series of real-valued descriptors from mathematical Knot Theory. The extent to which a structure contains unusual configurations can then be judged from this fingerprint. The method is not confined to a particular pre-defined topology or geometry (like a knot or a poke), and so, unlike existing methods, it is general. To achieve this our new algorithm, GISA, as a key novelty produces the descriptors, so called Gauss integrals, not only for the full chains of a protein but for all its sub-chains. This allows fingerprinting on any scale from local to global. The Gauss integrals are known to be effective descriptors of global protein folds. Applying GISA to sets of several thousand high resolution structures, we first show how the most basic Gauss integral, the writhe, enables swift identification of pre-defined geometries such as pokes and links. We then apply GISA with no restrictions on geometry, to show how it allows identifying rare conformations by finding rare invariant values only. In this unrestricted search, pokes and links are still found, but also knotted conformations, as well as more highly entangled configurations not previously described. Thus, an application of the basic scan method in GISA’s tool-box revealed 10 known cases of knots as the top positive writhe cases, while placing at the top of the negative writhe 14 cases in cis-trans isomerases sharing a spatial motif of little secondary structure content, which possibly has gone unnoticed. Possible general applicat…
bibliographic citation: Grønbæk et al. (2020) GISA: using Gauss Integrals to identify rare conformations in protein structures. PeerJ 8:e9159 https://doi.org/10.7717/peerj.9159
date submitted: 2019-09-30
date accepted: 2020-04-18
issued: 2020-06-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grønbæk
  given name: Christian
author list: Agent
  family name: Hamelryck
  given name: Thomas
author list: Agent
  family name: Røgen
  given name: Peter
doi: 10.7717/peerj.9159
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-11
copyright: ©2020 Grønbæk et al.
attribution name: Grønbæk et al.

Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment
type: item
type: AcademicArticle
description: Environmental DNA (eDNA) analysis provides an efficient and objective approach for monitoring and assessing ecological status; however, studies on the eDNA of aquatic insects, such as Ephemeroptera, Plecoptera, and Trichoptera (EPT), are limited despite its potential as a useful indicator of river health. Here, we investigated the community structures of aquatic insects using eDNA and evaluated the applicability of eDNA data for calculating assessment indices. Field surveys were conducted to sample river water for eDNA at six locations from upstream to downstream of two rivers in Japan in July and November 2016. Simultaneously, aquatic insects were collected using the traditional Surber net survey method. The communities of aquatic insects were revealed using eDNA by targeting the cytochrome oxidase subunit I gene in mitochondrial DNA via metabarcoding analyses. As a result, the eDNA revealed 63 families and 75 genera of aquatic insects, which was double than that detected by the Surber net survey (especially for families in Diptera and Hemiptera). The seasonal differences of communities were distinguished by both the eDNA and Surber net survey data. Furthermore, the total nitrogen concentration, a surrogate of organic pollution, showed positive correlations with biotic environmental assessment indices (i.e., EPT index and Chironomidae index) calculated using eDNA at the genus-level resolution but the indices calculated using the Surber net survey data. Our results demonstrated that eDNA analysis with higher taxonomic resolution can provide as a more sensitive environmental assessment index than the traditional method that requires biotic samples.
format: application/pdf
format: text/html
creator: Noriko Uchida
creator: Kengo Kubota
creator: Shunsuke Aita
creator: So Kazama
subject: Bioinformatics
subject: Ecosystem Science
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.9176
publisher: PeerJ Inc.
rights: © 2020 Uchida et al.
abstract: Environmental DNA (eDNA) analysis provides an efficient and objective approach for monitoring and assessing ecological status; however, studies on the eDNA of aquatic insects, such as Ephemeroptera, Plecoptera, and Trichoptera (EPT), are limited despite its potential as a useful indicator of river health. Here, we investigated the community structures of aquatic insects using eDNA and evaluated the applicability of eDNA data for calculating assessment indices. Field surveys were conducted to sample river water for eDNA at six locations from upstream to downstream of two rivers in Japan in July and November 2016. Simultaneously, aquatic insects were collected using the traditional Surber net survey method. The communities of aquatic insects were revealed using eDNA by targeting the cytochrome oxidase subunit I gene in mitochondrial DNA via metabarcoding analyses. As a result, the eDNA revealed 63 families and 75 genera of aquatic insects, which was double than that detected by the Surber net survey (especially for families in Diptera and Hemiptera). The seasonal differences of communities were distinguished by both the eDNA and Surber net survey data. Furthermore, the total nitrogen concentration, a surrogate of organic pollution, showed positive correlations with biotic environmental assessment indices (i.e., EPT index and Chironomidae index) calculated using eDNA at the genus-level resolution but the indices calculated using the Surber net survey data. Our results demonstrated that eDNA analysis with higher taxonomic resolution can provide as a more sensitive environmental assessment index than the traditional method that requires biotic samples.
bibliographic citation: Uchida et al. (2020) Aquatic insect community structure revealed by eDNA metabarcoding derives indices for environmental assessment. PeerJ 8:e9176 https://doi.org/10.7717/peerj.9176
date submitted: 2019-05-06
date accepted: 2020-04-21
issued: 2020-06-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uchida
  given name: Noriko
author list: Agent
  family name: Kubota
  given name: Kengo
author list: Agent
  family name: Aita
  given name: Shunsuke
author list: Agent
  family name: Kazama
  given name: So
doi: 10.7717/peerj.9176
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-11
copyright: © 2020 Uchida et al.
attribution name: Uchida et al.

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.

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