PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Enhancement of specific T-lymphocyte responses by monocyte-derived dendritic cells pulsed with E2 protein of human papillomavirus 16 and human p16INK4A
items: Non-parallel changes in songbird migration timing are not explained by changes in stopover duration
items: Recent advances in biochar application for water and wastewater treatment: a review
items: The ability of oriental magpies (Pica serica) to solve baited multiple-string problems
items: The association of EGF rs2237051 variant, serum EGF levels and generalized aggressive periodontitis: a preliminary study
items: The case for extended lifespan in cooperatively breeding mammals: a re-appraisal
items: Plasma antioxidants and oxidative stress status in obese women: correlation with cardiopulmonary response
items: Expression and protease characterization of a conserved protein YgjD in Vibrio harveyi
items: The influence of surrounding land cover on wetland habitat conditions: a case study of inland wetlands in South Korea
items: Mitochondrial DNA variation in the Italian Heavy Draught Horse

Enhancement of specific T-lymphocyte responses by monocyte-derived dendritic cells pulsed with E2 protein of human papillomavirus 16 and human p16INK4A
type: item
type: AcademicArticle
description: Introduction Prophylactic vaccines are already available for prevention of human papillomavirus (HPV) infection. However, we still await development of therapeutic vaccines with high efficiency for stimulating specific T lymphocytes to clear HPV infection. Objective This study investigates the potential for subunits of human p16INK4a protein and E2 protein of HPV16 to stimulate dendritic cells and enhance the specific response of T lymphocytes against HPV-infected cells. Methodology Immunogenic epitopes of HPV16 E2 and p16INK4a proteins were predicted through the common HLA class I and II alleles present in the Thai population. Then, monocyte-derived dendritic cells (MDCs) were pulsed with HPV16 E2 and/or p16INK4a protein s and their maturity assessed. MDCs pulsed with either or both of these proteins at optimal concentrations were used for activation of autologous T lymphocytes and IFN-γ production was measured for specific response function. Results HPV16 E2 and p16INK4a proteins contain various immunogenic epitopes which can be presented by antigen-presenting cells via both HLA class I and II molecules. The stimulation of MDCs with either HPV16 E2 or p16INK4a proteins increased percentages and mean fluorescence intensity (MFI) of CD83+ MDCs in a dose-dependent manner. An optimum concentration of 250 ng/mL and 150 ng/mL of HPV16 E2 and p16INK4a proteins, respectively, stimulated MDCs via the MAPK pathway (confirmed by use of MAPK inhibitors). T lymphocytes could be activated by MDCs pulsed with these proteins, leading to high percentages of both CD4+ IFN-γ+ T lymphocytes and CD8+ IFN-γ+ T lymphocytes. The production of IFN-γ was higher in co-cultures containing MDCs pulsed with HPV16 E2 protein than those pulsed with p16INK4a. Interestingly, MDCs pulsed with a combination of HPV16 E2 and p16INK4a significantly increased IFN-γ production of T lymphocytes. The IFN-γ production was inhibited by both HLA class I and II blockade, particularly in co-cultures with MDCs p…
format: application/pdf
format: text/html
creator: Nuchsupha Sunthamala
creator: Neeranuch Sankla
creator: Jureeporn Chuerduangphui
creator: Piyawut Swangphon
creator: Wanchareeporn Boontun
creator: Supakpong Ngaochaiyaphum
creator: Weerayut Wongjampa
creator: Tipaya Ekalaksananan
creator: Chamsai Pientong
subject: Bioinformatics
subject: Microbiology
subject: Virology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.9213
publisher: PeerJ Inc.
rights: © 2020 Sunthamala et al.
abstract: Introduction Prophylactic vaccines are already available for prevention of human papillomavirus (HPV) infection. However, we still await development of therapeutic vaccines with high efficiency for stimulating specific T lymphocytes to clear HPV infection. Objective This study investigates the potential for subunits of human p16INK4a protein and E2 protein of HPV16 to stimulate dendritic cells and enhance the specific response of T lymphocytes against HPV-infected cells. Methodology Immunogenic epitopes of HPV16 E2 and p16INK4a proteins were predicted through the common HLA class I and II alleles present in the Thai population. Then, monocyte-derived dendritic cells (MDCs) were pulsed with HPV16 E2 and/or p16INK4a protein s and their maturity assessed. MDCs pulsed with either or both of these proteins at optimal concentrations were used for activation of autologous T lymphocytes and IFN-γ production was measured for specific response function. Results HPV16 E2 and p16INK4a proteins contain various immunogenic epitopes which can be presented by antigen-presenting cells via both HLA class I and II molecules. The stimulation of MDCs with either HPV16 E2 or p16INK4a proteins increased percentages and mean fluorescence intensity (MFI) of CD83+ MDCs in a dose-dependent manner. An optimum concentration of 250 ng/mL and 150 ng/mL of HPV16 E2 and p16INK4a proteins, respectively, stimulated MDCs via the MAPK pathway (confirmed by use of MAPK inhibitors). T lymphocytes could be activated by MDCs pulsed with these proteins, leading to high percentages of both CD4+ IFN-γ+ T lymphocytes and CD8+ IFN-γ+ T lymphocytes. The production of IFN-γ was higher in co-cultures containing MDCs pulsed with HPV16 E2 protein than those pulsed with p16INK4a. Interestingly, MDCs pulsed with a combination of HPV16 E2 and p16INK4a significantly increased IFN-γ production of T lymphocytes. The IFN-γ production was inhibited by both HLA class I and II blockade, particularly in co-cultures with MDCs p…
bibliographic citation: Sunthamala et al. (2020) Enhancement of specific T-lymphocyte responses by monocyte-derived dendritic cells pulsed with E2 protein of human papillomavirus 16 and human p16INK4A. PeerJ 8:e9213 https://doi.org/10.7717/peerj.9213
date submitted: 2020-01-06
date accepted: 2020-04-27
issued: 2020-05-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sunthamala
  given name: Nuchsupha
author list: Agent
  family name: Sankla
  given name: Neeranuch
author list: Agent
  family name: Chuerduangphui
  given name: Jureeporn
author list: Agent
  family name: Swangphon
  given name: Piyawut
author list: Agent
  family name: Boontun
  given name: Wanchareeporn
author list: Agent
  family name: Ngaochaiyaphum
  given name: Supakpong
author list: Agent
  family name: Wongjampa
  given name: Weerayut
author list: Agent
  family name: Ekalaksananan
  given name: Tipaya
author list: Agent
  family name: Pientong
  given name: Chamsai
doi: 10.7717/peerj.9213
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-20
copyright: © 2020 Sunthamala et al.
attribution name: Sunthamala et al.

Non-parallel changes in songbird migration timing are not explained by changes in stopover duration
type: item
type: AcademicArticle
description: Shifts in the timing of animal migration are widespread and well-documented; however, the mechanism underlying these changes is largely unknown. In this study, we test the hypothesis that systematic changes in stopover duration—the time that individuals spend resting and refueling at a site—are driving shifts in songbird migration timing. Specifically, we predicted that increases in stopover duration at our study site could generate increases in passage duration—the number of days that a study site is occupied by a particular species—by changing the temporal breadth of observations and vise versa. We analyzed an uninterrupted 46-year bird banding dataset from Massachusetts, USA using quantile regression, which allowed us to detect changes in early-and late-arriving birds, as well as changes in passage duration. We found that median spring migration had advanced by 1.04 days per decade; that these advances had strengthened over the last 13 years; and that early-and late-arriving birds were advancing in parallel, leading to negligible changes in the duration of spring passage at our site (+0.07 days per decade). In contrast, changes in fall migration were less consistent. Across species, we found that median fall migration had delayed by 0.80 days per decade, and that changes were stronger in late-arriving birds, leading to an average increase in passage duration of 0.45 days per decade. Trends in stopover duration, however, were weak and negative and, as a result, could not explain any changes in passage duration. We discuss, and provide some evidence, that changes in population age-structure, cryptic geographic variation, or shifts in resource availability are consistent with increases in fall passage duration. Moreover, we demonstrate the importance of evaluating changes across the entire phenological distribution, rather than just the mean, and stress this as an important consideration for future studies.
format: application/pdf
format: text/html
creator: Nicholas N. Dorian
creator: Trevor L. Lloyd-Evans
creator: J. Michael Reed
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Population Biology
description: doi:10.7717/peerj.8975
publisher: PeerJ Inc.
rights: © 2020 Dorian et al.
abstract: Shifts in the timing of animal migration are widespread and well-documented; however, the mechanism underlying these changes is largely unknown. In this study, we test the hypothesis that systematic changes in stopover duration—the time that individuals spend resting and refueling at a site—are driving shifts in songbird migration timing. Specifically, we predicted that increases in stopover duration at our study site could generate increases in passage duration—the number of days that a study site is occupied by a particular species—by changing the temporal breadth of observations and vise versa. We analyzed an uninterrupted 46-year bird banding dataset from Massachusetts, USA using quantile regression, which allowed us to detect changes in early-and late-arriving birds, as well as changes in passage duration. We found that median spring migration had advanced by 1.04 days per decade; that these advances had strengthened over the last 13 years; and that early-and late-arriving birds were advancing in parallel, leading to negligible changes in the duration of spring passage at our site (+0.07 days per decade). In contrast, changes in fall migration were less consistent. Across species, we found that median fall migration had delayed by 0.80 days per decade, and that changes were stronger in late-arriving birds, leading to an average increase in passage duration of 0.45 days per decade. Trends in stopover duration, however, were weak and negative and, as a result, could not explain any changes in passage duration. We discuss, and provide some evidence, that changes in population age-structure, cryptic geographic variation, or shifts in resource availability are consistent with increases in fall passage duration. Moreover, we demonstrate the importance of evaluating changes across the entire phenological distribution, rather than just the mean, and stress this as an important consideration for future studies.
bibliographic citation: Dorian et al. (2020) Non-parallel changes in songbird migration timing are not explained by changes in stopover duration. PeerJ 8:e8975 https://doi.org/10.7717/peerj.8975
date submitted: 2019-09-27
date accepted: 2020-03-24
issued: 2020-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dorian
  given name: Nicholas N.
author list: Agent
  family name: Lloyd-Evans
  given name: Trevor L.
author list: Agent
  family name: Reed
  given name: J. Michael
doi: 10.7717/peerj.8975
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-19
copyright: © 2020 Dorian et al.
attribution name: Dorian et al.

Recent advances in biochar application for water and wastewater treatment: a review
type: item
type: AcademicArticle
description: In the past decade, researchers have carried out a massive amount of research on the application of biochar for contaminants removal from aqueous solutions. As an emerging sorbent with great potential, biochar has shown significant advantages such as the broad sources of feedstocks, easy preparation process, and favorable surface and structural properties. This review provides an overview of recent advances in biochar application in water and wastewater treatment, including a brief discussion of the involved sorption mechanisms of contaminants removal, as well as the biochar modification methods. Furthermore, environmental concerns of biochar that need to be paid attention to and future research directions are put forward to promote the further application of biochar in practical water and wastewater treatment.
format: application/pdf
format: text/html
creator: Xiaoqing Wang
creator: Zizhang Guo
creator: Zhen Hu
creator: Jian Zhang
subject: Natural Resource Management
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.9164
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: In the past decade, researchers have carried out a massive amount of research on the application of biochar for contaminants removal from aqueous solutions. As an emerging sorbent with great potential, biochar has shown significant advantages such as the broad sources of feedstocks, easy preparation process, and favorable surface and structural properties. This review provides an overview of recent advances in biochar application in water and wastewater treatment, including a brief discussion of the involved sorption mechanisms of contaminants removal, as well as the biochar modification methods. Furthermore, environmental concerns of biochar that need to be paid attention to and future research directions are put forward to promote the further application of biochar in practical water and wastewater treatment.
bibliographic citation: Wang et al. (2020) Recent advances in biochar application for water and wastewater treatment: a review. PeerJ 8:e9164 https://doi.org/10.7717/peerj.9164
date submitted: 2019-11-07
date accepted: 2020-04-18
issued: 2020-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xiaoqing
author list: Agent
  family name: Guo
  given name: Zizhang
author list: Agent
  family name: Hu
  given name: Zhen
author list: Agent
  family name: Zhang
  given name: Jian
doi: 10.7717/peerj.9164
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-19
copyright: ©2020 Wang et al.
attribution name: Wang et al.

The ability of oriental magpies (Pica serica) to solve baited multiple-string problems
type: item
type: AcademicArticle
description: Background Baited multiple-string problems are commonly used in avian laboratory studies to evaluate complex cognition. Several bird species possess the ability to use a string pull for obtaining food. Methods We initially tested and trained 11 magpies to determine whether the oriental magpie (Pica sericia) possesses the ability to solve baited multiple-string problems. Eight of the birds obtained the bait by pulling, and were selected for formal multiple-string tasks in the second stage. Second stage tests were divided into seven tasks based on string configurations. Results Only two magpies were able to solve two tasks: one solved the task of parallel strings, and the other solved the task of slanted strings with the bait farther from the middle point between the two strings and selected the short string in the task of long-short strings. When faced with more difficult tasks (i.e., the task of slanted strings with the bait closer to the middle point between the two strings, the task with two crossing strings, and the task of continuity and discontinuity), the birds initially observed the tasks and chose instead to adopt simpler strategies based on the proximity principle, side bias strategies and trial-and-error learning. Our results indicate that the oriental magpie had a partial understanding of the principle of multiple-string problems but adopted simpler strategies.
format: application/pdf
format: text/html
creator: Lin Wang
creator: Jinxin Guo
creator: Heng jiu Tian
creator: Jinling Sui
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.9200
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Baited multiple-string problems are commonly used in avian laboratory studies to evaluate complex cognition. Several bird species possess the ability to use a string pull for obtaining food. Methods We initially tested and trained 11 magpies to determine whether the oriental magpie (Pica sericia) possesses the ability to solve baited multiple-string problems. Eight of the birds obtained the bait by pulling, and were selected for formal multiple-string tasks in the second stage. Second stage tests were divided into seven tasks based on string configurations. Results Only two magpies were able to solve two tasks: one solved the task of parallel strings, and the other solved the task of slanted strings with the bait farther from the middle point between the two strings and selected the short string in the task of long-short strings. When faced with more difficult tasks (i.e., the task of slanted strings with the bait closer to the middle point between the two strings, the task with two crossing strings, and the task of continuity and discontinuity), the birds initially observed the tasks and chose instead to adopt simpler strategies based on the proximity principle, side bias strategies and trial-and-error learning. Our results indicate that the oriental magpie had a partial understanding of the principle of multiple-string problems but adopted simpler strategies.
bibliographic citation: Wang et al. (2020) The ability of oriental magpies (Pica serica) to solve baited multiple-string problems. PeerJ 8:e9200 https://doi.org/10.7717/peerj.9200
date submitted: 2019-12-11
date accepted: 2020-04-24
issued: 2020-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Lin
author list: Agent
  family name: Guo
  given name: Jinxin
author list: Agent
  family name: Tian
  given name: Heng jiu
author list: Agent
  family name: Sui
  given name: Jinling
doi: 10.7717/peerj.9200
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-19
copyright: © 2020 Wang et al.
attribution name: Wang et al.

The association of EGF rs2237051 variant, serum EGF levels and generalized aggressive periodontitis: a preliminary study
type: item
type: AcademicArticle
description: Background Epidermal growth factor (EGF) is a pro-inflammatory small peptide that stimulates cell growth, proliferation and differentiation through binding to its receptor. EGF rs2237051 and serum EGF levels have been demonstrated to be related with a variety of diseases, including several tumors and inflammatory diseases. Therefore, this study aims to investigate the association of the EGF rs2237051 variant and serum EGF levels in Chinese patients with generalized aggressive periodontitis (GAgP). Material and Methods A case-control study was conducted among 216 patients with GAgP and 138 healthy controls. The clinical parameters of plaque index, probing depth, attachment loss and bleeding index were recorded. The EGF rs2237051 polymorphism was genotyped using time-of-flight mass spectrometry, and serum EGF levels were determined. Logistic and linear regression models were used to investigate the association between the genotypes of EGF rs2237051, serum EGF levels and GAgP risk. Results The AA genotype of EGF rs2237051 showed higher risk for GAgP than the combined genotypes GG and AG (adjusted OR = 1.65, 95% CI [1.06–2.57]). Increased serum EGF levels were associated with GAgP (adjusted OR = 1.18, 95% CI [1.14–1.22]). Moreover, the serum EGF level for the AA genotype was significantly higher than that for the AG/GG genotypes in patients with GAgP (adjusted β = 4.70, 95% CI [2.09–7.31]). Conclusion We demonstrated that EGF rs2237051 variant and the increased level of serum EGF were associated with the risk of GAgP, the serum EGF was up-regulated in patients with GAgP. It was indicated that serum EGF might be a biomarker of GAgP and EGF rs2237051 may be related to the genetic background of GAgP.
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format: text/html
creator: Xian’e Wang
creator: Wenjing Li
creator: Li Xu
creator: Ruifang Lu
creator: Huanxin Meng
subject: Genetics
subject: Dentistry
subject: Infectious Diseases
description: doi:10.7717/peerj.9212
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background Epidermal growth factor (EGF) is a pro-inflammatory small peptide that stimulates cell growth, proliferation and differentiation through binding to its receptor. EGF rs2237051 and serum EGF levels have been demonstrated to be related with a variety of diseases, including several tumors and inflammatory diseases. Therefore, this study aims to investigate the association of the EGF rs2237051 variant and serum EGF levels in Chinese patients with generalized aggressive periodontitis (GAgP). Material and Methods A case-control study was conducted among 216 patients with GAgP and 138 healthy controls. The clinical parameters of plaque index, probing depth, attachment loss and bleeding index were recorded. The EGF rs2237051 polymorphism was genotyped using time-of-flight mass spectrometry, and serum EGF levels were determined. Logistic and linear regression models were used to investigate the association between the genotypes of EGF rs2237051, serum EGF levels and GAgP risk. Results The AA genotype of EGF rs2237051 showed higher risk for GAgP than the combined genotypes GG and AG (adjusted OR = 1.65, 95% CI [1.06–2.57]). Increased serum EGF levels were associated with GAgP (adjusted OR = 1.18, 95% CI [1.14–1.22]). Moreover, the serum EGF level for the AA genotype was significantly higher than that for the AG/GG genotypes in patients with GAgP (adjusted β = 4.70, 95% CI [2.09–7.31]). Conclusion We demonstrated that EGF rs2237051 variant and the increased level of serum EGF were associated with the risk of GAgP, the serum EGF was up-regulated in patients with GAgP. It was indicated that serum EGF might be a biomarker of GAgP and EGF rs2237051 may be related to the genetic background of GAgP.
bibliographic citation: Wang et al. (2020) The association of EGF rs2237051 variant, serum EGF levels and generalized aggressive periodontitis: a preliminary study. PeerJ 8:e9212 https://doi.org/10.7717/peerj.9212
date submitted: 2020-02-17
date accepted: 2020-04-27
issued: 2020-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Xian’e
author list: Agent
  family name: Li
  given name: Wenjing
author list: Agent
  family name: Xu
  given name: Li
author list: Agent
  family name: Lu
  given name: Ruifang
author list: Agent
  family name: Meng
  given name: Huanxin
doi: 10.7717/peerj.9212
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-19
copyright: © 2020 Wang et al.
attribution name: Wang et al.

The case for extended lifespan in cooperatively breeding mammals: a re-appraisal
type: item
type: AcademicArticle
description: Recent comparative studies have suggested that cooperative breeding is associated with increases in maximum lifespan among mammals, replicating a pattern also seen in birds and insects. In this study, we re-examine the case for increased lifespan in mammalian cooperative breeders by analysing a large dataset of maximum longevity records. We did not find any consistent, strong evidence that cooperative breeders have longer lifespans than other mammals after having controlled for variation in body mass, mode of life and data quality. The only possible exception to this general trend is found in the African mole-rats (the Bathyergid family), where all members are relatively long-lived, but where the social, cooperatively breeding species appear to be much longer-lived than the solitary species. However, solitary mole-rat species have rarely been kept in captivity or followed longitudinally in the wild and so it seems likely that their maximum lifespan has been underestimated when compared to the highly researched social species. Although few subterranean mammals have received much attention in a captive or wild setting, current data instead supports a causal role of subterranean living on lifespan extension in mammals.
format: application/pdf
format: text/html
creator: Jack Thorley
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.9214
publisher: PeerJ Inc.
rights: © 2020 Thorley
abstract: Recent comparative studies have suggested that cooperative breeding is associated with increases in maximum lifespan among mammals, replicating a pattern also seen in birds and insects. In this study, we re-examine the case for increased lifespan in mammalian cooperative breeders by analysing a large dataset of maximum longevity records. We did not find any consistent, strong evidence that cooperative breeders have longer lifespans than other mammals after having controlled for variation in body mass, mode of life and data quality. The only possible exception to this general trend is found in the African mole-rats (the Bathyergid family), where all members are relatively long-lived, but where the social, cooperatively breeding species appear to be much longer-lived than the solitary species. However, solitary mole-rat species have rarely been kept in captivity or followed longitudinally in the wild and so it seems likely that their maximum lifespan has been underestimated when compared to the highly researched social species. Although few subterranean mammals have received much attention in a captive or wild setting, current data instead supports a causal role of subterranean living on lifespan extension in mammals.
bibliographic citation: Thorley (2020) The case for extended lifespan in cooperatively breeding mammals: a re-appraisal. PeerJ 8:e9214 https://doi.org/10.7717/peerj.9214
date submitted: 2019-09-20
date accepted: 2020-04-27
issued: 2020-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Thorley
  given name: Jack
doi: 10.7717/peerj.9214
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-19
copyright: © 2020 Thorley
attribution name: Thorley

Plasma antioxidants and oxidative stress status in obese women: correlation with cardiopulmonary response
type: item
type: AcademicArticle
description: Introduction A high body fat coupled with low cardiopulmonary fitness and an increase in oxidative stress has been connoted as contributing factors in developing cardiovascular comorbidities. This study aimed to investigate the correlation between antioxidants and oxidative stress status with cardiopulmonary responses in women of different body mass index (BMI). Subjects and Methods Eighty female adults were recruited and divided into three groups; normal weight (n = 23), overweight (n = 28) and obese (n = 29), according to their BMI. Blood samples were obtained prior to cardiopulmonary exercise testing. Plasma samples were separated by centrifugation and analysed for enzymatic antioxidant activity including catalase, glutathione peroxidase and superoxide dismutase. Non-enzymatic antioxidant activities were assessed using 2, 2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical scavenging and ferric reducing ability of plasma (FRAP) assays. To evaluate the oxidative stress status of subjects, levels of reactive oxygen species and malondialdehyde, the by-product of lipid peroxidation, were measured. Cardiopulmonary responses were analysed using cardiopulmonary exercise testing (CPET) which involved 15 various parameters such as peak oxygen consumption, metabolic equivalents and respiratory exchange ratio. Results The obese group had significantly lower ABTS radical scavenging and FRAP activities than the normal weight group. A higher catalase activity was observed in the obese group than the normal weight group. Spearman’s correlation showed an inverse relationship between catalase and peak oxygen consumption, while partial correlation analysis showed inverse correlations between superoxide dismutase and respiratory frequency, ABTS activity and oxygen pulse, and between ABTS activity and cardiac output. Conclusion Our results demonstrate a lower cardiovascular fitness and antioxidant capacity in obese women; the higher catalase activity may be a compe…
format: application/pdf
format: text/html
creator: Dyg Mastura Adenan
creator: Zulkarnain Jaafar
creator: Jaime Jacqueline Jayapalan
creator: Azlina Abdul Aziz
subject: Molecular Biology
subject: Public Health
subject: Women’s Health
description: doi:10.7717/peerj.9230
publisher: PeerJ Inc.
rights: © 2020 Adenan et al.
abstract: Introduction A high body fat coupled with low cardiopulmonary fitness and an increase in oxidative stress has been connoted as contributing factors in developing cardiovascular comorbidities. This study aimed to investigate the correlation between antioxidants and oxidative stress status with cardiopulmonary responses in women of different body mass index (BMI). Subjects and Methods Eighty female adults were recruited and divided into three groups; normal weight (n = 23), overweight (n = 28) and obese (n = 29), according to their BMI. Blood samples were obtained prior to cardiopulmonary exercise testing. Plasma samples were separated by centrifugation and analysed for enzymatic antioxidant activity including catalase, glutathione peroxidase and superoxide dismutase. Non-enzymatic antioxidant activities were assessed using 2, 2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radical scavenging and ferric reducing ability of plasma (FRAP) assays. To evaluate the oxidative stress status of subjects, levels of reactive oxygen species and malondialdehyde, the by-product of lipid peroxidation, were measured. Cardiopulmonary responses were analysed using cardiopulmonary exercise testing (CPET) which involved 15 various parameters such as peak oxygen consumption, metabolic equivalents and respiratory exchange ratio. Results The obese group had significantly lower ABTS radical scavenging and FRAP activities than the normal weight group. A higher catalase activity was observed in the obese group than the normal weight group. Spearman’s correlation showed an inverse relationship between catalase and peak oxygen consumption, while partial correlation analysis showed inverse correlations between superoxide dismutase and respiratory frequency, ABTS activity and oxygen pulse, and between ABTS activity and cardiac output. Conclusion Our results demonstrate a lower cardiovascular fitness and antioxidant capacity in obese women; the higher catalase activity may be a compe…
bibliographic citation: Adenan et al. (2020) Plasma antioxidants and oxidative stress status in obese women: correlation with cardiopulmonary response. PeerJ 8:e9230 https://doi.org/10.7717/peerj.9230
date submitted: 2020-01-06
date accepted: 2020-04-30
issued: 2020-05-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Adenan
  given name: Dyg Mastura
author list: Agent
  family name: Jaafar
  given name: Zulkarnain
author list: Agent
  family name: Jayapalan
  given name: Jaime Jacqueline
author list: Agent
  family name: Abdul Aziz
  given name: Azlina
doi: 10.7717/peerj.9230
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-19
copyright: ©2020 Adenan et al.
attribution name: Adenan et al.

Expression and protease characterization of a conserved protein YgjD in Vibrio harveyi
type: item
type: AcademicArticle
description: The glycopeptidase GCP and its homologue proteins are conserved and essential for survival of bacteria. The ygjD gene (Glycopeptidase homologue) was cloned from Vibrio harveyi strain SF-1. The gene consisted of 1,017 bp, which encodes a 338 amino acid polypeptide. The nucleotide sequence similarity of the ygjD gene with that of V. harveyi FDAARGOS 107 was 95%. The ygjD gene also showed similarities of 68%, 67% and 50% with those of Salmonella enterica, Escherichia coli and Bacillus cereus. The ygjD gene was expressed in E. coli BL21 (DE3) and the recombinant YgjD was purified by Ni2+ affinity chromatography column. The purified YgjD showed a specific 37 kDa band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and exhibited protease activities of 59,000 units/mg, 53,700 units/mg and 8,100 units/mg, respectively, on N-Acetyl-L-tyrosine ethyl ester monohydrate (ATEE), N-Benzoyl-L-tyrosine ethyl ester (BTEE) and N-Benzoyl-DL-arginine-4-nitroanilide hydrochloride (BAPNA) substrates. When the conserved amino acids of His111, Glu113 and His115 in the YgjD were replaced with alanine, respectively, the protease activities of the mutants were partly decreased. The two conserved His111 and His115 of YgjD were mutated and the protein lost the protease activity, which implied that the two amino acid played very important roles in maintaining its protease activity. The addition of the purified YgjD to the culture medium of V. harveyi strain SF-1 can effectively promote the bacteria growth. These results indicated that the protease activities may be involved in the survival of bacteria.
format: application/pdf
format: text/html
creator: Yayuan Zhang
creator: Jixiang Chen
creator: Yonggang Wang
creator: Yanlin Li
creator: Wenhong Rui
creator: Jiyi Zhang
creator: Dan Luo
subject: Agricultural Science
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
description: doi:10.7717/peerj.9061
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: The glycopeptidase GCP and its homologue proteins are conserved and essential for survival of bacteria. The ygjD gene (Glycopeptidase homologue) was cloned from Vibrio harveyi strain SF-1. The gene consisted of 1,017 bp, which encodes a 338 amino acid polypeptide. The nucleotide sequence similarity of the ygjD gene with that of V. harveyi FDAARGOS 107 was 95%. The ygjD gene also showed similarities of 68%, 67% and 50% with those of Salmonella enterica, Escherichia coli and Bacillus cereus. The ygjD gene was expressed in E. coli BL21 (DE3) and the recombinant YgjD was purified by Ni2+ affinity chromatography column. The purified YgjD showed a specific 37 kDa band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and exhibited protease activities of 59,000 units/mg, 53,700 units/mg and 8,100 units/mg, respectively, on N-Acetyl-L-tyrosine ethyl ester monohydrate (ATEE), N-Benzoyl-L-tyrosine ethyl ester (BTEE) and N-Benzoyl-DL-arginine-4-nitroanilide hydrochloride (BAPNA) substrates. When the conserved amino acids of His111, Glu113 and His115 in the YgjD were replaced with alanine, respectively, the protease activities of the mutants were partly decreased. The two conserved His111 and His115 of YgjD were mutated and the protein lost the protease activity, which implied that the two amino acid played very important roles in maintaining its protease activity. The addition of the purified YgjD to the culture medium of V. harveyi strain SF-1 can effectively promote the bacteria growth. These results indicated that the protease activities may be involved in the survival of bacteria.
bibliographic citation: Zhang et al. (2020) Expression and protease characterization of a conserved protein YgjD in Vibrio harveyi. PeerJ 8:e9061 https://doi.org/10.7717/peerj.9061
date submitted: 2019-12-26
date accepted: 2020-04-04
issued: 2020-05-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yayuan
author list: Agent
  family name: Chen
  given name: Jixiang
author list: Agent
  family name: Wang
  given name: Yonggang
author list: Agent
  family name: Li
  given name: Yanlin
author list: Agent
  family name: Rui
  given name: Wenhong
author list: Agent
  family name: Zhang
  given name: Jiyi
author list: Agent
  family name: Luo
  given name: Dan
doi: 10.7717/peerj.9061
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-18
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

The influence of surrounding land cover on wetland habitat conditions: a case study of inland wetlands in South Korea
type: item
type: AcademicArticle
description: Wetland ecosystems have been globally degraded and lost due to rapid urbanization and climate change. An assessment of national scale inventory, including wetland types and conditions, is urgently required to understand the big picture of endangered wetlands, such as where they are and how they look like. We analyzed the spatial patterns of each inland wetland type (brackish wetland was included) in South Korea and the relative importance of land cover categories on wetland conditions. The wetlands were grouped into four dominant types (riverine, lake, mountain, and human-made) according to their topography. Riverine wetlands constituted the largest area (71.3%). The relative ratio of wetlands in a well-conserved condition (i.e., “A” rank) was highest in riverine wetlands (23.8%), followed by mountain wetlands (22.1%). The higher proportion of grasslands was related to a better condition ranking, but the increasing bareland area had a negative impact on wetland conditions. We also found that wetlands located near wetland protected areas tend to be in a better condition compared to remote sites. Our results further support the importance of the condition of surrounding areas for wetland conservation.
format: application/pdf
format: text/html
creator: Ran-Young Im
creator: Taekyu Kim
creator: Chung-Yeol Baek
creator: Chang-Su Lee
creator: Song-Hyun Kim
creator: Jung-Hwan Lee
creator: Ji Yoon Kim
creator: Gea-Jae Joo
subject: Ecology
subject: Freshwater Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.9101
publisher: PeerJ Inc.
rights: © 2020 Im et al.
abstract: Wetland ecosystems have been globally degraded and lost due to rapid urbanization and climate change. An assessment of national scale inventory, including wetland types and conditions, is urgently required to understand the big picture of endangered wetlands, such as where they are and how they look like. We analyzed the spatial patterns of each inland wetland type (brackish wetland was included) in South Korea and the relative importance of land cover categories on wetland conditions. The wetlands were grouped into four dominant types (riverine, lake, mountain, and human-made) according to their topography. Riverine wetlands constituted the largest area (71.3%). The relative ratio of wetlands in a well-conserved condition (i.e., “A” rank) was highest in riverine wetlands (23.8%), followed by mountain wetlands (22.1%). The higher proportion of grasslands was related to a better condition ranking, but the increasing bareland area had a negative impact on wetland conditions. We also found that wetlands located near wetland protected areas tend to be in a better condition compared to remote sites. Our results further support the importance of the condition of surrounding areas for wetland conservation.
bibliographic citation: Im et al. (2020) The influence of surrounding land cover on wetland habitat conditions: a case study of inland wetlands in South Korea. PeerJ 8:e9101 https://doi.org/10.7717/peerj.9101
date submitted: 2019-11-11
date accepted: 2020-04-09
issued: 2020-05-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Im
  given name: Ran-Young
author list: Agent
  family name: Kim
  given name: Taekyu
author list: Agent
  family name: Baek
  given name: Chung-Yeol
author list: Agent
  family name: Lee
  given name: Chang-Su
author list: Agent
  family name: Kim
  given name: Song-Hyun
author list: Agent
  family name: Lee
  given name: Jung-Hwan
author list: Agent
  family name: Kim
  given name: Ji Yoon
author list: Agent
  family name: Joo
  given name: Gea-Jae
doi: 10.7717/peerj.9101
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-18
copyright: ©2020 Im et al.
attribution name: Im et al.

Mitochondrial DNA variation in the Italian Heavy Draught Horse
type: item
type: AcademicArticle
description: Background In the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook. Methodology To provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds. Results Among the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.
format: application/pdf
format: text/html
creator: Hovirag Lancioni
creator: Irene Cardinali
creator: Andrea Giontella
creator: Maria Teresa Antognoni
creator: Arianna Miglio
subject: Conservation Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.8996
publisher: PeerJ Inc.
rights: © 2020 Lancioni et al.
abstract: Background In the last decades, Italy as well as other developed countries have registered a decrease in the population size of many local horse breeds. The continuous crossbreeding has determined the dilution of genetic heritage of several native breeds. The Italian Heavy Draught Horse (IHD) is the only autochthonous Italian coldblooded horse among these breeds; therefore, it represents a resource to be preserved. In 1927, the first generation of this breed was officially created by crossing different Heavy Draught horses with local mares and recorded in a Studbook. Methodology To provide the first comprehensive overview of the genetic diversity of Italian Heavy Draught horses from Central Italy, we produced and phylogenetically analysed 52 mitochondrial DNA (mtDNA) control-region sequences. Furthermore, we evaluated data available from GenBank (N = 568) to have a more complete scenario and to understand the relationships with other European Heavy Draught horse breeds. Results Among the IHD samples that were analysed, we identified ten of the 17 haplogroups described in modern horses. Most of these sequences fell into L, G, and M lineages, thus showing the overall mtDNA legacy of the ancestral mares that were probably used at the initial stages of breeding selections a long time ago. The high mitochondrial haplotype diversity (Hd = 0.969) found in our samples reflected the multiple maternal origins of the horses. Our results highlighted a considerable percentage of haplotypes shared especially with Bardigiano and Hungarian Heavy Draught breeds. Furthermore, both the presence of four unique haplotypes detected in our samples and their absence among all equine mitochondrial published data demonstrate a mitochondrial peculiarity that needs to be further investigated and preserved with careful breeding practices.
bibliographic citation: Lancioni et al. (2020) Mitochondrial DNA variation in the Italian Heavy Draught Horse. PeerJ 8:e8996 https://doi.org/10.7717/peerj.8996
date submitted: 2019-11-28
date accepted: 2020-03-26
issued: 2020-05-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lancioni
  given name: Hovirag
author list: Agent
  family name: Cardinali
  given name: Irene
author list: Agent
  family name: Giontella
  given name: Andrea
author list: Agent
  family name: Antognoni
  given name: Maria Teresa
author list: Agent
  family name: Miglio
  given name: Arianna
doi: 10.7717/peerj.8996
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-05-15
copyright: ©2020 Lancioni et al.
attribution name: Lancioni et al.

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