PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Aichi Target 18 beyond 2020: mainstreaming Traditional Biodiversity Knowledge in the conservation and sustainable use of marine and coastal ecosystems
items: Expression of vitamin D 1α-hydroxylase in human gingival fibroblasts in vivo
items: Analysis of synonymous codon usage of transcriptome database in Rheum palmatum
items: A nature-based health intervention at a military healthcare center: a randomized, controlled, cross-over study
items: Limited effect of a highway barrier on the genetic structure of a gypsum soil specialist
items: A feasibility study to determine the use of baited pots in Greenland halibut (Reinhardtius hippoglossoides) fisheries, supported by the use of underwater video observations
items: Soluble expression and purification of Bluetongue Virus Type 1 (BTV1) structure protein VP2 in Escherichia coli and its immunogenicity in mice
items: In vitro anticandidal activity and gas chromatography-mass spectrometry (GC-MS) screening of Vitex agnus-castus leaf extracts
items: Serum metabolite profiling of a 4-Nitroquinoline-1-oxide-induced experimental oral carcinogenesis model using gas chromatography-mass spectrometry
items: Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2

Aichi Target 18 beyond 2020: mainstreaming Traditional Biodiversity Knowledge in the conservation and sustainable use of marine and coastal ecosystems
type: item
type: AcademicArticle
description: Indigenous Peoples and Local Communities (IPLCs) have inhabited coastal areas, the seas, and remote islands for millennia, and developed place-based traditional ancestral knowledge and diversified livelihoods associated with the biocultural use of marine and coastal ecosystems. Through their cultural traditions, customary wise practices, and holistic approaches to observe, monitor, understand, and appreciate the Natural World, IPLCs have been preserving, managing, and sustainably using seascapes and coastal landscapes, which has been essential for biodiversity conservation. The international community has more than ever recognized the central role of IPLCs in the conservation of biodiversity-rich ecosystems, in particular, for the achievement of the Global Biodiversity Targets determined by the Parties to the United Nations Convention on Biological Diversity to tackle biodiversity loss. However, much remains to be done to fully recognize and protect at national levels IPLCs’ Traditional Biodiversity Knowledge (TBK), ways of life, and their internationally recognized rights to inhabit, own, manage and govern traditional lands, territories, and waters, which are increasingly threatened. At the 2018 4th World Conference on Marine Biodiversity held in Montréal, Canada, eight themed working groups critically discussed progress to date and barriers that have prevented the achievement of the Aichi Biodiversity Targets agreed for the period 2011–2020, and priority actions for the Post-2020 Global Biodiversity Framework. Discussions in the “Application of Biodiversity Knowledge” working group focused on Targets 11 and 18 and the equal valuation of diverse Biodiversity Knowledge Systems (BKS). This Perspective Paper summarizes the 10 Priority Actions identified for a holistic biodiversity conservation, gender equality and human rights-based approach that strengthens the role of IPLCs as biodiversity conservation decision-makers and managers at national and international level…
format: application/pdf
format: text/html
creator: Paola Fajardo
creator: David Beauchesne
creator: Alberto Carbajal-López
creator: Rémi M. Daigle
creator: L. Denisse Fierro-Arcos
creator: Jesica Goldsmit
creator: Sabine Zajderman
creator: Juan I. Valdez-Hernández
creator: María Yolanda Terán Maigua
creator: Ronaldo A. Christofoletti
subject: Biodiversity
subject: Conservation Biology
subject: Marine Biology
subject: Science Policy
subject: Natural Resource Management
description: doi:10.7717/peerj.9616
publisher: PeerJ Inc.
rights: © 2021 Fajardo et al.
abstract: Indigenous Peoples and Local Communities (IPLCs) have inhabited coastal areas, the seas, and remote islands for millennia, and developed place-based traditional ancestral knowledge and diversified livelihoods associated with the biocultural use of marine and coastal ecosystems. Through their cultural traditions, customary wise practices, and holistic approaches to observe, monitor, understand, and appreciate the Natural World, IPLCs have been preserving, managing, and sustainably using seascapes and coastal landscapes, which has been essential for biodiversity conservation. The international community has more than ever recognized the central role of IPLCs in the conservation of biodiversity-rich ecosystems, in particular, for the achievement of the Global Biodiversity Targets determined by the Parties to the United Nations Convention on Biological Diversity to tackle biodiversity loss. However, much remains to be done to fully recognize and protect at national levels IPLCs’ Traditional Biodiversity Knowledge (TBK), ways of life, and their internationally recognized rights to inhabit, own, manage and govern traditional lands, territories, and waters, which are increasingly threatened. At the 2018 4th World Conference on Marine Biodiversity held in Montréal, Canada, eight themed working groups critically discussed progress to date and barriers that have prevented the achievement of the Aichi Biodiversity Targets agreed for the period 2011–2020, and priority actions for the Post-2020 Global Biodiversity Framework. Discussions in the “Application of Biodiversity Knowledge” working group focused on Targets 11 and 18 and the equal valuation of diverse Biodiversity Knowledge Systems (BKS). This Perspective Paper summarizes the 10 Priority Actions identified for a holistic biodiversity conservation, gender equality and human rights-based approach that strengthens the role of IPLCs as biodiversity conservation decision-makers and managers at national and international level…
bibliographic citation: Fajardo et al. (2021) Aichi Target 18 beyond 2020: mainstreaming Traditional Biodiversity Knowledge in the conservation and sustainable use of marine and coastal ecosystems. PeerJ 9:e9616 https://doi.org/10.7717/peerj.9616
date submitted: 2019-08-14
date accepted: 2020-07-06
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fajardo
  given name: Paola
author list: Agent
  family name: Beauchesne
  given name: David
author list: Agent
  family name: Carbajal-López
  given name: Alberto
author list: Agent
  family name: Daigle
  given name: Rémi M.
author list: Agent
  family name: Fierro-Arcos
  given name: L. Denisse
author list: Agent
  family name: Goldsmit
  given name: Jesica
author list: Agent
  family name: Zajderman
  given name: Sabine
author list: Agent
  family name: Valdez-Hernández
  given name: Juan I.
author list: Agent
  family name: Terán Maigua
  given name: María Yolanda
author list: Agent
  family name: Christofoletti
  given name: Ronaldo A.
doi: 10.7717/peerj.9616
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: © 2021 Fajardo et al.
attribution name: Fajardo et al.

Expression of vitamin D 1α-hydroxylase in human gingival fibroblasts in vivo
type: item
type: AcademicArticle
description: Background Vitamin D 1α-hydroxylase CYP27B1 is the key factor in the vitamin D pathway. Previously, we analyzed the expression of CYP27B1 in human gingival fibroblasts in vitro. In the present study, we analyzed the gingival expression of CYP27B1 in vivo. Methods Forty-two patients with periodontitis Stage IV Grade C and 33 controls were recruited. All patients with periodontitis had unsalvageable teeth and part of the wall of the periodontal pocket was resected and obtained after tooth extraction. All controls needed crown-lengthening surgery, and samples of gingiva resected during surgery were also harvested. All the individuals’ gingivae were used for immunohistochemistry and immunofluorescence. In addition, gingivae from seventeen subjects of the diseased group and twelve subjects of the control group were analyzed by real-time PCR. Results Expression of CYP27B1 was detected both in gingival epithelia and in gingival connective tissues, and the expression in connective tissues colocalized with vimentin, indicating that CYP27B1 protein is expressed in gingival fibroblasts. The expression of CYP27B1 mRNA in gingival connective tissues and the CYP27B1 staining scores in gingival fibroblasts in the diseased group were significantly higher than those in the control group. Conclusions Expression of CYP27B1 in human gingival tissues was detected, not only in the fibroblasts of gingival connective tissues, but also in the gingival epithelial cells, and might be positively correlated with periodontal inflammation.
format: application/pdf
format: text/html
creator: Kaining Liu
creator: Bing Han
creator: Jianxia Hou
creator: Jianyun Zhang
creator: Jing Su
creator: Huanxin Meng
subject: Cell Biology
subject: Molecular Biology
subject: Dentistry
subject: Infectious Diseases
subject: Histology
description: doi:10.7717/peerj.10279
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background Vitamin D 1α-hydroxylase CYP27B1 is the key factor in the vitamin D pathway. Previously, we analyzed the expression of CYP27B1 in human gingival fibroblasts in vitro. In the present study, we analyzed the gingival expression of CYP27B1 in vivo. Methods Forty-two patients with periodontitis Stage IV Grade C and 33 controls were recruited. All patients with periodontitis had unsalvageable teeth and part of the wall of the periodontal pocket was resected and obtained after tooth extraction. All controls needed crown-lengthening surgery, and samples of gingiva resected during surgery were also harvested. All the individuals’ gingivae were used for immunohistochemistry and immunofluorescence. In addition, gingivae from seventeen subjects of the diseased group and twelve subjects of the control group were analyzed by real-time PCR. Results Expression of CYP27B1 was detected both in gingival epithelia and in gingival connective tissues, and the expression in connective tissues colocalized with vimentin, indicating that CYP27B1 protein is expressed in gingival fibroblasts. The expression of CYP27B1 mRNA in gingival connective tissues and the CYP27B1 staining scores in gingival fibroblasts in the diseased group were significantly higher than those in the control group. Conclusions Expression of CYP27B1 in human gingival tissues was detected, not only in the fibroblasts of gingival connective tissues, but also in the gingival epithelial cells, and might be positively correlated with periodontal inflammation.
bibliographic citation: Liu et al. (2021) Expression of vitamin D 1α-hydroxylase in human gingival fibroblasts in vivo. PeerJ 9:e10279 https://doi.org/10.7717/peerj.10279
date submitted: 2020-06-24
date accepted: 2020-10-09
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Kaining
author list: Agent
  family name: Han
  given name: Bing
author list: Agent
  family name: Hou
  given name: Jianxia
author list: Agent
  family name: Zhang
  given name: Jianyun
author list: Agent
  family name: Su
  given name: Jing
author list: Agent
  family name: Meng
  given name: Huanxin
doi: 10.7717/peerj.10279
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Analysis of synonymous codon usage of transcriptome database in Rheum palmatum
type: item
type: AcademicArticle
description: Background Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. Methods In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. Results The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.
format: application/pdf
format: text/html
creator: Xiaowei Huo
creator: Sisi Liu
creator: Yimin Li
creator: Hao Wei
creator: Jing Gao
creator: Yonggang Yan
creator: Gang Zhang
creator: Mengmeng Liu
subject: Bioinformatics
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.10450
publisher: PeerJ Inc.
rights: © 2021 Huo et al.
abstract: Background Rheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 predicted CDSs from R. palmatum transcriptome. Methods In this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS. Results The average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms in R. palmatum.
bibliographic citation: Huo et al. (2021) Analysis of synonymous codon usage of transcriptome database in Rheum palmatum. PeerJ 9:e10450 https://doi.org/10.7717/peerj.10450
date submitted: 2020-06-26
date accepted: 2020-11-09
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huo
  given name: Xiaowei
author list: Agent
  family name: Liu
  given name: Sisi
author list: Agent
  family name: Li
  given name: Yimin
author list: Agent
  family name: Wei
  given name: Hao
author list: Agent
  family name: Gao
  given name: Jing
author list: Agent
  family name: Yan
  given name: Yonggang
author list: Agent
  family name: Zhang
  given name: Gang
author list: Agent
  family name: Liu
  given name: Mengmeng
doi: 10.7717/peerj.10450
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: ©2021 Huo et al.
attribution name: Huo et al.

A nature-based health intervention at a military healthcare center: a randomized, controlled, cross-over study
type: item
type: AcademicArticle
description: We describe a mixed qualitative and quantitative research study in a military facility regarding the role of nature in well-being. Study intervention included two 20-minute walks. One walk was in an intentionally designed woodland environment (Green Road) and the other was on a busy campus road in a medical treatment facility (Urban Road). Twelve volunteers from a military facility participated in both walks in a cross-over experimental design. The two walking sessions were randomly ordered and preceded by pre-walk instructions appropriate to each road’s characteristics and incorporated focused attention and present moment orientation. A semi-structured post-walk interview, the primary outcome, was conducted after the conclusion of each walk. Qualitative data analyses consisted of sentiments and themes by using NVivo 12 software. The Green Road was unanimously rated as positive (100%). Responses to Urban Road were evenly distributed among positive (33.3%), negative (33.3%), and neutral/mixed (33.3%) sentiments. The Green Road yielded predominantly positive themes such as enjoyment of nature, relaxation, and feelings of privacy and safety. Urban Road produced significantly more negative themes such as concerns for safety, dislike of noise and other noxious experiences. Quantitative assessment of distress and mindfulness with Distress Thermometer (DT) and Mindful Attention Awareness Scale-state version (MAAS) demonstrated that a walk on the Green Road significantly decreased distress and increased mindfulness compared to a walk on the Urban Road. We also observed that pre-walk instructions could direct attention to both obvious and subtle elements of experience and enhance awareness. Results support the notion that an intentional nature-based environment may produce significantly more positive experiences and result in health-promoting benefits in a military health-care setting compared to an urban environment. Future studies with clinical populations could advance ou…
format: application/pdf
format: text/html
creator: Rezvan Ameli
creator: Perry Skeath
creator: Preetha A. Abraham
creator: Samin Panahi
creator: Josh B. Kazman
creator: Frederick Foote
creator: Patricia A. Deuster
creator: Niha Ahmad
creator: Ann Berger
subject: Psychiatry and Psychology
subject: Public Health
description: doi:10.7717/peerj.10519
publisher: PeerJ Inc.
rights: © 2021 Ameli et al.
abstract: We describe a mixed qualitative and quantitative research study in a military facility regarding the role of nature in well-being. Study intervention included two 20-minute walks. One walk was in an intentionally designed woodland environment (Green Road) and the other was on a busy campus road in a medical treatment facility (Urban Road). Twelve volunteers from a military facility participated in both walks in a cross-over experimental design. The two walking sessions were randomly ordered and preceded by pre-walk instructions appropriate to each road’s characteristics and incorporated focused attention and present moment orientation. A semi-structured post-walk interview, the primary outcome, was conducted after the conclusion of each walk. Qualitative data analyses consisted of sentiments and themes by using NVivo 12 software. The Green Road was unanimously rated as positive (100%). Responses to Urban Road were evenly distributed among positive (33.3%), negative (33.3%), and neutral/mixed (33.3%) sentiments. The Green Road yielded predominantly positive themes such as enjoyment of nature, relaxation, and feelings of privacy and safety. Urban Road produced significantly more negative themes such as concerns for safety, dislike of noise and other noxious experiences. Quantitative assessment of distress and mindfulness with Distress Thermometer (DT) and Mindful Attention Awareness Scale-state version (MAAS) demonstrated that a walk on the Green Road significantly decreased distress and increased mindfulness compared to a walk on the Urban Road. We also observed that pre-walk instructions could direct attention to both obvious and subtle elements of experience and enhance awareness. Results support the notion that an intentional nature-based environment may produce significantly more positive experiences and result in health-promoting benefits in a military health-care setting compared to an urban environment. Future studies with clinical populations could advance ou…
bibliographic citation: Ameli et al. (2021) A nature-based health intervention at a military healthcare center: a randomized, controlled, cross-over study. PeerJ 9:e10519 https://doi.org/10.7717/peerj.10519
date submitted: 2020-07-29
date accepted: 2020-11-17
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Ameli
  given name: Rezvan
author list: Agent
  family name: Skeath
  given name: Perry
author list: Agent
  family name: Abraham
  given name: Preetha A.
author list: Agent
  family name: Panahi
  given name: Samin
author list: Agent
  family name: Kazman
  given name: Josh B.
author list: Agent
  family name: Foote
  given name: Frederick
author list: Agent
  family name: Deuster
  given name: Patricia A.
author list: Agent
  family name: Ahmad
  given name: Niha
author list: Agent
  family name: Berger
  given name: Ann
doi: 10.7717/peerj.10519
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: ©2021 Ameli et al.
attribution name: Ameli et al.

Limited effect of a highway barrier on the genetic structure of a gypsum soil specialist
type: item
type: AcademicArticle
description: Background Gypsum ecosystems are edaphic islands surrounded by a matrix that is inhospitable to gypsum soil plant specialists. These naturally fragmented landscapes are currently exacerbated due to man-made disturbances, jeopardising their valuable biodiversity. Concomitant action of other fragmentation drivers such as linear infrastructures may increase the already high threat to these specialists. Although some evidence suggest that gypsophytes are not evolutionary dead-ends and can respond to fragmentation by means of phenotypic plasticity, the simultaneous action of barriers to genetic flow can pose a severe hazard to their viability. Here, we evaluated the effect of a highway with heavy traffic on the genetic flow and diversity in the species Lepidium subulatum, a dominant Iberian shrubby gypsophyte. Methods We tested the possible existence of bottlenecks, and estimated the genetic diversity, gene flow and genetic structure in the remnant populations, exploring in detail the effect of a highway as a possible barrier. Results Results showed variability in genetic diversity, migrants and structure. The highway had a low impact on the species since populations can retain high levels of genetic diversity and genetic parameter, like FST and FIS, did not seem to be affected. The presence of some level of genetic flow in both sides along the highway could explain the relatively high genetic diversity in the habitat remnants. Discussion Natural fragmentation and their exacerbation by agriculture and linear infrastructures seem to be negligible for this species and do not limit its viability. The biological features, demographic dynamics and population structures of gypsum species seem to be a valuable, adaptive pre-requisite to be a soil specialist and to maintain its competitiveness with other species in such adverse stressful conditions.
format: application/pdf
format: text/html
creator: Irene Martín-Rodríguez
creator: Adrián Escudero
creator: Alfredo García-Fernández
subject: Ecology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
subject: Population Biology
description: doi:10.7717/peerj.10533
publisher: PeerJ Inc.
rights: © 2021 Martín-Rodríguez et al.
abstract: Background Gypsum ecosystems are edaphic islands surrounded by a matrix that is inhospitable to gypsum soil plant specialists. These naturally fragmented landscapes are currently exacerbated due to man-made disturbances, jeopardising their valuable biodiversity. Concomitant action of other fragmentation drivers such as linear infrastructures may increase the already high threat to these specialists. Although some evidence suggest that gypsophytes are not evolutionary dead-ends and can respond to fragmentation by means of phenotypic plasticity, the simultaneous action of barriers to genetic flow can pose a severe hazard to their viability. Here, we evaluated the effect of a highway with heavy traffic on the genetic flow and diversity in the species Lepidium subulatum, a dominant Iberian shrubby gypsophyte. Methods We tested the possible existence of bottlenecks, and estimated the genetic diversity, gene flow and genetic structure in the remnant populations, exploring in detail the effect of a highway as a possible barrier. Results Results showed variability in genetic diversity, migrants and structure. The highway had a low impact on the species since populations can retain high levels of genetic diversity and genetic parameter, like FST and FIS, did not seem to be affected. The presence of some level of genetic flow in both sides along the highway could explain the relatively high genetic diversity in the habitat remnants. Discussion Natural fragmentation and their exacerbation by agriculture and linear infrastructures seem to be negligible for this species and do not limit its viability. The biological features, demographic dynamics and population structures of gypsum species seem to be a valuable, adaptive pre-requisite to be a soil specialist and to maintain its competitiveness with other species in such adverse stressful conditions.
bibliographic citation: Martín-Rodríguez et al. (2021) Limited effect of a highway barrier on the genetic structure of a gypsum soil specialist. PeerJ 9:e10533 https://doi.org/10.7717/peerj.10533
date submitted: 2020-06-25
date accepted: 2020-11-19
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martín-Rodríguez
  given name: Irene
author list: Agent
  family name: Escudero
  given name: Adrián
author list: Agent
  family name: García-Fernández
  given name: Alfredo
doi: 10.7717/peerj.10533
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: © 2021 Martín-Rodríguez et al.
attribution name: Martín-Rodríguez et al.

A feasibility study to determine the use of baited pots in Greenland halibut (Reinhardtius hippoglossoides) fisheries, supported by the use of underwater video observations
type: item
type: AcademicArticle
description: High incidental catches of Greenland shark (Somniosus microcephalus) in Nunavut’s Greenland halibut (Reinhardtius hippoglossoides) fishery has led to studies on the feasibility of capturing Greenland halibut with baited pots. In this study, catch rates among six experimental pots are compared. In addition to this, underwater video observations of Greenland halibut interacting with two of these experimental pot types are quantified in order to help provide recommendations on future pot designs. Catch rates of Greenland halibut differed among pots with different entrance mesh types, and none of the pots produced substantial amounts of bycatch. Strings of pots were deployed within a narrow corridor between baited gillnets targeting Greenland halibut, which may have affected catch results. Video observations revealed Greenland halibut entangled by their teeth significantly more often in entrance funnels constructed with 50 mm than with 19 mm clear monofilament netting and the entrance rate was 45% higher with the 19 mm netting. Greenland halibut that successfully entered a pot repeatedly became entangled by their teeth in 58 mm netting used in the side and end panels and in a horizontal panel used to separate the pot into a lower and upper chamber. The majority (80%) of Greenland halibut were observed to approach a pot against the current. The downstream entrance was aligned with the current in 52% of the observed Greenland halibut approaches. Seventy percent of entry attempts and 67% of successful entries occurred when fish approached against the current and when the entrance was aligned with the current. These observations lead to recommendations that future studies consider developing a four entrance pot to ensure an entrance is always aligned with bottom currents. Based on these observations of entanglements, it is recommended to use 19 mm clear monofilament netting in the entrance funnel, 100 mm polyethylene netting in the exterior panels, and 19 mm polypropylene n…
format: application/pdf
format: text/html
creator: Margaret H. Folkins
creator: Scott M. Grant
creator: Philip Walsh
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.10536
publisher: PeerJ Inc.
rights: © 2021 Folkins et al.
abstract: High incidental catches of Greenland shark (Somniosus microcephalus) in Nunavut’s Greenland halibut (Reinhardtius hippoglossoides) fishery has led to studies on the feasibility of capturing Greenland halibut with baited pots. In this study, catch rates among six experimental pots are compared. In addition to this, underwater video observations of Greenland halibut interacting with two of these experimental pot types are quantified in order to help provide recommendations on future pot designs. Catch rates of Greenland halibut differed among pots with different entrance mesh types, and none of the pots produced substantial amounts of bycatch. Strings of pots were deployed within a narrow corridor between baited gillnets targeting Greenland halibut, which may have affected catch results. Video observations revealed Greenland halibut entangled by their teeth significantly more often in entrance funnels constructed with 50 mm than with 19 mm clear monofilament netting and the entrance rate was 45% higher with the 19 mm netting. Greenland halibut that successfully entered a pot repeatedly became entangled by their teeth in 58 mm netting used in the side and end panels and in a horizontal panel used to separate the pot into a lower and upper chamber. The majority (80%) of Greenland halibut were observed to approach a pot against the current. The downstream entrance was aligned with the current in 52% of the observed Greenland halibut approaches. Seventy percent of entry attempts and 67% of successful entries occurred when fish approached against the current and when the entrance was aligned with the current. These observations lead to recommendations that future studies consider developing a four entrance pot to ensure an entrance is always aligned with bottom currents. Based on these observations of entanglements, it is recommended to use 19 mm clear monofilament netting in the entrance funnel, 100 mm polyethylene netting in the exterior panels, and 19 mm polypropylene n…
bibliographic citation: Folkins et al. (2021) A feasibility study to determine the use of baited pots in Greenland halibut (Reinhardtius hippoglossoides) fisheries, supported by the use of underwater video observations. PeerJ 9:e10536 https://doi.org/10.7717/peerj.10536
date submitted: 2020-05-14
date accepted: 2020-11-19
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Folkins
  given name: Margaret H.
author list: Agent
  family name: Grant
  given name: Scott M.
author list: Agent
  family name: Walsh
  given name: Philip
doi: 10.7717/peerj.10536
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: ©2021 Folkins et al.
attribution name: Folkins et al.

Soluble expression and purification of Bluetongue Virus Type 1 (BTV1) structure protein VP2 in Escherichia coli and its immunogenicity in mice
type: item
type: AcademicArticle
description: Background The VP2 on the surface of the virus particle is the main structural protein of BTV, which can induce the host to produce neutralizing antibodies and play an important role in the antiviral immunity process. This study aimed to obtain the soluble VP2 and analyze its immunogenicity. Methods The gene encoding the full-length VP2 of BTV1 was amplified by PCR. The products from restriction enzyme digestion and ligase reaction between VP2 and vector pET-28a were transformed into E.coli DH5α. After PCR and sequencing detection, the positive plasmid PET28a-VP2 was transformed into E.coli BL21(DE3) and Rosetta(DE3) competent cells, expression induced by IPTG. The fusion protein was expressed in the optimized conditions with the induction of IPTG, purified by affinity chromatography and identified by SDS-PAGE and Western blotting. A total of 5 Balb/c mice aged 6–8 weeks were immunized with the fusion protein at a dose of 30 µg per mouse. Each mouse was immunized three times at an interval of 3 weeks. Results The recombinant plasmid PET28a-VP2 was successfully constructed. The expression strains were induced by 0.4 mmol/L IPTG at 16 °C for 10 h, and BTV1 VP2 was expressed in a soluble form. The purity of the recombinant VP2 protein (∼109 kDa) was about 90% in the concentration at 0.2 mg/ml afterpurification. The purified VP2 had good immunoreactivity with BTV1 positive serum. Taken together, thisstudy offered a route for producing soluble BTV VP2, which retains activity and immunogenicity, to bebeneficial to the research on developing BTV vaccine, and lay the foundation for further research on BTV.
format: application/pdf
format: text/html
creator: Aiping Wang
creator: Jiajia Yin
creator: Jingming Zhou
creator: Hongfang Ma
creator: Yumei Chen
creator: Hongliang Liu
creator: Yanhua Qi
creator: Chao Liang
creator: Yankai Liu
creator: Jinge Li
creator: Gaiping Zhang
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.10543
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background The VP2 on the surface of the virus particle is the main structural protein of BTV, which can induce the host to produce neutralizing antibodies and play an important role in the antiviral immunity process. This study aimed to obtain the soluble VP2 and analyze its immunogenicity. Methods The gene encoding the full-length VP2 of BTV1 was amplified by PCR. The products from restriction enzyme digestion and ligase reaction between VP2 and vector pET-28a were transformed into E.coli DH5α. After PCR and sequencing detection, the positive plasmid PET28a-VP2 was transformed into E.coli BL21(DE3) and Rosetta(DE3) competent cells, expression induced by IPTG. The fusion protein was expressed in the optimized conditions with the induction of IPTG, purified by affinity chromatography and identified by SDS-PAGE and Western blotting. A total of 5 Balb/c mice aged 6–8 weeks were immunized with the fusion protein at a dose of 30 µg per mouse. Each mouse was immunized three times at an interval of 3 weeks. Results The recombinant plasmid PET28a-VP2 was successfully constructed. The expression strains were induced by 0.4 mmol/L IPTG at 16 °C for 10 h, and BTV1 VP2 was expressed in a soluble form. The purity of the recombinant VP2 protein (∼109 kDa) was about 90% in the concentration at 0.2 mg/ml afterpurification. The purified VP2 had good immunoreactivity with BTV1 positive serum. Taken together, thisstudy offered a route for producing soluble BTV VP2, which retains activity and immunogenicity, to bebeneficial to the research on developing BTV vaccine, and lay the foundation for further research on BTV.
bibliographic citation: Wang et al. (2021) Soluble expression and purification of Bluetongue Virus Type 1 (BTV1) structure protein VP2 in Escherichia coli and its immunogenicity in mice. PeerJ 9:e10543 https://doi.org/10.7717/peerj.10543
date submitted: 2020-06-12
date accepted: 2020-11-20
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Aiping
author list: Agent
  family name: Yin
  given name: Jiajia
author list: Agent
  family name: Zhou
  given name: Jingming
author list: Agent
  family name: Ma
  given name: Hongfang
author list: Agent
  family name: Chen
  given name: Yumei
author list: Agent
  family name: Liu
  given name: Hongliang
author list: Agent
  family name: Qi
  given name: Yanhua
author list: Agent
  family name: Liang
  given name: Chao
author list: Agent
  family name: Liu
  given name: Yankai
author list: Agent
  family name: Li
  given name: Jinge
author list: Agent
  family name: Zhang
  given name: Gaiping
doi: 10.7717/peerj.10543
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: ©2021 Wang et al.
attribution name: Wang et al.

In vitro anticandidal activity and gas chromatography-mass spectrometry (GC-MS) screening of Vitex agnus-castus leaf extracts
type: item
type: AcademicArticle
description: Background Candida infections are becoming more drug resistant; it is necessary to search for alternative medications to treat them. Therefore, the present study estimates the anticandidal activity of Vitex agnus-castus (VA-C) leaf extracts. Methods We used the agar well diffusion method to assess the anticandidal activity of three different VA-C leaf extracts (ethanol, methanol, and water) against three Candida species (Candida tropicalis, Candida albicans, and Candida ciferrii). The minimum inhibitory concentration (MIC) was estimated using the two-fold dilution method and the minimum fungicidal concentration (MFC) was determined using the classic pour plate technique. The MFC/MIC ratio was calculated to estimate the microbicidal or microbiostatic activity. A gas chromatography mass spectrometer was used to screen the phytochemicals of the VA-C leaf extracts (ethanol, methanol, and water). Results All VA-C extracts ethanol, methanol, and water were significantly inhibited the growth of the test Candida species and the inhibition activity depended on the solvent used and the Candida species. The results showed that C. tropicalis was the most highly inhibited by all extracts followed by C. albicans and C. ciferrii. The MIC values were 12.5–25 µg/ml, and MFC values were 25–100 µg/ml. The ratios of MFC/MIC were two-fold to four-fold which was considered candidacidal activity. Ninety-five phytochemical compounds were identified by the GC-MS assay for the VA-C leaf extracts. The total number of compounds per extract differed. Methanol had 43 compounds, ethanol had 47 compounds, and water had 52 compounds. The highest compound concentrations were: 4,5-Dichloro-1,3-dioxolan-2-one in ethanol and methanol, 1H-Indene, 2,3-dihydro-1,1,2,3,3-pentamethyl in ethanol, Isobutyl 4-hydroxybenzoate in methanol, and Benzoic acid and 4-hydroxy- in water. These phytochemical compounds belong to different bioactive chemical group such as polyphenols, fatty acids, terpenes, terpenoids, st…
format: application/pdf
format: text/html
creator: Ibtisam Mohammed Ababutain
creator: Azzah Ibrahim Alghamdi
subject: Biochemistry
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.10561
publisher: PeerJ Inc.
rights: © 2021 Ababutain and Alghamdi
abstract: Background Candida infections are becoming more drug resistant; it is necessary to search for alternative medications to treat them. Therefore, the present study estimates the anticandidal activity of Vitex agnus-castus (VA-C) leaf extracts. Methods We used the agar well diffusion method to assess the anticandidal activity of three different VA-C leaf extracts (ethanol, methanol, and water) against three Candida species (Candida tropicalis, Candida albicans, and Candida ciferrii). The minimum inhibitory concentration (MIC) was estimated using the two-fold dilution method and the minimum fungicidal concentration (MFC) was determined using the classic pour plate technique. The MFC/MIC ratio was calculated to estimate the microbicidal or microbiostatic activity. A gas chromatography mass spectrometer was used to screen the phytochemicals of the VA-C leaf extracts (ethanol, methanol, and water). Results All VA-C extracts ethanol, methanol, and water were significantly inhibited the growth of the test Candida species and the inhibition activity depended on the solvent used and the Candida species. The results showed that C. tropicalis was the most highly inhibited by all extracts followed by C. albicans and C. ciferrii. The MIC values were 12.5–25 µg/ml, and MFC values were 25–100 µg/ml. The ratios of MFC/MIC were two-fold to four-fold which was considered candidacidal activity. Ninety-five phytochemical compounds were identified by the GC-MS assay for the VA-C leaf extracts. The total number of compounds per extract differed. Methanol had 43 compounds, ethanol had 47 compounds, and water had 52 compounds. The highest compound concentrations were: 4,5-Dichloro-1,3-dioxolan-2-one in ethanol and methanol, 1H-Indene, 2,3-dihydro-1,1,2,3,3-pentamethyl in ethanol, Isobutyl 4-hydroxybenzoate in methanol, and Benzoic acid and 4-hydroxy- in water. These phytochemical compounds belong to different bioactive chemical group such as polyphenols, fatty acids, terpenes, terpenoids, st…
bibliographic citation: Ababutain et al. (2021) In vitro anticandidal activity and gas chromatography-mass spectrometry (GC-MS) screening of Vitex agnus-castus leaf extracts. PeerJ 9:e10561 https://doi.org/10.7717/peerj.10561
date submitted: 2020-08-06
date accepted: 2020-11-22
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ababutain
  given name: Ibtisam Mohammed
author list: Agent
  family name: Alghamdi
  given name: Azzah Ibrahim
doi: 10.7717/peerj.10561
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: © 2021 Ababutain and Alghamdi
attribution name: Ababutain and Alghamdi

Serum metabolite profiling of a 4-Nitroquinoline-1-oxide-induced experimental oral carcinogenesis model using gas chromatography-mass spectrometry
type: item
type: AcademicArticle
description: Background Oral cancer progresses from hyperplastic epithelial lesions through dysplasia to invasive carcinoma. The critical needs in oral cancer treatment are expanding our knowledge of malignant tumour progression and the development of useful approaches to prevent dysplastic lesions. This study was designed to gain insights into the underlying metabolic transformations that occur during the process of oral carcinogenesis. Methods We used gas chromatography-mass spectrometry (GC-MS) in conjunction with multivariate statistical techniques to observe alterations in serum metabolites in a 4-Nitroquinoline 1-oxide (4NQO)-induced rat tongue carcinogenesis model. Thirty-eight male rats were randomly divided into two groups, including the 4NQO-induced model group of 30 rats and the healthy control group of five rats. Animals were sacrificed at weeks 9, 13, 20, 24, and 32, post-4NQO treatment. Tissue samples were collected for histopathological examinations and blood samples were collected for metabolomic analysis. Partial least squares discriminate analysis (PLS-DA) models generated from GC-MS metabolic profile data showed robust discrimination from rats with oral premalignant and malignant lesions induced by 4NQO, and normal controls. Results The results found 16 metabolites associated with 4NQO-induced rat tongue carcinogenesis. Dysregulated arachidonic acid, fatty acid, and glycine metabolism, as well as disturbed tricarboxylic acid (TCA) cycle and mitochondrial respiratory chains were observed in the animal model. The PLS-DA models of metabolomic results demonstrated good separations between the 4NQO-induced model group and the normal control group. Conclusion We found several metabolites modulated by 4NQO and provide a good reference for further study of early diagnosis in oral cancer.
format: application/pdf
format: text/html
creator: Shuyun Ge
creator: Haiwen Zhou
creator: Zengtong Zhou
creator: Lin Liu
creator: Jianing Lou
subject: Dentistry
subject: Hematology
subject: Oncology
subject: Metabolic Sciences
description: doi:10.7717/peerj.10619
publisher: PeerJ Inc.
rights: © 2021 Ge et al.
abstract: Background Oral cancer progresses from hyperplastic epithelial lesions through dysplasia to invasive carcinoma. The critical needs in oral cancer treatment are expanding our knowledge of malignant tumour progression and the development of useful approaches to prevent dysplastic lesions. This study was designed to gain insights into the underlying metabolic transformations that occur during the process of oral carcinogenesis. Methods We used gas chromatography-mass spectrometry (GC-MS) in conjunction with multivariate statistical techniques to observe alterations in serum metabolites in a 4-Nitroquinoline 1-oxide (4NQO)-induced rat tongue carcinogenesis model. Thirty-eight male rats were randomly divided into two groups, including the 4NQO-induced model group of 30 rats and the healthy control group of five rats. Animals were sacrificed at weeks 9, 13, 20, 24, and 32, post-4NQO treatment. Tissue samples were collected for histopathological examinations and blood samples were collected for metabolomic analysis. Partial least squares discriminate analysis (PLS-DA) models generated from GC-MS metabolic profile data showed robust discrimination from rats with oral premalignant and malignant lesions induced by 4NQO, and normal controls. Results The results found 16 metabolites associated with 4NQO-induced rat tongue carcinogenesis. Dysregulated arachidonic acid, fatty acid, and glycine metabolism, as well as disturbed tricarboxylic acid (TCA) cycle and mitochondrial respiratory chains were observed in the animal model. The PLS-DA models of metabolomic results demonstrated good separations between the 4NQO-induced model group and the normal control group. Conclusion We found several metabolites modulated by 4NQO and provide a good reference for further study of early diagnosis in oral cancer.
bibliographic citation: Ge et al. (2021) Serum metabolite profiling of a 4-Nitroquinoline-1-oxide-induced experimental oral carcinogenesis model using gas chromatography-mass spectrometry. PeerJ 9:e10619 https://doi.org/10.7717/peerj.10619
date submitted: 2020-06-24
date accepted: 2020-11-30
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ge
  given name: Shuyun
author list: Agent
  family name: Zhou
  given name: Haiwen
author list: Agent
  family name: Zhou
  given name: Zengtong
author list: Agent
  family name: Liu
  given name: Lin
author list: Agent
  family name: Lou
  given name: Jianing
doi: 10.7717/peerj.10619
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: ©2021 Ge et al.
attribution name: Ge et al.

Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2
type: item
type: AcademicArticle
description: SARS-CoV-2 genome encodes four structural proteins that include the spike glycoprotein, membrane protein, envelope protein and nucleocapsid phosphoprotein (N-protein). The N-protein interacts with viral genomic RNA and helps in packaging. As SARS-CoV-2 spread to almost all countries worldwide within 2–3 months, it also acquired mutations in its RNA genome. Therefore, this study was conducted with an aim to identify the variations present in N-protein of SARS-CoV-2. Here, we analysed 4,163 reported sequence of N-protein from United States of America (USA) and compared them with the first reported sequence from Wuhan, China. Our study identified 107 mutations that reside all over the N-protein. Further, we show the high rate of mutations in intrinsically disordered regions (IDRs) of N-protein. Our study show 45% residues of IDR2 harbour mutations. The RNA-binding domain (RBD) and dimerization domain of N-protein also have mutations at key residues. We further measured the effect of these mutations on N-protein stability and dynamicity and our data reveals that multiple mutations can cause considerable alterations. Altogether, our data strongly suggests that N-protein is one of the mutational hotspot proteins of SARS-CoV-2 that is changing rapidly and these mutations can potentially interferes with various aspects of N-protein functions including its interaction with RNA, oligomerization and signalling events.
format: application/pdf
format: text/html
creator: Gajendra Kumar Azad
subject: Biochemistry
subject: Genetics
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.10666
publisher: PeerJ Inc.
rights: © 2021 Azad
abstract: SARS-CoV-2 genome encodes four structural proteins that include the spike glycoprotein, membrane protein, envelope protein and nucleocapsid phosphoprotein (N-protein). The N-protein interacts with viral genomic RNA and helps in packaging. As SARS-CoV-2 spread to almost all countries worldwide within 2–3 months, it also acquired mutations in its RNA genome. Therefore, this study was conducted with an aim to identify the variations present in N-protein of SARS-CoV-2. Here, we analysed 4,163 reported sequence of N-protein from United States of America (USA) and compared them with the first reported sequence from Wuhan, China. Our study identified 107 mutations that reside all over the N-protein. Further, we show the high rate of mutations in intrinsically disordered regions (IDRs) of N-protein. Our study show 45% residues of IDR2 harbour mutations. The RNA-binding domain (RBD) and dimerization domain of N-protein also have mutations at key residues. We further measured the effect of these mutations on N-protein stability and dynamicity and our data reveals that multiple mutations can cause considerable alterations. Altogether, our data strongly suggests that N-protein is one of the mutational hotspot proteins of SARS-CoV-2 that is changing rapidly and these mutations can potentially interferes with various aspects of N-protein functions including its interaction with RNA, oligomerization and signalling events.
bibliographic citation: Azad (2021) Identification and molecular characterization of mutations in nucleocapsid phosphoprotein of SARS-CoV-2. PeerJ 9:e10666 https://doi.org/10.7717/peerj.10666
date submitted: 2020-06-28
date accepted: 2020-12-08
issued: 2021-01-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Azad
  given name: Gajendra Kumar
doi: 10.7717/peerj.10666
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-04
copyright: © 2021 Azad
attribution name: Azad

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