PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam
items: Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China
items: Sex difference in the association between triglyceride and intracerebral bleeding risk after intravenous thrombolysis for acute ischemic stroke, a multi-center retrospective study
items: Associations between fundamental movement skills and accelerometer-measured physical activity in Chinese children: the mediating role of cardiorespiratory fitness
items: Squatting biomechanics following physiotherapist-led care or hip arthroscopy for femoroacetabular impingement syndrome: a secondary analysis from a randomised controlled trial
items: Optimization of polysaccharide conditions and analysis of antioxidant capacity in the co-culture of Sanghuangporus vaninii and Pleurotus sapidus
items: Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes
items: Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches
items: Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max
items: Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.)

Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam
type: item
type: AcademicArticle
description: Background White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is …
format: application/pdf
format: text/html
creator: Nam-Hai Truong
creator: Thi-Thu-Hong Le
creator: Hong-Duong Nguyen
creator: Hong-Thanh Nguyen
creator: Trong-Khoa Dao
creator: Thi-Minh-Nguyet Tran
creator: Huyen-Linh Tran
creator: Dinh-Trong Nguyen
creator: Thi-Quy Nguyen
creator: Thi-Hong-Thao Phan
creator: Thi-Huyen Do
creator: Ngoc-Han Phan
creator: Thi-Cam-Nhung Ngo
creator: Van-Van Vu
subject: Biochemistry
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
subject: Mycology
description: doi:10.7717/peerj.17553
publisher: PeerJ Inc.
rights: © 2024 Truong et al.
abstract: Background White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is …
bibliographic citation: Truong et al. (2024) Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam. PeerJ 12:e17553 https://doi.org/10.7717/peerj.17553
date submitted: 2023-11-28
date accepted: 2024-05-20
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Truong
  given name: Nam-Hai
author list: Agent
  family name: Le
  given name: Thi-Thu-Hong
author list: Agent
  family name: Nguyen
  given name: Hong-Duong
author list: Agent
  family name: Nguyen
  given name: Hong-Thanh
author list: Agent
  family name: Dao
  given name: Trong-Khoa
author list: Agent
  family name: Tran
  given name: Thi-Minh-Nguyet
author list: Agent
  family name: Tran
  given name: Huyen-Linh
author list: Agent
  family name: Nguyen
  given name: Dinh-Trong
author list: Agent
  family name: Nguyen
  given name: Thi-Quy
author list: Agent
  family name: Phan
  given name: Thi-Hong-Thao
author list: Agent
  family name: Do
  given name: Thi-Huyen
author list: Agent
  family name: Phan
  given name: Ngoc-Han
author list: Agent
  family name: Ngo
  given name: Thi-Cam-Nhung
author list: Agent
  family name: Vu
  given name: Van-Van
doi: 10.7717/peerj.17553
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: ©2024 Truong et al.
attribution name: Truong et al.

Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China
type: item
type: AcademicArticle
description: Background Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribu…
format: application/pdf
format: text/html
creator: Xiangnan Liu
creator: Meizhen Wang
creator: Shiqiang Song
creator: Qing Ma
creator: Zhaoping Yang
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.17554
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background Gymnospermium kiangnanense is the only species distributed in the subtropical region within the spring ephemeral genus Gymnospermium. Extensive human exploitation and habitat destruction have resulted in a rapid shrink of G. kiangnanense populations. This study utilizes microsatellite markers to analyze the genetic diversity and structure and to deduce historical population events of extant populations of G. kiangnanense. Methods A total of 143 individuals from eight extant populations of G. kiangnanense, including two populations from Anhui Province and six populations from Zhejiang Province, were analyzed with using 21 pairs of microsatellite markers. Genetic diversity indices were calculated using Cervus, GENEPOP, GenALEX. Population structure was assessed using genetic distance (UPGMA), principal coordinate analysis (PCoA), Bayesian clustering method (STRUCTURE), and molecular variation analysis of variance (AMOVA). Population history events were inferred using DIYABC. Results The studied populations of G. kiangnanense exhibited a low level of genetic diversity (He = 0.179, I = 0.286), but a high degree of genetic differentiation (FST = 0.521). The mean value of gene flow (Nm) among populations was 1.082, indicating prevalent gene exchange via pollen dispersal. Phylogeographic analyses suggested that the populations of G. kiangnanense were divided into two lineages, Zhejiang (ZJ) and Anhui (AH). These two lineages were separated by the Huangshan-Tianmu Mountain Range. AMOVA analysis revealed that 36.59% of total genetic variation occurred between the two groups. The ZJ lineage was further divided into the Hangzhou (ZJH) and Zhuji (ZJZ) lineages, separated by the Longmen Mountain and Fuchun River. DIYABC analyses suggested that the ZJ and AH lineages were separated at 5.592 ka, likely due to the impact of Holocene climate change and human activities. Subsequently, the ZJZ lineage diverged from the ZJH lineage around 2.112 ka. Given the limited distribu…
bibliographic citation: Liu et al. (2024) Population structure and diversification of Gymnospermium kiangnanense, a plant species with extremely small populations endemic to eastern China. PeerJ 12:e17554 https://doi.org/10.7717/peerj.17554
date submitted: 2024-02-02
date accepted: 2024-05-20
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Xiangnan
author list: Agent
  family name: Wang
  given name: Meizhen
author list: Agent
  family name: Song
  given name: Shiqiang
author list: Agent
  family name: Ma
  given name: Qing
author list: Agent
  family name: Yang
  given name: Zhaoping
doi: 10.7717/peerj.17554
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: © 2024 Liu et al.
attribution name: Liu et al.

Sex difference in the association between triglyceride and intracerebral bleeding risk after intravenous thrombolysis for acute ischemic stroke, a multi-center retrospective study
type: item
type: AcademicArticle
description: Background Whether the relationship of intracerebral bleeding risk with lipid profile may vary by sex remains unclear. This study aims to investigate potential sex differences in the association between lipid profile and the risk of symptomatic intracerebral hemorrhage (sICH) in patients with acute ischemic stroke (AIS) who received intravenous thrombolysis using recombinant tissue plasminogen activator (r-tPA). Methods This multicenter retrospective observational study analyzed patients with AIS treated with intravenous r-tPA. sICH was defined as a worsening of 4 or higher points in the National Institutes of Health Stroke Scale (NIHSS) score within 36 hours after intravenous thrombolysis in any hemorrhage subtype. We assessed the odds ratio (OR) with 95% confidence interval (CI) of lipid profile for sICH for each sex using logistic regression models adjusted for potential confounding factors. Results Of 957 participants (median age 68 (interquartile range, 59–75), men 628 (65.6%)), 56 sICH events (36 (5.7%) in men and 20 (6.1%) in women) were observed. The risk of sICH in men decreased with increasing serum levels of triglyceride after adjustment for confounding factors (vs lowest tertile, medium tertile OR 0.39, 95% CI [0.17–0.91], top tertile OR 0.33, 95% CI [0.13–0.84], overall p = 0.021; per point increase, adjusted OR 0.29, 95% CI [0.13–0.63], p = 0.002). Neither serum levels of total cholesterol nor low-density lipoprotein (LDL) was associated with sICH in men. In women, there was no association between any of the lipid levels and the risk of sICH. Conclusions This study indicated that the association between serum levels of triglyceride and sICH may vary by sex. In men, increased triglyceride levels decrease the risk of sICH; in women, this association was lost. Further studies on the biological mechanisms for sex differences in stroke risk associated with triglyceride are needed.
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creator: Qilin Yuan
creator: Ying Han
creator: Shuangfang Fang
creator: Hanhan Lei
creator: Huapin Huang
creator: Huiying Lin
creator: Xiaomin Wu
creator: Ronghua Chen
creator: Zhiting Chen
creator: Jie Chen
creator: Hangfeng Li
creator: Nan Liu
creator: Houwei Du
subject: Cardiology
subject: Hematology
subject: Neurology
subject: Metabolic Sciences
description: doi:10.7717/peerj.17558
publisher: PeerJ Inc.
rights: © 2024 Yuan et al.
abstract: Background Whether the relationship of intracerebral bleeding risk with lipid profile may vary by sex remains unclear. This study aims to investigate potential sex differences in the association between lipid profile and the risk of symptomatic intracerebral hemorrhage (sICH) in patients with acute ischemic stroke (AIS) who received intravenous thrombolysis using recombinant tissue plasminogen activator (r-tPA). Methods This multicenter retrospective observational study analyzed patients with AIS treated with intravenous r-tPA. sICH was defined as a worsening of 4 or higher points in the National Institutes of Health Stroke Scale (NIHSS) score within 36 hours after intravenous thrombolysis in any hemorrhage subtype. We assessed the odds ratio (OR) with 95% confidence interval (CI) of lipid profile for sICH for each sex using logistic regression models adjusted for potential confounding factors. Results Of 957 participants (median age 68 (interquartile range, 59–75), men 628 (65.6%)), 56 sICH events (36 (5.7%) in men and 20 (6.1%) in women) were observed. The risk of sICH in men decreased with increasing serum levels of triglyceride after adjustment for confounding factors (vs lowest tertile, medium tertile OR 0.39, 95% CI [0.17–0.91], top tertile OR 0.33, 95% CI [0.13–0.84], overall p = 0.021; per point increase, adjusted OR 0.29, 95% CI [0.13–0.63], p = 0.002). Neither serum levels of total cholesterol nor low-density lipoprotein (LDL) was associated with sICH in men. In women, there was no association between any of the lipid levels and the risk of sICH. Conclusions This study indicated that the association between serum levels of triglyceride and sICH may vary by sex. In men, increased triglyceride levels decrease the risk of sICH; in women, this association was lost. Further studies on the biological mechanisms for sex differences in stroke risk associated with triglyceride are needed.
bibliographic citation: Yuan et al. (2024) Sex difference in the association between triglyceride and intracerebral bleeding risk after intravenous thrombolysis for acute ischemic stroke, a multi-center retrospective study. PeerJ 12:e17558 https://doi.org/10.7717/peerj.17558
date submitted: 2023-12-21
date accepted: 2024-05-21
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Qilin
author list: Agent
  family name: Han
  given name: Ying
author list: Agent
  family name: Fang
  given name: Shuangfang
author list: Agent
  family name: Lei
  given name: Hanhan
author list: Agent
  family name: Huang
  given name: Huapin
author list: Agent
  family name: Lin
  given name: Huiying
author list: Agent
  family name: Wu
  given name: Xiaomin
author list: Agent
  family name: Chen
  given name: Ronghua
author list: Agent
  family name: Chen
  given name: Zhiting
author list: Agent
  family name: Chen
  given name: Jie
author list: Agent
  family name: Li
  given name: Hangfeng
author list: Agent
  family name: Liu
  given name: Nan
author list: Agent
  family name: Du
  given name: Houwei
doi: 10.7717/peerj.17558
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: ©2024 Yuan et al.
attribution name: Yuan et al.

Associations between fundamental movement skills and accelerometer-measured physical activity in Chinese children: the mediating role of cardiorespiratory fitness
type: item
type: AcademicArticle
description: Background and purpose The associations of fundamental motor skills (FMS), health-related physical fitness (e.g., cardiorespiratory fitness, CRF), and moderate-vigorous physical activity (MVPA) have been demonstrated in Western children, but these associations have not yet been validated in a sample of Chinese children. The aims of this study, therefore, were to examine the association between FMS subdomains and MVPA in a sample of Chinese children and to evaluate whether this association is mediated by CRF. Methods A cross-sectional study consisting of 311 children aged 8–12 years (49.2% girls; mean age = 9.9 years) from Shanghai was conducted. FMS, CRF and MVPA were assessed using the Test of Gross Motor Development-3rd Edition, Progressive Aerobic Cardiovascular Endurance Run and ActiGraph GT3X accelerometers. Preacher & Hayes’s bootstrap method was used to test the mediating effects of CRF on the association between FMS and MVPA. Results CRF fully mediated the association between total FMS and MVPA in girls (indirect effects, b = 0.21, 95% CI [0.07–0.37]), while the mediation was only partial in boys (indirect effects, b = 0.12, 95% CI [0.01–0.26]). CRF fully mediated the association between locomotor skills and MVPA in girls (indirect effects, b = 0.27, 95% CI [0.09– 0.51]), whereas CRF partially mediated the association between object control skills and MVPA in boys (indirect effects, b = 0.15, 95% CI [0.18–0.35]). Conclusion In order to better design and implement sex-specific interventions aiming to increase MVPA, it is essential to consider FMS subdomains and CRF alongside the sex differences in the association between them.
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format: text/html
creator: Dingyi Zhang
creator: Sitong Chen
creator: Fei Xin
creator: Clemens Drenowatz
creator: Xiaoqing Hu
creator: Yan Tang
subject: Epidemiology
subject: Kinesiology
subject: Pediatrics
subject: Public Health
subject: Sports Medicine
description: doi:10.7717/peerj.17564
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background and purpose The associations of fundamental motor skills (FMS), health-related physical fitness (e.g., cardiorespiratory fitness, CRF), and moderate-vigorous physical activity (MVPA) have been demonstrated in Western children, but these associations have not yet been validated in a sample of Chinese children. The aims of this study, therefore, were to examine the association between FMS subdomains and MVPA in a sample of Chinese children and to evaluate whether this association is mediated by CRF. Methods A cross-sectional study consisting of 311 children aged 8–12 years (49.2% girls; mean age = 9.9 years) from Shanghai was conducted. FMS, CRF and MVPA were assessed using the Test of Gross Motor Development-3rd Edition, Progressive Aerobic Cardiovascular Endurance Run and ActiGraph GT3X accelerometers. Preacher & Hayes’s bootstrap method was used to test the mediating effects of CRF on the association between FMS and MVPA. Results CRF fully mediated the association between total FMS and MVPA in girls (indirect effects, b = 0.21, 95% CI [0.07–0.37]), while the mediation was only partial in boys (indirect effects, b = 0.12, 95% CI [0.01–0.26]). CRF fully mediated the association between locomotor skills and MVPA in girls (indirect effects, b = 0.27, 95% CI [0.09– 0.51]), whereas CRF partially mediated the association between object control skills and MVPA in boys (indirect effects, b = 0.15, 95% CI [0.18–0.35]). Conclusion In order to better design and implement sex-specific interventions aiming to increase MVPA, it is essential to consider FMS subdomains and CRF alongside the sex differences in the association between them.
bibliographic citation: Zhang et al. (2024) Associations between fundamental movement skills and accelerometer-measured physical activity in Chinese children: the mediating role of cardiorespiratory fitness. PeerJ 12:e17564 https://doi.org/10.7717/peerj.17564
date submitted: 2024-02-02
date accepted: 2024-05-22
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Dingyi
author list: Agent
  family name: Chen
  given name: Sitong
author list: Agent
  family name: Xin
  given name: Fei
author list: Agent
  family name: Drenowatz
  given name: Clemens
author list: Agent
  family name: Hu
  given name: Xiaoqing
author list: Agent
  family name: Tang
  given name: Yan
doi: 10.7717/peerj.17564
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Squatting biomechanics following physiotherapist-led care or hip arthroscopy for femoroacetabular impingement syndrome: a secondary analysis from a randomised controlled trial
type: item
type: AcademicArticle
description: Background Femoroacetabular impingement syndrome (FAIS) can cause hip pain and chondrolabral damage that may be managed non-operatively or surgically. Squatting motions require large degrees of hip flexion and underpin many daily and sporting tasks but may cause hip impingement and provoke pain. Differential effects of physiotherapist-led care and arthroscopy on biomechanics during squatting have not been examined previously. This study explored differences in 12-month changes in kinematics and moments during squatting between patients with FAIS treated with a physiotherapist-led intervention (Personalised Hip Therapy, PHT) and arthroscopy. Methods A subsample (n = 36) of participants with FAIS enrolled in a multi-centre, pragmatic, two-arm superiority randomised controlled trial underwent three-dimensional motion analysis during squatting at baseline and 12-months following random allocation to PHT (n = 17) or arthroscopy (n = 19). Changes in time-series and peak trunk, pelvis, and hip biomechanics, and squat velocity and maximum depth were explored between treatment groups. Results No significant differences in 12-month changes were detected between PHT and arthroscopy groups. Compared to baseline, the arthroscopy group squatted slower at follow-up (descent: mean difference −0.04 m∙s−1 (95%CI [−0.09 to 0.01]); ascent: −0.05 m∙s−1 [−0.11 to 0.01]%). No differences in squat depth were detected between or within groups. After adjusting for speed, trunk flexion was greater in both treatment groups at follow-up compared to baseline (descent: PHT 7.50° [−14.02 to −0.98]%; ascent: PHT 7.29° [−14.69 to 0.12]%, arthroscopy 16.32° [−32.95 to 0.30]%). Compared to baseline, both treatment groups exhibited reduced anterior pelvic tilt (descent: PHT 8.30° [0.21–16.39]%, arthroscopy −10.95° [−5.54 to 16.34]%; ascent: PHT −7.98° [−0.38 to 16.35]%, arthroscopy −10.82° [3.82–17.81]%), hip flexion (descent: PHT −11.86° [1.67–22.05]%, arthroscopy −16.78° [8.55–22.01]%; ascent: PHT −1…
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format: text/html
creator: Tamara M. Grant
creator: David J. Saxby
creator: Claudio Pizzolato
creator: Trevor Savage
creator: Kim Bennell
creator: Edward Dickenson
creator: Jillian Eyles
creator: Nadine Foster
creator: Michelle Hall
creator: David Hunter
creator: David Lloyd
creator: Rob Molnar
creator: Nicholas Murphy
creator: John O’Donnell
creator: Parminder Singh
creator: Libby Spiers
creator: Phong Tran
creator: Laura E. Diamond
subject: Orthopedics
subject: Biomechanics
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.17567
publisher: PeerJ Inc.
rights: © 2024 Grant et al.
abstract: Background Femoroacetabular impingement syndrome (FAIS) can cause hip pain and chondrolabral damage that may be managed non-operatively or surgically. Squatting motions require large degrees of hip flexion and underpin many daily and sporting tasks but may cause hip impingement and provoke pain. Differential effects of physiotherapist-led care and arthroscopy on biomechanics during squatting have not been examined previously. This study explored differences in 12-month changes in kinematics and moments during squatting between patients with FAIS treated with a physiotherapist-led intervention (Personalised Hip Therapy, PHT) and arthroscopy. Methods A subsample (n = 36) of participants with FAIS enrolled in a multi-centre, pragmatic, two-arm superiority randomised controlled trial underwent three-dimensional motion analysis during squatting at baseline and 12-months following random allocation to PHT (n = 17) or arthroscopy (n = 19). Changes in time-series and peak trunk, pelvis, and hip biomechanics, and squat velocity and maximum depth were explored between treatment groups. Results No significant differences in 12-month changes were detected between PHT and arthroscopy groups. Compared to baseline, the arthroscopy group squatted slower at follow-up (descent: mean difference −0.04 m∙s−1 (95%CI [−0.09 to 0.01]); ascent: −0.05 m∙s−1 [−0.11 to 0.01]%). No differences in squat depth were detected between or within groups. After adjusting for speed, trunk flexion was greater in both treatment groups at follow-up compared to baseline (descent: PHT 7.50° [−14.02 to −0.98]%; ascent: PHT 7.29° [−14.69 to 0.12]%, arthroscopy 16.32° [−32.95 to 0.30]%). Compared to baseline, both treatment groups exhibited reduced anterior pelvic tilt (descent: PHT 8.30° [0.21–16.39]%, arthroscopy −10.95° [−5.54 to 16.34]%; ascent: PHT −7.98° [−0.38 to 16.35]%, arthroscopy −10.82° [3.82–17.81]%), hip flexion (descent: PHT −11.86° [1.67–22.05]%, arthroscopy −16.78° [8.55–22.01]%; ascent: PHT −1…
bibliographic citation: Grant et al. (2024) Squatting biomechanics following physiotherapist-led care or hip arthroscopy for femoroacetabular impingement syndrome: a secondary analysis from a randomised controlled trial. PeerJ 12:e17567 https://doi.org/10.7717/peerj.17567
date submitted: 2024-02-23
date accepted: 2024-05-23
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grant
  given name: Tamara M.
author list: Agent
  family name: Saxby
  given name: David J.
author list: Agent
  family name: Pizzolato
  given name: Claudio
author list: Agent
  family name: Savage
  given name: Trevor
author list: Agent
  family name: Bennell
  given name: Kim
author list: Agent
  family name: Dickenson
  given name: Edward
author list: Agent
  family name: Eyles
  given name: Jillian
author list: Agent
  family name: Foster
  given name: Nadine
author list: Agent
  family name: Hall
  given name: Michelle
author list: Agent
  family name: Hunter
  given name: David
author list: Agent
  family name: Lloyd
  given name: David
author list: Agent
  family name: Molnar
  given name: Rob
author list: Agent
  family name: Murphy
  given name: Nicholas
author list: Agent
  family name: O’Donnell
  given name: John
author list: Agent
  family name: Singh
  given name: Parminder
author list: Agent
  family name: Spiers
  given name: Libby
author list: Agent
  family name: Tran
  given name: Phong
author list: Agent
  family name: Diamond
  given name: Laura E.
doi: 10.7717/peerj.17567
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: © 2024 Grant et al.
attribution name: Grant et al.

Optimization of polysaccharide conditions and analysis of antioxidant capacity in the co-culture of Sanghuangporus vaninii and Pleurotus sapidus
type: item
type: AcademicArticle
description: Fungal polysaccharides are commonly utilized in the food industry and biomedical fields as a natural and safe immune modulator. Co-culturing is a valuable method for enhancing the production of secondary metabolites. This study used intracellular polysaccharide (IPS) content as a screening index, co-culturing seven different fungi with Sanghuangporus vaninii. The seed pre-culture liquid culture time was selected through screening, and conditions were assessed using single factor experimentation, a Plackett-Burman (PB) design, and response surface methodology (RSM) optimization. RSM optimization was conducted, leading to the measurement of antioxidant capacity. Results indicated that the co-culture of S. vaninii and Pleurotus sapidus exhibited the most effective outcome. Specifically, pre-culturing S. vaninii and P. sapidus seed cultures for 2 days and 0 days, respectively, followed by co-culturing, significantly increased IPS content compared to single-strain culturing. Further optimization of co-culture conditions revealed that yeast extract concentration, liquid volume, and S. vaninii inoculum ratio notably influenced IPS content in the order of yeast extract concentration > liquid volume > S. vaninii inoculum ratio. Under the optimal conditions, IPS content reached 69.9626 mg/g, a 17.04% increase from pre-optimization co-culture conditions. Antioxidant capacity testing demonstrated that co-cultured IPS exhibited greater scavenging abilities for DPPH and ABTS free radicals compared to single strain cultures. These findings highlight the potential of co-culturing S. vaninii and P. sapidus to enhance IPS content and improve antioxidant capacity, presenting an effective strategy for increasing fungal polysaccharide production.
format: application/pdf
format: text/html
creator: Yuantian Lu
creator: Di Liu
subject: Biotechnology
subject: Food Science and Technology
subject: Mycology
description: doi:10.7717/peerj.17571
publisher: PeerJ Inc.
rights: © 2024 Lu and Liu
abstract: Fungal polysaccharides are commonly utilized in the food industry and biomedical fields as a natural and safe immune modulator. Co-culturing is a valuable method for enhancing the production of secondary metabolites. This study used intracellular polysaccharide (IPS) content as a screening index, co-culturing seven different fungi with Sanghuangporus vaninii. The seed pre-culture liquid culture time was selected through screening, and conditions were assessed using single factor experimentation, a Plackett-Burman (PB) design, and response surface methodology (RSM) optimization. RSM optimization was conducted, leading to the measurement of antioxidant capacity. Results indicated that the co-culture of S. vaninii and Pleurotus sapidus exhibited the most effective outcome. Specifically, pre-culturing S. vaninii and P. sapidus seed cultures for 2 days and 0 days, respectively, followed by co-culturing, significantly increased IPS content compared to single-strain culturing. Further optimization of co-culture conditions revealed that yeast extract concentration, liquid volume, and S. vaninii inoculum ratio notably influenced IPS content in the order of yeast extract concentration > liquid volume > S. vaninii inoculum ratio. Under the optimal conditions, IPS content reached 69.9626 mg/g, a 17.04% increase from pre-optimization co-culture conditions. Antioxidant capacity testing demonstrated that co-cultured IPS exhibited greater scavenging abilities for DPPH and ABTS free radicals compared to single strain cultures. These findings highlight the potential of co-culturing S. vaninii and P. sapidus to enhance IPS content and improve antioxidant capacity, presenting an effective strategy for increasing fungal polysaccharide production.
bibliographic citation: Lu et al. (2024) Optimization of polysaccharide conditions and analysis of antioxidant capacity in the co-culture of Sanghuangporus vaninii and Pleurotus sapidus. PeerJ 12:e17571 https://doi.org/10.7717/peerj.17571
date submitted: 2024-01-23
date accepted: 2024-05-23
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lu
  given name: Yuantian
author list: Agent
  family name: Liu
  given name: Di
doi: 10.7717/peerj.17571
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: © 2024 Lu and Liu
attribution name: Lu and Liu

Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes
type: item
type: AcademicArticle
description: Background Enhancing detection of cryptic snakes is critical for the development of conservation and management strategies; yet, finding methods that provide adequate detection remains challenging. Issues with detecting snakes can be particularly problematic for some species, like the invasive Burmese python (Python bivittatus) in the Florida Everglades. Methods Using multiple survey methods, we predicted that our ability to detect pythons, larger snakes and all other snakes would be enhanced with the use of live mammalian lures (domesticated rabbits; Oryctolagus cuniculus). Specifically, we used visual surveys, python detection dogs, and time-lapse game cameras to determine if domesticated rabbits were an effective lure. Results Time-lapse game cameras detected almost 40 times more snakes (n = 375, treatment = 245, control = 130) than visual surveys (n = 10). We recorded 21 independent detections of pythons at treatment pens (with lures) and one detection at a control pen (without lures). In addition, we found larger snakes, and all other snakes were 165% and 74% more likely to be detected at treatment pens compared to control pens, respectively. Time-lapse cameras detected almost 40 times more snakes than visual surveys; we did not detect any pythons with python detection dogs. Conclusions Our study presents compelling evidence that the detection of snakes is improved by coupling live mammalian lures with time-lapse game cameras. Although the identification of smaller snake species was limited, this was due to pixel resolution, which could be improved by changing the camera focal length. For larger snakes with individually distinctive patterns, this method could potentially be used to identify unique individuals and thus allow researchers to estimate population dynamics.
format: application/pdf
format: text/html
creator: Marina McCampbell
creator: McKayla Spencer
creator: Kristen Hart
creator: Gabrielle Link
creator: Andrew Watson
creator: Robert McCleery
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.17577
publisher: PeerJ Inc.
rights: © 2024
abstract: Background Enhancing detection of cryptic snakes is critical for the development of conservation and management strategies; yet, finding methods that provide adequate detection remains challenging. Issues with detecting snakes can be particularly problematic for some species, like the invasive Burmese python (Python bivittatus) in the Florida Everglades. Methods Using multiple survey methods, we predicted that our ability to detect pythons, larger snakes and all other snakes would be enhanced with the use of live mammalian lures (domesticated rabbits; Oryctolagus cuniculus). Specifically, we used visual surveys, python detection dogs, and time-lapse game cameras to determine if domesticated rabbits were an effective lure. Results Time-lapse game cameras detected almost 40 times more snakes (n = 375, treatment = 245, control = 130) than visual surveys (n = 10). We recorded 21 independent detections of pythons at treatment pens (with lures) and one detection at a control pen (without lures). In addition, we found larger snakes, and all other snakes were 165% and 74% more likely to be detected at treatment pens compared to control pens, respectively. Time-lapse cameras detected almost 40 times more snakes than visual surveys; we did not detect any pythons with python detection dogs. Conclusions Our study presents compelling evidence that the detection of snakes is improved by coupling live mammalian lures with time-lapse game cameras. Although the identification of smaller snake species was limited, this was due to pixel resolution, which could be improved by changing the camera focal length. For larger snakes with individually distinctive patterns, this method could potentially be used to identify unique individuals and thus allow researchers to estimate population dynamics.
bibliographic citation: McCampbell et al. (2024) Mammalian lures monitored with time-lapse cameras increase detection of pythons and other snakes. PeerJ 12:e17577 https://doi.org/10.7717/peerj.17577
date submitted: 2023-09-21
date accepted: 2024-05-24
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: McCampbell
  given name: Marina
author list: Agent
  family name: Spencer
  given name: McKayla
author list: Agent
  family name: Hart
  given name: Kristen
author list: Agent
  family name: Link
  given name: Gabrielle
author list: Agent
  family name: Watson
  given name: Andrew
author list: Agent
  family name: McCleery
  given name: Robert
doi: 10.7717/peerj.17577
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24

Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches
type: item
type: AcademicArticle
description: Abiotic stress tolerance breeding programs present a spectrum of perspectives, yet definitive solutions remain elusive, with each approach carrying its own set of advantages and disadvantages. This study systematically evaluates extant methodologies, comparing plant performance across varied genotypes and selection traits under optimal and stress conditions. The objective is to elucidate prevailing ambiguities. Ten homozygous lines (F8 generation) were assessed using a randomized block design alongside five control varieties, with four replicates cultivated under well-watered and deficit water conditions. It is noteworthy that six of the ten homozygous lines were cultivated exclusively under well-watered conditions (F3 to F7), while four lines experienced deficit water conditions (F3 to F7). All five control varieties underwent cultivation under both conditions. These findings underscore the necessity for tailored breeding programs attuned to specific environmental exigencies, recognizing that individual traits manifest divergent responses to varying conditions. It is evident that certain traits exhibit marked disparities under well-watered conditions, while others evince heightened differentiation under water deficit conditions. Significantly, our analysis reveals a pronounced interaction between irrigation regimes and selection traits, which serves to underscore the nuanced interplay between genotype and environmental stress.
format: application/pdf
format: text/html
creator: Hatice Kübra Gören
creator: Uğur Tan
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.17584
publisher: PeerJ Inc.
rights: © 2024 Gören and Tan
abstract: Abiotic stress tolerance breeding programs present a spectrum of perspectives, yet definitive solutions remain elusive, with each approach carrying its own set of advantages and disadvantages. This study systematically evaluates extant methodologies, comparing plant performance across varied genotypes and selection traits under optimal and stress conditions. The objective is to elucidate prevailing ambiguities. Ten homozygous lines (F8 generation) were assessed using a randomized block design alongside five control varieties, with four replicates cultivated under well-watered and deficit water conditions. It is noteworthy that six of the ten homozygous lines were cultivated exclusively under well-watered conditions (F3 to F7), while four lines experienced deficit water conditions (F3 to F7). All five control varieties underwent cultivation under both conditions. These findings underscore the necessity for tailored breeding programs attuned to specific environmental exigencies, recognizing that individual traits manifest divergent responses to varying conditions. It is evident that certain traits exhibit marked disparities under well-watered conditions, while others evince heightened differentiation under water deficit conditions. Significantly, our analysis reveals a pronounced interaction between irrigation regimes and selection traits, which serves to underscore the nuanced interplay between genotype and environmental stress.
bibliographic citation: Gören et al. (2024) Unraveling the complexities of drought stress in cotton: a multifaceted analysis of selection criteria and breeding approaches. PeerJ 12:e17584 https://doi.org/10.7717/peerj.17584
date submitted: 2024-03-20
date accepted: 2024-05-27
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gören
  given name: Hatice Kübra
author list: Agent
  family name: Tan
  given name: Uğur
doi: 10.7717/peerj.17584
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: ©2024 Gören and Tan
attribution name: Gören and Tan

Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max
type: item
type: AcademicArticle
description: Background Glutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean (Glycine max (L.) Merr.), one of the most important crops worldwide. Methods In this study, we performed genome-wide identification and characterization of GS, GOGAT, and NR genes in soybean under abiotic and nitrogen stress conditions. Results We identified a total of 10 GS genes, six GOGAT genes, and four NR genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of GS, GOGAT, and NR genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding.
format: application/pdf
format: text/html
creator: Hind Abdelmonim Elsanosi
creator: Tiantian Zhu
creator: Guisheng Zhou
creator: Li Song
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.17590
publisher: PeerJ Inc.
rights: © 2024 Elsanosi et al.
abstract: Background Glutamine synthetase (GS), glutamate synthase (GOGAT), and nitrate reductase (NR) are key enzymes involved in nitrogen assimilation and metabolism in plants. However, the systematic analysis of these gene families lacked reports in soybean (Glycine max (L.) Merr.), one of the most important crops worldwide. Methods In this study, we performed genome-wide identification and characterization of GS, GOGAT, and NR genes in soybean under abiotic and nitrogen stress conditions. Results We identified a total of 10 GS genes, six GOGAT genes, and four NR genes in the soybean genome. Phylogenetic analysis revealed the presence of multiple isoforms for each gene family, indicating their functional diversification. The distribution of these genes on soybean chromosomes was uneven, with segmental duplication events contributing to their expansion. Within the nitrogen assimilation genes (NAGs) group, there was uniformity in the exon-intron structure and the presence of conserved motifs in NAGs. Furthermore, analysis of cis-elements in NAG promoters indicated complex regulation of their expression. RT-qPCR analysis of seven soybean NAGs under various abiotic stresses, including nitrogen deficiency, drought-nitrogen, and salinity, revealed distinct regulatory patterns. Most NAGs exhibited up-regulation under nitrogen stress, while diverse expression patterns were observed under salt and drought-nitrogen stress, indicating their crucial role in nitrogen assimilation and abiotic stress tolerance. These findings offer valuable insights into the genomic organization and expression profiles of GS, GOGAT, and NR genes in soybean under nitrogen and abiotic stress conditions. The results have potential applications in the development of stress-resistant soybean varieties through genetic engineering and breeding.
bibliographic citation: Elsanosi et al. (2024) Genomic organization and expression profiles of nitrogen assimilation genes in Glycine max. PeerJ 12:e17590 https://doi.org/10.7717/peerj.17590
date submitted: 2024-04-02
date accepted: 2024-05-28
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Elsanosi
  given name: Hind Abdelmonim
author list: Agent
  family name: Zhu
  given name: Tiantian
author list: Agent
  family name: Zhou
  given name: Guisheng
author list: Agent
  family name: Song
  given name: Li
doi: 10.7717/peerj.17590
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: © 2024 Elsanosi et al.
attribution name: Elsanosi et al.

Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.)
type: item
type: AcademicArticle
description: Background Tungsten (W) is an emerging heavy metal pollutant, yet research remains scarce on the biomonitor and sensitive biomarkers for W contamination. Methods In this study, celery and pepper were chosen as study subjects and subjected to exposure cultivation in solutions with five different levels of W. The physiological and biochemical toxicities of W on these two plants were systematically analyzed. The feasibility of utilizing celery and pepper as biomonitor organisms for W contamination was explored and indicative biomarkers were screened. Results The results indicated that W could inhibit plants’ root length, shoot height, and fresh weight while concurrently promoting membrane lipid peroxidation. Additionally, W enhanced the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and total antioxidant capacity (TAOC) to counteract oxidative damage. From a physiological perspective, pepper exhibited potential as a biomonitor for W contamination. Biochemical indicators suggested that SOD could serve as a sensitive biomarker for W in celery, while TAOC and POD were more suitable for the roots and leaves of pepper. In conclusion, our study investigated the toxic effects of W on celery and pepper, contributing to the understanding of W’s environmental toxicity. Furthermore, it provided insights for selecting biomonitor organisms and sensitive biomarkers for W contamination.
format: application/pdf
format: text/html
creator: Qi Li
creator: Xiaojun Zheng
creator: Ming Chen
subject: Agricultural Science
subject: Plant Science
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.17601
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background Tungsten (W) is an emerging heavy metal pollutant, yet research remains scarce on the biomonitor and sensitive biomarkers for W contamination. Methods In this study, celery and pepper were chosen as study subjects and subjected to exposure cultivation in solutions with five different levels of W. The physiological and biochemical toxicities of W on these two plants were systematically analyzed. The feasibility of utilizing celery and pepper as biomonitor organisms for W contamination was explored and indicative biomarkers were screened. Results The results indicated that W could inhibit plants’ root length, shoot height, and fresh weight while concurrently promoting membrane lipid peroxidation. Additionally, W enhanced the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and total antioxidant capacity (TAOC) to counteract oxidative damage. From a physiological perspective, pepper exhibited potential as a biomonitor for W contamination. Biochemical indicators suggested that SOD could serve as a sensitive biomarker for W in celery, while TAOC and POD were more suitable for the roots and leaves of pepper. In conclusion, our study investigated the toxic effects of W on celery and pepper, contributing to the understanding of W’s environmental toxicity. Furthermore, it provided insights for selecting biomonitor organisms and sensitive biomarkers for W contamination.
bibliographic citation: Li et al. (2024) Ecotoxicological effects of tungsten on celery (Apium graveolens L) and pepper (Capsicum spp.). PeerJ 12:e17601 https://doi.org/10.7717/peerj.17601
date submitted: 2024-01-09
date accepted: 2024-05-29
issued: 2024-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Qi
author list: Agent
  family name: Zheng
  given name: Xiaojun
author list: Agent
  family name: Chen
  given name: Ming
doi: 10.7717/peerj.17601
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-24
copyright: ©2024 Li et al.
attribution name: Li et al.

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