PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: First fossil species of family Hyidae (Arachnida: Pseudoscorpiones) confirms 99 million years of ecological stasis in a Gondwanan lineage
items: https://peerj.com/articles/17583
items: Possible eucynodont (Synapsida: Cynodontia) tracks from a lacustrine facies in the Lower Jurassic Moenave Formation of southwestern Utah
items: The effects of occupational disruption during COVID-19 lockdowns on health: a cross-sectional study
items: Shoulder mobility and strength impairments in patients with rotator cuff related shoulder pain: a systematic review and meta analysis
items: The association between antiphospholipid syndrome and atrial fibrillation: a single center retrospective case-control study
items: Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length
items: Novel roles of κ-opioid receptor in myocardial ischemia-reperfusion injury
items: Recovery of deep-sea meiofauna community in Kaikōura Canyon following an earthquake-triggered turbidity flow
items: TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets

First fossil species of family Hyidae (Arachnida: Pseudoscorpiones) confirms 99 million years of ecological stasis in a Gondwanan lineage
type: item
type: AcademicArticle
description: Burmese amber preserves a diverse assemblage of Cretaceous arachnids, and among pseudoscorpions (Arachnida: Pseudoscorpiones), ten species in five families have already been named. Here, we describe a new fossil species from Burmese amber in the pseudoscorpion family Hyidae, providing detailed measurements, photographs and 3D-models from synchrotron scanning. Based on morphology, the new fossil, Hya fynni sp. nov. is placed in the genus Hya, and is nearly identical to extant species in the genus, except for the position of trichobothrium est on the pedipalpal chela, thereby indicating extreme morphological stasis in this invertebrate lineage over the last 99 million years. Hya fynni represents the first described fossil species in Hyidae, and the third described Burmese fossil in the superfamily Neobisioidea. It also joins the garypinid, Amblyolpium burmiticum, in representing the oldest fossil records for extant pseudoscorpion genera. Considering proposed divergence dates, the newly described fossil species bolsters a Gondwanan origin for Hyidae, and provides evidence for the “Late Jurassic Rifting” hypothesis for the Burma Terrane, in which this landmass rifted from Gondwana in the Late Jurassic and collided with Eurasia by the Cretaceous/Eocene. Like Hya species today, H. fynni likely inhabited humicolous microhabitats in tropical forests on the Burma Terrane, supporting ecological niche stasis for this family since the Mesozoic.
format: application/pdf
format: text/html
creator: Liza M. Röschmann
creator: Mark S. Harvey
creator: Yanmeng Hou
creator: Danilo Harms
creator: Ulrich Kotthoff
creator: Jörg U. Hammel
creator: Dong Ren
creator: Stephanie F. Loria
subject: Biodiversity
subject: Biogeography
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.17515
publisher: PeerJ Inc.
rights: © 2024 Röschmann et al.
abstract: Burmese amber preserves a diverse assemblage of Cretaceous arachnids, and among pseudoscorpions (Arachnida: Pseudoscorpiones), ten species in five families have already been named. Here, we describe a new fossil species from Burmese amber in the pseudoscorpion family Hyidae, providing detailed measurements, photographs and 3D-models from synchrotron scanning. Based on morphology, the new fossil, Hya fynni sp. nov. is placed in the genus Hya, and is nearly identical to extant species in the genus, except for the position of trichobothrium est on the pedipalpal chela, thereby indicating extreme morphological stasis in this invertebrate lineage over the last 99 million years. Hya fynni represents the first described fossil species in Hyidae, and the third described Burmese fossil in the superfamily Neobisioidea. It also joins the garypinid, Amblyolpium burmiticum, in representing the oldest fossil records for extant pseudoscorpion genera. Considering proposed divergence dates, the newly described fossil species bolsters a Gondwanan origin for Hyidae, and provides evidence for the “Late Jurassic Rifting” hypothesis for the Burma Terrane, in which this landmass rifted from Gondwana in the Late Jurassic and collided with Eurasia by the Cretaceous/Eocene. Like Hya species today, H. fynni likely inhabited humicolous microhabitats in tropical forests on the Burma Terrane, supporting ecological niche stasis for this family since the Mesozoic.
bibliographic citation: Röschmann et al. (2024) First fossil species of family Hyidae (Arachnida: Pseudoscorpiones) confirms 99 million years of ecological stasis in a Gondwanan lineage. PeerJ 12:e17515 https://doi.org/10.7717/peerj.17515
date submitted: 2024-02-29
date accepted: 2024-05-13
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Röschmann
  given name: Liza M.
author list: Agent
  family name: Harvey
  given name: Mark S.
author list: Agent
  family name: Hou
  given name: Yanmeng
author list: Agent
  family name: Harms
  given name: Danilo
author list: Agent
  family name: Kotthoff
  given name: Ulrich
author list: Agent
  family name: Hammel
  given name: Jörg U.
author list: Agent
  family name: Ren
  given name: Dong
author list: Agent
  family name: Loria
  given name: Stephanie F.
doi: 10.7717/peerj.17515
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: © 2024 Röschmann et al.
attribution name: Röschmann et al.

https://peerj.com/articles/17583
type: item
type: AcademicArticle
title: Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: a prospective, open label, controlled, randomized, comparative, proof of concept study
description: Background Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®-a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated. Methods A total of 30 participants with type 2 diabetes and hyperlipidaemia were recruited for this study. The microbiome profile of the 15 participants (test arm) was evaluated using whole genome shotgun metagenomics and personalized nutritional recommendations based on their microbiota profile were provided. The remaining 15 participants (control arm) were provided with diabetic nutritional guidance for 3 months. Clinical and anthropometric parameters such as HbA1c, systolic/diastolic pressure, c-reactive protein levels and microbiota composition were measured and compared during the study. Results The test arm (microbiome-based nutrition) showed a statistically significant decrease in HbA1c level from 8.30 (95% confidence interval (CI), [7.74–8.85]) to 6.67 (95% CI [6.2–7.05]), p < 0.001 after 90 days. The test arm also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130 mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure (p < 0.05), after the microbiome-based personalized dietary intervention. The int…
format: application/pdf
format: text/html
creator: Gopalakrishna Kallapura
creator: Anthony Surya Prakash
creator: Kumar Sankaran
creator: Prabhath Manjappa
creator: Prayagraj Chaudhary
creator: Sanjay Ambhore
creator: Debojyoti Dhar
subject: Microbiology
subject: Clinical Trials
subject: Diabetes and Endocrinology
subject: Nutrition
subject: Metabolic Sciences
description: doi:10.7717/peerj.17583
publisher: PeerJ Inc.
rights: © 2024 Kallapura et al.
abstract: Background Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®-a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated. Methods A total of 30 participants with type 2 diabetes and hyperlipidaemia were recruited for this study. The microbiome profile of the 15 participants (test arm) was evaluated using whole genome shotgun metagenomics and personalized nutritional recommendations based on their microbiota profile were provided. The remaining 15 participants (control arm) were provided with diabetic nutritional guidance for 3 months. Clinical and anthropometric parameters such as HbA1c, systolic/diastolic pressure, c-reactive protein levels and microbiota composition were measured and compared during the study. Results The test arm (microbiome-based nutrition) showed a statistically significant decrease in HbA1c level from 8.30 (95% confidence interval (CI), [7.74–8.85]) to 6.67 (95% CI [6.2–7.05]), p < 0.001 after 90 days. The test arm also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130 mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure (p < 0.05), after the microbiome-based personalized dietary intervention. The int…
bibliographic citation: Kallapura et al. (2024) Microbiota based personalized nutrition improves hyperglycaemia and hypertension parameters and reduces inflammation: a prospective, open label, controlled, randomized, comparative, proof of concept study. PeerJ 12:e17583 https://doi.org/10.7717/peerj.17583
date submitted: 2024-01-19
date accepted: 2024-05-27
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kallapura
  given name: Gopalakrishna
author list: Agent
  family name: Prakash
  given name: Anthony Surya
author list: Agent
  family name: Sankaran
  given name: Kumar
author list: Agent
  family name: Manjappa
  given name: Prabhath
author list: Agent
  family name: Chaudhary
  given name: Prayagraj
author list: Agent
  family name: Ambhore
  given name: Sanjay
author list: Agent
  family name: Dhar
  given name: Debojyoti
doi: 10.7717/peerj.17583
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: © 2024 Kallapura et al.
attribution name: Kallapura et al.

Possible eucynodont (Synapsida: Cynodontia) tracks from a lacustrine facies in the Lower Jurassic Moenave Formation of southwestern Utah
type: item
type: AcademicArticle
description: Eight fossil tetrapod footprints from lake-shore deposits in the Lower Jurassic Moenave Formation at the St. George Dinosaur Discovery Site (SGDS) in southwestern Utah cannot be assigned to the prevalent dinosaurian (Anomoepus, Eubrontes, Gigandipus, Grallator, Kayentapus) or crocodyliform (Batrachopus) ichnotaxa at the site. The tridactyl and tetradactyl footprints are incomplete, consisting of digit- and digit-tip-only imprints. Seven of the eight are likely pes prints; the remaining specimen is a possible manus print. The pes prints have digit imprint morphologies and similar anterior projections and divarication angles to those of Brasilichnium, an ichnotaxon found primarily in eolian paleoenvironments attributed to eucynodont synapsids. Although their incompleteness prevents clear referral to Brasilichnium, the SGDS tracks nevertheless suggest a eucynodont track maker and thus represent a rare, Early Mesozoic occurrence of such tracks outside of an eolian paleoenvironment.
format: application/pdf
format: text/html
creator: Holly Hurtado
creator: Jerald D. Harris
creator: Andrew R.C. Milner
subject: Animal Behavior
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17591
publisher: PeerJ Inc.
rights: © 2024 Hurtado et al.
abstract: Eight fossil tetrapod footprints from lake-shore deposits in the Lower Jurassic Moenave Formation at the St. George Dinosaur Discovery Site (SGDS) in southwestern Utah cannot be assigned to the prevalent dinosaurian (Anomoepus, Eubrontes, Gigandipus, Grallator, Kayentapus) or crocodyliform (Batrachopus) ichnotaxa at the site. The tridactyl and tetradactyl footprints are incomplete, consisting of digit- and digit-tip-only imprints. Seven of the eight are likely pes prints; the remaining specimen is a possible manus print. The pes prints have digit imprint morphologies and similar anterior projections and divarication angles to those of Brasilichnium, an ichnotaxon found primarily in eolian paleoenvironments attributed to eucynodont synapsids. Although their incompleteness prevents clear referral to Brasilichnium, the SGDS tracks nevertheless suggest a eucynodont track maker and thus represent a rare, Early Mesozoic occurrence of such tracks outside of an eolian paleoenvironment.
bibliographic citation: Hurtado et al. (2024) Possible eucynodont (Synapsida: Cynodontia) tracks from a lacustrine facies in the Lower Jurassic Moenave Formation of southwestern Utah. PeerJ 12:e17591 https://doi.org/10.7717/peerj.17591
date submitted: 2023-07-24
date accepted: 2024-05-28
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hurtado
  given name: Holly
author list: Agent
  family name: Harris
  given name: Jerald D.
author list: Agent
  family name: Milner
  given name: Andrew R.C.
doi: 10.7717/peerj.17591
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Hurtado et al.
attribution name: Hurtado et al.

The effects of occupational disruption during COVID-19 lockdowns on health: a cross-sectional study
type: item
type: AcademicArticle
description: The disruption in daily activity performance during COVID-19 lockdowns is widely understood to have impacted health, but a better understanding of how restricted performance of specific activities are associated with health is needed. This cross-sectional study answers the following question: How were changes in the performance of 16 daily activities associated with health during COVID-19 lockdowns? A total of 116 participants completed an online survey rating their health before and during COVID-19 lockdowns and comparing their recollection of the performance of 16 activities before COVID-19 with their performance during lockdowns. Multiple stepwise linear regression analysis was used to estimate the relationship between self-reported changes in activities during lockdowns and concurrent (during-lockdown) health status, while controlling for pre-COVID-19 health status. Only changes in activities that were uniquely and significantly associated with lockdown health status were retained in the final model. Health before COVID-19 accounted for 3.7% (P = 0.039) of the variance in health during COVID-19 lockdowns. After controlling for health before COVID-19, five types of activity were significantly and uniquely predictive of health during lockdowns, together accounting for 48.3% of the variance. These activities and the variances they accounted for were rest and sleep (29.5%, P < 0.001), play and recreational activities (8%, P < 0.001), work (4.8%, P = 0.002), personal hygiene (3.2%, P = 0.01), and healthy eating (2.8%, P = 0.013). The study suggests that these five types of activity should be prioritized in policy or interventions when participation in activity is constrained by lockdowns or comparable factors.
format: application/pdf
format: text/html
creator: Bernard Austin Kigunda Muriithi
creator: R. Curtis Bay
subject: Epidemiology
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.17594
publisher: PeerJ Inc.
rights: © 2024 Muriithi and Bay
abstract: The disruption in daily activity performance during COVID-19 lockdowns is widely understood to have impacted health, but a better understanding of how restricted performance of specific activities are associated with health is needed. This cross-sectional study answers the following question: How were changes in the performance of 16 daily activities associated with health during COVID-19 lockdowns? A total of 116 participants completed an online survey rating their health before and during COVID-19 lockdowns and comparing their recollection of the performance of 16 activities before COVID-19 with their performance during lockdowns. Multiple stepwise linear regression analysis was used to estimate the relationship between self-reported changes in activities during lockdowns and concurrent (during-lockdown) health status, while controlling for pre-COVID-19 health status. Only changes in activities that were uniquely and significantly associated with lockdown health status were retained in the final model. Health before COVID-19 accounted for 3.7% (P = 0.039) of the variance in health during COVID-19 lockdowns. After controlling for health before COVID-19, five types of activity were significantly and uniquely predictive of health during lockdowns, together accounting for 48.3% of the variance. These activities and the variances they accounted for were rest and sleep (29.5%, P < 0.001), play and recreational activities (8%, P < 0.001), work (4.8%, P = 0.002), personal hygiene (3.2%, P = 0.01), and healthy eating (2.8%, P = 0.013). The study suggests that these five types of activity should be prioritized in policy or interventions when participation in activity is constrained by lockdowns or comparable factors.
bibliographic citation: Muriithi et al. (2024) The effects of occupational disruption during COVID-19 lockdowns on health: a cross-sectional study. PeerJ 12:e17594 https://doi.org/10.7717/peerj.17594
date submitted: 2023-12-22
date accepted: 2024-05-28
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Muriithi
  given name: Bernard Austin Kigunda
author list: Agent
  family name: Bay
  given name: R. Curtis
doi: 10.7717/peerj.17594
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Muriithi and Bay
attribution name: Muriithi and Bay

Shoulder mobility and strength impairments in patients with rotator cuff related shoulder pain: a systematic review and meta analysis
type: item
type: AcademicArticle
description: Background The methods previously proposed in the literature to assess patients with rotator cuff related shoulder pain, based on special orthopedic tests to precisely identify the structure causing the shoulder symptoms have been recently challenged. This opens the possibility of a different way of physical examination. Objective To analyze the differences in shoulder range of motion, strength and thoracic kyphosis between rotator cuff related shoulder pain patients and an asymptomatic group. Method The protocol of the present research was registered in the International Prospective Register of Systematic Review (PROSPERO) (registration number CRD42021258924). Database search of observational studies was conducted in MEDLINE, EMBASE, WOS and CINHAL until July 2023, which assessed shoulder or neck neuro-musculoskeletal non-invasive physical examination compared to an asymptomatic group. Two investigators assessed eligibility and study quality. The Newcastle Ottawa Scale was used to evaluate the methodology quality. Results Eight studies (N = 604) were selected for the quantitative analysis. Meta-analysis showed statistical differences with large effect for shoulder flexion (I2 = 91.7%, p < 0.01, HG = −1.30), external rotation (I2 = 83.2%, p < 0.01, HG = −1.16) and internal rotation range of motion (I2 = 0%, p < 0.01, HG = −1.32). Regarding to shoulder strength; only internal rotation strength showed statistical differences with small effect (I2 = 42.8%, p < 0.05, HG = −0.3). Conclusions There is moderate to strong evidence that patients with rotator cuff related shoulder pain present less shoulder flexion, internal and external rotation range of motion and less internal rotation strength than asymptomatic individuals.
format: application/pdf
format: text/html
creator: Daniel Manoso-Hernando
creator: Javier Bailón-Cerezo
creator: Santiago Angulo-Díaz-Parreño
creator: Álvaro Reina-Varona
creator: Ignacio Elizagaray-García
creator: Alfonso Gil-Martínez
subject: Anesthesiology and Pain Management
subject: Kinesiology
subject: Orthopedics
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.17604
publisher: PeerJ Inc.
rights: © 2024 Manoso-Hernando et al.
abstract: Background The methods previously proposed in the literature to assess patients with rotator cuff related shoulder pain, based on special orthopedic tests to precisely identify the structure causing the shoulder symptoms have been recently challenged. This opens the possibility of a different way of physical examination. Objective To analyze the differences in shoulder range of motion, strength and thoracic kyphosis between rotator cuff related shoulder pain patients and an asymptomatic group. Method The protocol of the present research was registered in the International Prospective Register of Systematic Review (PROSPERO) (registration number CRD42021258924). Database search of observational studies was conducted in MEDLINE, EMBASE, WOS and CINHAL until July 2023, which assessed shoulder or neck neuro-musculoskeletal non-invasive physical examination compared to an asymptomatic group. Two investigators assessed eligibility and study quality. The Newcastle Ottawa Scale was used to evaluate the methodology quality. Results Eight studies (N = 604) were selected for the quantitative analysis. Meta-analysis showed statistical differences with large effect for shoulder flexion (I2 = 91.7%, p < 0.01, HG = −1.30), external rotation (I2 = 83.2%, p < 0.01, HG = −1.16) and internal rotation range of motion (I2 = 0%, p < 0.01, HG = −1.32). Regarding to shoulder strength; only internal rotation strength showed statistical differences with small effect (I2 = 42.8%, p < 0.05, HG = −0.3). Conclusions There is moderate to strong evidence that patients with rotator cuff related shoulder pain present less shoulder flexion, internal and external rotation range of motion and less internal rotation strength than asymptomatic individuals.
bibliographic citation: Manoso-Hernando et al. (2024) Shoulder mobility and strength impairments in patients with rotator cuff related shoulder pain: a systematic review and meta analysis. PeerJ 12:e17604 https://doi.org/10.7717/peerj.17604
date submitted: 2024-01-15
date accepted: 2024-05-30
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manoso-Hernando
  given name: Daniel
author list: Agent
  family name: Bailón-Cerezo
  given name: Javier
author list: Agent
  family name: Angulo-Díaz-Parreño
  given name: Santiago
author list: Agent
  family name: Reina-Varona
  given name: Álvaro
author list: Agent
  family name: Elizagaray-García
  given name: Ignacio
author list: Agent
  family name: Gil-Martínez
  given name: Alfonso
doi: 10.7717/peerj.17604
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Manoso-Hernando et al.
attribution name: Manoso-Hernando et al.

The association between antiphospholipid syndrome and atrial fibrillation: a single center retrospective case-control study
type: item
type: AcademicArticle
description: Antiphospholipid syndrome (APS) is a systemic autoimmune syndrome characterized by arterial or venous thrombosis, pregnancy complications and thrombocytopenia. The aim of this study is to investigate the association between APS and atrial fibrillation (AF) among patients in Peking University People’s Hospital. A single center retrospective study was conducted. Cases were hospitalized patients diagnosed with AF by a cardiologist while the control group patients did not exhibit cardiac diseases. The results of the study revealed that in multivariable logistic regression, APS, anticardiolipin antibody (aCL) positivity and anti-beta-2-glycoprotein antibody (anti-β2GPI) positivity are independent risk factors of AF. APS, aCL positivity and anti-β2GPI positivity are statistically different between AF patients and non-AF patients. Forthcoming studies are needed to clarify the potential link between APS and AF.
format: application/pdf
format: text/html
creator: Zechuan Zhou
creator: Yuansheng Liu
subject: Allergy and Clinical Immunology
subject: Cardiology
subject: Immunology
subject: Internal Medicine
subject: Rheumatology
description: doi:10.7717/peerj.17617
publisher: PeerJ Inc.
rights: © 2024 Zhou and Liu
abstract: Antiphospholipid syndrome (APS) is a systemic autoimmune syndrome characterized by arterial or venous thrombosis, pregnancy complications and thrombocytopenia. The aim of this study is to investigate the association between APS and atrial fibrillation (AF) among patients in Peking University People’s Hospital. A single center retrospective study was conducted. Cases were hospitalized patients diagnosed with AF by a cardiologist while the control group patients did not exhibit cardiac diseases. The results of the study revealed that in multivariable logistic regression, APS, anticardiolipin antibody (aCL) positivity and anti-beta-2-glycoprotein antibody (anti-β2GPI) positivity are independent risk factors of AF. APS, aCL positivity and anti-β2GPI positivity are statistically different between AF patients and non-AF patients. Forthcoming studies are needed to clarify the potential link between APS and AF.
bibliographic citation: Zhou et al. (2024) The association between antiphospholipid syndrome and atrial fibrillation: a single center retrospective case-control study. PeerJ 12:e17617 https://doi.org/10.7717/peerj.17617
date submitted: 2024-04-01
date accepted: 2024-05-31
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zechuan
author list: Agent
  family name: Liu
  given name: Yuansheng
doi: 10.7717/peerj.17617
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Zhou and Liu
attribution name: Zhou and Liu

Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length
type: item
type: AcademicArticle
description: Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding (PDCB) protein that associates with the plasmodesmata contributes to cell wall extension. Given that the elongation of cotton fiber cells correlates with the dynamics of the cell wall, this protein can be related to the cotton fiber elongation. This study sought to identify PDCB family members within the Gossypium. hirsutum genome and to elucidate their expression profiles. A total of 45 distinct family members were observed through the identification and screening processes. The analysis of their physicochemical properties revealed the similarity in the amino acid composition and molecular weight across most members. The phylogenetic analysis facilitated the construction of an evolutionary tree, categorizing these members into five groups mainly distributed on 20 chromosomes. The fine mapping results facilitated a tissue-specific examination of group V, revealing that the expression level of GhPDCB9 peaked five days after flowering. The VIGS experiments resulted in a marked decrease in the gene expression level and a significant reduction in the mature fiber length, averaging a shortening of 1.43–4.77 mm. The results indicated that GhPDCB9 played a pivotal role in the cotton fiber development and served as a candidate for enhancing cotton yield.
format: application/pdf
format: text/html
creator: Haibo Zhang
creator: Xianghui Xiao
creator: Ziyin Li
creator: Yu Chen
creator: Pengtao Li
creator: Renhai Peng
creator: Quanwei Lu
creator: Youwu Wang
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.17625
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Plasmodesmata are transmembrane channels embedded within the cell wall that can facilitate the intercellular communication in plants. Plasmodesmata callose-binding (PDCB) protein that associates with the plasmodesmata contributes to cell wall extension. Given that the elongation of cotton fiber cells correlates with the dynamics of the cell wall, this protein can be related to the cotton fiber elongation. This study sought to identify PDCB family members within the Gossypium. hirsutum genome and to elucidate their expression profiles. A total of 45 distinct family members were observed through the identification and screening processes. The analysis of their physicochemical properties revealed the similarity in the amino acid composition and molecular weight across most members. The phylogenetic analysis facilitated the construction of an evolutionary tree, categorizing these members into five groups mainly distributed on 20 chromosomes. The fine mapping results facilitated a tissue-specific examination of group V, revealing that the expression level of GhPDCB9 peaked five days after flowering. The VIGS experiments resulted in a marked decrease in the gene expression level and a significant reduction in the mature fiber length, averaging a shortening of 1.43–4.77 mm. The results indicated that GhPDCB9 played a pivotal role in the cotton fiber development and served as a candidate for enhancing cotton yield.
bibliographic citation: Zhang et al. (2024) Exploring the plasmodesmata callose-binding protein gene family in upland cotton: unraveling insights for enhancing fiber length. PeerJ 12:e17625 https://doi.org/10.7717/peerj.17625
date submitted: 2024-01-28
date accepted: 2024-06-02
issued: 2024-06-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Haibo
author list: Agent
  family name: Xiao
  given name: Xianghui
author list: Agent
  family name: Li
  given name: Ziyin
author list: Agent
  family name: Chen
  given name: Yu
author list: Agent
  family name: Li
  given name: Pengtao
author list: Agent
  family name: Peng
  given name: Renhai
author list: Agent
  family name: Lu
  given name: Quanwei
author list: Agent
  family name: Wang
  given name: Youwu
doi: 10.7717/peerj.17625
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-26
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

Novel roles of κ-opioid receptor in myocardial ischemia-reperfusion injury
type: item
type: AcademicArticle
description: Acute heart attack is the primary cause of cardiovascular-related death worldwide. A common treatment is reperfusion of ischemic tissue, which can cause irreversible damage to the myocardium. The number of mitochondria in cardiomyocytes is large, which generate adenosine triphosphate (ATP) to sustain proper cardiac contractile function, and mitochondrial dysfunction plays a crucial role in cell death during myocardial ischemia-reperfusion, leading to an increasing number of studies investigating the impact of mitochondria on ischemia-reperfusion injury. The disarray of mitochondrial dynamics, excessive Ca2+ accumulation, activation of mitochondrial permeable transition pores, swelling of mitochondria, ultimately the death of cardiomyocyte are the consequences of ischemia-reperfusion injury. κ-opioid receptors can alleviate mitochondrial dysfunction, regulate mitochondrial dynamics, mitigate myocardial ischemia-reperfusion injury, exert protective effects on myocardium. The mechanism of κ-OR activation during myocardial ischemia-reperfusion to regulate mitochondrial dynamics and reduce myocardial ischemia-reperfusion injury will be discussed, so as to provide theoretical basis for the protection of ischemic myocardium.
format: application/pdf
format: text/html
creator: Wen Zhang
creator: Qi Zhang
creator: Yali Liu
creator: Jianming Pei
creator: Na Feng
subject: Biochemistry
subject: Cell Biology
subject: Cardiology
description: doi:10.7717/peerj.17333
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Acute heart attack is the primary cause of cardiovascular-related death worldwide. A common treatment is reperfusion of ischemic tissue, which can cause irreversible damage to the myocardium. The number of mitochondria in cardiomyocytes is large, which generate adenosine triphosphate (ATP) to sustain proper cardiac contractile function, and mitochondrial dysfunction plays a crucial role in cell death during myocardial ischemia-reperfusion, leading to an increasing number of studies investigating the impact of mitochondria on ischemia-reperfusion injury. The disarray of mitochondrial dynamics, excessive Ca2+ accumulation, activation of mitochondrial permeable transition pores, swelling of mitochondria, ultimately the death of cardiomyocyte are the consequences of ischemia-reperfusion injury. κ-opioid receptors can alleviate mitochondrial dysfunction, regulate mitochondrial dynamics, mitigate myocardial ischemia-reperfusion injury, exert protective effects on myocardium. The mechanism of κ-OR activation during myocardial ischemia-reperfusion to regulate mitochondrial dynamics and reduce myocardial ischemia-reperfusion injury will be discussed, so as to provide theoretical basis for the protection of ischemic myocardium.
bibliographic citation: Zhang et al. (2024) Novel roles of κ-opioid receptor in myocardial ischemia-reperfusion injury. PeerJ 12:e17333 https://doi.org/10.7717/peerj.17333
date submitted: 2024-01-18
date accepted: 2024-04-12
issued: 2024-06-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Wen
author list: Agent
  family name: Zhang
  given name: Qi
author list: Agent
  family name: Liu
  given name: Yali
author list: Agent
  family name: Pei
  given name: Jianming
author list: Agent
  family name: Feng
  given name: Na
doi: 10.7717/peerj.17333
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-25
copyright: ©2024 Zhang et al.
attribution name: Zhang et al.

Recovery of deep-sea meiofauna community in Kaikōura Canyon following an earthquake-triggered turbidity flow
type: item
type: AcademicArticle
description: Turbidity flows can transport massive amounts of sediment across large distances with dramatic, long-lasting impacts on deep-sea benthic communities. The 2016 Mw 7.8 Kaikōura Earthquake triggered a canyon-flushing event in Kaikōura Canyon, New Zealand, which included significant submarine mass wasting, debris, and turbidity flows. This event provided an excellent opportunity to investigate the effects of large-scale natural disturbance on benthic ecosystems. Benthic meiofauna community structure before and after the event was analysed from a time series of sediment cores collected 10 years and 6 years before, and 10 weeks, 10 months, and 4 years after the disturbance. Immediately after the 2016 event abundances of all meiofauna dramatically decreased. Four years later the meiofauna community had recovered and was no longer distinguishable from the pre-event community. However, the nematode component of the community was similar, but not fully comparable to the pre-event community by 4 years after the disturbance. Community recovery was systematically correlated to changes in the physical characteristics of the habitat caused by the disturbance, using physical and biochemical variables derived from sediment cores, namely: sediment texture, organic matter, and pigment content. While these environmental variables explained relatively little of the overall variability in meiofauna community structure, particle size, food availability and quality were significant components. The minimum threshold time for the meiofauna community to fully recover was estimated to be between 3.9 and 4.7 years, although the predicted recovery time for the nematode community was longer, between 4.6 and 5 years. We consider the management implications of this study in comparison to the few studies of large-scale disturbances in the deep sea, in terms of their relevance to the efficacy of the marine reserve that encompasses Kaikōura Canyon, along with potential implications for our understandi…
format: application/pdf
format: text/html
creator: Katharine T. Bigham
creator: Daniel Leduc
creator: Ashley A. Rowden
creator: David A. Bowden
creator: Scott D. Nodder
creator: Alan R. Orpin
subject: Ecology
subject: Environmental Sciences
subject: Marine Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.17367
publisher: PeerJ Inc.
rights: © 2024 Bigham et al.
abstract: Turbidity flows can transport massive amounts of sediment across large distances with dramatic, long-lasting impacts on deep-sea benthic communities. The 2016 Mw 7.8 Kaikōura Earthquake triggered a canyon-flushing event in Kaikōura Canyon, New Zealand, which included significant submarine mass wasting, debris, and turbidity flows. This event provided an excellent opportunity to investigate the effects of large-scale natural disturbance on benthic ecosystems. Benthic meiofauna community structure before and after the event was analysed from a time series of sediment cores collected 10 years and 6 years before, and 10 weeks, 10 months, and 4 years after the disturbance. Immediately after the 2016 event abundances of all meiofauna dramatically decreased. Four years later the meiofauna community had recovered and was no longer distinguishable from the pre-event community. However, the nematode component of the community was similar, but not fully comparable to the pre-event community by 4 years after the disturbance. Community recovery was systematically correlated to changes in the physical characteristics of the habitat caused by the disturbance, using physical and biochemical variables derived from sediment cores, namely: sediment texture, organic matter, and pigment content. While these environmental variables explained relatively little of the overall variability in meiofauna community structure, particle size, food availability and quality were significant components. The minimum threshold time for the meiofauna community to fully recover was estimated to be between 3.9 and 4.7 years, although the predicted recovery time for the nematode community was longer, between 4.6 and 5 years. We consider the management implications of this study in comparison to the few studies of large-scale disturbances in the deep sea, in terms of their relevance to the efficacy of the marine reserve that encompasses Kaikōura Canyon, along with potential implications for our understandi…
bibliographic citation: Bigham et al. (2024) Recovery of deep-sea meiofauna community in Kaikōura Canyon following an earthquake-triggered turbidity flow. PeerJ 12:e17367 https://doi.org/10.7717/peerj.17367
date submitted: 2024-01-12
date accepted: 2024-04-18
issued: 2024-06-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bigham
  given name: Katharine T.
author list: Agent
  family name: Leduc
  given name: Daniel
author list: Agent
  family name: Rowden
  given name: Ashley A.
author list: Agent
  family name: Bowden
  given name: David A.
author list: Agent
  family name: Nodder
  given name: Scott D.
author list: Agent
  family name: Orpin
  given name: Alan R.
doi: 10.7717/peerj.17367
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-25
copyright: ©2024 Bigham et al.
attribution name: Bigham et al.

TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets
type: item
type: AcademicArticle
description: TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X’s predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user’s web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researcher…
format: application/pdf
format: text/html
creator: Vincent T. Metzger
creator: Daniel C. Cannon
creator: Jeremy J. Yang
creator: Stephen L. Mathias
creator: Cristian G. Bologa
creator: Anna Waller
creator: Stephan C. Schürer
creator: Dušica Vidović
creator: Keith J. Kelleher
creator: Timothy K. Sheils
creator: Lars Juhl Jensen
creator: Christophe G. Lambert
creator: Tudor I. Oprea
creator: Jeremy S. Edwards
subject: Bioinformatics
subject: Computational Biology
subject: Translational Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.17470
publisher: PeerJ Inc.
rights: © 2024 Metzger et al.
abstract: TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org. TIN-X uses natural language processing to identify disease and protein mentions within PubMed content using previously published tools for named entity recognition (NER) of gene/protein and disease names. Target data is obtained from the Target Central Resource Database (TCRD). Two important metrics, novelty and importance, are computed from this data and when plotted as log(importance) vs. log(novelty), aid the user in visually exploring the novelty of drug targets and their associated importance to diseases. TIN-X Version 3.0 has been significantly improved with an expanded dataset, modernized architecture including a REST API, and an improved user interface (UI). The dataset has been expanded to include not only PubMed publication titles and abstracts, but also full-text articles when available. This results in approximately 9-fold more target/disease associations compared to previous versions of TIN-X. Additionally, the TIN-X database containing this expanded dataset is now hosted in the cloud via Amazon RDS. Recent enhancements to the UI focuses on making it more intuitive for users to find diseases or drug targets of interest while providing a new, sortable table-view mode to accompany the existing plot-view mode. UI improvements also help the user browse the associated PubMed publications to explore and understand the basis of TIN-X’s predicted association between a specific disease and a target of interest. While implementing these upgrades, computational resources are balanced between the webserver and the user’s web browser to achieve adequate performance while accommodating the expanded dataset. Together, these advances aim to extend the duration that users can benefit from TIN-X while providing both an expanded dataset and new features that researcher…
bibliographic citation: Metzger et al. (2024) TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets. PeerJ 12:e17470 https://doi.org/10.7717/peerj.17470
date submitted: 2023-05-10
date accepted: 2024-05-06
issued: 2024-06-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Metzger
  given name: Vincent T.
author list: Agent
  family name: Cannon
  given name: Daniel C.
author list: Agent
  family name: Yang
  given name: Jeremy J.
author list: Agent
  family name: Mathias
  given name: Stephen L.
author list: Agent
  family name: Bologa
  given name: Cristian G.
author list: Agent
  family name: Waller
  given name: Anna
author list: Agent
  family name: Schürer
  given name: Stephan C.
author list: Agent
  family name: Vidović
  given name: Dušica
author list: Agent
  family name: Kelleher
  given name: Keith J.
author list: Agent
  family name: Sheils
  given name: Timothy K.
author list: Agent
  family name: Jensen
  given name: Lars Juhl
author list: Agent
  family name: Lambert
  given name: Christophe G.
author list: Agent
  family name: Oprea
  given name: Tudor I.
author list: Agent
  family name: Edwards
  given name: Jeremy S.
doi: 10.7717/peerj.17470
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-25
copyright: © 2024 Metzger et al.
attribution name: Metzger et al.

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