PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bayesian multistate models for measuring invasive carp movement and evaluating telemetry array performance
items: Ferroptosis-related gene transferrin receptor protein 1 expression correlates with the prognosis and tumor immune microenvironment in cervical cancer
items: Chemical composition and egg production capacity throughout bloom development of ctenophore Mnemiopsis leidyi in the northern Adriatic Sea
items: Associations of 24-hour movement guidelines adherence with fruit and vegetable intake in university students
items: Modelling take-off moment arms in an ornithocheiraean pterosaur
items: Genome sequencing and CAZymes repertoire analysis of Diaporthe eres P3-1W causing postharvest fruit rot of ‘Hongyang’ kiwifruit in China
items: Within-host adaptive speciation of commensal yoyo clams leads to ecological exclusion, not co-existence
items: The effectiveness of different attentional foci on the acquisition of sport-specific motor skills in healthy adults: a systematic review with network meta-analysis
items: Research progress on the effects of postharvest storage methods on melon quality
items: A glycolysis-related signature to improve the current treatment and prognostic evaluation for breast cancer

Bayesian multistate models for measuring invasive carp movement and evaluating telemetry array performance
type: item
type: AcademicArticle
description: Understanding the movement patterns of an invasive species can be a powerful tool in designing effective management and control strategies. Here, we used a Bayesian multistate model to investigate the movement of two invasive carp species, silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), using acoustic telemetry. The invaded portions of the Illinois and Des Plaines Rivers, USA, are a high priority management zone in the broader efforts to combat the spread of invasive carps from reaching the Laurentian Great Lakes. Our main objective was to characterize the rates of upstream and downstream movements by carps between river pools that are maintained by navigation lock and dam structures. However, we also aimed to evaluate the efficacy of the available telemetry infrastructure to monitor carp movements through this system. We found that, on a monthly basis, most individuals of both species remained within their current river pools: averaging 76.2% of silver carp and 75.5% of bighead carp. Conversely, a smaller proportion of silver carp, averaging 14.2%, and bighead carp, averaging 13.9%, moved to downstream river pools. Movements towards upstream pools were the least likely for both species, with silver carp at an average of 6.7% and bighead carp at 7.9%. The highest probabilities for upstream movements were for fish originating from the three most downstream river pools, where most of the population recruitment occurs. However, our evaluation of the telemetry array’s effectiveness indicated low probability to detect fish in this portion of the river. We provide insights to enhance the placement and use of these monitoring tools, aiming to deepen our comprehension of these species’ movement patterns in the system.
format: application/pdf
format: text/html
creator: Jessica C. Stanton
creator: Marybeth K. Brey
creator: Alison A. Coulter
creator: David R. Stewart
creator: Brent Knights
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.17834
publisher: PeerJ Inc.
rights: © 2024 Stanton et al.
abstract: Understanding the movement patterns of an invasive species can be a powerful tool in designing effective management and control strategies. Here, we used a Bayesian multistate model to investigate the movement of two invasive carp species, silver carp (Hypophthalmichthys molitrix) and bighead carp (H. nobilis), using acoustic telemetry. The invaded portions of the Illinois and Des Plaines Rivers, USA, are a high priority management zone in the broader efforts to combat the spread of invasive carps from reaching the Laurentian Great Lakes. Our main objective was to characterize the rates of upstream and downstream movements by carps between river pools that are maintained by navigation lock and dam structures. However, we also aimed to evaluate the efficacy of the available telemetry infrastructure to monitor carp movements through this system. We found that, on a monthly basis, most individuals of both species remained within their current river pools: averaging 76.2% of silver carp and 75.5% of bighead carp. Conversely, a smaller proportion of silver carp, averaging 14.2%, and bighead carp, averaging 13.9%, moved to downstream river pools. Movements towards upstream pools were the least likely for both species, with silver carp at an average of 6.7% and bighead carp at 7.9%. The highest probabilities for upstream movements were for fish originating from the three most downstream river pools, where most of the population recruitment occurs. However, our evaluation of the telemetry array’s effectiveness indicated low probability to detect fish in this portion of the river. We provide insights to enhance the placement and use of these monitoring tools, aiming to deepen our comprehension of these species’ movement patterns in the system.
bibliographic citation: Stanton et al. (2024) Bayesian multistate models for measuring invasive carp movement and evaluating telemetry array performance. PeerJ 12:e17834 https://doi.org/10.7717/peerj.17834
date submitted: 2024-02-23
date accepted: 2024-07-09
issued: 2024-08-06
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Stanton
  given name: Jessica C.
author list: Agent
  family name: Brey
  given name: Marybeth K.
author list: Agent
  family name: Coulter
  given name: Alison A.
author list: Agent
  family name: Stewart
  given name: David R.
author list: Agent
  family name: Knights
  given name: Brent
doi: 10.7717/peerj.17834
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-06
copyright: ©2024 Stanton et al.
attribution name: Stanton et al.

Ferroptosis-related gene transferrin receptor protein 1 expression correlates with the prognosis and tumor immune microenvironment in cervical cancer
type: item
type: AcademicArticle
description: Background Ferroptosis is a non-apoptotic iron-dependent form of cell death implicated in various cancer pathologies. However, its precise role in tumor growth and progression of cervical cancer (CC) remains unclear. Transferrin receptor protein 1 (TFRC), a key molecule associated with ferroptosis, has been identified as influencing a broad range of pathological processes in different cancers. However, the prognostic significance of TFRC in CC remains unclear. The present study utilized bioinformatics to explore the significance of the ferroptosis-related gene TFRC in the progression and prognosis of CC. Methods We obtained RNA sequencing data and corresponding clinical information on patients with CC from The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx) and Gene Expression Omnibus (GEO) databases. Using least absolute shrinkage and selection operator (LASSO) Cox regression, we then generated a multigene signature of five ferroptosis-related genes (FRGs) for the prognostic prediction of CC. We investigated the relationship between TFRC gene expression and immune cell infiltration by employing single-sample GSEA (ssGSEA) analysis. The potential functional role of the TFRC gene was evaluated through gene set enrichment analysis (GSEA). Immunohistochemistry and qPCR was employed to assess TFRC mRNA and protein expression in 33 cases of cervical cancer. Furthermore, the relationship between TFRC mRNA expression and overall survival (OS) was investigated in patients. Results CC samples had significantly higher TFRC gene expression levels than normal tissue samples. Higher TFRC gene expression levels were strongly associated with higher cancer T stages and OS events. The findings of multivariate analyses illustrated that the OS in CC patients with high TFRC expression is shorter than in patients with low TFRC expression. Significant increases were observed in the levels of TFRC mRNA and protein expression in patients diagnosed with CC. Conclusion Increase…
format: application/pdf
format: text/html
creator: Xiujuan Shang
creator: Hongdong Wang
creator: Jin Gu
creator: Xiaohui Zhao
creator: Jing Zhang
creator: Bohao Sun
creator: Xinming Zhu
subject: Bioinformatics
subject: Cell Biology
subject: Pathology
subject: Women’s Health
description: doi:10.7717/peerj.17842
publisher: PeerJ Inc.
rights: © 2024 Shang et al.
abstract: Background Ferroptosis is a non-apoptotic iron-dependent form of cell death implicated in various cancer pathologies. However, its precise role in tumor growth and progression of cervical cancer (CC) remains unclear. Transferrin receptor protein 1 (TFRC), a key molecule associated with ferroptosis, has been identified as influencing a broad range of pathological processes in different cancers. However, the prognostic significance of TFRC in CC remains unclear. The present study utilized bioinformatics to explore the significance of the ferroptosis-related gene TFRC in the progression and prognosis of CC. Methods We obtained RNA sequencing data and corresponding clinical information on patients with CC from The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx) and Gene Expression Omnibus (GEO) databases. Using least absolute shrinkage and selection operator (LASSO) Cox regression, we then generated a multigene signature of five ferroptosis-related genes (FRGs) for the prognostic prediction of CC. We investigated the relationship between TFRC gene expression and immune cell infiltration by employing single-sample GSEA (ssGSEA) analysis. The potential functional role of the TFRC gene was evaluated through gene set enrichment analysis (GSEA). Immunohistochemistry and qPCR was employed to assess TFRC mRNA and protein expression in 33 cases of cervical cancer. Furthermore, the relationship between TFRC mRNA expression and overall survival (OS) was investigated in patients. Results CC samples had significantly higher TFRC gene expression levels than normal tissue samples. Higher TFRC gene expression levels were strongly associated with higher cancer T stages and OS events. The findings of multivariate analyses illustrated that the OS in CC patients with high TFRC expression is shorter than in patients with low TFRC expression. Significant increases were observed in the levels of TFRC mRNA and protein expression in patients diagnosed with CC. Conclusion Increase…
bibliographic citation: Shang et al. (2024) Ferroptosis-related gene transferrin receptor protein 1 expression correlates with the prognosis and tumor immune microenvironment in cervical cancer. PeerJ 12:e17842 https://doi.org/10.7717/peerj.17842
date submitted: 2024-04-02
date accepted: 2024-07-10
issued: 2024-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shang
  given name: Xiujuan
author list: Agent
  family name: Wang
  given name: Hongdong
author list: Agent
  family name: Gu
  given name: Jin
author list: Agent
  family name: Zhao
  given name: Xiaohui
author list: Agent
  family name: Zhang
  given name: Jing
author list: Agent
  family name: Sun
  given name: Bohao
author list: Agent
  family name: Zhu
  given name: Xinming
doi: 10.7717/peerj.17842
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-06
copyright: © 2024 Shang et al.
attribution name: Shang et al.

Chemical composition and egg production capacity throughout bloom development of ctenophore Mnemiopsis leidyi in the northern Adriatic Sea
type: item
type: AcademicArticle
description: High abundances of gelatinous zooplankton (GZ) can significantly impact marine ecosystem by acting as both sink and source of organic matter (OM) and nutrients. The decay of GZ bloom can introduce significant amount of OM to the ocean interior, with its variability influenced by GZ life traits and environmental factors, impacting microbial communities vital to marine biogeochemical cycles. The invasive ctenophores Mnemiopsis leidyi has formed massive blooms in the northern Adriatic Sea since 2016. However, the variability in the chemical composition and egg production of blooming populations, as well as the role of environmental factors in governing this variability, remains largely unknown. Our analysis of biometry, chemical composition, and fecundity of M. leidyi sampled in the Gulf of Trieste in 2021 revealed stable carbon and nitrogen content throughout bloom development, with no significant correlation with seawater temperature, salinity, oxygen, and chlorophyll a concentration. Although the studied population exhibited homogeneity in terms of biometry and chemical composition, the number of produced eggs varied substantially, showing no clear correlation with environmental variables and being somewhat lower than previously reported for the study area and other Mediterranean areas. We observed a positive correlation between the wet weight of individuals and the percentage of hatched eggs, as well as a significant positive correlation between the percentage of hatched eggs and ambient seawater temperature. Additionally, we noted that the speed of hatching decreased with decreasing seawater temperature in autumn, corresponding to the end of M. leidyi bloom.
format: application/pdf
format: text/html
creator: Kevin Rečnik
creator: Katja Klun
creator: Lovrenc Lipej
creator: Alenka Malej
creator: Tinkara Tinta
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.17844
publisher: PeerJ Inc.
rights: © 2024 Rečnik et al.
abstract: High abundances of gelatinous zooplankton (GZ) can significantly impact marine ecosystem by acting as both sink and source of organic matter (OM) and nutrients. The decay of GZ bloom can introduce significant amount of OM to the ocean interior, with its variability influenced by GZ life traits and environmental factors, impacting microbial communities vital to marine biogeochemical cycles. The invasive ctenophores Mnemiopsis leidyi has formed massive blooms in the northern Adriatic Sea since 2016. However, the variability in the chemical composition and egg production of blooming populations, as well as the role of environmental factors in governing this variability, remains largely unknown. Our analysis of biometry, chemical composition, and fecundity of M. leidyi sampled in the Gulf of Trieste in 2021 revealed stable carbon and nitrogen content throughout bloom development, with no significant correlation with seawater temperature, salinity, oxygen, and chlorophyll a concentration. Although the studied population exhibited homogeneity in terms of biometry and chemical composition, the number of produced eggs varied substantially, showing no clear correlation with environmental variables and being somewhat lower than previously reported for the study area and other Mediterranean areas. We observed a positive correlation between the wet weight of individuals and the percentage of hatched eggs, as well as a significant positive correlation between the percentage of hatched eggs and ambient seawater temperature. Additionally, we noted that the speed of hatching decreased with decreasing seawater temperature in autumn, corresponding to the end of M. leidyi bloom.
bibliographic citation: Rečnik et al. (2024) Chemical composition and egg production capacity throughout bloom development of ctenophore Mnemiopsis leidyi in the northern Adriatic Sea. PeerJ 12:e17844 https://doi.org/10.7717/peerj.17844
date submitted: 2024-02-16
date accepted: 2024-07-10
issued: 2024-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Rečnik
  given name: Kevin
author list: Agent
  family name: Klun
  given name: Katja
author list: Agent
  family name: Lipej
  given name: Lovrenc
author list: Agent
  family name: Malej
  given name: Alenka
author list: Agent
  family name: Tinta
  given name: Tinkara
doi: 10.7717/peerj.17844
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-06
copyright: ©2024 Rečnik et al.
attribution name: Rečnik et al.

Associations of 24-hour movement guidelines adherence with fruit and vegetable intake in university students
type: item
type: AcademicArticle
description: Background Unhealthy eating habits, such as low vegetable and fruit intake, are associated with many health problems. 24-h movement behaviors have been reported to be positively associated with numerous health-related outcomes. Despite the importance of these two modifiable lifestyle behaviors in building healthy habits in university students, there is a paucity of relevant research in this population. Therefore, this study aims to examine the correlation between compliance with 24-h movement guideline (24-h MG) and intake of fruits and vegetables (IFV) in Chinese university students. Methods This study investigated the relationship between the compliance with 24-h MG and IFV in 1,793 Chinese university students using a convenience sampling method online. Physical activity (PA) and sedentary behavior (SB) were assessed by the International Physical Activity Questionnaire-Short Form, while sleep was measured using the Pittsburgh Sleep Quality Index. The Chinese version of the Health Promoting Lifestyle Profile II was used to measure IFV. Generalized linear models were applied to examine the correlation between compliance with the 24-h MG and eating habits. Results The proportion of participants who routinely consumed vegetables and fruits was 24.6% and 43.1%, respectively, while the proportion of meeting the three 24-h MG and a combination of any two guidelines was 27.8% and 40.1%, respectively. Meeting all three guidelines was associated with a greater IFV intake compared to not meeting either guideline. Meeting all three guidelines (OR = 2.42 [1.63, 3.58]) and the combination of moderate to vigorous PA (MVPA) and sleep (OR = 2.06 [1.37, 3.10]) were positively associated with the frequency of vegetable consumption (p < 0.05). As well, meeting all three guidelines (OR = 2.06 [1.37, 3.10]), the combination of MVPA and sleep (OR = 1.72 [1.04, 2.84]), and sleep only (OR = 1.88 [1.21, 2.92]) were positively associated with fruits consumption (p < 0.05). Conclusion Almost…
format: application/pdf
format: text/html
creator: Yao Zhang
creator: Xingyi Yang
creator: Zhen Yang
creator: Xinli Chi
creator: Sitong Chen
subject: Global Health
subject: Health Policy
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.17875
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background Unhealthy eating habits, such as low vegetable and fruit intake, are associated with many health problems. 24-h movement behaviors have been reported to be positively associated with numerous health-related outcomes. Despite the importance of these two modifiable lifestyle behaviors in building healthy habits in university students, there is a paucity of relevant research in this population. Therefore, this study aims to examine the correlation between compliance with 24-h movement guideline (24-h MG) and intake of fruits and vegetables (IFV) in Chinese university students. Methods This study investigated the relationship between the compliance with 24-h MG and IFV in 1,793 Chinese university students using a convenience sampling method online. Physical activity (PA) and sedentary behavior (SB) were assessed by the International Physical Activity Questionnaire-Short Form, while sleep was measured using the Pittsburgh Sleep Quality Index. The Chinese version of the Health Promoting Lifestyle Profile II was used to measure IFV. Generalized linear models were applied to examine the correlation between compliance with the 24-h MG and eating habits. Results The proportion of participants who routinely consumed vegetables and fruits was 24.6% and 43.1%, respectively, while the proportion of meeting the three 24-h MG and a combination of any two guidelines was 27.8% and 40.1%, respectively. Meeting all three guidelines was associated with a greater IFV intake compared to not meeting either guideline. Meeting all three guidelines (OR = 2.42 [1.63, 3.58]) and the combination of moderate to vigorous PA (MVPA) and sleep (OR = 2.06 [1.37, 3.10]) were positively associated with the frequency of vegetable consumption (p < 0.05). As well, meeting all three guidelines (OR = 2.06 [1.37, 3.10]), the combination of MVPA and sleep (OR = 1.72 [1.04, 2.84]), and sleep only (OR = 1.88 [1.21, 2.92]) were positively associated with fruits consumption (p < 0.05). Conclusion Almost…
bibliographic citation: Zhang et al. (2024) Associations of 24-hour movement guidelines adherence with fruit and vegetable intake in university students. PeerJ 12:e17875 https://doi.org/10.7717/peerj.17875
date submitted: 2024-03-12
date accepted: 2024-07-16
issued: 2024-08-06
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yao
author list: Agent
  family name: Yang
  given name: Xingyi
author list: Agent
  family name: Yang
  given name: Zhen
author list: Agent
  family name: Chi
  given name: Xinli
author list: Agent
  family name: Chen
  given name: Sitong
doi: 10.7717/peerj.17875
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-06
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Modelling take-off moment arms in an ornithocheiraean pterosaur
type: item
type: AcademicArticle
description: Take-off is a vital part of powered flight which likely constrains the size of birds, yet extinct pterosaurs are known to have reached far larger sizes. Three different hypothesised take-off motions (bipedal burst launching, bipedal countermotion launching, and quadrupedal launching) have been proposed as explanations for how pterosaurs became airborne and circumvented this proposed morphological limit. We have constructed a computational musculoskeletal model of a 5 m wingspan ornithocheiraean pterosaur, reconstructing thirty-four key muscles to estimate the muscle moment arms throughout the three hypothesised take-off motions. Range of motion constrained hypothetical kinematic sequences for bipedal and quadrupedal take-off motions were modelled after extant flying vertebrates. Across our simulations we did not find higher hindlimb moment arms for bipedal take-off motions or noticeably higher forelimb moment arms in the forelimb for quadrupedal take-off motions. Despite this, in all our models we found the muscles utilised in the quadrupedal take-off have the largest total launch applicable moment arms throughout the entire take-off sequences and for the take-off pose. This indicates the potential availability of higher leverage for a quadrupedal take-off than hypothesised bipedal motions in pterosaurs pending further examination of muscle forces.
format: application/pdf
format: text/html
creator: Benjamin W. Griffin
creator: Elizabeth Martin-Silverstone
creator: Rodrigo V. Pêgas
creator: Erik Anthony Meilak
creator: Fabiana R. Costa
creator: Colin Palmer
creator: Emily J. Rayfield
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17678
publisher: PeerJ Inc.
rights: © 2024 Griffin et al.
abstract: Take-off is a vital part of powered flight which likely constrains the size of birds, yet extinct pterosaurs are known to have reached far larger sizes. Three different hypothesised take-off motions (bipedal burst launching, bipedal countermotion launching, and quadrupedal launching) have been proposed as explanations for how pterosaurs became airborne and circumvented this proposed morphological limit. We have constructed a computational musculoskeletal model of a 5 m wingspan ornithocheiraean pterosaur, reconstructing thirty-four key muscles to estimate the muscle moment arms throughout the three hypothesised take-off motions. Range of motion constrained hypothetical kinematic sequences for bipedal and quadrupedal take-off motions were modelled after extant flying vertebrates. Across our simulations we did not find higher hindlimb moment arms for bipedal take-off motions or noticeably higher forelimb moment arms in the forelimb for quadrupedal take-off motions. Despite this, in all our models we found the muscles utilised in the quadrupedal take-off have the largest total launch applicable moment arms throughout the entire take-off sequences and for the take-off pose. This indicates the potential availability of higher leverage for a quadrupedal take-off than hypothesised bipedal motions in pterosaurs pending further examination of muscle forces.
bibliographic citation: Griffin et al. (2024) Modelling take-off moment arms in an ornithocheiraean pterosaur. PeerJ 12:e17678 https://doi.org/10.7717/peerj.17678
date submitted: 2023-09-07
date accepted: 2024-06-12
issued: 2024-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Griffin
  given name: Benjamin W.
author list: Agent
  family name: Martin-Silverstone
  given name: Elizabeth
author list: Agent
  family name: Pêgas
  given name: Rodrigo V.
author list: Agent
  family name: Meilak
  given name: Erik Anthony
author list: Agent
  family name: Costa
  given name: Fabiana R.
author list: Agent
  family name: Palmer
  given name: Colin
author list: Agent
  family name: Rayfield
  given name: Emily J.
doi: 10.7717/peerj.17678
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-05
copyright: ©2024 Griffin et al.
attribution name: Griffin et al.

Genome sequencing and CAZymes repertoire analysis of Diaporthe eres P3-1W causing postharvest fruit rot of ‘Hongyang’ kiwifruit in China
type: item
type: AcademicArticle
description: Postharvest rot caused by various fungal pathogens is a damaging disease affecting kiwifruit production and quality, resulting in significant annual economic losses. This study focused on isolating the strain P3-1W, identified as Diaporthe eres, as the causal agent of ‘Hongyang’ postharvest rot disease in China. The investigation highlighted cell wall degrading enzymes (CWDEs) as crucial pathogenic factors. Specially, the enzymatic activities of cellulase, β-galactosidase, polygalacturonase, and pectin methylesterases peaked significantly on the second day after infection of D. eres P3-1W. To gain a comprehensive understanding of these CWDEs, the genome of this strain was sequenced using PacBio and Illumina sequencing technologies. The analysis revealed that the genome of D. eres P3-1W spans 58,489,835 bp, with an N50 of 5,939,879 bp and a GC content of 50.7%. A total of 15,407 total protein-coding genes (PCGs) were predicted and functionally annotated. Notably, 857 carbohydrate-active enzymes (CAZymes) were identified in D. eres P3-1W, with 521 CWDEs consisting of 374 glycoside hydrolases (GHs), 108 carbohydrate esterase (CEs) and 91 polysaccharide lyases (PLs). Additionally, 221 auxiliary activities (AAs), 91 glycosyltransferases (GTs), and 108 carbohydrate binding modules (CBMs) were detected. These findings offer valuable insights into the CAZymes of D. eres P3-1W.
format: application/pdf
format: text/html
creator: Li-Zhen Ling
creator: Ling-Ling Chen
creator: Zhen-Zhen Liu
creator: Lan-Ying Luo
creator: Si-Han Tai
creator: Shu-Dong Zhang
subject: Agricultural Science
subject: Genomics
subject: Microbiology
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.17715
publisher: PeerJ Inc.
rights: © 2024 Ling et al.
abstract: Postharvest rot caused by various fungal pathogens is a damaging disease affecting kiwifruit production and quality, resulting in significant annual economic losses. This study focused on isolating the strain P3-1W, identified as Diaporthe eres, as the causal agent of ‘Hongyang’ postharvest rot disease in China. The investigation highlighted cell wall degrading enzymes (CWDEs) as crucial pathogenic factors. Specially, the enzymatic activities of cellulase, β-galactosidase, polygalacturonase, and pectin methylesterases peaked significantly on the second day after infection of D. eres P3-1W. To gain a comprehensive understanding of these CWDEs, the genome of this strain was sequenced using PacBio and Illumina sequencing technologies. The analysis revealed that the genome of D. eres P3-1W spans 58,489,835 bp, with an N50 of 5,939,879 bp and a GC content of 50.7%. A total of 15,407 total protein-coding genes (PCGs) were predicted and functionally annotated. Notably, 857 carbohydrate-active enzymes (CAZymes) were identified in D. eres P3-1W, with 521 CWDEs consisting of 374 glycoside hydrolases (GHs), 108 carbohydrate esterase (CEs) and 91 polysaccharide lyases (PLs). Additionally, 221 auxiliary activities (AAs), 91 glycosyltransferases (GTs), and 108 carbohydrate binding modules (CBMs) were detected. These findings offer valuable insights into the CAZymes of D. eres P3-1W.
bibliographic citation: Ling et al. (2024) Genome sequencing and CAZymes repertoire analysis of Diaporthe eres P3-1W causing postharvest fruit rot of ‘Hongyang’ kiwifruit in China. PeerJ 12:e17715 https://doi.org/10.7717/peerj.17715
date submitted: 2024-02-26
date accepted: 2024-06-18
issued: 2024-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ling
  given name: Li-Zhen
author list: Agent
  family name: Chen
  given name: Ling-Ling
author list: Agent
  family name: Liu
  given name: Zhen-Zhen
author list: Agent
  family name: Luo
  given name: Lan-Ying
author list: Agent
  family name: Tai
  given name: Si-Han
author list: Agent
  family name: Zhang
  given name: Shu-Dong
doi: 10.7717/peerj.17715
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-05
copyright: © 2024 Ling et al.
attribution name: Ling et al.

Within-host adaptive speciation of commensal yoyo clams leads to ecological exclusion, not co-existence
type: item
type: AcademicArticle
description: Symbionts dominate planetary diversity and three primary symbiont diversification processes have been proposed: co-speciation with hosts, speciation by host-switching, and within-host speciation. The last mechanism is prevalent among members of an extraordinary marine symbiosis in the Indian River Lagoon, Florida, composed of a host mantis shrimp, Lysiosquilla scabricauda, and seven host-specific commensal vasconielline “yoyo” clams (Galeommatoidea) that collectively occupy two distinct niches: burrow-wall-attached, and host-attached/ectocommensal. This within-host symbiont radiation provides a natural experiment to test how symbiont coexistence patterns are regulated in a common ancestral habitat. The competitive exclusion principle predicts that sister taxa produced by adaptive speciation (with distinct morphologies and within-burrow niches) are most likely to coexist whereas the neutral theory predicts no difference among adaptive and non-adaptive sister taxa co-occurrence. To test these predictions, we engaged in (1) field-censusing commensal species assemblages; (2) trophic niche analyses; (3) laboratory behavioral observations. Although predicted by both models, the field census found no mixed-niche commensal assemblages: multi-species burrows were exclusively composed of burrow-wall commensals. Their co-occurrence matched random assembly process expectations, but presence of the single ectocommensal species had a highly significant negative effect on recruitment of all burrow-wall commensal species (P < 0.001), including on its burrow-wall commensal sister species (P < 0.001). Our stable isotope data indicated that commensals are suspension feeders and that co-occurring burrow-wall commensals may exhibit trophic niche differentiation. The artificial burrow behavioral experiment yielded no evidence of spatial segregation among burrow-wall commensals, and it was terminated by a sudden breakdown of the host-commensal relationship resulting in a mass mortality of…
format: application/pdf
format: text/html
creator: Teal A. Harrison
creator: Ryutaro Goto
creator: Jingchun Li
creator: Diarmaid Ó Foighil
subject: Ecology
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.17753
publisher: PeerJ Inc.
rights: © 2024 Harrison et al.
abstract: Symbionts dominate planetary diversity and three primary symbiont diversification processes have been proposed: co-speciation with hosts, speciation by host-switching, and within-host speciation. The last mechanism is prevalent among members of an extraordinary marine symbiosis in the Indian River Lagoon, Florida, composed of a host mantis shrimp, Lysiosquilla scabricauda, and seven host-specific commensal vasconielline “yoyo” clams (Galeommatoidea) that collectively occupy two distinct niches: burrow-wall-attached, and host-attached/ectocommensal. This within-host symbiont radiation provides a natural experiment to test how symbiont coexistence patterns are regulated in a common ancestral habitat. The competitive exclusion principle predicts that sister taxa produced by adaptive speciation (with distinct morphologies and within-burrow niches) are most likely to coexist whereas the neutral theory predicts no difference among adaptive and non-adaptive sister taxa co-occurrence. To test these predictions, we engaged in (1) field-censusing commensal species assemblages; (2) trophic niche analyses; (3) laboratory behavioral observations. Although predicted by both models, the field census found no mixed-niche commensal assemblages: multi-species burrows were exclusively composed of burrow-wall commensals. Their co-occurrence matched random assembly process expectations, but presence of the single ectocommensal species had a highly significant negative effect on recruitment of all burrow-wall commensal species (P < 0.001), including on its burrow-wall commensal sister species (P < 0.001). Our stable isotope data indicated that commensals are suspension feeders and that co-occurring burrow-wall commensals may exhibit trophic niche differentiation. The artificial burrow behavioral experiment yielded no evidence of spatial segregation among burrow-wall commensals, and it was terminated by a sudden breakdown of the host-commensal relationship resulting in a mass mortality of…
bibliographic citation: Harrison et al. (2024) Within-host adaptive speciation of commensal yoyo clams leads to ecological exclusion, not co-existence. PeerJ 12:e17753 https://doi.org/10.7717/peerj.17753
date submitted: 2024-03-04
date accepted: 2024-06-25
issued: 2024-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harrison
  given name: Teal A.
author list: Agent
  family name: Goto
  given name: Ryutaro
author list: Agent
  family name: Li
  given name: Jingchun
author list: Agent
  family name: Ó Foighil
  given name: Diarmaid
doi: 10.7717/peerj.17753
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-05
copyright: ©2024 Harrison et al.
attribution name: Harrison et al.

The effectiveness of different attentional foci on the acquisition of sport-specific motor skills in healthy adults: a systematic review with network meta-analysis
type: item
type: AcademicArticle
description: Background The acquisition of motor skills is a key element in many sports. A motor learning principle, which is frequently used to support skill acquisition is the application of different attentional foci. The effectiveness of different attentional foci on performance and the learning of motor skills has been investigated in various sports using randomised controlled trials. The aim of the present study was to investigate the effectiveness of different attentional foci (such as external (EFA) and internal attentional foci (IFA), but also holistic and switching foci) on the performance and learning of a sport-specific motor task in healthy individuals. Methods This study was a systematic review with network meta-analysis. We followed the Prisma reporting guideline and the Cochrane handbook for systematic reviews. Cinahl, Embase, Medline and Cochrane Central were searched for eligible studies. Network meta-analyses were performed for the post-acquisition, retention and transfer test endpoints. Results Twelve studies were included in the review. At post-acquisition an EFA was the most effective intervention compared to the control intervention (SMD: 0.9855; 95% CI [0.4–1.57]; p: 0.001). At the retention and transfer test endpoints, a holistic focus of attention had the highest effectiveness compared to an IFA (SMD 0.75; 95% CI [−0.1 to 1.6]; p: 0.09) and (SMD 1.16; 95% CI [0.47–1.86]; p: 0.001). Discussion For all three endpoints, we analysed a greater effectiveness of an EFA and holistic focus compared to an IFA. Several promising different attentional focus interventions were identified. The largest effects were analysed for a holistic focus. However, only one study used this intervention and therefore there remains uncertainty about the effectiveness. With regard to the inconsistency observed, the analysis at post-acquisition should be interpreted with caution. Modified versions of the EFA were the imagined and the dynamic EFA. Both were only explored in single st…
format: application/pdf
format: text/html
creator: Emmanuel Favre-Bulle
creator: Siri Nyfeler
creator: Chloé Schorderet
creator: Gaia Risso
creator: Michela Bassolino
creator: Karl Martin Sattelmayer
subject: Neuroscience
subject: Kinesiology
description: doi:10.7717/peerj.17799
publisher: PeerJ Inc.
rights: © 2024 Favre-Bulle et al.
abstract: Background The acquisition of motor skills is a key element in many sports. A motor learning principle, which is frequently used to support skill acquisition is the application of different attentional foci. The effectiveness of different attentional foci on performance and the learning of motor skills has been investigated in various sports using randomised controlled trials. The aim of the present study was to investigate the effectiveness of different attentional foci (such as external (EFA) and internal attentional foci (IFA), but also holistic and switching foci) on the performance and learning of a sport-specific motor task in healthy individuals. Methods This study was a systematic review with network meta-analysis. We followed the Prisma reporting guideline and the Cochrane handbook for systematic reviews. Cinahl, Embase, Medline and Cochrane Central were searched for eligible studies. Network meta-analyses were performed for the post-acquisition, retention and transfer test endpoints. Results Twelve studies were included in the review. At post-acquisition an EFA was the most effective intervention compared to the control intervention (SMD: 0.9855; 95% CI [0.4–1.57]; p: 0.001). At the retention and transfer test endpoints, a holistic focus of attention had the highest effectiveness compared to an IFA (SMD 0.75; 95% CI [−0.1 to 1.6]; p: 0.09) and (SMD 1.16; 95% CI [0.47–1.86]; p: 0.001). Discussion For all three endpoints, we analysed a greater effectiveness of an EFA and holistic focus compared to an IFA. Several promising different attentional focus interventions were identified. The largest effects were analysed for a holistic focus. However, only one study used this intervention and therefore there remains uncertainty about the effectiveness. With regard to the inconsistency observed, the analysis at post-acquisition should be interpreted with caution. Modified versions of the EFA were the imagined and the dynamic EFA. Both were only explored in single st…
bibliographic citation: Favre-Bulle et al. (2024) The effectiveness of different attentional foci on the acquisition of sport-specific motor skills in healthy adults: a systematic review with network meta-analysis. PeerJ 12:e17799 https://doi.org/10.7717/peerj.17799
date submitted: 2024-02-28
date accepted: 2024-07-02
issued: 2024-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Favre-Bulle
  given name: Emmanuel
author list: Agent
  family name: Nyfeler
  given name: Siri
author list: Agent
  family name: Schorderet
  given name: Chloé
author list: Agent
  family name: Risso
  given name: Gaia
author list: Agent
  family name: Bassolino
  given name: Michela
author list: Agent
  family name: Sattelmayer
  given name: Karl Martin
doi: 10.7717/peerj.17799
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-05
copyright: © 2024 Favre-Bulle et al.
attribution name: Favre-Bulle et al.

Research progress on the effects of postharvest storage methods on melon quality
type: item
type: AcademicArticle
description: Background As an important global agricultural cash crop, melon has a long history of cultivation and a wide planting area. The physiological metabolism of melon after harvest is relatively strong; if not properly stored, melon is easily invaded by external pathogens during transportation, resulting in economic losses and greatly limiting its production, development and market supply. Therefore, the storage and freshness of melon are the main challenges in realizing the annual supply of melon, so postharvest storage has received increasing amounts of attention from researchers. Methods This study used academic, PubMed, and Web of Science resources to retrieve keywords related to postharvest storage and melon quality; read, refined, classified, and sorted the retrieved literature; sorted and summarized the relevant research results; and finally completed this article. Results This article reviews the mechanism and effects of physical, chemical and biological preservation techniques on the sensory quality, compound contents and respiratory physiological activities of different varieties of melon fruits. When maintaining normal metabolism and not producing physiological disorders, melon inhibits cell wall metabolism, reactive oxygen species metabolism and the ethylene biosynthesis pathway, etc., to the greatest extent during postharvest storage, thereby reducing the material consumption of fruits, delaying the ripening and senescence process, and prolonging the postharvest life and shelf life. Conclusion The literature provides a theoretical basis for postharvest preservation technology in the melon industry in the future and provides corresponding guidance for the development of the melon industry.
format: application/pdf
format: text/html
creator: Haofei Wang
creator: Jiayi Cui
creator: Rui Bao
creator: Hui Zhang
creator: Zi Zhao
creator: Xuanye Chen
creator: Zhangfei Wu
creator: Chaonan Wang
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.17800
publisher: PeerJ Inc.
rights: © 2024 Wang et al.
abstract: Background As an important global agricultural cash crop, melon has a long history of cultivation and a wide planting area. The physiological metabolism of melon after harvest is relatively strong; if not properly stored, melon is easily invaded by external pathogens during transportation, resulting in economic losses and greatly limiting its production, development and market supply. Therefore, the storage and freshness of melon are the main challenges in realizing the annual supply of melon, so postharvest storage has received increasing amounts of attention from researchers. Methods This study used academic, PubMed, and Web of Science resources to retrieve keywords related to postharvest storage and melon quality; read, refined, classified, and sorted the retrieved literature; sorted and summarized the relevant research results; and finally completed this article. Results This article reviews the mechanism and effects of physical, chemical and biological preservation techniques on the sensory quality, compound contents and respiratory physiological activities of different varieties of melon fruits. When maintaining normal metabolism and not producing physiological disorders, melon inhibits cell wall metabolism, reactive oxygen species metabolism and the ethylene biosynthesis pathway, etc., to the greatest extent during postharvest storage, thereby reducing the material consumption of fruits, delaying the ripening and senescence process, and prolonging the postharvest life and shelf life. Conclusion The literature provides a theoretical basis for postharvest preservation technology in the melon industry in the future and provides corresponding guidance for the development of the melon industry.
bibliographic citation: Wang et al. (2024) Research progress on the effects of postharvest storage methods on melon quality. PeerJ 12:e17800 https://doi.org/10.7717/peerj.17800
date submitted: 2024-03-20
date accepted: 2024-07-02
issued: 2024-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Haofei
author list: Agent
  family name: Cui
  given name: Jiayi
author list: Agent
  family name: Bao
  given name: Rui
author list: Agent
  family name: Zhang
  given name: Hui
author list: Agent
  family name: Zhao
  given name: Zi
author list: Agent
  family name: Chen
  given name: Xuanye
author list: Agent
  family name: Wu
  given name: Zhangfei
author list: Agent
  family name: Wang
  given name: Chaonan
doi: 10.7717/peerj.17800
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-05
copyright: ©2024 Wang et al.
attribution name: Wang et al.

A glycolysis-related signature to improve the current treatment and prognostic evaluation for breast cancer
type: item
type: AcademicArticle
description: Background As a heterogeneous malignancy, breast cancer (BRCA) shows high incidence and mortality. Discovering novel molecular markers and developing reliable prognostic models may improve the survival of BCRA. Methods The RNA-seq data of BRCA patients were collected from the training set The Cancer Genome Atlas (TCGA)-BRCA and validation set GSE20685 in the Gene Expression Omnibus (GEO) databases. The “GSVA” R package was used to calculate the glycolysis score for each patient, based on which all the patients were divided into different glycolysis groups. The “limma” package was employed to perform differentially expression genes (DEGs) analysis. Key signature genes were selected by performing un/multivariate and least absolute shrinkage and selection operator (LASSO) C regression and used to develop a RiskScore model. The ESTIMATE and MCP-Counter algorithms were used for quantifying immune infiltration level. The functions of the genes were validated using Western blot, colony formation, transwell and wound-healing assay. Results The glycolysis score and prognostic analysis showed that high glycolysis score was related to tumorigenesis pathway and a poor prognosis in BRCA as overactive glycolysis inhibited the normal functions of immune cells. Subsequently, we screened five key prognostic genes using the LASSO Cox regression analysis and used them to establish a RiskScore with a high classification efficiency. Based on the results of the RiskScore, it was found that patients in the high-risk group had significantly unfavorable immune infiltration and prognostic outcomes. A nomogram integrating the RiskScore could well predict the prognosis for BRCA patients. Knockdown of PSCA suppressed cell proliferation, invasion and migration of BRCA cells. Conclusion This study developed a glycolysis-related signature with five genes to distinguish between high-risk and low-risk BRCA patients. A nomogram developed on the basis of the RiskScore was reliable to predict BRCA surv…
format: application/pdf
format: text/html
creator: Sijie Feng
creator: Linwei Ning
creator: Huizhen Zhang
creator: Zhenhui Wang
creator: Yunkun Lu
subject: Bioinformatics
subject: Cell Biology
subject: Immunology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.17861
publisher: PeerJ Inc.
rights: © 2024 Feng et al.
abstract: Background As a heterogeneous malignancy, breast cancer (BRCA) shows high incidence and mortality. Discovering novel molecular markers and developing reliable prognostic models may improve the survival of BCRA. Methods The RNA-seq data of BRCA patients were collected from the training set The Cancer Genome Atlas (TCGA)-BRCA and validation set GSE20685 in the Gene Expression Omnibus (GEO) databases. The “GSVA” R package was used to calculate the glycolysis score for each patient, based on which all the patients were divided into different glycolysis groups. The “limma” package was employed to perform differentially expression genes (DEGs) analysis. Key signature genes were selected by performing un/multivariate and least absolute shrinkage and selection operator (LASSO) C regression and used to develop a RiskScore model. The ESTIMATE and MCP-Counter algorithms were used for quantifying immune infiltration level. The functions of the genes were validated using Western blot, colony formation, transwell and wound-healing assay. Results The glycolysis score and prognostic analysis showed that high glycolysis score was related to tumorigenesis pathway and a poor prognosis in BRCA as overactive glycolysis inhibited the normal functions of immune cells. Subsequently, we screened five key prognostic genes using the LASSO Cox regression analysis and used them to establish a RiskScore with a high classification efficiency. Based on the results of the RiskScore, it was found that patients in the high-risk group had significantly unfavorable immune infiltration and prognostic outcomes. A nomogram integrating the RiskScore could well predict the prognosis for BRCA patients. Knockdown of PSCA suppressed cell proliferation, invasion and migration of BRCA cells. Conclusion This study developed a glycolysis-related signature with five genes to distinguish between high-risk and low-risk BRCA patients. A nomogram developed on the basis of the RiskScore was reliable to predict BRCA surv…
bibliographic citation: Feng et al. (2024) A glycolysis-related signature to improve the current treatment and prognostic evaluation for breast cancer. PeerJ 12:e17861 https://doi.org/10.7717/peerj.17861
date submitted: 2024-04-30
date accepted: 2024-07-14
issued: 2024-08-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Sijie
author list: Agent
  family name: Ning
  given name: Linwei
author list: Agent
  family name: Zhang
  given name: Huizhen
author list: Agent
  family name: Wang
  given name: Zhenhui
author list: Agent
  family name: Lu
  given name: Yunkun
doi: 10.7717/peerj.17861
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-08-05
copyright: © 2024 Feng et al.
attribution name: Feng et al.

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