PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Use of the traditional halibut hook of the Makah Tribe, the čibu⋅d, reduces bycatch in recreational halibut fisheries
items: Conservation implications of using an imitation carnivore to assess rarely used refuges as critical habitat features in an alpine ungulate
items: Genome-wide characterization of the Zn(II)2Cys6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress
items: Epiphytic bryophyte biomass estimation on tree trunks and upscaling in tropical montane cloud forests
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

Use of the traditional halibut hook of the Makah Tribe, the čibu⋅d, reduces bycatch in recreational halibut fisheries
type: item
type: AcademicArticle
description: A previous study found that use of the traditional halibut hook (čibu⋅d) of the Makah Tribe in present day recreational Pacific halibut (Hippoglossus stenolepis) fisheries significantly reduced bycatch compared to paired 8/0 circle hooks. The study also found that the čibu⋅d had a significantly reduced catch of halibut, but that the reduction may have been due to manufacturing flaws in the čibu⋅d used in the study. In this two-phased study, we first compared the fishing performance of redesigned čibu⋅d made from four different materials: brass, stainless steel, plastic, and wood. In the second phase, we compared the fishing performance of the brass čibu⋅d with two common recreational fishing set-ups: a single large 16/0 circle hook and paired 8/0 circle hooks. The fishing performance of the redesigned čibu⋅d was not statistically different for čibu⋅d made of brass, stainless steel, or plastic. However, the čibu⋅d made from wood had significantly lower catch of halibut than the other čibu⋅d. We selected the brass čibu⋅d for the second phase of the study for continuity with the previous study of čibu⋅d and found that it had significantly less bycatch and a lower bycatch ratio than both the paired 8/0 and single 16/0 circle hooks. No significant differences were found in catch rates of halibut for paired 8/0 circle hooks, 16/0 circle hook, and the brass čibu⋅d. This study demonstrates that the improved catching performance of čibu⋅d on halibut and reduced bycatch compared to other popular approaches can be achieved by using brass čibu⋅d. Managers of recreational halibut fisheries should consider the use of čibu⋅d in areas where bycatch is a concern.
format: application/pdf
format: text/html
creator: Joseph R. Petersen
creator: Jonathan J. Scordino
creator: Cole I. Svec
creator: Reginald H. Buttram
creator: Maria R. Gonzalez
creator: Joe Scordino
subject: Anthropology
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.9288
publisher: PeerJ Inc.
rights: © 2020 Petersen et al.
abstract: A previous study found that use of the traditional halibut hook (čibu⋅d) of the Makah Tribe in present day recreational Pacific halibut (Hippoglossus stenolepis) fisheries significantly reduced bycatch compared to paired 8/0 circle hooks. The study also found that the čibu⋅d had a significantly reduced catch of halibut, but that the reduction may have been due to manufacturing flaws in the čibu⋅d used in the study. In this two-phased study, we first compared the fishing performance of redesigned čibu⋅d made from four different materials: brass, stainless steel, plastic, and wood. In the second phase, we compared the fishing performance of the brass čibu⋅d with two common recreational fishing set-ups: a single large 16/0 circle hook and paired 8/0 circle hooks. The fishing performance of the redesigned čibu⋅d was not statistically different for čibu⋅d made of brass, stainless steel, or plastic. However, the čibu⋅d made from wood had significantly lower catch of halibut than the other čibu⋅d. We selected the brass čibu⋅d for the second phase of the study for continuity with the previous study of čibu⋅d and found that it had significantly less bycatch and a lower bycatch ratio than both the paired 8/0 and single 16/0 circle hooks. No significant differences were found in catch rates of halibut for paired 8/0 circle hooks, 16/0 circle hook, and the brass čibu⋅d. This study demonstrates that the improved catching performance of čibu⋅d on halibut and reduced bycatch compared to other popular approaches can be achieved by using brass čibu⋅d. Managers of recreational halibut fisheries should consider the use of čibu⋅d in areas where bycatch is a concern.
bibliographic citation: Petersen et al. (2020) Use of the traditional halibut hook of the Makah Tribe, the čibu⋅d, reduces bycatch in recreational halibut fisheries. PeerJ 8:e9288 https://doi.org/10.7717/peerj.9288
date submitted: 2020-02-18
date accepted: 2020-05-13
issued: 2020-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Petersen
  given name: Joseph R.
author list: Agent
  family name: Scordino
  given name: Jonathan J.
author list: Agent
  family name: Svec
  given name: Cole I.
author list: Agent
  family name: Buttram
  given name: Reginald H.
author list: Agent
  family name: Gonzalez
  given name: Maria R.
author list: Agent
  family name: Scordino
  given name: Joe
doi: 10.7717/peerj.9288
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: ©2020 Petersen et al.
attribution name: Petersen et al.

Conservation implications of using an imitation carnivore to assess rarely used refuges as critical habitat features in an alpine ungulate
type: item
type: AcademicArticle
description: Understanding relationships between animals and their habitat is a central goal in ecology with important implications for conservation. Misidentified habitat requirements can have serious repercussions because land protection or reintroductions might occur in less than optimal habitat. Studies of resource selection have greatly facilitated an understanding of ecological relationships but can be improved when vital yet infrequently utilized habitat features are more fully described. A critical element for many prey species is escape terrain or some other form of refuge to avoid predation. Mountain goats (Oreamnos americanus) are well known for their use of cliffs to avoid predation, but a survey of the literature revealed at least twelve different approximations of goat escape terrain, ranging from > 25° to > 50° slopes. Here, we seek to (1) enhance estimates of mountain goat escape terrain and antipredator behavior, and (2) highlight the limitations of the assumption that the time an animal spends in an area is proportional to importance. To improve estimates of goat escape terrain, we conducted field work across two years (2014–15) in Glacier National Park, Montana USA and manipulated apparent predation risk by exposing mountain goats to a threatening simulated grizzly bear (Ursus arctos) treatment and a non-threatening ungulate (control) treatment. Mountain goats moved in response to the simulated bear but not in response to the simulated ungulate, with shorter latencies to move for subjects in larger groups and at shorter distances to the simulated threat. Through a used-unused resource selection function we tested 22 landscape variables to describe the use of escape terrain. Proximity to slopes greater than 60° best explained the locations to which mountain goats fled after exposure to the simulated bear, and the average slope of these escape locations was 56.5° (±14.1 S.D.). Our results suggest that mountain goat escape terrain be considered at slopes of 60° a…
format: application/pdf
format: text/html
creator: Wesley Sarmento
creator: Joel Berger
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.9296
publisher: PeerJ Inc.
rights: © 2020 Sarmento and and Berger
abstract: Understanding relationships between animals and their habitat is a central goal in ecology with important implications for conservation. Misidentified habitat requirements can have serious repercussions because land protection or reintroductions might occur in less than optimal habitat. Studies of resource selection have greatly facilitated an understanding of ecological relationships but can be improved when vital yet infrequently utilized habitat features are more fully described. A critical element for many prey species is escape terrain or some other form of refuge to avoid predation. Mountain goats (Oreamnos americanus) are well known for their use of cliffs to avoid predation, but a survey of the literature revealed at least twelve different approximations of goat escape terrain, ranging from > 25° to > 50° slopes. Here, we seek to (1) enhance estimates of mountain goat escape terrain and antipredator behavior, and (2) highlight the limitations of the assumption that the time an animal spends in an area is proportional to importance. To improve estimates of goat escape terrain, we conducted field work across two years (2014–15) in Glacier National Park, Montana USA and manipulated apparent predation risk by exposing mountain goats to a threatening simulated grizzly bear (Ursus arctos) treatment and a non-threatening ungulate (control) treatment. Mountain goats moved in response to the simulated bear but not in response to the simulated ungulate, with shorter latencies to move for subjects in larger groups and at shorter distances to the simulated threat. Through a used-unused resource selection function we tested 22 landscape variables to describe the use of escape terrain. Proximity to slopes greater than 60° best explained the locations to which mountain goats fled after exposure to the simulated bear, and the average slope of these escape locations was 56.5° (±14.1 S.D.). Our results suggest that mountain goat escape terrain be considered at slopes of 60° a…
bibliographic citation: Sarmento et al. (2020) Conservation implications of using an imitation carnivore to assess rarely used refuges as critical habitat features in an alpine ungulate. PeerJ 8:e9296 https://doi.org/10.7717/peerj.9296
date submitted: 2019-03-29
date accepted: 2020-05-14
issued: 2020-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sarmento
  given name: Wesley
author list: Agent
  family name: Berger
  given name: Joel
doi: 10.7717/peerj.9296
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: ©2020 Sarmento and Berger
attribution name: Sarmento and and Berger

Genome-wide characterization of the Zn(II)2Cys6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress
type: item
type: AcademicArticle
description: Pleurotus ostreatus is one of the most widely cultivated mushrooms in China. The regulatory mechanisms of fruiting body formation and the response to heat stress in P. ostreatus are main research focuses. The Zn(II)2Cys6 family is one of the largest families of transcriptional factors and plays important roles in multiple biological processes in fungi. In this study, we identified 66 zinc cluster proteins in P. ostreatus (PoZCPs) through a genome-wide search. The PoZCPs were classified into 15 types according to their zinc cluster domain. Physical and chemical property analyses showed a huge diversity among the PoZCPs. Phylogenetic analysis of PoZCPs classified these proteins into six groups and conserved motif combinations and similar gene structures were observed in each group. The expression profiles of these PoZCP genes during different developmental stages and under heat stress were further investigated by RNA-sequencing (RNA-seq), revealing diverse expression patterns. A total of 13 PoZCPs that may participate in development or the heat stress response were selected for validation of their expression levels through real-time quantitative PCR (RT-qPCR) analysis, and some developmental stage-specific and heat stress-responsive candidates were identified. The findings contribute to our understanding of the roles and regulatory mechanisms of ZCPs in P. ostreatus.
format: application/pdf
format: text/html
creator: Zhihao Hou
creator: Qiang Chen
creator: Mengran Zhao
creator: Chenyang Huang
creator: Xiangli Wu
subject: Agricultural Science
subject: Bioinformatics
subject: Cell Biology
subject: Microbiology
subject: Mycology
description: doi:10.7717/peerj.9336
publisher: PeerJ Inc.
rights: © 2020 Hou et al.
abstract: Pleurotus ostreatus is one of the most widely cultivated mushrooms in China. The regulatory mechanisms of fruiting body formation and the response to heat stress in P. ostreatus are main research focuses. The Zn(II)2Cys6 family is one of the largest families of transcriptional factors and plays important roles in multiple biological processes in fungi. In this study, we identified 66 zinc cluster proteins in P. ostreatus (PoZCPs) through a genome-wide search. The PoZCPs were classified into 15 types according to their zinc cluster domain. Physical and chemical property analyses showed a huge diversity among the PoZCPs. Phylogenetic analysis of PoZCPs classified these proteins into six groups and conserved motif combinations and similar gene structures were observed in each group. The expression profiles of these PoZCP genes during different developmental stages and under heat stress were further investigated by RNA-sequencing (RNA-seq), revealing diverse expression patterns. A total of 13 PoZCPs that may participate in development or the heat stress response were selected for validation of their expression levels through real-time quantitative PCR (RT-qPCR) analysis, and some developmental stage-specific and heat stress-responsive candidates were identified. The findings contribute to our understanding of the roles and regulatory mechanisms of ZCPs in P. ostreatus.
bibliographic citation: Hou et al. (2020) Genome-wide characterization of the Zn(II)2Cys6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress. PeerJ 8:e9336 https://doi.org/10.7717/peerj.9336
date submitted: 2020-02-19
date accepted: 2020-05-20
issued: 2020-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hou
  given name: Zhihao
author list: Agent
  family name: Chen
  given name: Qiang
author list: Agent
  family name: Zhao
  given name: Mengran
author list: Agent
  family name: Huang
  given name: Chenyang
author list: Agent
  family name: Wu
  given name: Xiangli
doi: 10.7717/peerj.9336
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: © 2020 Hou et al.
attribution name: Hou et al.

Epiphytic bryophyte biomass estimation on tree trunks and upscaling in tropical montane cloud forests
type: item
type: AcademicArticle
description: Epiphytic bryophytes (EB) are some of the most commonly found plant species in tropical montane cloud forests, and they play a disproportionate role in influencing the terrestrial hydrological and nutrient cycles. However, it is difficult to estimate the abundance of EB due to the nature of their “epiphytic” habitat. This study proposes an allometric scaling approach implemented in twenty-one 30 × 30 m plots across an elevation range in 16,773 ha tropical montane cloud forests of northeastern Taiwan to measure EB biomass, a primary metric for indicating plant abundance and productivity. A general allometry was developed to estimate EB biomass of 100 cm2 circular-shaped mats (n = 131) with their central depths. We developed a new point-intercept instrument to rapidly measure the depths of EB along tree trunks below 300 cm from the ground level (sampled stem surface area (SSA)) (n = 210). Biomass of EB of each point measure was derived using the general allometry and was aggregated across each SSA, and its performance was evaluated. Total EB biomass of a tree was estimated by referring to an in-situ conversion model and was interpolated for all trees in the plots (n = 1451). Finally, we assessed EB biomass density at the plot scale of the study region. The general EB biomass-depth allometry showed that the depth of an EB mat was a salient variable for biomass estimation (R2 = 0.72, p < 0.001). The performance of upscaling from mats to SSA was satisfactory, which allowed us to further estimate mean (±standard deviation) EB biomass of the 21 plots (272 ± 104 kg ha−1). Since a significant relationship between tree size and EB abundance is commonly found, regional EB biomass may be mapped by integrating our method and three-dimensional remotely sensed airborne data.
format: application/pdf
format: text/html
creator: Guan-Yu Lai
creator: Hung-Chi Liu
creator: Ariel J. Kuo
creator: Cho-ying Huang
subject: Ecology
subject: Ecosystem Science
subject: Natural Resource Management
subject: Biogeochemistry
subject: Forestry
description: doi:10.7717/peerj.9351
publisher: PeerJ Inc.
rights: © 2020 Lai et al.
abstract: Epiphytic bryophytes (EB) are some of the most commonly found plant species in tropical montane cloud forests, and they play a disproportionate role in influencing the terrestrial hydrological and nutrient cycles. However, it is difficult to estimate the abundance of EB due to the nature of their “epiphytic” habitat. This study proposes an allometric scaling approach implemented in twenty-one 30 × 30 m plots across an elevation range in 16,773 ha tropical montane cloud forests of northeastern Taiwan to measure EB biomass, a primary metric for indicating plant abundance and productivity. A general allometry was developed to estimate EB biomass of 100 cm2 circular-shaped mats (n = 131) with their central depths. We developed a new point-intercept instrument to rapidly measure the depths of EB along tree trunks below 300 cm from the ground level (sampled stem surface area (SSA)) (n = 210). Biomass of EB of each point measure was derived using the general allometry and was aggregated across each SSA, and its performance was evaluated. Total EB biomass of a tree was estimated by referring to an in-situ conversion model and was interpolated for all trees in the plots (n = 1451). Finally, we assessed EB biomass density at the plot scale of the study region. The general EB biomass-depth allometry showed that the depth of an EB mat was a salient variable for biomass estimation (R2 = 0.72, p < 0.001). The performance of upscaling from mats to SSA was satisfactory, which allowed us to further estimate mean (±standard deviation) EB biomass of the 21 plots (272 ± 104 kg ha−1). Since a significant relationship between tree size and EB abundance is commonly found, regional EB biomass may be mapped by integrating our method and three-dimensional remotely sensed airborne data.
bibliographic citation: Lai et al. (2020) Epiphytic bryophyte biomass estimation on tree trunks and upscaling in tropical montane cloud forests. PeerJ 8:e9351 https://doi.org/10.7717/peerj.9351
date submitted: 2020-01-15
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: Lai
  given name: Guan-Yu
author list: Agent
  family name: Liu
  given name: Hung-Chi
author list: Agent
  family name: Kuo
  given name: Ariel J.
author list: Agent
  family name: Huang
  given name: Cho-ying
doi: 10.7717/peerj.9351
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-12
copyright: © 2020 Lai et al.
attribution name: Lai et al.

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.

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