PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Pyrolyzed and unpyrolyzed residues enhance maize yield under varying rates of application and fertilization regimes
items: Modulation of the gut microbiota by processed food and natural food: evidence from the Siniperca chuatsi microbiome
items: https://peerj.com/articles/17525
items: Screening and verification of proteins that interact with the anthocyanin-related transcription factor PbrMYB114 in ‘Yuluxiang’ pear
items: Maize residue retention shapes soil microbial communities and co-occurrence networks upon freeze-thawing cycles
items: Ferrostatin-1 inhibits fibroblast fibrosis in keloid by inhibiting ferroptosis
items: Using linear measurements to diagnose the ecological habitat of Spinosaurus
items: Integrative systematic revision of the Montseny brook newt (Calotriton arnoldi), with the description of a new subspecies
items: When and where? Day-night alterations in wild boar space use captured by a generalized additive mixed model
items: Altered vaginal cervical microbiota diversity contributes to HPV-induced cervical cancer via inflammation regulation

Pyrolyzed and unpyrolyzed residues enhance maize yield under varying rates of application and fertilization regimes
type: item
type: AcademicArticle
description: Biochar is increasingly gaining popularity due to its extensive recommendation as a potential solution for addressing the concerns of food security and climate change in agroecosystems, with biochar application for increased carbon sequestration, enhanced soil fertility, improved soil health, and increased crop yield and quality. There have been multiple studies on crop yield utilizing various biochar types and application amounts; however, none have focused on the influence of diverse biochar types at various pyrolysis temperatures with different application amounts and the integration of fertilizer regimes in maize crops. Therefore, a two-year factorial field experiment was designed in a temperate Himalayan region of India (THRI) to evaluate the residual effect of different biochar on maize yield under different pyrolysis temperatures, various application rates and fertilizer regimes. The study included three factors viz., amendment type (factor 1), rate of application (factor 2) and fertilizer regime (factor 3). Amendment type included 7 treatments: No biochar- control (A1), apple biochar @ 400 °C pyrolysis temperature (A2), apple biochar @ 600 °C pyrolysis temperature (A3), apple residue biomass (A4), dal weed biochar @ 400 °C pyrolysis temperature (A5), dal weed biochar @ 600 °C pyrolysis temperatures (A6), and dal weed residue biomass (A7). The rate of application included 3 levels: Low (L- 1 t ha−1), medium (M- 2 t ha−1), and high (H- 3 t ha−1). At the same time, the fertilizer regimes included 2 treatments: No fertilizer (N) and recommended dose of fertilizer (F). The results revealed that among the various amendment type, rate of application and fertilizer regimes, the A3 amendment, H rate of application and F fertilizer regime gave the best maize growth and productivity outcome. Results revealed that among the different pyrolyzed residues used, the A3 amendment had the highest plant height (293.87 cm), most kernels cob−1 (535.75), highest soil plant analys…
format: application/pdf
format: text/html
creator: Owais Ali Wani
creator: Farida Akhter
creator: Shamal Shasang Kumar
creator: Raihana Habib Kanth
creator: Zahoor Ahmed Dar
creator: Subhash Babu
creator: Nazir Hussain
creator: Syed Sheraz Mahdi
creator: Abed Alataway
creator: Ahmed Z. Dewidar
creator: Mohamed A. Mattar
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.17513
publisher: PeerJ Inc.
rights: © 2024 Wani et al.
abstract: Biochar is increasingly gaining popularity due to its extensive recommendation as a potential solution for addressing the concerns of food security and climate change in agroecosystems, with biochar application for increased carbon sequestration, enhanced soil fertility, improved soil health, and increased crop yield and quality. There have been multiple studies on crop yield utilizing various biochar types and application amounts; however, none have focused on the influence of diverse biochar types at various pyrolysis temperatures with different application amounts and the integration of fertilizer regimes in maize crops. Therefore, a two-year factorial field experiment was designed in a temperate Himalayan region of India (THRI) to evaluate the residual effect of different biochar on maize yield under different pyrolysis temperatures, various application rates and fertilizer regimes. The study included three factors viz., amendment type (factor 1), rate of application (factor 2) and fertilizer regime (factor 3). Amendment type included 7 treatments: No biochar- control (A1), apple biochar @ 400 °C pyrolysis temperature (A2), apple biochar @ 600 °C pyrolysis temperature (A3), apple residue biomass (A4), dal weed biochar @ 400 °C pyrolysis temperature (A5), dal weed biochar @ 600 °C pyrolysis temperatures (A6), and dal weed residue biomass (A7). The rate of application included 3 levels: Low (L- 1 t ha−1), medium (M- 2 t ha−1), and high (H- 3 t ha−1). At the same time, the fertilizer regimes included 2 treatments: No fertilizer (N) and recommended dose of fertilizer (F). The results revealed that among the various amendment type, rate of application and fertilizer regimes, the A3 amendment, H rate of application and F fertilizer regime gave the best maize growth and productivity outcome. Results revealed that among the different pyrolyzed residues used, the A3 amendment had the highest plant height (293.87 cm), most kernels cob−1 (535.75), highest soil plant analys…
bibliographic citation: Wani et al. (2024) Pyrolyzed and unpyrolyzed residues enhance maize yield under varying rates of application and fertilization regimes. PeerJ 12:e17513 https://doi.org/10.7717/peerj.17513
date submitted: 2023-11-28
date accepted: 2024-05-13
issued: 2024-06-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wani
  given name: Owais Ali
author list: Agent
  family name: Akhter
  given name: Farida
author list: Agent
  family name: Kumar
  given name: Shamal Shasang
author list: Agent
  family name: Kanth
  given name: Raihana Habib
author list: Agent
  family name: Dar
  given name: Zahoor Ahmed
author list: Agent
  family name: Babu
  given name: Subhash
author list: Agent
  family name: Hussain
  given name: Nazir
author list: Agent
  family name: Mahdi
  given name: Syed Sheraz
author list: Agent
  family name: Alataway
  given name: Abed
author list: Agent
  family name: Dewidar
  given name: Ahmed Z.
author list: Agent
  family name: Mattar
  given name: Mohamed A.
doi: 10.7717/peerj.17513
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-14
copyright: ©2024 Wani et al.
attribution name: Wani et al.

Modulation of the gut microbiota by processed food and natural food: evidence from the Siniperca chuatsi microbiome
type: item
type: AcademicArticle
description: Habitual dietary changes have the potential to induce alterations in the host’s gut microbiota. Mandarin fish (Siniperca chuatsi), an aquatic vertebrate species with distinct feeding habits, were fed with natural feeds (NF) and artificial feeds (AF) to simulate the effects of natural and processed food consumption on host gut microbiota assemblages. The results showed that the alpha diversity index was reduced in the AF diet treatment, as lower abundance and diversity of the gut microbiota were observed, which could be attributed to the colonized microorganisms of the diet itself and the incorporation of plant-derived proteins or carbohydrates. The β-diversity analysis indicated that the two dietary treatments were associated with distinct bacterial communities. The AF diet had a significantly higher abundance of Bacteroidota and a lower abundance of Actinomycetota, Acidobacteriota, and Chloroflexota compared to the NF group. In addition, Bacteroidota was the biomarker in the gut of mandarin fish from the AF treatment, while Acidobacteriota was distinguished in the NF treatments. Additionally, the increased abundance of Bacteroidota in the AF diet group contributed to the improved fermentation and nutrient assimilation, as supported by the metabolic functional prediction and transcriptome verification. Overall, the present work used the mandarin fish as a vertebrate model to uncover the effects of habitual dietary changes on the evolution of the host microbiota, which may provide potential insights for the substitution of natural foods by processed foods in mammals.
format: application/pdf
format: text/html
creator: Hongyan Li
creator: Shuhui Niu
creator: Houjun Pan
creator: Guangjun Wang
creator: Jun Xie
creator: Jingjing Tian
creator: Kai Zhang
creator: Yun Xia
creator: Zhifei Li
creator: Ermeng Yu
creator: Wenping Xie
creator: Wangbao Gong
subject: Aquaculture, Fisheries and Fish Science
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.17520
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Habitual dietary changes have the potential to induce alterations in the host’s gut microbiota. Mandarin fish (Siniperca chuatsi), an aquatic vertebrate species with distinct feeding habits, were fed with natural feeds (NF) and artificial feeds (AF) to simulate the effects of natural and processed food consumption on host gut microbiota assemblages. The results showed that the alpha diversity index was reduced in the AF diet treatment, as lower abundance and diversity of the gut microbiota were observed, which could be attributed to the colonized microorganisms of the diet itself and the incorporation of plant-derived proteins or carbohydrates. The β-diversity analysis indicated that the two dietary treatments were associated with distinct bacterial communities. The AF diet had a significantly higher abundance of Bacteroidota and a lower abundance of Actinomycetota, Acidobacteriota, and Chloroflexota compared to the NF group. In addition, Bacteroidota was the biomarker in the gut of mandarin fish from the AF treatment, while Acidobacteriota was distinguished in the NF treatments. Additionally, the increased abundance of Bacteroidota in the AF diet group contributed to the improved fermentation and nutrient assimilation, as supported by the metabolic functional prediction and transcriptome verification. Overall, the present work used the mandarin fish as a vertebrate model to uncover the effects of habitual dietary changes on the evolution of the host microbiota, which may provide potential insights for the substitution of natural foods by processed foods in mammals.
bibliographic citation: Li et al. (2024) Modulation of the gut microbiota by processed food and natural food: evidence from the Siniperca chuatsi microbiome. PeerJ 12:e17520 https://doi.org/10.7717/peerj.17520
date submitted: 2024-01-17
date accepted: 2024-05-15
issued: 2024-06-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Hongyan
author list: Agent
  family name: Niu
  given name: Shuhui
author list: Agent
  family name: Pan
  given name: Houjun
author list: Agent
  family name: Wang
  given name: Guangjun
author list: Agent
  family name: Xie
  given name: Jun
author list: Agent
  family name: Tian
  given name: Jingjing
author list: Agent
  family name: Zhang
  given name: Kai
author list: Agent
  family name: Xia
  given name: Yun
author list: Agent
  family name: Li
  given name: Zhifei
author list: Agent
  family name: Yu
  given name: Ermeng
author list: Agent
  family name: Xie
  given name: Wenping
author list: Agent
  family name: Gong
  given name: Wangbao
doi: 10.7717/peerj.17520
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-14
copyright: © 2024 Li et al.
attribution name: Li et al.

https://peerj.com/articles/17525
type: item
type: AcademicArticle
title: Effects of combined aerobic and resistance training on glycemic control, blood pressure, inflammation, cardiorespiratory fitness and quality of life in patients with type 2 diabetes and overweight/obesity: a systematic review and meta-analysis
description: Background Structured aerobic or resistance training alone seems to be a beneficial tool for improving glucose homeostasis, chronic systemic inflammation, resting cardiovascular function, and mental health in people with obesity and type 2 diabetes mellitus (T2DM). The aim of the present study was to synthesize the available data on the effectiveness of combined aerobic and resistance training (CART) on glycemic control, blood pressure, inflammation, cardiorespiratory fitness (CRF), and quality of life (QoL) in overweight and obese individuals with T2DM. Methods A database search was carried out in PubMed, Web of Science, Scopus, Science Direct, Cochrane Library, and Google Scholar from inception up to May 2023. The Cochrane risk of bias tool was used to assess eligible studies, and the GRADE method to evaluate the reliability of evidence. A random-effects model was used, and data were analyzed using standardized mean differences and 95% confidence intervals. The study protocol was registered in the International Prospective Register of Systematic Reviews (ID: CRD42022355612). Results A total of 21,612 studies were retrieved; 20 studies were included, and data were extracted from 1,192 participants (mean age: 57 ± 7 years) who met the eligibility criteria. CART demonstrated significant improvements in body mass index, glycated hemoglobin, systolic and diastolic blood pressure, C-reactive protein, tumor necrosis factor-alpha, interleukin-6, CRF, and QoL compared to ST. These findings highlight the significance of exercise interventions such as CART as essential elements within comprehensive diabetes management strategies, ultimately enhancing overall health outcomes in individuals with T2DM and overweight/obesity.No differences were found in resting heart rate between CART and ST. An uncertain risk of bias and poor quality of evidence were found among the eligible studies. Conclusion These outcomes show clear evidence considering the positive role of CART in inducing…
format: application/pdf
format: text/html
creator: Sameer Badri AL-Mhanna
creator: Alexios Batrakoulis
creator: Wan Syaheedah Wan Ghazali
creator: Mahaneem Mohamed
creator: Abdulaziz Aldayel
creator: Maha H. Alhussain
creator: Hafeez Abiola Afolabi
creator: Yusuf Wada
creator: Mehmet Gülü
creator: Safaa Elkholi
creator: Bishir Daku Abubakar
creator: Daniel Rojas-Valverde
subject: Diabetes and Endocrinology
subject: Public Health
subject: Obesity
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.17525
publisher: PeerJ Inc.
rights: © 2024 AL-Mhanna et al.
abstract: Background Structured aerobic or resistance training alone seems to be a beneficial tool for improving glucose homeostasis, chronic systemic inflammation, resting cardiovascular function, and mental health in people with obesity and type 2 diabetes mellitus (T2DM). The aim of the present study was to synthesize the available data on the effectiveness of combined aerobic and resistance training (CART) on glycemic control, blood pressure, inflammation, cardiorespiratory fitness (CRF), and quality of life (QoL) in overweight and obese individuals with T2DM. Methods A database search was carried out in PubMed, Web of Science, Scopus, Science Direct, Cochrane Library, and Google Scholar from inception up to May 2023. The Cochrane risk of bias tool was used to assess eligible studies, and the GRADE method to evaluate the reliability of evidence. A random-effects model was used, and data were analyzed using standardized mean differences and 95% confidence intervals. The study protocol was registered in the International Prospective Register of Systematic Reviews (ID: CRD42022355612). Results A total of 21,612 studies were retrieved; 20 studies were included, and data were extracted from 1,192 participants (mean age: 57 ± 7 years) who met the eligibility criteria. CART demonstrated significant improvements in body mass index, glycated hemoglobin, systolic and diastolic blood pressure, C-reactive protein, tumor necrosis factor-alpha, interleukin-6, CRF, and QoL compared to ST. These findings highlight the significance of exercise interventions such as CART as essential elements within comprehensive diabetes management strategies, ultimately enhancing overall health outcomes in individuals with T2DM and overweight/obesity.No differences were found in resting heart rate between CART and ST. An uncertain risk of bias and poor quality of evidence were found among the eligible studies. Conclusion These outcomes show clear evidence considering the positive role of CART in inducing…
bibliographic citation: AL-Mhanna et al. (2024) Effects of combined aerobic and resistance training on glycemic control, blood pressure, inflammation, cardiorespiratory fitness and quality of life in patients with type 2 diabetes and overweight/obesity: a systematic review and meta-analysis. PeerJ 12:e17525 https://doi.org/10.7717/peerj.17525
date submitted: 2024-01-18
date accepted: 2024-05-16
issued: 2024-06-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: AL-Mhanna
  given name: Sameer Badri
author list: Agent
  family name: Batrakoulis
  given name: Alexios
author list: Agent
  family name: Wan Ghazali
  given name: Wan Syaheedah
author list: Agent
  family name: Mohamed
  given name: Mahaneem
author list: Agent
  family name: Aldayel
  given name: Abdulaziz
author list: Agent
  family name: Alhussain
  given name: Maha H.
author list: Agent
  family name: Afolabi
  given name: Hafeez Abiola
author list: Agent
  family name: Wada
  given name: Yusuf
author list: Agent
  family name: Gülü
  given name: Mehmet
author list: Agent
  family name: Elkholi
  given name: Safaa
author list: Agent
  family name: Abubakar
  given name: Bishir Daku
author list: Agent
  family name: Rojas-Valverde
  given name: Daniel
doi: 10.7717/peerj.17525
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-14
copyright: © 2024 AL-Mhanna et al.
attribution name: AL-Mhanna et al.

Screening and verification of proteins that interact with the anthocyanin-related transcription factor PbrMYB114 in ‘Yuluxiang’ pear
type: item
type: AcademicArticle
description: Despite extensive research highlighting the pivotal role of MYB transcription factors in regulating anthocyanin biosynthesis, the interactive regulatory network involving these MYB factors in pear fruits remains inadequately characterized. In this study, the anthocyanin-regulatory gene PbrMYB114 was successfully cloned from ‘Yuluxiang’ pear (Pyrus bretschneideri) fruits, and its influence on anthocyanin accumulation was confirmed through transient expression assays. Specifically, the co-transformation of PbrMYB114 with its partner PbrbHLH3 in pears served to validate the functional role of PbrMYB114. Subsequently, PbrMYB114 was employed as bait in a yeast two-hybrid screening assay, using a ‘Yuluxiang’ pear protein library, which led to the identification of 25 interacting proteins. Further validation of the interactions between PbrMYB114 and PbrMT2/PbrMT3 was conducted. Investigations into the role of PbrMT2 and PbrMT3 in ‘Duli’ seedlings (Pyrus betulaefolia) revealed their potential to enhance anthocyanin accumulation. The outcomes of these studies provide novel insights into the protein network that regulates pear anthocyanin biosynthesis, particularly the functional interactions among PbrMYB114 and associated proteins.
format: application/pdf
format: text/html
creator: Qingwei Liu
creator: Ge Gao
creator: Chen Shang
creator: Tong Li
creator: Yadong Wang
creator: Liulin Li
creator: Xinxin Feng
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.17540
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Despite extensive research highlighting the pivotal role of MYB transcription factors in regulating anthocyanin biosynthesis, the interactive regulatory network involving these MYB factors in pear fruits remains inadequately characterized. In this study, the anthocyanin-regulatory gene PbrMYB114 was successfully cloned from ‘Yuluxiang’ pear (Pyrus bretschneideri) fruits, and its influence on anthocyanin accumulation was confirmed through transient expression assays. Specifically, the co-transformation of PbrMYB114 with its partner PbrbHLH3 in pears served to validate the functional role of PbrMYB114. Subsequently, PbrMYB114 was employed as bait in a yeast two-hybrid screening assay, using a ‘Yuluxiang’ pear protein library, which led to the identification of 25 interacting proteins. Further validation of the interactions between PbrMYB114 and PbrMT2/PbrMT3 was conducted. Investigations into the role of PbrMT2 and PbrMT3 in ‘Duli’ seedlings (Pyrus betulaefolia) revealed their potential to enhance anthocyanin accumulation. The outcomes of these studies provide novel insights into the protein network that regulates pear anthocyanin biosynthesis, particularly the functional interactions among PbrMYB114 and associated proteins.
bibliographic citation: Liu et al. (2024) Screening and verification of proteins that interact with the anthocyanin-related transcription factor PbrMYB114 in ‘Yuluxiang’ pear. PeerJ 12:e17540 https://doi.org/10.7717/peerj.17540
date submitted: 2024-02-14
date accepted: 2024-05-19
issued: 2024-06-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Qingwei
author list: Agent
  family name: Gao
  given name: Ge
author list: Agent
  family name: Shang
  given name: Chen
author list: Agent
  family name: Li
  given name: Tong
author list: Agent
  family name: Wang
  given name: Yadong
author list: Agent
  family name: Li
  given name: Liulin
author list: Agent
  family name: Feng
  given name: Xinxin
doi: 10.7717/peerj.17540
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-14
copyright: © 2024 Liu et al.
attribution name: Liu et al.

Maize residue retention shapes soil microbial communities and co-occurrence networks upon freeze-thawing cycles
type: item
type: AcademicArticle
description: Maize residue retention is an effective agricultural practice for improving soil fertility in black soil region, where suffered from long freezing-thawing periods and intense freeze-thawing (FT) cycles. However, very few studies have examined the influence of maize residue retention on soil microbial communities under FT cycles. We investigated the response of soil microbial communities and co-occurrence networks to maize residue retention at different FT intensities over 12 cycles using a microcosm experiment conditioned in a temperature incubator. Our results indicated that maize residue retention induced dramatic shifts in soil archaeal, bacterial and fungal communities towards copiotroph-dominated communities. Maize residue retention consistently reduced soil fungal richness across all cycles, but this effect was weaker for archaea and bacteria. Normalized stochastic ratio analysis revealed that maize residue retention significantly enhanced the deterministic process of archaeal, bacterial and fungal communities. Although FT intensity significantly impacted soil respiration, it did not induce profound changes in soil microbial diversity and community composition. Co-occurrence network analysis revealed that maize residue retention simplified prokaryotic network, while did not impact fungal network complexity. The network robustness index suggested that maize residue retention enhanced the fungal network stability, but reduced prokaryotic network stability. Moreover, the fungal network in severe FT treatment harbored the most abundant keystone taxa, mainly being cold-adapted fungi. By identifying modules in networks, we observed that prokaryotic Module #1 and fungal Module #3 were enhanced by maize residue retention and contributed greatly to soil quality. Together, our results showed that maize residue retention exerted stronger influence on soil microbial communities and co-occurrence network patterns than FT intensity and highlighted the potential of microbial…
format: application/pdf
format: text/html
creator: Yang Yu
creator: Quankuan Guo
creator: Shuhan Zhang
creator: Yupeng Guan
creator: Nana Jiang
creator: Yang Zhang
creator: Rong Mao
creator: Keyu Bai
creator: Salimjan Buriyev
creator: Nuriddin Samatov
creator: Ximei Zhang
creator: Wei Yang
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.17543
publisher: PeerJ Inc.
rights: © 2024 Yu et al.
abstract: Maize residue retention is an effective agricultural practice for improving soil fertility in black soil region, where suffered from long freezing-thawing periods and intense freeze-thawing (FT) cycles. However, very few studies have examined the influence of maize residue retention on soil microbial communities under FT cycles. We investigated the response of soil microbial communities and co-occurrence networks to maize residue retention at different FT intensities over 12 cycles using a microcosm experiment conditioned in a temperature incubator. Our results indicated that maize residue retention induced dramatic shifts in soil archaeal, bacterial and fungal communities towards copiotroph-dominated communities. Maize residue retention consistently reduced soil fungal richness across all cycles, but this effect was weaker for archaea and bacteria. Normalized stochastic ratio analysis revealed that maize residue retention significantly enhanced the deterministic process of archaeal, bacterial and fungal communities. Although FT intensity significantly impacted soil respiration, it did not induce profound changes in soil microbial diversity and community composition. Co-occurrence network analysis revealed that maize residue retention simplified prokaryotic network, while did not impact fungal network complexity. The network robustness index suggested that maize residue retention enhanced the fungal network stability, but reduced prokaryotic network stability. Moreover, the fungal network in severe FT treatment harbored the most abundant keystone taxa, mainly being cold-adapted fungi. By identifying modules in networks, we observed that prokaryotic Module #1 and fungal Module #3 were enhanced by maize residue retention and contributed greatly to soil quality. Together, our results showed that maize residue retention exerted stronger influence on soil microbial communities and co-occurrence network patterns than FT intensity and highlighted the potential of microbial…
bibliographic citation: Yu et al. (2024) Maize residue retention shapes soil microbial communities and co-occurrence networks upon freeze-thawing cycles. PeerJ 12:e17543 https://doi.org/10.7717/peerj.17543
date submitted: 2024-01-30
date accepted: 2024-05-19
issued: 2024-06-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Yang
author list: Agent
  family name: Guo
  given name: Quankuan
author list: Agent
  family name: Zhang
  given name: Shuhan
author list: Agent
  family name: Guan
  given name: Yupeng
author list: Agent
  family name: Jiang
  given name: Nana
author list: Agent
  family name: Zhang
  given name: Yang
author list: Agent
  family name: Mao
  given name: Rong
author list: Agent
  family name: Bai
  given name: Keyu
author list: Agent
  family name: Buriyev
  given name: Salimjan
author list: Agent
  family name: Samatov
  given name: Nuriddin
author list: Agent
  family name: Zhang
  given name: Ximei
author list: Agent
  family name: Yang
  given name: Wei
doi: 10.7717/peerj.17543
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-14
copyright: ©2024 Yu et al.
attribution name: Yu et al.

Ferrostatin-1 inhibits fibroblast fibrosis in keloid by inhibiting ferroptosis
type: item
type: AcademicArticle
description: Background Keloid is a chronic proliferative fibrotic disease caused by abnormal fibroblasts proliferation and excessive extracellular matrix (ECM) production. Numerous fibrotic disorders are significantly influenced by ferroptosis, and targeting ferroptosis can effectively mitigate fibrosis development. This study aimed to investigate the role and mechanism of ferroptosis in keloid development. Methods Keloid tissues from keloid patients and normal skin tissues from healthy controls were collected. Iron content, lipid peroxidation (LPO) level, and the mRNA and protein expression of ferroptosis-related genes including solute carrier family 7 member 11 (SLC7A11), glutathione peroxidase 4 (GPX4), transferrin receptor (TFRC), and nuclear factor erythroid 2-related factor 2 (Nrf2) were determined. Mitochondrial morphology was observed using transmission electron microscopy (TEM). Keloid fibroblasts (KFs) were isolated from keloid tissues, and treated with ferroptosis inhibitor ferrostatin-1 (fer-1) or ferroptosis activator erastin. Iron content, ferroptosis-related marker levels, LPO level, mitochondrial membrane potential, ATP content, and mitochondrial morphology in KFs were detected. Furthermore, the protein levels of α-smooth muscle actin (α-SMA), collagen I, and collagen III were measured to investigate whether ferroptosis affect fibrosis in KFs. Results We found that iron content and LPO level were substantially elevated in keloid tissues and KFs. SLC7A11, GPX4, and Nrf2 were downregulated and TFRC was upregulated in keloid tissues and KFs. Mitochondria in keloid tissues and KFs exhibited ferroptosis-related pathology. Fer-1 treatment reduced iron content, restrained ferroptosis and mitochondrial dysfunction in KFs, Moreover, ferrostatin-1 restrained the protein expression of α-SMA, collagen I, and collagen III in KFs. Whereas erastin treatment showed the opposite results. Conclusion Ferroptosis exists in keloid. Ferrostatin-1 restrained ECM deposition and fibrosi…
format: application/pdf
format: text/html
creator: Liu Yang
creator: Xiuli Li
creator: Yanli Wang
subject: Biochemistry
subject: Cell Biology
subject: Dermatology
description: doi:10.7717/peerj.17551
publisher: PeerJ Inc.
rights: © 2024 Yang et al.
abstract: Background Keloid is a chronic proliferative fibrotic disease caused by abnormal fibroblasts proliferation and excessive extracellular matrix (ECM) production. Numerous fibrotic disorders are significantly influenced by ferroptosis, and targeting ferroptosis can effectively mitigate fibrosis development. This study aimed to investigate the role and mechanism of ferroptosis in keloid development. Methods Keloid tissues from keloid patients and normal skin tissues from healthy controls were collected. Iron content, lipid peroxidation (LPO) level, and the mRNA and protein expression of ferroptosis-related genes including solute carrier family 7 member 11 (SLC7A11), glutathione peroxidase 4 (GPX4), transferrin receptor (TFRC), and nuclear factor erythroid 2-related factor 2 (Nrf2) were determined. Mitochondrial morphology was observed using transmission electron microscopy (TEM). Keloid fibroblasts (KFs) were isolated from keloid tissues, and treated with ferroptosis inhibitor ferrostatin-1 (fer-1) or ferroptosis activator erastin. Iron content, ferroptosis-related marker levels, LPO level, mitochondrial membrane potential, ATP content, and mitochondrial morphology in KFs were detected. Furthermore, the protein levels of α-smooth muscle actin (α-SMA), collagen I, and collagen III were measured to investigate whether ferroptosis affect fibrosis in KFs. Results We found that iron content and LPO level were substantially elevated in keloid tissues and KFs. SLC7A11, GPX4, and Nrf2 were downregulated and TFRC was upregulated in keloid tissues and KFs. Mitochondria in keloid tissues and KFs exhibited ferroptosis-related pathology. Fer-1 treatment reduced iron content, restrained ferroptosis and mitochondrial dysfunction in KFs, Moreover, ferrostatin-1 restrained the protein expression of α-SMA, collagen I, and collagen III in KFs. Whereas erastin treatment showed the opposite results. Conclusion Ferroptosis exists in keloid. Ferrostatin-1 restrained ECM deposition and fibrosi…
bibliographic citation: Yang et al. (2024) Ferrostatin-1 inhibits fibroblast fibrosis in keloid by inhibiting ferroptosis. PeerJ 12:e17551 https://doi.org/10.7717/peerj.17551
date submitted: 2024-02-02
date accepted: 2024-05-20
issued: 2024-06-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Liu
author list: Agent
  family name: Li
  given name: Xiuli
author list: Agent
  family name: Wang
  given name: Yanli
doi: 10.7717/peerj.17551
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-14
copyright: ©2024 Yang et al.
attribution name: Yang et al.

Using linear measurements to diagnose the ecological habitat of Spinosaurus
type: item
type: AcademicArticle
description: Much of the ecological discourse surrounding the polarising theropod Spinosaurus has centred on qualitative discussions. Using a quantitative multivariate data analytical approach on size-adjusted linear measurements of the skull, we examine patterns in skull shape across a range of sauropsid clades and three ecological realms (terrestrial, semi-aquatic, and aquatic). We utilise cluster analyses to identify emergent properties of the data which associate properties of skull shape with ecological realm occupancy. Results revealed terrestrial ecologies to be significantly distinct from both semi- and fully aquatic ecologies, the latter two were not significantly different. Spinosaurids (including Spinosaurus) plotted away from theropods in morphospace and close to both marine taxa and wading birds. The position of nares and the degree of rostral elongation had the greatest effect on categorisation. Comparisons of supervised (k-means) and unsupervised clustering demonstrated categorising taxa into three groups (ecological realms) was inappropriate and suggested instead that cluster division is based on morphological adaptations to feeding on aquatic versus terrestrial food items. The relative position of the nares in longirostrine taxa is associated with which skull bones are elongated. Rostral elongation is observed by either elongating the maxilla and the premaxilla or by elongating the maxilla only. This results in the nares positioned towards the orbits or towards the anterior end of the rostrum respectively, with implications on available feeding methods. Spinosaurids, especially Spinosaurus, show elongation in the maxilla-premaxilla complex, achieving similar functional outcomes to elongation of the premaxilla seen in birds, particularly large-bodied piscivorous taxa. Such a skull construction would bolster “stand-and-wait” predation of aquatic prey to a greater extent than serving other proposed feeding methods.
format: application/pdf
format: text/html
creator: Sean Smart
creator: Manabu Sakamoto
subject: Ecology
subject: Paleontology
subject: Zoology
subject: Data Science
description: doi:10.7717/peerj.17544
publisher: PeerJ Inc.
rights: © 2024 Smart and Sakamoto
abstract: Much of the ecological discourse surrounding the polarising theropod Spinosaurus has centred on qualitative discussions. Using a quantitative multivariate data analytical approach on size-adjusted linear measurements of the skull, we examine patterns in skull shape across a range of sauropsid clades and three ecological realms (terrestrial, semi-aquatic, and aquatic). We utilise cluster analyses to identify emergent properties of the data which associate properties of skull shape with ecological realm occupancy. Results revealed terrestrial ecologies to be significantly distinct from both semi- and fully aquatic ecologies, the latter two were not significantly different. Spinosaurids (including Spinosaurus) plotted away from theropods in morphospace and close to both marine taxa and wading birds. The position of nares and the degree of rostral elongation had the greatest effect on categorisation. Comparisons of supervised (k-means) and unsupervised clustering demonstrated categorising taxa into three groups (ecological realms) was inappropriate and suggested instead that cluster division is based on morphological adaptations to feeding on aquatic versus terrestrial food items. The relative position of the nares in longirostrine taxa is associated with which skull bones are elongated. Rostral elongation is observed by either elongating the maxilla and the premaxilla or by elongating the maxilla only. This results in the nares positioned towards the orbits or towards the anterior end of the rostrum respectively, with implications on available feeding methods. Spinosaurids, especially Spinosaurus, show elongation in the maxilla-premaxilla complex, achieving similar functional outcomes to elongation of the premaxilla seen in birds, particularly large-bodied piscivorous taxa. Such a skull construction would bolster “stand-and-wait” predation of aquatic prey to a greater extent than serving other proposed feeding methods.
bibliographic citation: Smart et al. (2024) Using linear measurements to diagnose the ecological habitat of Spinosaurus. PeerJ 12:e17544 https://doi.org/10.7717/peerj.17544
date submitted: 2023-10-17
date accepted: 2024-05-19
issued: 2024-06-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smart
  given name: Sean
author list: Agent
  family name: Sakamoto
  given name: Manabu
doi: 10.7717/peerj.17544
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-13
copyright: © 2024 Smart and Sakamoto
attribution name: Smart and Sakamoto

Integrative systematic revision of the Montseny brook newt (Calotriton arnoldi), with the description of a new subspecies
type: item
type: AcademicArticle
description: The Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small, isolated massif in northeast Spain, is considered the only Critically Endangered urodele in Europe. Its restricted range is divided by a deep valley that acts as an impassable barrier to dispersal, separating two isolated metapopulations (Western and Eastern) that correspond to independent lineages with different evolutionary trajectories, based on genetic and genomic data. Here, we address the ecological differentiation between lineages and discuss its potential effect on the phenotypic distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanus ssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described taxa.
format: application/pdf
format: text/html
creator: Adrián Talavera
creator: Emilio Valbuena-Ureña
creator: Bernat Burriel-Carranza
creator: Gabriel Mochales-Riaño
creator: Dean C. Adams
creator: Fèlix Amat
creator: Francesc Carbonell
creator: Salvador Carranza
subject: Conservation Biology
subject: Genomics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.17550
publisher: PeerJ Inc.
rights: © 2024 Talavera et al.
abstract: The Montseny brook newt (Calotriton arnoldi), a glacial relict endemic to a small, isolated massif in northeast Spain, is considered the only Critically Endangered urodele in Europe. Its restricted range is divided by a deep valley that acts as an impassable barrier to dispersal, separating two isolated metapopulations (Western and Eastern) that correspond to independent lineages with different evolutionary trajectories, based on genetic and genomic data. Here, we address the ecological differentiation between lineages and discuss its potential effect on the phenotypic distinctness of each lineage. Based on multiple lines of evidence, we formally describe the Western Montseny brook newt as a new subspecies: Calotriton arnoldi laietanus ssp. nov. Finally, our study underscores the importance of considering taxonomic progress in the conservation policies of endangered species, ensuring appropriate management and protection of the newly described taxa.
bibliographic citation: Talavera et al. (2024) Integrative systematic revision of the Montseny brook newt (Calotriton arnoldi), with the description of a new subspecies. PeerJ 12:e17550 https://doi.org/10.7717/peerj.17550
date submitted: 2024-01-30
date accepted: 2024-05-20
issued: 2024-06-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Talavera
  given name: Adrián
author list: Agent
  family name: Valbuena-Ureña
  given name: Emilio
author list: Agent
  family name: Burriel-Carranza
  given name: Bernat
author list: Agent
  family name: Mochales-Riaño
  given name: Gabriel
author list: Agent
  family name: Adams
  given name: Dean C.
author list: Agent
  family name: Amat
  given name: Fèlix
author list: Agent
  family name: Carbonell
  given name: Francesc
author list: Agent
  family name: Carranza
  given name: Salvador
doi: 10.7717/peerj.17550
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-13
copyright: © 2024 Talavera et al.
attribution name: Talavera et al.

When and where? Day-night alterations in wild boar space use captured by a generalized additive mixed model
type: item
type: AcademicArticle
description: Wild boar (Sus scrofa), an abundant species across Europe, is often subjected to management in agro-ecosystems in order to control population size, or to scare them away from agricultural fields to safeguard crop yields. Wild boar management can benefit from a better understanding on changes in its space use across the diel cycle (i.e., diel space use) in relation to variable hunting pressures or other factors. Here, we estimate wild boar diel space use in an agro-ecosystem in central Belgium during four consecutive “growing seasons” (i.e., April–September). To achieve this, we fit generalized additive mixed models (GAMMs) to camera trap data of wild boar aggregated over 1-h periods. Our results reveal that wild boar are predominantly nocturnal in all of the hunting management zones in Meerdaal, with activity peaks around sunrise and sunset. Hunting events in our study area tend to take place around sunrise and sunset, while non-lethal human activities occur during sunlight hours. Our GAMM reveals that wild boar use different areas throughout the diel cycle. During the day, wild boar utilized areas in the centre of the forest, possibly to avoid human activities during daytime. During the night, they foraged near (or in) agricultural fields. A post hoc comparison of space use maps of wild boar in Meerdaal revealed that their diurnal and nocturnal space use were uncorrelated. We did not find sufficient evidence to prove that wild boar spatiotemporally avoid hunters. Finally, our work reveals the potential of GAMMs to model variation in space across 24-h periods from camera trap data, an application that will be useful to address a range of ecological questions. However, to test the robustness of this approach we advise that it should be compared against telemetry-based methods to derive diel space use.
format: application/pdf
format: text/html
creator: Martijn Bollen
creator: Jim Casaer
creator: Thomas Neyens
creator: Natalie Beenaerts
subject: Animal Behavior
subject: Ecology
subject: Data Science
subject: Population Biology
description: doi:10.7717/peerj.17390
publisher: PeerJ Inc.
rights: © 2024 Bollen et al.
abstract: Wild boar (Sus scrofa), an abundant species across Europe, is often subjected to management in agro-ecosystems in order to control population size, or to scare them away from agricultural fields to safeguard crop yields. Wild boar management can benefit from a better understanding on changes in its space use across the diel cycle (i.e., diel space use) in relation to variable hunting pressures or other factors. Here, we estimate wild boar diel space use in an agro-ecosystem in central Belgium during four consecutive “growing seasons” (i.e., April–September). To achieve this, we fit generalized additive mixed models (GAMMs) to camera trap data of wild boar aggregated over 1-h periods. Our results reveal that wild boar are predominantly nocturnal in all of the hunting management zones in Meerdaal, with activity peaks around sunrise and sunset. Hunting events in our study area tend to take place around sunrise and sunset, while non-lethal human activities occur during sunlight hours. Our GAMM reveals that wild boar use different areas throughout the diel cycle. During the day, wild boar utilized areas in the centre of the forest, possibly to avoid human activities during daytime. During the night, they foraged near (or in) agricultural fields. A post hoc comparison of space use maps of wild boar in Meerdaal revealed that their diurnal and nocturnal space use were uncorrelated. We did not find sufficient evidence to prove that wild boar spatiotemporally avoid hunters. Finally, our work reveals the potential of GAMMs to model variation in space across 24-h periods from camera trap data, an application that will be useful to address a range of ecological questions. However, to test the robustness of this approach we advise that it should be compared against telemetry-based methods to derive diel space use.
bibliographic citation: Bollen et al. (2024) When and where? Day-night alterations in wild boar space use captured by a generalized additive mixed model. PeerJ 12:e17390 https://doi.org/10.7717/peerj.17390
date submitted: 2023-09-28
date accepted: 2024-04-23
issued: 2024-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bollen
  given name: Martijn
author list: Agent
  family name: Casaer
  given name: Jim
author list: Agent
  family name: Neyens
  given name: Thomas
author list: Agent
  family name: Beenaerts
  given name: Natalie
doi: 10.7717/peerj.17390
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-12
copyright: ©2024 Bollen et al.
attribution name: Bollen et al.

Altered vaginal cervical microbiota diversity contributes to HPV-induced cervical cancer via inflammation regulation
type: item
type: AcademicArticle
description: Background Cancer has surpassed infectious diseases and heart ailments, taking the top spot in the disease hierarchy. Cervical cancer is a significant concern for women due to high incidence and mortality rates, linked to the human papillomavirus (HPV). HPV infection leads to precancerous lesions progressing to cervical cancer. The cervix’s external os, near the vagina, hosts various microorganisms. Evidence points to the link between vaginal microbiota and HPV-induced cervical cancer. Cervical cancer onset aligns with an imbalanced Th1/Th2 immune response, but the role of vaginal microbiota in modulating this imbalance is unclear. Methods In this study, we collected vaginal samples from 99 HPV-infected patients across varying degrees of lesions, alongside control groups. These samples underwent bacterial DNA sequencing. Additionally, we employed Elisa kits to quantify the protein expression levels of Th1/Th2 cytokines IL2, IL12, IL5, IL13, and TNFa within the centrifuged supernatant of vaginal-cervical secretions from diverse research subjects. Subsequently, correlation analyses were conducted between inflammatory factors and vaginal microbiota. Results Our findings highlighted a correlation between decreased Lactobacillus and increased Gardenerella presence with HPV-induced cervical cancer. Functionally, our predictive analysis revealed the predominant enrichment of the ABC transporter within the vaginal microbiota of cervical cancer patients. Notably, these microbiota alterations exhibited correlations with the production of Th1/Th2 cytokines, which are intimately tied to tumor immunity. Conclusions This study suggests the potential involvement of vaginal microbiota in the progression of HPV-induced cervical cancer through Th1/Th2 cytokine regulation. This novel insight offers a fresh perspective for early cervical cancer diagnosis and future prevention strategies.
format: application/pdf
format: text/html
creator: Yiheng Yang
creator: Jufan Zhu
creator: Renqian Feng
creator: Mengfei Han
creator: Fenghua Chen
creator: Yan Hu
subject: Bioinformatics
subject: Gynecology and Obstetrics
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.17415
publisher: PeerJ Inc.
rights: © 2024 Yang et al.
abstract: Background Cancer has surpassed infectious diseases and heart ailments, taking the top spot in the disease hierarchy. Cervical cancer is a significant concern for women due to high incidence and mortality rates, linked to the human papillomavirus (HPV). HPV infection leads to precancerous lesions progressing to cervical cancer. The cervix’s external os, near the vagina, hosts various microorganisms. Evidence points to the link between vaginal microbiota and HPV-induced cervical cancer. Cervical cancer onset aligns with an imbalanced Th1/Th2 immune response, but the role of vaginal microbiota in modulating this imbalance is unclear. Methods In this study, we collected vaginal samples from 99 HPV-infected patients across varying degrees of lesions, alongside control groups. These samples underwent bacterial DNA sequencing. Additionally, we employed Elisa kits to quantify the protein expression levels of Th1/Th2 cytokines IL2, IL12, IL5, IL13, and TNFa within the centrifuged supernatant of vaginal-cervical secretions from diverse research subjects. Subsequently, correlation analyses were conducted between inflammatory factors and vaginal microbiota. Results Our findings highlighted a correlation between decreased Lactobacillus and increased Gardenerella presence with HPV-induced cervical cancer. Functionally, our predictive analysis revealed the predominant enrichment of the ABC transporter within the vaginal microbiota of cervical cancer patients. Notably, these microbiota alterations exhibited correlations with the production of Th1/Th2 cytokines, which are intimately tied to tumor immunity. Conclusions This study suggests the potential involvement of vaginal microbiota in the progression of HPV-induced cervical cancer through Th1/Th2 cytokine regulation. This novel insight offers a fresh perspective for early cervical cancer diagnosis and future prevention strategies.
bibliographic citation: Yang et al. (2024) Altered vaginal cervical microbiota diversity contributes to HPV-induced cervical cancer via inflammation regulation. PeerJ 12:e17415 https://doi.org/10.7717/peerj.17415
date submitted: 2023-11-03
date accepted: 2024-04-28
issued: 2024-06-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Yiheng
author list: Agent
  family name: Zhu
  given name: Jufan
author list: Agent
  family name: Feng
  given name: Renqian
author list: Agent
  family name: Han
  given name: Mengfei
author list: Agent
  family name: Chen
  given name: Fenghua
author list: Agent
  family name: Hu
  given name: Yan
doi: 10.7717/peerj.17415
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-06-12
copyright: © 2024 Yang et al.
attribution name: Yang et al.

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