PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effects of quarantine on Physical Activity prevalence in Italian Adults: a pilot study
items: Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands
items: Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach
items: Association between clinical oral health status and perceived oral health in different age groups
items: Distorted body schema after mastectomy with immediate breast reconstruction: a 4-month follow up study
items: An in silico study of how histone tail conformation affects the binding affinity of ING family proteins
items: MicroRNA-21 as a potential biomarker for detecting esophageal carcinoma in Asian populations: a meta-analysis
items: Irradiation with carbon ion beams affects soybean nutritional quality in early generations
items: Rapid restructurization of conformationally-distinct alpha-synuclein amyloid fibrils at an elevated temperature
items: Progressive overload without progressing load? The effects of load or repetition progression on muscular adaptations

Effects of quarantine on Physical Activity prevalence in Italian Adults: a pilot study
type: item
type: AcademicArticle
description: Background COVID-19 is a respiratory disease that caused a global pandemic status in March 2020. Due to its fast diffusion, many governments adopted forced solutions including social restrictions, which could negatively affect citizens’ habits as physical activity. Our study aimed to investigate how and why the physical activity prevalence varied from the period before the quarantine up to the period after it, and understand what citizens thought of physical inactivity COVID-19 related to and whether they were satisfied with physical activity promotion during the lockdown. Methods A new questionnaire was created and administered online. A sample of 749 interviews (female = 552 (73.7%), male = 197 (26.3%)) was collected and analysed. Results The prevalence of people who were older than 50 years reduced both during and after the lockdown (P < 0.05) and the most common reason for which they have quitted physical activity practice was related to psychological problems (lockdown = 64.57%; post-lockdown = 62.17%). In addition, youngers seemed to be more sensitive than elders to unhealthy consequences generated by forced isolation (P < 0.05), and they believed that children/adolescents and older adults practised an insufficient amount of physical activity and/or sport, which could negatively impact public health. Conclusions Although many strategies were implemented during the lockdown to promote regular physical activity practice, several results suggested that quarantine negatively affected citizens’ habits. The future government should focus on adequate measures to improve health behaviours.
format: application/pdf
format: text/html
creator: Mario Mauro
creator: Stefania Toselli
creator: Silvia Bonazzi
creator: Alessia Grigoletto
creator: Stefania Cataldi
creator: Gianpiero Greco
creator: Pasqualino Maietta Latessa
subject: Global Health
subject: Health Policy
subject: Kinesiology
subject: Public Health
subject: COVID-19
description: doi:10.7717/peerj.14123
publisher: PeerJ Inc.
rights: © 2022 Mauro et al.
abstract: Background COVID-19 is a respiratory disease that caused a global pandemic status in March 2020. Due to its fast diffusion, many governments adopted forced solutions including social restrictions, which could negatively affect citizens’ habits as physical activity. Our study aimed to investigate how and why the physical activity prevalence varied from the period before the quarantine up to the period after it, and understand what citizens thought of physical inactivity COVID-19 related to and whether they were satisfied with physical activity promotion during the lockdown. Methods A new questionnaire was created and administered online. A sample of 749 interviews (female = 552 (73.7%), male = 197 (26.3%)) was collected and analysed. Results The prevalence of people who were older than 50 years reduced both during and after the lockdown (P < 0.05) and the most common reason for which they have quitted physical activity practice was related to psychological problems (lockdown = 64.57%; post-lockdown = 62.17%). In addition, youngers seemed to be more sensitive than elders to unhealthy consequences generated by forced isolation (P < 0.05), and they believed that children/adolescents and older adults practised an insufficient amount of physical activity and/or sport, which could negatively impact public health. Conclusions Although many strategies were implemented during the lockdown to promote regular physical activity practice, several results suggested that quarantine negatively affected citizens’ habits. The future government should focus on adequate measures to improve health behaviours.
bibliographic citation: Mauro et al. (2022) Effects of quarantine on Physical Activity prevalence in Italian Adults: a pilot study. PeerJ 10:e14123 https://doi.org/10.7717/peerj.14123
date submitted: 2022-07-28
date accepted: 2022-09-06
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mauro
  given name: Mario
author list: Agent
  family name: Toselli
  given name: Stefania
author list: Agent
  family name: Bonazzi
  given name: Silvia
author list: Agent
  family name: Grigoletto
  given name: Alessia
author list: Agent
  family name: Cataldi
  given name: Stefania
author list: Agent
  family name: Greco
  given name: Gianpiero
author list: Agent
  family name: Maietta Latessa
  given name: Pasqualino
doi: 10.7717/peerj.14123
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Mauro et al.
attribution name: Mauro et al.

Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands
type: item
type: AcademicArticle
description: In recent years, a rare edible mushroom Stropharia rugosoannulata has become popular. S. rugosoannulata has the characteristics of easy cultivation, low cost, high output value, and low labor requirement, making its economic benefits significantly superior to those of other planting industries. Accumulating research demonstrates that cultivating edible fungus is advantageous for farming soil. The present experiment used idle croplands in winter for S. rugosoannulata cultivation. We explored the effects of S. rugosoannulata cultivation on soil properties and soil microbial community structure in paddy and dry fields, respectively. We cultivated S. rugosoannulata in the fields after planting chili and rice, respectively. The results showed that Chili-S. rugosoannulata and Rice-S. rugosoannulata planting patterns increased the yield, quality and amino acid content of S. rugosoannulata. By analyzing the soil properties, we found that the Chili-S. rugosoannulata and Rice-S. rugosoannulata cropping patterns increased the total nitrogen, available phosphorus, soil organic carbon, and available potassium content of the soil. We used 16s amplicons for bacteria and internal transcribed spacer (ITS) region for fungi to analyze the microbial communities in rhizosphere soils. Notably, S. rugosoannulata cultivation significantly increased the abundance of beneficial microorganisms such as Chloroflexi, Cladosporium and Mortierella and reduce the abundance of Botryotrichumin and Archaeorhizomyces. We consider S. rugosoannulata cultivation in cropland can improve soil properties, regulate the community structure of soil microorganisms, increase the expression abundance of beneficial organisms and ultimately improve the S. rugosoannulata yield and lay a good foundation for a new round of crops after this edible mushroom cultivation.
format: application/pdf
format: text/html
creator: Shaojun Tang
creator: Tingting Fan
creator: Lei Jin
creator: Pin Lei
creator: Chenxia Shao
creator: Shenlian Wu
creator: Yi Yang
creator: Yuelin He
creator: Rui Ren
creator: Jun Xu
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Mycology
subject: Soil Science
description: doi:10.7717/peerj.14130
publisher: PeerJ Inc.
rights: © 2022 Tang et al.
abstract: In recent years, a rare edible mushroom Stropharia rugosoannulata has become popular. S. rugosoannulata has the characteristics of easy cultivation, low cost, high output value, and low labor requirement, making its economic benefits significantly superior to those of other planting industries. Accumulating research demonstrates that cultivating edible fungus is advantageous for farming soil. The present experiment used idle croplands in winter for S. rugosoannulata cultivation. We explored the effects of S. rugosoannulata cultivation on soil properties and soil microbial community structure in paddy and dry fields, respectively. We cultivated S. rugosoannulata in the fields after planting chili and rice, respectively. The results showed that Chili-S. rugosoannulata and Rice-S. rugosoannulata planting patterns increased the yield, quality and amino acid content of S. rugosoannulata. By analyzing the soil properties, we found that the Chili-S. rugosoannulata and Rice-S. rugosoannulata cropping patterns increased the total nitrogen, available phosphorus, soil organic carbon, and available potassium content of the soil. We used 16s amplicons for bacteria and internal transcribed spacer (ITS) region for fungi to analyze the microbial communities in rhizosphere soils. Notably, S. rugosoannulata cultivation significantly increased the abundance of beneficial microorganisms such as Chloroflexi, Cladosporium and Mortierella and reduce the abundance of Botryotrichumin and Archaeorhizomyces. We consider S. rugosoannulata cultivation in cropland can improve soil properties, regulate the community structure of soil microorganisms, increase the expression abundance of beneficial organisms and ultimately improve the S. rugosoannulata yield and lay a good foundation for a new round of crops after this edible mushroom cultivation.
bibliographic citation: Tang et al. (2022) Soil microbial diversity and functional capacity associated with the production of edible mushroom Stropharia rugosoannulata in croplands. PeerJ 10:e14130 https://doi.org/10.7717/peerj.14130
date submitted: 2022-08-15
date accepted: 2022-09-06
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tang
  given name: Shaojun
author list: Agent
  family name: Fan
  given name: Tingting
author list: Agent
  family name: Jin
  given name: Lei
author list: Agent
  family name: Lei
  given name: Pin
author list: Agent
  family name: Shao
  given name: Chenxia
author list: Agent
  family name: Wu
  given name: Shenlian
author list: Agent
  family name: Yang
  given name: Yi
author list: Agent
  family name: He
  given name: Yuelin
author list: Agent
  family name: Ren
  given name: Rui
author list: Agent
  family name: Xu
  given name: Jun
doi: 10.7717/peerj.14130
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Tang et al.
attribution name: Tang et al.

Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach
type: item
type: AcademicArticle
description: MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.
format: application/pdf
format: text/html
creator: Reza Arshinchi Bonab
creator: Seyedehsadaf Asfa
creator: Panagiota Kontou
creator: Gökhan Karakülah
creator: Athanasia Pavlopoulou
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.14149
publisher: PeerJ Inc.
rights: © 2022 Arshinchi Bonab et al.
abstract: MicroRNAs represent major regulatory components of the disease epigenome and they constitute powerful biomarkers for the accurate diagnosis and prognosis of various diseases, including cancers. The advent of high-throughput technologies facilitated the generation of a vast amount of miRNA-cancer association data. Computational approaches have been utilized widely to effectively analyze and interpret these data towards the identification of miRNA signatures for diverse types of cancers. Herein, a novel computational workflow was applied to discover core sets of miRNA interactions for the major groups of neoplastic diseases by employing network-based methods. To this end, miRNA-cancer association data from four comprehensive publicly available resources were utilized for constructing miRNA-centered networks for each major group of neoplasms. The corresponding miRNA-miRNA interactions were inferred based on shared functionally related target genes. The topological attributes of the generated networks were investigated in order to detect clusters of highly interconnected miRNAs that form core modules in each network. Those modules that exhibited the highest degree of mutual exclusivity were selected from each graph. In this way, neoplasm-specific miRNA modules were identified that could represent potential signatures for the corresponding diseases.
bibliographic citation: Arshinchi Bonab et al. (2022) Identification of neoplasm-specific signatures of miRNA interactions by employing a systems biology approach. PeerJ 10:e14149 https://doi.org/10.7717/peerj.14149
date submitted: 2022-04-28
date accepted: 2022-09-07
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arshinchi Bonab
  given name: Reza
author list: Agent
  family name: Asfa
  given name: Seyedehsadaf
author list: Agent
  family name: Kontou
  given name: Panagiota
author list: Agent
  family name: Karakülah
  given name: Gökhan
author list: Agent
  family name: Pavlopoulou
  given name: Athanasia
doi: 10.7717/peerj.14149
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: ©2022 Arshinchi Bonab et al.
attribution name: Arshinchi Bonab et al.

Association between clinical oral health status and perceived oral health in different age groups
type: item
type: AcademicArticle
description: Objective The perceived oral health refers to the very own perception of a person’s oral health (OH). This study aims to explore the association of perceived oral health status (PSR-OHS) with clinically determined OHS in three age groups: young adults, adults and older adults. This study also aims to identify demographic, socio-economic and/or clinical factors that influence PSR-OHS. Methods A cross-sectional study was conducted in ten different dental hospitals of Pakistan. The one-way ANOVA test was used to analyze patient’s demographic distribution with PSR-OHS and oral functions. The complex sample general linear model was used to determine association between clinical OH and PSR-OHS. Analyses of each age group were conducted separately. Results A total of 1,804 outdoor patients participated in the study, out of which 660 were young adults, 685 adults and 459 were older adults. Overall self-perception of all age groups about their oral health was ‘good’ (mean = 3.71). Female gender and education status were a significant factor in young adults and adults. Family income affected PSR-OHS of only the adult age group. Frequent visit to dental clinic and preventive reason of dental attendance were associated with good PSR-OHS. DMFT score, prosthesis score and periodontal score also affected the PSR-OHS of individuals. Association between PSR-OHS and clinical examination was confirmed by complex general linear model. Conclusion There are differences in the perceived oral health status of young adults, adults and older adults. The variables, age, education, family income, DMFT score, prosthesis score and periodontal score directly influence the self-perception of individuals.
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format: text/html
creator: Ayesha Fahim
creator: Rizwan Mahmood
creator: Irsam Haider
creator: Mamoona Luqman
creator: Ifra Ikhlaq
creator: Tariq Mahmood
creator: Mohammad Khursheed Alam
subject: Dentistry
subject: Public Health
description: doi:10.7717/peerj.14152
publisher: PeerJ Inc.
rights: © 2022 Fahim et al.
abstract: Objective The perceived oral health refers to the very own perception of a person’s oral health (OH). This study aims to explore the association of perceived oral health status (PSR-OHS) with clinically determined OHS in three age groups: young adults, adults and older adults. This study also aims to identify demographic, socio-economic and/or clinical factors that influence PSR-OHS. Methods A cross-sectional study was conducted in ten different dental hospitals of Pakistan. The one-way ANOVA test was used to analyze patient’s demographic distribution with PSR-OHS and oral functions. The complex sample general linear model was used to determine association between clinical OH and PSR-OHS. Analyses of each age group were conducted separately. Results A total of 1,804 outdoor patients participated in the study, out of which 660 were young adults, 685 adults and 459 were older adults. Overall self-perception of all age groups about their oral health was ‘good’ (mean = 3.71). Female gender and education status were a significant factor in young adults and adults. Family income affected PSR-OHS of only the adult age group. Frequent visit to dental clinic and preventive reason of dental attendance were associated with good PSR-OHS. DMFT score, prosthesis score and periodontal score also affected the PSR-OHS of individuals. Association between PSR-OHS and clinical examination was confirmed by complex general linear model. Conclusion There are differences in the perceived oral health status of young adults, adults and older adults. The variables, age, education, family income, DMFT score, prosthesis score and periodontal score directly influence the self-perception of individuals.
bibliographic citation: Fahim et al. (2022) Association between clinical oral health status and perceived oral health in different age groups. PeerJ 10:e14152 https://doi.org/10.7717/peerj.14152
date submitted: 2022-01-11
date accepted: 2022-09-07
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fahim
  given name: Ayesha
author list: Agent
  family name: Mahmood
  given name: Rizwan
author list: Agent
  family name: Haider
  given name: Irsam
author list: Agent
  family name: Luqman
  given name: Mamoona
author list: Agent
  family name: Ikhlaq
  given name: Ifra
author list: Agent
  family name: Mahmood
  given name: Tariq
author list: Agent
  family name: Alam
  given name: Mohammad Khursheed
doi: 10.7717/peerj.14152
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Fahim et al.
attribution name: Fahim et al.

Distorted body schema after mastectomy with immediate breast reconstruction: a 4-month follow up study
type: item
type: AcademicArticle
description: Background After breast cancer, some patients report residual pain-related upper limb disability without physical impairment. Although pain and altered proprioception are known to affect the working body schema (WBS), there is little available evidence investigating the WBS of breast cancer survivors (BrCS). WBS—body representations in the brain—affect the “neuromatrix” that modulates pain sensitivity and the threshold for threatening stimuli. The aim of this study was to investigate whether WBS was disrupted after mastectomy with immediate breast reconstruction (IBR) for breast cancer and whether pain and proprioceptive changes affected WBS. Methods Thirty-five BrCS participated in the 4-month follow-up study. They were observed at 1 and 4 months postoperatively. The main outcome measures were the left right judgement test (LRJT) results, absolute angle error, pectoralis minor length index (PMI), pain, and Quick-Disabilities of the Arm, Shoulder, and Hand (Q-DASH) score. They were measured at each observation, and parametric tests were performed to identify the nature of WBS. Results Both the reaction time and accuracy of the hand LRJT were poorer than those of the foot and back LRJT (p < 0.001). The hand LRJT reaction time and accuracy were unchanged over the total follow-up period (p = 0.77 and p = 0.47, respectively). There was a weak correlation between the LRJT reaction time and PMI (r = −0.26, p = 0.07), pain severity (r = 0.37, p = 0.02), and Q-DASH score (r = 0.37, p = 0.02). There was also a weak correlation between LRJT accuracy and Q-DASH score (r = −0.31, p = 0.04). The LRJT accuracy of BrCS who underwent surgery on their dominant side was higher than that of BrCS who underwent surgery on their non-dominant side (p = 0.002). Regression analysis found a weak but significant relationship between the early hand LRJT results and late pain severity (adjusted R2 = 0.179, p = 0.007). A similar relationship was found between early hand LRJT results and Q-DASH s…
format: application/pdf
format: text/html
creator: Asall Kim
creator: Eun Joo Yang
creator: Myungki Ji
creator: Jaewon Beom
creator: Chunghwi Yi
subject: Neuroscience
subject: Anesthesiology and Pain Management
subject: Surgery and Surgical Specialties
subject: Women’s Health
subject: Rehabilitation
description: doi:10.7717/peerj.14157
publisher: PeerJ Inc.
rights: © 2022 Kim et al.
abstract: Background After breast cancer, some patients report residual pain-related upper limb disability without physical impairment. Although pain and altered proprioception are known to affect the working body schema (WBS), there is little available evidence investigating the WBS of breast cancer survivors (BrCS). WBS—body representations in the brain—affect the “neuromatrix” that modulates pain sensitivity and the threshold for threatening stimuli. The aim of this study was to investigate whether WBS was disrupted after mastectomy with immediate breast reconstruction (IBR) for breast cancer and whether pain and proprioceptive changes affected WBS. Methods Thirty-five BrCS participated in the 4-month follow-up study. They were observed at 1 and 4 months postoperatively. The main outcome measures were the left right judgement test (LRJT) results, absolute angle error, pectoralis minor length index (PMI), pain, and Quick-Disabilities of the Arm, Shoulder, and Hand (Q-DASH) score. They were measured at each observation, and parametric tests were performed to identify the nature of WBS. Results Both the reaction time and accuracy of the hand LRJT were poorer than those of the foot and back LRJT (p < 0.001). The hand LRJT reaction time and accuracy were unchanged over the total follow-up period (p = 0.77 and p = 0.47, respectively). There was a weak correlation between the LRJT reaction time and PMI (r = −0.26, p = 0.07), pain severity (r = 0.37, p = 0.02), and Q-DASH score (r = 0.37, p = 0.02). There was also a weak correlation between LRJT accuracy and Q-DASH score (r = −0.31, p = 0.04). The LRJT accuracy of BrCS who underwent surgery on their dominant side was higher than that of BrCS who underwent surgery on their non-dominant side (p = 0.002). Regression analysis found a weak but significant relationship between the early hand LRJT results and late pain severity (adjusted R2 = 0.179, p = 0.007). A similar relationship was found between early hand LRJT results and Q-DASH s…
bibliographic citation: Kim et al. (2022) Distorted body schema after mastectomy with immediate breast reconstruction: a 4-month follow up study. PeerJ 10:e14157 https://doi.org/10.7717/peerj.14157
date submitted: 2022-06-27
date accepted: 2022-09-08
issued: 2022-10-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Asall
author list: Agent
  family name: Yang
  given name: Eun Joo
author list: Agent
  family name: Ji
  given name: Myungki
author list: Agent
  family name: Beom
  given name: Jaewon
author list: Agent
  family name: Yi
  given name: Chunghwi
doi: 10.7717/peerj.14157
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-03
copyright: © 2022 Kim et al.
attribution name: Kim et al.

An in silico study of how histone tail conformation affects the binding affinity of ING family proteins
type: item
type: AcademicArticle
description: Background Due to its intrinsically disordered nature, the histone tail is conformationally heterogenic. Therefore, it provides specific binding sites for different binding proteins or factors through reversible post-translational modifications (PTMs). For instance, experimental studies stated that the ING family binds with the histone tail that has methylation on the lysine in position 4. However, numerous complexes featuring a methylated fourth lysine residue of the histone tail can be found in the UniProt database. So the question arose if other factors like the conformation of the histone tail affect the binding affinity. Methods The crystal structure of the PHD finger domain from the proteins ING1, ING2, ING4, and ING5 are docked to four histone H3 tails with two different conformations using Haddock 2.4 and ClusPro. The best four models for each combination are selected and a two-sample t-test is performed to compare the binding affinities of helical conformations vs. linear conformations using Prodigy. The protein-protein interactions are examined using LigPlot. Results The linear histone conformations in predicted INGs-histone H3 complexes exhibit statistically significant higher binding affinity than their helical counterparts (confidence level of 99%). The outputs of predicted models generated by the molecular docking programs Haddock 2.4 and ClusPro are comparable, and the obtained protein-protein interaction patterns are consistent with experimentally confirmed binding patterns. Conclusion The results show that the conformation of the histone tail is significantly affecting the binding affinity of the docking protein. Herewith, this in silico study demonstrated in detail the binding preference of the ING protein family to histone H3 tail. Further research on the effect of certain PTMs on the final tail conformation and the interaction between those factors seem to be promising for a better understanding of epigenetics.
format: application/pdf
format: text/html
creator: Nadir Gül
creator: Ahmet Yıldız
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.14029
publisher: PeerJ Inc.
rights: © 2022 Gül and Yıldız
abstract: Background Due to its intrinsically disordered nature, the histone tail is conformationally heterogenic. Therefore, it provides specific binding sites for different binding proteins or factors through reversible post-translational modifications (PTMs). For instance, experimental studies stated that the ING family binds with the histone tail that has methylation on the lysine in position 4. However, numerous complexes featuring a methylated fourth lysine residue of the histone tail can be found in the UniProt database. So the question arose if other factors like the conformation of the histone tail affect the binding affinity. Methods The crystal structure of the PHD finger domain from the proteins ING1, ING2, ING4, and ING5 are docked to four histone H3 tails with two different conformations using Haddock 2.4 and ClusPro. The best four models for each combination are selected and a two-sample t-test is performed to compare the binding affinities of helical conformations vs. linear conformations using Prodigy. The protein-protein interactions are examined using LigPlot. Results The linear histone conformations in predicted INGs-histone H3 complexes exhibit statistically significant higher binding affinity than their helical counterparts (confidence level of 99%). The outputs of predicted models generated by the molecular docking programs Haddock 2.4 and ClusPro are comparable, and the obtained protein-protein interaction patterns are consistent with experimentally confirmed binding patterns. Conclusion The results show that the conformation of the histone tail is significantly affecting the binding affinity of the docking protein. Herewith, this in silico study demonstrated in detail the binding preference of the ING protein family to histone H3 tail. Further research on the effect of certain PTMs on the final tail conformation and the interaction between those factors seem to be promising for a better understanding of epigenetics.
bibliographic citation: Gül et al. (2022) An in silico study of how histone tail conformation affects the binding affinity of ING family proteins. PeerJ 10:e14029 https://doi.org/10.7717/peerj.14029
date submitted: 2022-05-30
date accepted: 2022-08-16
issued: 2022-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gül
  given name: Nadir
author list: Agent
  family name: Yıldız
  given name: Ahmet
doi: 10.7717/peerj.14029
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-30
copyright: ©2022 Gül and Yıldız
attribution name: Gül and Yıldız

MicroRNA-21 as a potential biomarker for detecting esophageal carcinoma in Asian populations: a meta-analysis
type: item
type: AcademicArticle
description: Background MicroRNA-21 (miR-21) is significantly expressed in a variety of cancers and could be used as a tumor biomarker. However, the results are varied, and no studies on the diagnostic usefulness of miR-21 in Asian esophageal cancer (EC) patients have been published. This meta-analysis was aimed at exploring whether miR-21 can be used as a diagnostic marker and assessing its effectiveness. Methods The relevant literature was identified in six main databases: Ovid MEDLINE, PsycINFO, PubMed MEDLINE, Embase, Web of Science, and the Cochrane Library. Two researchers independently selected the literature based on the inclusion and exclusion criteria, extracted data, and evaluated the risk of bias. The meta-analysis was carried out using Review Manager 5.4, Meta-Disc 1.4 and STATA 15.1 software. In the end, 987 patients from 12 different studies were included. Quality evaluation of diagnostic accuracy studies 2 (QUADAS—2) was used to examine the risk of bias. Results The pooled sensitivity (SEN) was 0.72 (95% CI [0.69–0.75]), the pooled specificity (SPE) was 0.78 (95% CI [0.75–0.81]), the pooled positive likelihood ratio (PLR) was 2.87 (95% CI [2.28–3.59]), the pooled negative likelihood ratio (NLR) was 0.36 (95% CI [0.31–0.43]), the pooled diagnostic odds ratio (DOR) was 10.00 (95% CI [7.73–12.95]), and the area under the curve 0.82 (95% CI [0.79–0.85]). A Deeks’ funnel plot shows that there was no publication bias (P = 0.99). Conclusion Our findings suggest miR-21 might be the potential biomarker for detecting EC in Asian populations, with a good diagnostic value.
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format: text/html
creator: Zheng Han
creator: Lingbo Pan
creator: Bangjie Lu
creator: Huixia Zhu
subject: Molecular Biology
subject: Clinical Trials
subject: Epidemiology
subject: Oncology
subject: Otorhinolaryngology
description: doi:10.7717/peerj.14048
publisher: PeerJ Inc.
rights: © 2022 Han et al.
abstract: Background MicroRNA-21 (miR-21) is significantly expressed in a variety of cancers and could be used as a tumor biomarker. However, the results are varied, and no studies on the diagnostic usefulness of miR-21 in Asian esophageal cancer (EC) patients have been published. This meta-analysis was aimed at exploring whether miR-21 can be used as a diagnostic marker and assessing its effectiveness. Methods The relevant literature was identified in six main databases: Ovid MEDLINE, PsycINFO, PubMed MEDLINE, Embase, Web of Science, and the Cochrane Library. Two researchers independently selected the literature based on the inclusion and exclusion criteria, extracted data, and evaluated the risk of bias. The meta-analysis was carried out using Review Manager 5.4, Meta-Disc 1.4 and STATA 15.1 software. In the end, 987 patients from 12 different studies were included. Quality evaluation of diagnostic accuracy studies 2 (QUADAS—2) was used to examine the risk of bias. Results The pooled sensitivity (SEN) was 0.72 (95% CI [0.69–0.75]), the pooled specificity (SPE) was 0.78 (95% CI [0.75–0.81]), the pooled positive likelihood ratio (PLR) was 2.87 (95% CI [2.28–3.59]), the pooled negative likelihood ratio (NLR) was 0.36 (95% CI [0.31–0.43]), the pooled diagnostic odds ratio (DOR) was 10.00 (95% CI [7.73–12.95]), and the area under the curve 0.82 (95% CI [0.79–0.85]). A Deeks’ funnel plot shows that there was no publication bias (P = 0.99). Conclusion Our findings suggest miR-21 might be the potential biomarker for detecting EC in Asian populations, with a good diagnostic value.
bibliographic citation: Han et al. (2022) MicroRNA-21 as a potential biomarker for detecting esophageal carcinoma in Asian populations: a meta-analysis. PeerJ 10:e14048 https://doi.org/10.7717/peerj.14048
date submitted: 2022-06-07
date accepted: 2022-08-22
issued: 2022-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Zheng
author list: Agent
  family name: Pan
  given name: Lingbo
author list: Agent
  family name: Lu
  given name: Bangjie
author list: Agent
  family name: Zhu
  given name: Huixia
doi: 10.7717/peerj.14048
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-30
copyright: © 2022 Han et al.
attribution name: Han et al.

Irradiation with carbon ion beams affects soybean nutritional quality in early generations
type: item
type: AcademicArticle
description: As people’s demand for healthy diet increases, improving soybean seed nutritional quality is becoming as important as yield. Carbon ion beam radiation (CIBR) is an effective method to create soybean mutants, and thus breeding cultivars with better seed nutritional quality. In this study, the high-yield soybean line ‘Dongsheng 28’ was used, and three CIBR doses (100, 120, and 140 Gy) were used to explore the characteristics of quality separation and variation in the offspring of early mutant populations. Eleven quality traits, including protein, oil, sucrose, soluble sugar, iron (Fe), manganese (Mn), zinc (Zn), cupper (Cu), daidzin, glycitin, and genistin concentrations were analyzed in the M2 and M3 generations. The results revealed that the range of protein and oil concentration of all three CIBR doses changed by 38.5–42.9% and 18.8–23.8% in the M2 and M3 generations, respectively, while soluble sugar and sucrose concentrations changed by 48.1–123.4 and 22.7–74.7 mg/g, with significant effects by 140 Gy across the two generations. Therefore, around the optimum range, a higher CIBR dose is better for high protein, oil, and sugar varieties selection. In general, irradiation raised isoflavone concentrations, but 140 Gy had an inhibitory effect on isoflavone concentrations in the M3 generation. Although a variety could not be released in the M2 or M3 generation, the results of this study have important guiding significance for the targeted cultivation of specific nutritional quality materials. For instance, a lower irradiation dose is preferable when breeding targets are higher isoflavones and Mn concentrations. It is essential to increase the irradiation dose if the breeding targets contain high levels of protein, oil, sucrose, soluble sugars, Fe, Zn, and Cu.
format: application/pdf
format: text/html
creator: Changkai Liu
creator: Xue Wang
creator: Yansheng Li
creator: Heng Chen
creator: Qiuying Zhang
creator: Xiaobing Liu
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.14080
publisher: PeerJ Inc.
rights: © 2022 Liu et al.
abstract: As people’s demand for healthy diet increases, improving soybean seed nutritional quality is becoming as important as yield. Carbon ion beam radiation (CIBR) is an effective method to create soybean mutants, and thus breeding cultivars with better seed nutritional quality. In this study, the high-yield soybean line ‘Dongsheng 28’ was used, and three CIBR doses (100, 120, and 140 Gy) were used to explore the characteristics of quality separation and variation in the offspring of early mutant populations. Eleven quality traits, including protein, oil, sucrose, soluble sugar, iron (Fe), manganese (Mn), zinc (Zn), cupper (Cu), daidzin, glycitin, and genistin concentrations were analyzed in the M2 and M3 generations. The results revealed that the range of protein and oil concentration of all three CIBR doses changed by 38.5–42.9% and 18.8–23.8% in the M2 and M3 generations, respectively, while soluble sugar and sucrose concentrations changed by 48.1–123.4 and 22.7–74.7 mg/g, with significant effects by 140 Gy across the two generations. Therefore, around the optimum range, a higher CIBR dose is better for high protein, oil, and sugar varieties selection. In general, irradiation raised isoflavone concentrations, but 140 Gy had an inhibitory effect on isoflavone concentrations in the M3 generation. Although a variety could not be released in the M2 or M3 generation, the results of this study have important guiding significance for the targeted cultivation of specific nutritional quality materials. For instance, a lower irradiation dose is preferable when breeding targets are higher isoflavones and Mn concentrations. It is essential to increase the irradiation dose if the breeding targets contain high levels of protein, oil, sucrose, soluble sugars, Fe, Zn, and Cu.
bibliographic citation: Liu et al. (2022) Irradiation with carbon ion beams affects soybean nutritional quality in early generations. PeerJ 10:e14080 https://doi.org/10.7717/peerj.14080
date submitted: 2022-04-29
date accepted: 2022-08-29
issued: 2022-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Changkai
author list: Agent
  family name: Wang
  given name: Xue
author list: Agent
  family name: Li
  given name: Yansheng
author list: Agent
  family name: Chen
  given name: Heng
author list: Agent
  family name: Zhang
  given name: Qiuying
author list: Agent
  family name: Liu
  given name: Xiaobing
doi: 10.7717/peerj.14080
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-30
copyright: © 2022 Liu et al.
attribution name: Liu et al.

Rapid restructurization of conformationally-distinct alpha-synuclein amyloid fibrils at an elevated temperature
type: item
type: AcademicArticle
description: Protein aggregation in the form of amyloid fibrils is linked with the onset and progression of more than 30 amyloidoses, including multiple neurodegenerative disorders, such as Alzheimer’s or Parkinson’s disease. Despite countless studies and years of research, the process of such aggregate formation is still not fully understood. One peculiar aspect of amyloids is that they appear to be capable of undergoing structural rearrangements even after the fibrils have already formed. Such a phenomenon was reported to occur in the case of alpha-synuclein and amyloid beta aggregates after a long period of incubation. In this work, we examine whether incubation at an elevated temperature can induce the restructurization of four different conformation alpha-synuclein amyloid fibrils. We show that this structural alteration occurs in a relatively brief time period, when the aggregates are incubated at 60 °C. Additionally, it appears that during this process multiple conformationally-distinct alpha-synuclein fibrils all shift towards an identical secondary structure.
format: application/pdf
format: text/html
creator: Mantas Ziaunys
creator: Andrius Sakalauskas
creator: Kamile Mikalauskaite
creator: Vytautas Smirnovas
subject: Biochemistry
subject: Biophysics
subject: Molecular Biology
description: doi:10.7717/peerj.14137
publisher: PeerJ Inc.
rights: © 2022 Ziaunys et al.
abstract: Protein aggregation in the form of amyloid fibrils is linked with the onset and progression of more than 30 amyloidoses, including multiple neurodegenerative disorders, such as Alzheimer’s or Parkinson’s disease. Despite countless studies and years of research, the process of such aggregate formation is still not fully understood. One peculiar aspect of amyloids is that they appear to be capable of undergoing structural rearrangements even after the fibrils have already formed. Such a phenomenon was reported to occur in the case of alpha-synuclein and amyloid beta aggregates after a long period of incubation. In this work, we examine whether incubation at an elevated temperature can induce the restructurization of four different conformation alpha-synuclein amyloid fibrils. We show that this structural alteration occurs in a relatively brief time period, when the aggregates are incubated at 60 °C. Additionally, it appears that during this process multiple conformationally-distinct alpha-synuclein fibrils all shift towards an identical secondary structure.
bibliographic citation: Ziaunys et al. (2022) Rapid restructurization of conformationally-distinct alpha-synuclein amyloid fibrils at an elevated temperature. PeerJ 10:e14137 https://doi.org/10.7717/peerj.14137
date submitted: 2022-06-02
date accepted: 2022-09-06
issued: 2022-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ziaunys
  given name: Mantas
author list: Agent
  family name: Sakalauskas
  given name: Andrius
author list: Agent
  family name: Mikalauskaite
  given name: Kamile
author list: Agent
  family name: Smirnovas
  given name: Vytautas
doi: 10.7717/peerj.14137
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-30
copyright: © 2022 Ziaunys et al.
attribution name: Ziaunys et al.

Progressive overload without progressing load? The effects of load or repetition progression on muscular adaptations
type: item
type: AcademicArticle
description: Background Progressive overload is a principle of resistance training exercise program design that typically relies on increasing load to increase neuromuscular demand to facilitate further adaptations. However, little attention has been given to another way of increasing demand—increasing the number of repetitions. Objective This study aimed to compare the effects of two resistance training programs: (1) increasing load while keeping repetition range constant vs (2) increasing repetitions while keeping load constant. We aimed to compare the effects of these programs on lower body muscle hypertrophy, muscle strength, and muscle endurance in resistance-trained individuals over an 8-week study period. Methods Forty-three participants with at least 1 year of consistent lower body resistance training experience were randomly assigned to one of two experimental, parallel groups: A group that aimed to increase load while keeping repetitions constant (LOAD: n = 22; 13 men, nine women) or a group that aimed to increase repetitions while keeping load constant (REPS: n = 21; 14 men, seven women). Subjects performed four sets of four lower body exercises (back squat, leg extension, straight-leg calf raise, and seated calf raise) twice per week. We assessed one repetition maximum (1RM) in the Smith machine squat, muscular endurance in the leg extension, countermovement jump height, and muscle thickness along the quadriceps and calf muscles. Between-group effects were estimated using analyses of covariance, adjusted for pre-intervention scores and sex. Results Rectus femoris growth modestly favored REPS (adjusted effect estimate (CI90%), sum of sites: 2.8 mm [−0.5, 5.8]). Alternatively, dynamic strength increases slightly favored LOAD (2.0 kg [−2.4, 7.8]), with differences of questionable practical significance. No other notable between-group differences were found across outcomes (muscle thicknesses, <1 mm; endurance, <1%; countermovement jump, 0.1 cm; body fat, <1%; leg segmen…
format: application/pdf
format: text/html
creator: Daniel Plotkin
creator: Max Coleman
creator: Derrick Van Every
creator: Jaime Maldonado
creator: Douglas Oberlin
creator: Michael Israetel
creator: Jared Feather
creator: Andrew Alto
creator: Andrew D. Vigotsky
creator: Brad J. Schoenfeld
subject: Anatomy and Physiology
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.14142
publisher: PeerJ Inc.
rights: © 2022 Plotkin et al.
abstract: Background Progressive overload is a principle of resistance training exercise program design that typically relies on increasing load to increase neuromuscular demand to facilitate further adaptations. However, little attention has been given to another way of increasing demand—increasing the number of repetitions. Objective This study aimed to compare the effects of two resistance training programs: (1) increasing load while keeping repetition range constant vs (2) increasing repetitions while keeping load constant. We aimed to compare the effects of these programs on lower body muscle hypertrophy, muscle strength, and muscle endurance in resistance-trained individuals over an 8-week study period. Methods Forty-three participants with at least 1 year of consistent lower body resistance training experience were randomly assigned to one of two experimental, parallel groups: A group that aimed to increase load while keeping repetitions constant (LOAD: n = 22; 13 men, nine women) or a group that aimed to increase repetitions while keeping load constant (REPS: n = 21; 14 men, seven women). Subjects performed four sets of four lower body exercises (back squat, leg extension, straight-leg calf raise, and seated calf raise) twice per week. We assessed one repetition maximum (1RM) in the Smith machine squat, muscular endurance in the leg extension, countermovement jump height, and muscle thickness along the quadriceps and calf muscles. Between-group effects were estimated using analyses of covariance, adjusted for pre-intervention scores and sex. Results Rectus femoris growth modestly favored REPS (adjusted effect estimate (CI90%), sum of sites: 2.8 mm [−0.5, 5.8]). Alternatively, dynamic strength increases slightly favored LOAD (2.0 kg [−2.4, 7.8]), with differences of questionable practical significance. No other notable between-group differences were found across outcomes (muscle thicknesses, <1 mm; endurance, <1%; countermovement jump, 0.1 cm; body fat, <1%; leg segmen…
bibliographic citation: Plotkin et al. (2022) Progressive overload without progressing load? The effects of load or repetition progression on muscular adaptations. PeerJ 10:e14142 https://doi.org/10.7717/peerj.14142
date submitted: 2022-06-30
date accepted: 2022-09-07
issued: 2022-09-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Plotkin
  given name: Daniel
author list: Agent
  family name: Coleman
  given name: Max
author list: Agent
  family name: Van Every
  given name: Derrick
author list: Agent
  family name: Maldonado
  given name: Jaime
author list: Agent
  family name: Oberlin
  given name: Douglas
author list: Agent
  family name: Israetel
  given name: Michael
author list: Agent
  family name: Feather
  given name: Jared
author list: Agent
  family name: Alto
  given name: Andrew
author list: Agent
  family name: Vigotsky
  given name: Andrew D.
author list: Agent
  family name: Schoenfeld
  given name: Brad J.
doi: 10.7717/peerj.14142
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-09-30
copyright: © 2022 Plotkin et al.
attribution name: Plotkin et al.

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