PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Traumatic spinal cord injury: identifying independent risk factors and predictive model development for symptomatic urinary tract infections
items: Synchrony on the reef: how environmental factors shape coral spawning patterns in Acropora corals in the Maldives
items: A hundred species, mostly new—first assessment of ribbon worm diversity and distribution in Oman
items: Alleviation of dextran sulfate sodium (DSS)-induced colitis in mice through the antioxidative effects of muscone via the MyD88/p38 MAPK signalling pathway
items: Unveiling the role of gasdermin B in cancer and inflammatory disease: from molecular mechanisms to therapeutic strategies
items: SK4 potentially modulates the alternative splicing profile associated with papillary thyroid cancer development in BHT101 cells
items: An ethogram of facial behaviour in domestic horses: evolutionary perspectives on form and function
items: A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information
items: Biochar-mediated changes in nutrient distribution and leaching patterns: insights from a soil column study
items: Xenobiotic resistance in mosquito eggs: current understanding and data gaps

Traumatic spinal cord injury: identifying independent risk factors and predictive model development for symptomatic urinary tract infections
type: item
type: AcademicArticle
description: Background Traumatic spinal cord injury (TSCI) is commonly associated with urinary tract infections (UTIs), with a reported prevalence ranging from 31.7% to 68%. Symptomatic UTIs can result in serious complications, including chronic kidney damage and recurrent infections. The objective of this study was to identify independent risk factors and develop a predictive model for symptomatic UTIs in TSCI patients, thereby providing valuable insights for prevention and management strategies. Methods A retrospective study was conducted at the China Rehabilitation Research Center, involving 168 TSCI patients admitted between January 1, 2020, and August 1, 2024. Symptomatic UTIs were diagnosed using Delphi consensus criteria, which integrated clinical symptoms, urinalysis, and culture confirmation. Comprehensive clinical data, including demographic characteristics, injury profiles, and laboratory parameters, were systematically extracted from the hospital information system. Potential risk factors were initially screened using univariable logistic regression, with statistically significant variables subsequently analyzed in a multivariable logistic regression model to identify independent predictors. A predictive model for symptomatic UTIs was constructed using the regression coefficients. The model’s performance was evaluated using the area under the receiver operating characteristic curve (AUC), calibration with the Hosmer-Lemeshow test, and internal validation through bootstrap resampling. Results The incidence of symptomatic UTIs was 57.14%, with the majority presenting with fever (65.07%) and Escherichia coli infections (44.52%). Prolonged hospitalization (OR = 1.005, 95% CI [1.001–1.010]) and cumulative antibiotic exposure (OR = 1.011, 95% CI [1.000–1.022]) were identified as independent risk factors. The predictive model, which incorporated these factors, demonstrated strong discrimination (AUC = 0.81, 95% CI [0.746–0.879]) and good calibration (P = 0.44). Conclusions…
format: application/pdf
format: text/html
creator: Huayong Du
creator: Zehui Li
creator: Jinming Zhang
creator: Xiaoxin Wang
creator: Yingli Jing
creator: Degang Yang
creator: Jianjun Li
subject: Neurology
subject: Urology
subject: Healthcare Services
subject: Rehabilitation
description: doi:10.7717/peerj.19473
publisher: PeerJ Inc.
rights: © 2025 Du et al.
abstract: Background Traumatic spinal cord injury (TSCI) is commonly associated with urinary tract infections (UTIs), with a reported prevalence ranging from 31.7% to 68%. Symptomatic UTIs can result in serious complications, including chronic kidney damage and recurrent infections. The objective of this study was to identify independent risk factors and develop a predictive model for symptomatic UTIs in TSCI patients, thereby providing valuable insights for prevention and management strategies. Methods A retrospective study was conducted at the China Rehabilitation Research Center, involving 168 TSCI patients admitted between January 1, 2020, and August 1, 2024. Symptomatic UTIs were diagnosed using Delphi consensus criteria, which integrated clinical symptoms, urinalysis, and culture confirmation. Comprehensive clinical data, including demographic characteristics, injury profiles, and laboratory parameters, were systematically extracted from the hospital information system. Potential risk factors were initially screened using univariable logistic regression, with statistically significant variables subsequently analyzed in a multivariable logistic regression model to identify independent predictors. A predictive model for symptomatic UTIs was constructed using the regression coefficients. The model’s performance was evaluated using the area under the receiver operating characteristic curve (AUC), calibration with the Hosmer-Lemeshow test, and internal validation through bootstrap resampling. Results The incidence of symptomatic UTIs was 57.14%, with the majority presenting with fever (65.07%) and Escherichia coli infections (44.52%). Prolonged hospitalization (OR = 1.005, 95% CI [1.001–1.010]) and cumulative antibiotic exposure (OR = 1.011, 95% CI [1.000–1.022]) were identified as independent risk factors. The predictive model, which incorporated these factors, demonstrated strong discrimination (AUC = 0.81, 95% CI [0.746–0.879]) and good calibration (P = 0.44). Conclusions…
bibliographic citation: Du et al. (2025) Traumatic spinal cord injury: identifying independent risk factors and predictive model development for symptomatic urinary tract infections. PeerJ 13:e19473 https://doi.org/10.7717/peerj.19473
date submitted: 2024-12-01
date accepted: 2025-04-24
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Huayong
author list: Agent
  family name: Li
  given name: Zehui
author list: Agent
  family name: Zhang
  given name: Jinming
author list: Agent
  family name: Wang
  given name: Xiaoxin
author list: Agent
  family name: Jing
  given name: Yingli
author list: Agent
  family name: Yang
  given name: Degang
author list: Agent
  family name: Li
  given name: Jianjun
doi: 10.7717/peerj.19473
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: ©2025 Du et al.
attribution name: Du et al.

Synchrony on the reef: how environmental factors shape coral spawning patterns in Acropora corals in the Maldives
type: item
type: AcademicArticle
description: Elucidating our knowledge on the reproductive phenology of scleractinian corals and the environmental drivers of reproductive synchronicity is pivotal for assessing gene flow between populations and the potential for ecosystem recovery. The timing of gamete release in sessile broadcast spawning corals is key to successful reproduction; and is dependent on a complex interaction between an organism’s genes and external environmental factors. In this study we assessed the effect of various environmental factors on the spawning timing and synchronicity of Acropora corals in the Maldives. A total of 3,026 colonies from 24 species of Acropora were recorded spawning between October 2021 and May 2024: 1,709 from 20 species in North Male Atoll and 1,317 from 18 species in Baa Atoll. Generalised linear models (GLMs) were used to estimate the effect of average daily wind speed (mph), total daily precipitation (mm), tide depth (m), and mean sea surface temperature (SST) over a 30-day period prior to spawning, on the proportion of colonies to spawn per day and the spawning day deviation to full moon. Models were run for all Acropora corals, and three species in which more than 30 days of spawning were observed enabling robust statistical models to be tested: A. secale, A. tenuis, and A. humilis, to determine the presence of species-specific relationships. Based on additional GLMs, we found that a change in SST does not determine the likelihood of Acropora spawning to occur in a given month, but does significantly predict the number of Acropora colonies to spawn per month. We also found that the relationship between SST and spawning as a predictor of probability or synchronicity on a monthly temporal scale can be species specific. We found a significant, positive correlation between daily precipitation levels and the proportion of Acropora colonies to spawn per day, however, there were some variations between species. Additionally, a higher proportion of Acropora colonies spawned…
format: application/pdf
format: text/html
creator: Kate Sheridan
creator: Margaux A.A. Monfared
creator: Simon P. Dixon
creator: Amelia J.F. Errington
creator: Thomas Le Berre
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.19447
publisher: PeerJ Inc.
rights: © 2025 Sheridan et al.
abstract: Elucidating our knowledge on the reproductive phenology of scleractinian corals and the environmental drivers of reproductive synchronicity is pivotal for assessing gene flow between populations and the potential for ecosystem recovery. The timing of gamete release in sessile broadcast spawning corals is key to successful reproduction; and is dependent on a complex interaction between an organism’s genes and external environmental factors. In this study we assessed the effect of various environmental factors on the spawning timing and synchronicity of Acropora corals in the Maldives. A total of 3,026 colonies from 24 species of Acropora were recorded spawning between October 2021 and May 2024: 1,709 from 20 species in North Male Atoll and 1,317 from 18 species in Baa Atoll. Generalised linear models (GLMs) were used to estimate the effect of average daily wind speed (mph), total daily precipitation (mm), tide depth (m), and mean sea surface temperature (SST) over a 30-day period prior to spawning, on the proportion of colonies to spawn per day and the spawning day deviation to full moon. Models were run for all Acropora corals, and three species in which more than 30 days of spawning were observed enabling robust statistical models to be tested: A. secale, A. tenuis, and A. humilis, to determine the presence of species-specific relationships. Based on additional GLMs, we found that a change in SST does not determine the likelihood of Acropora spawning to occur in a given month, but does significantly predict the number of Acropora colonies to spawn per month. We also found that the relationship between SST and spawning as a predictor of probability or synchronicity on a monthly temporal scale can be species specific. We found a significant, positive correlation between daily precipitation levels and the proportion of Acropora colonies to spawn per day, however, there were some variations between species. Additionally, a higher proportion of Acropora colonies spawned…
bibliographic citation: Sheridan et al. (2025) Synchrony on the reef: how environmental factors shape coral spawning patterns in Acropora corals in the Maldives. PeerJ 13:e19447 https://doi.org/10.7717/peerj.19447
date submitted: 2024-11-13
date accepted: 2025-04-20
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sheridan
  given name: Kate
author list: Agent
  family name: Monfared
  given name: Margaux A.A.
author list: Agent
  family name: Dixon
  given name: Simon P.
author list: Agent
  family name: Errington
  given name: Amelia J.F.
author list: Agent
  family name: Le Berre
  given name: Thomas
doi: 10.7717/peerj.19447
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: ©2025 Sheridan et al.
attribution name: Sheridan et al.

A hundred species, mostly new—first assessment of ribbon worm diversity and distribution in Oman
type: item
type: AcademicArticle
description: Background Biodiversity is a key characteristic of any ecosystem but remains largely undescribed for most marine animals. Ribbon worms (phylum Nemertea), a diverse but poorly sampled phylum ubiquitous in the world’s oceans, are a case in point. Aside from their function as predators in marine communities, nemerteans are biomedically relevant because they produce diverse toxins, and some impact bivalve, decapod, and glass eel fisheries. Identification of nemerteans is challenging because many species look alike. The task is further complicated by many descriptions being based on preserved specimens, and therefore lacking characters of external appearance of live specimens. Characters of internal anatomy form the basis of traditional systematics but are more recently shown to be of little use in distinguishing between closely related species. This makes DNA data essential in species descriptions, and assessments of diversity and distribution. Methods In a first modern survey of the phylum in Arabian waters, we collected nemerteans from a variety of habitats, focusing sampling on hard-bottom substrata, especially coral reefs. Specimens were triple-documented with photos, morphological vouchers, and DNA barcodes. Species delineation was based on morphology and Cytochrome Oxidase I sequences. Sequences and associated data are deposited in public databases, and vouchers at the Florida Museum of Natural History. Results We documented 107 nemertean species in Oman, where none were previously known. This doubles the number of genetically characterized nemertean species for the entire Indo-West Pacific—a testament to how poorly sampled the phylum is in the most biodiverse marine region of the world. As many as 98% of the species were undescribed, and 93% are not documented outside Arabia. Half of the species were rare, and most—cryptic. Undescribed species were assigned unique alphanumeric temporary names for tracking in the literature and public databases. Estimates of sourc…
format: application/pdf
format: text/html
creator: Svetlana Maslakova
creator: Irina Cherneva
creator: Ethan Kahn
creator: Audrey Wong
creator: Gustav Paulay
subject: Biogeography
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.19438
publisher: PeerJ Inc.
rights: © 2025 Maslakova et al.
abstract: Background Biodiversity is a key characteristic of any ecosystem but remains largely undescribed for most marine animals. Ribbon worms (phylum Nemertea), a diverse but poorly sampled phylum ubiquitous in the world’s oceans, are a case in point. Aside from their function as predators in marine communities, nemerteans are biomedically relevant because they produce diverse toxins, and some impact bivalve, decapod, and glass eel fisheries. Identification of nemerteans is challenging because many species look alike. The task is further complicated by many descriptions being based on preserved specimens, and therefore lacking characters of external appearance of live specimens. Characters of internal anatomy form the basis of traditional systematics but are more recently shown to be of little use in distinguishing between closely related species. This makes DNA data essential in species descriptions, and assessments of diversity and distribution. Methods In a first modern survey of the phylum in Arabian waters, we collected nemerteans from a variety of habitats, focusing sampling on hard-bottom substrata, especially coral reefs. Specimens were triple-documented with photos, morphological vouchers, and DNA barcodes. Species delineation was based on morphology and Cytochrome Oxidase I sequences. Sequences and associated data are deposited in public databases, and vouchers at the Florida Museum of Natural History. Results We documented 107 nemertean species in Oman, where none were previously known. This doubles the number of genetically characterized nemertean species for the entire Indo-West Pacific—a testament to how poorly sampled the phylum is in the most biodiverse marine region of the world. As many as 98% of the species were undescribed, and 93% are not documented outside Arabia. Half of the species were rare, and most—cryptic. Undescribed species were assigned unique alphanumeric temporary names for tracking in the literature and public databases. Estimates of sourc…
bibliographic citation: Maslakova et al. (2025) A hundred species, mostly new—first assessment of ribbon worm diversity and distribution in Oman. PeerJ 13:e19438 https://doi.org/10.7717/peerj.19438
date submitted: 2025-02-13
date accepted: 2025-04-16
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maslakova
  given name: Svetlana
author list: Agent
  family name: Cherneva
  given name: Irina
author list: Agent
  family name: Kahn
  given name: Ethan
author list: Agent
  family name: Wong
  given name: Audrey
author list: Agent
  family name: Paulay
  given name: Gustav
doi: 10.7717/peerj.19438
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: ©2025 Maslakova et al.
attribution name: Maslakova et al.

Alleviation of dextran sulfate sodium (DSS)-induced colitis in mice through the antioxidative effects of muscone via the MyD88/p38 MAPK signalling pathway
type: item
type: AcademicArticle
description: Background Inflammatory bowel disease (IBD) is characterized by chronic inflammation. Ulcerative colitis (UC) is a subtype of IBD. The symptoms of UC include inflammation, damage to crypts, and ulceration. UC patients frequently experience comorbid psychological disorders. Muscone has notable anti-inflammatory, antioxidative, and antidementia properties. Our study aimed to investigate the potential of muscone to alleviate colitis, the underlying mechanisms, and the signalling pathways involved. Methods C57BL/6 mice were administered dextran sulfate sodium (DSS) to induce colitis. The SMART v3.0 (Panlab, Barcelona, Spain) was used to measure parameters in the open field test and the tail suspension test to assess depression and anxiety. Gait changes were analysed using the DigiGait™ imaging system. The severity of colitis was assessed through body weight loss, stool consistency, gross bleeding, and histopathological evaluation. Proteins related to anti-inflammatory and antioxidative effects were analysed in dissociated tissues using mouse-specific commercial enzyme-linked immunosorbent assay (ELISA) kits. Results Muscone treatment reduced gross bleeding and histopathological damage scores and increased the ratio of colon length to body weight. Gait analysis revealed improvements in swing time, brake time, propulsive time, stance duration, stride duration, stride length, stride frequency, and paw area with muscone treatment. However, muscone treatment did not improve the distance travelled or the time spent in the open field test, nor did it affect the immobility duration in the tail suspension test. We observed that the expression of claudin-1, occludin, and zonula occludens-1 (ZO-1) increased in response to treatment with muscone. Muscone treatment downregulated the expression of interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-17 (IL-17), interleukin-33 (IL-33), and tumour necrosis factor-α (TNF-α), while increasing the expression of interleukin-4 (IL-4) a…
format: application/pdf
format: text/html
creator: Gang Yao
creator: Jian Zhang
creator: Lingyan Zhang
creator: Hai Zhao
creator: Shuguang Wu
creator: Hongmei Yang
creator: Jiangwei Yu
subject: Biochemistry
subject: Gastroenterology and Hepatology
subject: Pharmacology
description: doi:10.7717/peerj.19397
publisher: PeerJ Inc.
rights: © 2025 Yao et al.
abstract: Background Inflammatory bowel disease (IBD) is characterized by chronic inflammation. Ulcerative colitis (UC) is a subtype of IBD. The symptoms of UC include inflammation, damage to crypts, and ulceration. UC patients frequently experience comorbid psychological disorders. Muscone has notable anti-inflammatory, antioxidative, and antidementia properties. Our study aimed to investigate the potential of muscone to alleviate colitis, the underlying mechanisms, and the signalling pathways involved. Methods C57BL/6 mice were administered dextran sulfate sodium (DSS) to induce colitis. The SMART v3.0 (Panlab, Barcelona, Spain) was used to measure parameters in the open field test and the tail suspension test to assess depression and anxiety. Gait changes were analysed using the DigiGait™ imaging system. The severity of colitis was assessed through body weight loss, stool consistency, gross bleeding, and histopathological evaluation. Proteins related to anti-inflammatory and antioxidative effects were analysed in dissociated tissues using mouse-specific commercial enzyme-linked immunosorbent assay (ELISA) kits. Results Muscone treatment reduced gross bleeding and histopathological damage scores and increased the ratio of colon length to body weight. Gait analysis revealed improvements in swing time, brake time, propulsive time, stance duration, stride duration, stride length, stride frequency, and paw area with muscone treatment. However, muscone treatment did not improve the distance travelled or the time spent in the open field test, nor did it affect the immobility duration in the tail suspension test. We observed that the expression of claudin-1, occludin, and zonula occludens-1 (ZO-1) increased in response to treatment with muscone. Muscone treatment downregulated the expression of interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-17 (IL-17), interleukin-33 (IL-33), and tumour necrosis factor-α (TNF-α), while increasing the expression of interleukin-4 (IL-4) a…
bibliographic citation: Yao et al. (2025) Alleviation of dextran sulfate sodium (DSS)-induced colitis in mice through the antioxidative effects of muscone via the MyD88/p38 MAPK signalling pathway. PeerJ 13:e19397 https://doi.org/10.7717/peerj.19397
date submitted: 2024-07-09
date accepted: 2025-04-09
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yao
  given name: Gang
author list: Agent
  family name: Zhang
  given name: Jian
author list: Agent
  family name: Zhang
  given name: Lingyan
author list: Agent
  family name: Zhao
  given name: Hai
author list: Agent
  family name: Wu
  given name: Shuguang
author list: Agent
  family name: Yang
  given name: Hongmei
author list: Agent
  family name: Yu
  given name: Jiangwei
doi: 10.7717/peerj.19397
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: ©2025 Yao et al.
attribution name: Yao et al.

Unveiling the role of gasdermin B in cancer and inflammatory disease: from molecular mechanisms to therapeutic strategies
type: item
type: AcademicArticle
description: Gasdermin B (GSDMB) is a member of the gasdermin (GSDM) protein family, primarily known for mediating pyroptosis, an inflammatory form of programmed cell death. Recent studies have revealed the diverse molecular functions of GSDMB and its close association with various diseases, particularly cancers (e.g., breast cancer, gastric cancer, bladder cancer) and inflammatory diseases (e.g., asthma, inflammatory bowel disease). At the molecular level, GSDMB induces pyroptosis by forming pores in the cell membrane, leading to membrane rupture. This function is common across the GSDM protein family; however, GSDMB also exhibits unique non-pyroptotic functions, such as modulating cell proliferation, migration, and immune responses. In multiple cancers, including breast cancer, gastric cancer, and cervical cancer, high expression of GSDMB correlates with poor prognosis, promoting cancer cell proliferation, invasion, and metastasis through interactions with signaling pathways such as STAT3 and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK). Additionally, GSDMB influences the immune microenvironment through its pyroptotic activity, playing a role in the initiation and regulation of inflammation. Upon activation, it can directly cleave target cells via its N-terminal domain, contributing significantly to chronic inflammatory diseases and NK cell-mediated antibacterial responses. In conclusion, as a multifunctional protein, GSDMB not only participates in pyroptosis but also regulates non-pyroptotic processes, playing an important role in cancer progression and inflammatory diseases. Further elucidating the detailed mechanisms of GSDMB may offer novel therapeutic avenues for these conditions.
format: application/pdf
format: text/html
creator: Weixiao Yang
creator: Xu Hu
creator: Xiang Li
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.19392
publisher: PeerJ Inc.
rights: © 2025 Yang et al.
abstract: Gasdermin B (GSDMB) is a member of the gasdermin (GSDM) protein family, primarily known for mediating pyroptosis, an inflammatory form of programmed cell death. Recent studies have revealed the diverse molecular functions of GSDMB and its close association with various diseases, particularly cancers (e.g., breast cancer, gastric cancer, bladder cancer) and inflammatory diseases (e.g., asthma, inflammatory bowel disease). At the molecular level, GSDMB induces pyroptosis by forming pores in the cell membrane, leading to membrane rupture. This function is common across the GSDM protein family; however, GSDMB also exhibits unique non-pyroptotic functions, such as modulating cell proliferation, migration, and immune responses. In multiple cancers, including breast cancer, gastric cancer, and cervical cancer, high expression of GSDMB correlates with poor prognosis, promoting cancer cell proliferation, invasion, and metastasis through interactions with signaling pathways such as STAT3 and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK). Additionally, GSDMB influences the immune microenvironment through its pyroptotic activity, playing a role in the initiation and regulation of inflammation. Upon activation, it can directly cleave target cells via its N-terminal domain, contributing significantly to chronic inflammatory diseases and NK cell-mediated antibacterial responses. In conclusion, as a multifunctional protein, GSDMB not only participates in pyroptosis but also regulates non-pyroptotic processes, playing an important role in cancer progression and inflammatory diseases. Further elucidating the detailed mechanisms of GSDMB may offer novel therapeutic avenues for these conditions.
bibliographic citation: Yang et al. (2025) Unveiling the role of gasdermin B in cancer and inflammatory disease: from molecular mechanisms to therapeutic strategies. PeerJ 13:e19392 https://doi.org/10.7717/peerj.19392
date submitted: 2024-12-09
date accepted: 2025-04-08
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Weixiao
author list: Agent
  family name: Hu
  given name: Xu
author list: Agent
  family name: Li
  given name: Xiang
doi: 10.7717/peerj.19392
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: ©2025 Yang et al.
attribution name: Yang et al.

SK4 potentially modulates the alternative splicing profile associated with papillary thyroid cancer development in BHT101 cells
type: item
type: AcademicArticle
description: Papillary thyroid cancer (PTC) is an ever-increasing cancer type worldwide, and greatly decreases the life quality and affects survival time of patients during its development and progression, but the underlying mechanisms and key factors for PTC progression are not clear. Recent studies demonstrated the potassium channel protein SK4 participates in the progression of many cancers, while it lacks the molecular mechanism study for SK4 function. In this study, we performed functional and molecular explorations for SK4 by overexpressing its level in thyroid cancer BHT101 cells. Cellular proliferation and invasion experiments were performed to assess the influences of SK4 on cell behaviors. Further, whole transcriptome sequencing (RNA-seq) analysis helped us systematically investigated the targets of SK4, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs), and validated several related DEGs and RASEs by RT-qPCR experiment. In thyroid cancer patients, SK4 expression was completely lost in normal tissues and significantly increased in every stage of tumor tissues compared with normal tissues, which probably results from the low DNA methylation level at its promoter region. Consistent with previous study, SK4 overexpression (SK4-OE) promoted proliferation and invasion ability of BHT10 cells compared with negative control (NC). By analyzing the RNA-seq data, we detected dozens of DEGs and found that up DEGs were enriched in negative regulation of apoptotic progress, including VTCN1, MSX1, FATE1, TEK, and PRAMEF2. More importantly, we found SK4-OE globally changed the alternative splicing (AS) pattern and identified 1,639 RASEs. The genes of RASEs were enriched in DNA damage/repair, viral process, translation, and mRNA splicing pathways, which were tightly associated with the pathogenesis and progression of cancers. The splicing regulatory genes from regulated alternative splicing genes (RASGs) could partly explain the reason of…
format: application/pdf
format: text/html
creator: Alimujiang Wupuer
creator: Xuekelaiti Kuerban
creator: Gong Ye
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.19391
publisher: PeerJ Inc.
rights: © 2025 Wupuer et al.
abstract: Papillary thyroid cancer (PTC) is an ever-increasing cancer type worldwide, and greatly decreases the life quality and affects survival time of patients during its development and progression, but the underlying mechanisms and key factors for PTC progression are not clear. Recent studies demonstrated the potassium channel protein SK4 participates in the progression of many cancers, while it lacks the molecular mechanism study for SK4 function. In this study, we performed functional and molecular explorations for SK4 by overexpressing its level in thyroid cancer BHT101 cells. Cellular proliferation and invasion experiments were performed to assess the influences of SK4 on cell behaviors. Further, whole transcriptome sequencing (RNA-seq) analysis helped us systematically investigated the targets of SK4, including differentially expressed genes (DEGs) and regulated alternative splicing events (RASEs), and validated several related DEGs and RASEs by RT-qPCR experiment. In thyroid cancer patients, SK4 expression was completely lost in normal tissues and significantly increased in every stage of tumor tissues compared with normal tissues, which probably results from the low DNA methylation level at its promoter region. Consistent with previous study, SK4 overexpression (SK4-OE) promoted proliferation and invasion ability of BHT10 cells compared with negative control (NC). By analyzing the RNA-seq data, we detected dozens of DEGs and found that up DEGs were enriched in negative regulation of apoptotic progress, including VTCN1, MSX1, FATE1, TEK, and PRAMEF2. More importantly, we found SK4-OE globally changed the alternative splicing (AS) pattern and identified 1,639 RASEs. The genes of RASEs were enriched in DNA damage/repair, viral process, translation, and mRNA splicing pathways, which were tightly associated with the pathogenesis and progression of cancers. The splicing regulatory genes from regulated alternative splicing genes (RASGs) could partly explain the reason of…
bibliographic citation: Wupuer et al. (2025) SK4 potentially modulates the alternative splicing profile associated with papillary thyroid cancer development in BHT101 cells. PeerJ 13:e19391 https://doi.org/10.7717/peerj.19391
date submitted: 2024-08-01
date accepted: 2025-04-08
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wupuer
  given name: Alimujiang
author list: Agent
  family name: Kuerban
  given name: Xuekelaiti
author list: Agent
  family name: Ye
  given name: Gong
doi: 10.7717/peerj.19391
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: ©2025 Wupuer et al.
attribution name: Wupuer et al.

An ethogram of facial behaviour in domestic horses: evolutionary perspectives on form and function
type: item
type: AcademicArticle
description: Understanding cause and function of animal facial behaviour can provide key insights into the animal’s cognitive and emotional state. The Equine Facial Action Coding System (EquiFACS) has characterised a wide range of equine (Equus caballus) facial movements (Action Units (AU) and Descriptors (AD)). However, there is still a lack of systematic documentation of whether and how these AUs and ADs are combined to produce discrete configurations of facial behaviour in horses. The aim of this study was to provide a systematically derived ethogram of equine facial behaviour in the domestic horse across positive, negative and neutral social interactions. Facial behaviour was recorded during horse-horse interactions occurring during affiliative (non-play), play, agonistic and attentional contexts, based on the coding of contextual behaviour. Using EquiFACS, a bank of 805 AU/AD combinations, across 22 distinct behaviours, was created. Network analysis techniques (NetFACS) were used to establish the facial movements significantly associated with each context. Domestic horses use a wide range of distinct facial behaviours, which are defined and described in our ethogram. Interestingly, there were marked similarities between the play faces of horses and the open mouth play faces of primates and carnivores, adding weight to the hypothesis that these facial behaviours are deep rooted in mammalian biology. We also defined a new EquiFACS Action Unit, AUH21, facial tightener (platysma), which makes the underlying facial structures appear more prominent. This AU is found in humans and gibbons, but no other species studied, and its addition to EquiFACS will enhance cross-species comparisons and potentially facilitate the attribution of emotional state and assessment of pain in horses. Our equine facial behaviour ethogram will be invaluable in future work exploring equine emotion, welfare, social behaviour, and perception, as well as having direct applications for those working with and…
format: application/pdf
format: text/html
creator: Kate Lewis
creator: Sebastian D. McBride
creator: Jérôme Micheletta
creator: Matthew O. Parker
creator: Alan V. Rincon
creator: Jen Wathan
creator: Leanne Proops
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.19309
publisher: PeerJ Inc.
rights: © 2025 Lewis et al.
abstract: Understanding cause and function of animal facial behaviour can provide key insights into the animal’s cognitive and emotional state. The Equine Facial Action Coding System (EquiFACS) has characterised a wide range of equine (Equus caballus) facial movements (Action Units (AU) and Descriptors (AD)). However, there is still a lack of systematic documentation of whether and how these AUs and ADs are combined to produce discrete configurations of facial behaviour in horses. The aim of this study was to provide a systematically derived ethogram of equine facial behaviour in the domestic horse across positive, negative and neutral social interactions. Facial behaviour was recorded during horse-horse interactions occurring during affiliative (non-play), play, agonistic and attentional contexts, based on the coding of contextual behaviour. Using EquiFACS, a bank of 805 AU/AD combinations, across 22 distinct behaviours, was created. Network analysis techniques (NetFACS) were used to establish the facial movements significantly associated with each context. Domestic horses use a wide range of distinct facial behaviours, which are defined and described in our ethogram. Interestingly, there were marked similarities between the play faces of horses and the open mouth play faces of primates and carnivores, adding weight to the hypothesis that these facial behaviours are deep rooted in mammalian biology. We also defined a new EquiFACS Action Unit, AUH21, facial tightener (platysma), which makes the underlying facial structures appear more prominent. This AU is found in humans and gibbons, but no other species studied, and its addition to EquiFACS will enhance cross-species comparisons and potentially facilitate the attribution of emotional state and assessment of pain in horses. Our equine facial behaviour ethogram will be invaluable in future work exploring equine emotion, welfare, social behaviour, and perception, as well as having direct applications for those working with and…
bibliographic citation: Lewis et al. (2025) An ethogram of facial behaviour in domestic horses: evolutionary perspectives on form and function. PeerJ 13:e19309 https://doi.org/10.7717/peerj.19309
date submitted: 2024-09-05
date accepted: 2025-03-20
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lewis
  given name: Kate
author list: Agent
  family name: McBride
  given name: Sebastian D.
author list: Agent
  family name: Micheletta
  given name: Jérôme
author list: Agent
  family name: Parker
  given name: Matthew O.
author list: Agent
  family name: Rincon
  given name: Alan V.
author list: Agent
  family name: Wathan
  given name: Jen
author list: Agent
  family name: Proops
  given name: Leanne
doi: 10.7717/peerj.19309
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: ©2025 Lewis et al.
attribution name: Lewis et al.

A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information
type: item
type: AcademicArticle
description: Understanding the behavior of microbial consortia is crucial for predicting metabolite production by microorganisms. Genome-scale network reconstructions enable the computation of metabolic interactions and specific associations within microbial consortia underpinning the production of different metabolites. In the context of the human gut, butyrate is a central metabolite produced by bacteria that plays a key role within the gut microbiome impacting human health. Despite its importance, there is a lack of computational methods capable of predicting its production as a function of the consortium composition. Here, we present a novel machine-learning approach leveraging automatically generated genome-scale metabolic models to tackle this limitation. Briefly, all consortia made of two up to 13 members from a pool of 19 bacteria with known genomes, including at least one butyrate producer from a pool of three known producer species, were built and their (maximum) in silico butyrate production simulated. Using network-derived descriptors from each bacteria, butyrate production by the above consortia was used as training data for various machine learning models. The performance of the algorithms was evaluated using k-fold cross-validation and new experimental data, displaying a Pearson correlation coefficient exceeding 0.75 for the predicted and observed butyrate production in two bacteria consortia. While consortia with more than two bacteria showed generally worse predictions, the best machine-learning models still outperformed predictions from genome-scale metabolic models alone. Overall, this approach provides a valuable tool and framework for probing promising butyrate-producing consortia on a large scale, guiding experimentation, and more importantly, predicting metabolic production by consortia.
format: application/pdf
format: text/html
creator: Claudia Silva-Andrade
creator: Sergio Hernández
creator: Pedro Saa
creator: Ernesto Perez-Rueda
creator: Daniel Garrido
creator: Alberto J. Martin
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
description: doi:10.7717/peerj.19296
publisher: PeerJ Inc.
rights: © 2025 Silva-Andrade et al.
abstract: Understanding the behavior of microbial consortia is crucial for predicting metabolite production by microorganisms. Genome-scale network reconstructions enable the computation of metabolic interactions and specific associations within microbial consortia underpinning the production of different metabolites. In the context of the human gut, butyrate is a central metabolite produced by bacteria that plays a key role within the gut microbiome impacting human health. Despite its importance, there is a lack of computational methods capable of predicting its production as a function of the consortium composition. Here, we present a novel machine-learning approach leveraging automatically generated genome-scale metabolic models to tackle this limitation. Briefly, all consortia made of two up to 13 members from a pool of 19 bacteria with known genomes, including at least one butyrate producer from a pool of three known producer species, were built and their (maximum) in silico butyrate production simulated. Using network-derived descriptors from each bacteria, butyrate production by the above consortia was used as training data for various machine learning models. The performance of the algorithms was evaluated using k-fold cross-validation and new experimental data, displaying a Pearson correlation coefficient exceeding 0.75 for the predicted and observed butyrate production in two bacteria consortia. While consortia with more than two bacteria showed generally worse predictions, the best machine-learning models still outperformed predictions from genome-scale metabolic models alone. Overall, this approach provides a valuable tool and framework for probing promising butyrate-producing consortia on a large scale, guiding experimentation, and more importantly, predicting metabolic production by consortia.
bibliographic citation: Silva-Andrade et al. (2025) A machine-learning approach for predicting butyrate production by microbial consortia using metabolic network information. PeerJ 13:e19296 https://doi.org/10.7717/peerj.19296
date submitted: 2024-09-25
date accepted: 2025-03-19
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva-Andrade
  given name: Claudia
author list: Agent
  family name: Hernández
  given name: Sergio
author list: Agent
  family name: Saa
  given name: Pedro
author list: Agent
  family name: Perez-Rueda
  given name: Ernesto
author list: Agent
  family name: Garrido
  given name: Daniel
author list: Agent
  family name: Martin
  given name: Alberto J.
doi: 10.7717/peerj.19296
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: © 2025 Silva-Andrade et al.
attribution name: Silva-Andrade et al.

Biochar-mediated changes in nutrient distribution and leaching patterns: insights from a soil column study
type: item
type: AcademicArticle
description: Background Nutrient leaching threatens sustainable agriculture by depleting soil fertility and contaminating groundwater. Biochar offers a promising solution, but its effectiveness varies with feedstock, production, and application rates. Specifically, the potential of hazelnut husk biochar for nutrient retention and soil improvement has not been extensively studied, leaving a gap in understanding its practical applications and optimal usage in different soil types and crop systems. Methods This study investigated the influence of hazelnut husk biochar application on leachate properties, soil column characteristics, and nutrient dynamics over a 112-day period. The experiment employed a randomized split-plot design with four hazelnut husk biochar application rates (0%, 0.5%, 1%, and 2%) on sandy loam soil. Leaching events were conducted six times over 112 days of incubation period, simulating irrigation and fertilizer application for potato cultivation. Leachates were collected at each leaching event for analysis of pH, electrical conductivity (EC), and various nutrient contents. Following the experiment, soil samples were analyzed at three depths to assess nutrient content. Results The study revealed significant temporal dynamics in nutrient concentrations across different leaching events, emphasizing the impact of biochar on nutrient retention. Phosphorus (P) concentrations, for instance, decreased from 0.220 mg L−1 to 0.176 mg L−1 over four leaching events in the 2.0% biochar treatment. Similarly, potassium (K) concentrations declined from 6.44 mg L−1 to 3.76 mg L−1, indicating improved nutrient retention with biochar application. These findings contrast with the control (0% biochar), where nutrient leaching was more pronounced. While biochar had little effect on nitrate leaching, its inherent P content and adsorption characteristics influenced P leaching. Higher biochar application rates resulted in significant changes in soil properties and nutrient concentratio…
format: application/pdf
format: text/html
creator: Elif Gunal
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.18823
publisher: PeerJ Inc.
rights: © 2025 Gunal
abstract: Background Nutrient leaching threatens sustainable agriculture by depleting soil fertility and contaminating groundwater. Biochar offers a promising solution, but its effectiveness varies with feedstock, production, and application rates. Specifically, the potential of hazelnut husk biochar for nutrient retention and soil improvement has not been extensively studied, leaving a gap in understanding its practical applications and optimal usage in different soil types and crop systems. Methods This study investigated the influence of hazelnut husk biochar application on leachate properties, soil column characteristics, and nutrient dynamics over a 112-day period. The experiment employed a randomized split-plot design with four hazelnut husk biochar application rates (0%, 0.5%, 1%, and 2%) on sandy loam soil. Leaching events were conducted six times over 112 days of incubation period, simulating irrigation and fertilizer application for potato cultivation. Leachates were collected at each leaching event for analysis of pH, electrical conductivity (EC), and various nutrient contents. Following the experiment, soil samples were analyzed at three depths to assess nutrient content. Results The study revealed significant temporal dynamics in nutrient concentrations across different leaching events, emphasizing the impact of biochar on nutrient retention. Phosphorus (P) concentrations, for instance, decreased from 0.220 mg L−1 to 0.176 mg L−1 over four leaching events in the 2.0% biochar treatment. Similarly, potassium (K) concentrations declined from 6.44 mg L−1 to 3.76 mg L−1, indicating improved nutrient retention with biochar application. These findings contrast with the control (0% biochar), where nutrient leaching was more pronounced. While biochar had little effect on nitrate leaching, its inherent P content and adsorption characteristics influenced P leaching. Higher biochar application rates resulted in significant changes in soil properties and nutrient concentratio…
bibliographic citation: Gunal (2025) Biochar-mediated changes in nutrient distribution and leaching patterns: insights from a soil column study. PeerJ 13:e18823 https://doi.org/10.7717/peerj.18823
date submitted: 2024-05-12
date accepted: 2024-12-16
issued: 2025-05-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gunal
  given name: Elif
doi: 10.7717/peerj.18823
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-28
copyright: © 2025 Gunal
attribution name: Gunal

Xenobiotic resistance in mosquito eggs: current understanding and data gaps
type: item
type: AcademicArticle
description: Of all mosquito life stages, the egg continues to be the least understood and most vulnerable relative to exposure to external environmental stressors. The propensity of mosquitoes to lay eggs in or near aquatic environments exposes them to a variety of xenobiotic compounds. Owing to their increased use, two xenobiotics, antibiotics and insecticides are increasingly being detected in aquatic ecosystems. Both antibiotics and insecticides are known for their ovicidal effects. Prior to the formation of the serosal cuticle, mosquito eggs are potentially exposed to antibiotics and insecticides due to the permeability of the egg membrane. This short review attempts to summarize the current understanding and to identify the data gaps pertaining to the exposure of mosquito eggs to xenobiotics. The role of male mosquitoes in the propagation of xenobiotic resistance, something that’s been sparsely studied, is also discussed. Additionally, we address the implications of these data gaps relative to the overall objectives of vector control and public health.
format: application/pdf
format: text/html
creator: Uday Turaga
creator: Steven T. Peper
creator: Carlos J. Garcia
creator: Steven M. Presley
subject: Developmental Biology
subject: Entomology
subject: Toxicology
subject: Zoology
subject: Public Health
description: doi:10.7717/peerj.19523
publisher: PeerJ Inc.
rights: © 2025 Turaga et al.
abstract: Of all mosquito life stages, the egg continues to be the least understood and most vulnerable relative to exposure to external environmental stressors. The propensity of mosquitoes to lay eggs in or near aquatic environments exposes them to a variety of xenobiotic compounds. Owing to their increased use, two xenobiotics, antibiotics and insecticides are increasingly being detected in aquatic ecosystems. Both antibiotics and insecticides are known for their ovicidal effects. Prior to the formation of the serosal cuticle, mosquito eggs are potentially exposed to antibiotics and insecticides due to the permeability of the egg membrane. This short review attempts to summarize the current understanding and to identify the data gaps pertaining to the exposure of mosquito eggs to xenobiotics. The role of male mosquitoes in the propagation of xenobiotic resistance, something that’s been sparsely studied, is also discussed. Additionally, we address the implications of these data gaps relative to the overall objectives of vector control and public health.
bibliographic citation: Turaga et al. (2025) Xenobiotic resistance in mosquito eggs: current understanding and data gaps. PeerJ 13:e19523 https://doi.org/10.7717/peerj.19523
date submitted: 2024-12-02
date accepted: 2025-05-05
issued: 2025-05-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Turaga
  given name: Uday
author list: Agent
  family name: Peper
  given name: Steven T.
author list: Agent
  family name: Garcia
  given name: Carlos J.
author list: Agent
  family name: Presley
  given name: Steven M.
doi: 10.7717/peerj.19523
volume: 13
issn: 2167-8359
publication name: PeerJ
publication date: 2025-05-27
copyright: © 2025 Turaga et al.
attribution name: Turaga et al.

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