title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=111 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Applications and prospects of phosphoproteomics in renal disease research link: https://peerj.com/articles/18950 last-modified: 2025-03-20 description: IntroductionPhosphoproteomics, an advanced branch of molecular biology, utilizes specific techniques such as mass spectrometry, affinity chromatography, and bioinformatics analysis to explore protein phosphorylation, shedding light on the cellular mechanisms that drive various biological processes. This field has become instrumental in advancing our understanding of renal diseases, from identifying underlying mechanisms to pinpointing new therapeutic targets.Areas coveredThis review will discuss the evolution of phosphoproteomics from its early experimental observations to its current application in renal disease research using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We will explore its role in the identification of disease biomarkers, the elucidation of pathogenic mechanisms, and the development of novel therapeutic strategies. Additionally, the potential of phosphoproteomics in enhancing drug discovery and improving treatment outcomes for renal diseases will be highlighted.Expert opinionPhosphoproteomics is rapidly transforming renal disease research by offering unprecedented insights into cellular processes. Utilizing techniques such as LC-MS/MS, it enables the identification of novel biomarkers and therapeutic targets, enhancing our understanding of drug mechanisms. This field promises significant advancements in the diagnosis and treatment of renal diseases, shifting towards more personalized and effective therapeutic strategies. As the technology evolves, its integration into clinical practice is pivotal for revolutionizing renal healthcare. creator: XueJia Zheng creator: LingLing Zhou creator: TianTian Xu creator: GuoYing Wang creator: YaLi Peng creator: ChunMei Wen creator: MengYao Wu creator: HuiHui Tao creator: Yong Dai uri: https://doi.org/10.7717/peerj.18950 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Zheng et al. title: Phylogeny of Cassieae based on seed morphological and ITS evidence link: https://peerj.com/articles/18947 last-modified: 2025-03-20 description: The Cassieae tribe, comprising economically significant species, is understudied in terms of phylogenetics within China. This study aimed to elucidate the taxonomic status and systematic relationships among Cassieae species by integrating seed coat micro-morphological characteristics with molecular data from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. (1) The results indicate that the tribe is classified into seven distinct clades; Clade V consists of Chamaecrista, which is characterized by primarily monosymmetric flowers with occasional asymmetry, the presence of extrafloral nectaries (EFNs), five or ten stamens, and pods that dehisce elastically. Clade VI is associated with Senna, which displays polysymmetric or monosymmetric flowers, uniformly ten stamens or occasionally three staminodes, variable presence of EFNs, and predominantly indehiscent pods, with rare instances of slit dehiscence. Clade VII is characterized by the presence of Cassia, which exhibits polysymmetric flowers, consistently ten stamens—three of which are elongated and curved, typically exceeding the length of the petals—and indehiscent pods. (2) The monophyly of Cassia and Senna was strongly supported, with Cassia grouping closely with Senna, but distantly from Chamaecrista. (3) It is noteworthy that Senna occidentail and Senna sophera are confirmed as sister taxa, while Senna corymbosa and S. bicapsularis are confirmed as sister taxa. By integrating molecular biology and morphological taxonomy, this research enhances our comprehension of the phylogenetic relationships and evolutionary history within the Cassieae tribe in China. creator: Jing Cai creator: Chuang Yang creator: Leyang Wang creator: Jiaqing He creator: Qiang Wang uri: https://doi.org/10.7717/peerj.18947 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Cai et al. title: Female philopatry may influence antipredatory behavior in a solitary mammal link: https://peerj.com/articles/18933 last-modified: 2025-03-20 description: Whether neighboring individuals are related or not has a number of important ecological & evolutionary ramifications. Kin selection resulting from philopatry can play an important role in social and antipredatory behavior. Ground squirrels exhibit alarm vocalizations in the presence of predators; however, the degree to which kin selection shapes alarm calling behavior varies with species ecology and the degree of relatedness between neighbors. We studied a solitary ground squirrel species that exhibits sex-biased calling propensity to determine if female philopatry may be responsible for sex differences in antipredatory behavior observed in our population. We used double digest restriction-site associated DNA sequencing (ddRADseq) to sample the genomes of Harris’s antelope squirrel (Ammospermophilus harrisii) to determine the relatedness between individuals and test whether genetic and geographic distance were correlated. We found that geographic distance had a positive relationship with genetic distance, and that this relationship was sex-dependent, suggesting male-biased dispersal. Our results provide supporting evidence that female philopatry may be responsible for higher calling propensity observed in female squirrels, potentially influencing antipredatory behavior in this species via kin selection. Our findings add to a growing body of evidence that philopatry is an important ecological driver influencing sociospatial organization in solitary species. creator: Alexandra Burnett creator: Michelle Hein creator: Natalie Payne creator: Karla L. Vargas creator: Melanie Culver creator: John L. Koprowski uri: https://doi.org/10.7717/peerj.18933 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Burnett et al. title: Assessment of YouTube videos on post-dural puncture headache: a cross-sectional study link: https://peerj.com/articles/19151 last-modified: 2025-03-19 description: BackgroundPost-dural puncture headache (PDPH) is a common complication of central neuroaxis anesthesia or analgesia, causing severe headaches. YouTube is widely used for health information, but the reliability and quality of PDPH-related content are unclear. This study evaluates the content adequacy, reliability, and quality of YouTube videos on PDPH.MethodsThis cross-sectional study analyzed English-language YouTube videos on PDPH with good audiovisual quality. Two independent reviewers assessed the videos using the DISCERN instrument, Journal of American Medical Association (JAMA) benchmark criteria, and Global Quality Scale (GQS). Correlations between video characteristics and their reliability, content adequacy, and quality scores were examined.ResultsOut of 71 videos, 42.3% were uploaded by health-related websites, 36.6% by physicians, and 21.1% by patients. Strong correlations were found between DISCERN, JAMA, and GQS scores (p < 0.001). Videos from physicians and health-related websites had significantly higher scores than those from patients (p < 0.001). No significant correlations were observed between descriptive characteristics and scores (p > 0.05).ConclusionYouTube videos on PDPH uploaded by health-related websites or physicians are more reliable, adequate, and higher in quality than those uploaded by patients. Source credibility is crucial for evaluating medical information on YouTube. creator: Seher İlhan creator: Turan Evran uri: https://doi.org/10.7717/peerj.19151 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2025 İlhan and Evran title: Epidemiology of kerosene poisoning in Saudi Arabia: a retrospective analysis link: https://peerj.com/articles/19094 last-modified: 2025-03-19 description: BackgroundLimited national studies exist on the epidemiology of kerosene poisoning in Saudi Arabia. This study aimed to determine the frequency, demographic distribution, geographic patterns, and seasonal variations of kerosene poisoning incidents in Saudi Arabia from January 2019 to December 2021.MethodsThis retrospective cross-sectional study utilized data on all reported kerosene poisoning cases from the National Poisoning Surveillance System. Cross-tabulation with chi-square tests assessed the relationships between poisoning cases and key variables such as gender, age group, and region.ResultsA total of 460 kerosene poisoning cases were documented: 32.2% in 2019, 37.2% in 2020, and 30.6% in 2021. Saudi nationals comprised 97.6% of cases, and the male populace felt more influenced (60.9%) than females (39.1%), although the variation that was found was not proven to be statistically significant (p = 0.912). Out of all age groups, kids between the ages of 1 and 5 were the ones to be primarily affected, accounting for 87.6% of cases (p = 0.029). Most incidents occurred in residential settings (83.7%) and involved oral ingestion (91.7%, p < 0.001). Regionally, the AlQrayat Region reported the highest number of cases (53%), followed by the Northern Borders (18%) and AlJouf (15.7%), with incidents peaking during the colder months. Hospital admissions accounted for 41.3% of cases, while discharges against medical advice (DAMA) increased notably from 8.1% in 2019 to 28.4% in 2021.ConclusionKerosene poisoning in Saudi Arabia predominantly affects young children and occurs in residential settings, with higher concentrations in northern regions during colder months. Public health interventions focusing on parental education, safe kerosene storage practices, and region-specific prevention strategies are essential to reduce the burden of kerosene poisoning and improve outcomes. creator: Bassam M. Hakami creator: Randa Mohammed Nooh creator: Ali Ahmed Asiri uri: https://doi.org/10.7717/peerj.19094 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hakami et al. title: Effects of different grazing intensities on plant species diversity at different spatial scales in a desert steppe in Inner Mongolia link: https://peerj.com/articles/19087 last-modified: 2025-03-19 description: The effect of grazing intensity on plant diversity has been widely studied. In this study, desert steppes with different grazing intensities (no grazing (CK), light grazing (LG), moderate grazing (MG), heavy grazing (HG), and extremely heavy grazing (EG)) in Inner Mongolia were selected to study the changes in species diversity at different spatial scales (α, β, and γ diversity) and the α diversity of different plant groups (dominant species, common species, and rare species).The results showed that the α, β, and γ diversity first decreased and then increased with increasing grazing intensity, and β diversity was observed to be the most sensitive index to the grazing intensity. Grazing had the greatest impact on the α diversity of rare species and the least impact on the α diversity of common species. Therefore, rare species are of great significance for the maintenance and assessment of biodiversity. We concluded that grazing leads to a sensitive response of β diversity, and this sensitive phenomenon is mainly affected by rare species. The results could provide scientific bases for the protection of plant diversity and sustainable grazing in desert steppes. creator: Changlin Xue creator: Shijie Lv creator: Yanling Wu creator: Jie Yun creator: Rui Dong creator: Wentao Wang uri: https://doi.org/10.7717/peerj.19087 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Xue et al. title: A comprehensive prognostic and immunological analysis of hexokinase domain containing protein-1 (HKDC1) in pan-cancer link: https://peerj.com/articles/19083 last-modified: 2025-03-19 description: BackgroundCurrently, research on the role of hexokinase domain-containing protein-1 (HKDC1) in neoplasm metabolism remains sparse. This study seeks to conduct a thorough investigation of HKDC1’s potential functions across thirty-three different tumor types, utilizing data obtained from The Cancer Genome Atlas (TCGA).MethodWe conducted a thorough data extraction from the TCGA database, subsequently employing R (version 4.2.2) and its associated software packages for detailed analysis. Our investigation centered on evaluating the differential expression and prognostic significance of HKDC1, while also examining its connections to tumor heterogeneity, mutation profiles, and RNA modifications. Furthermore, we analyzed the relationship between HKDC1 expression and tumor immunity utilizing the TIMER analysis approach.ResultsA comprehensive analysis of various tumor types has revealed that HKDC1 is significantly upregulated in many malignant tumors. Importantly, patients with elevated HKDC1 levels in their tumor tissues often experience poorer prognoses. The association between HKDC1 expression, immune cell infiltration, and the existence of immune checkpoints suggests a possible connection between the tumor microenvironment and HKDC1, alongside tumor advancement. Gene set enrichment analysis (GSEA) further substantiates the idea that HKDC1 may play a role in several critical pathways and biological processes associated with neoplasm. Additionally, the overexpression of HKDC1 is influenced by promoter methylation and alterations in DNA copy number amplification. Furthermore, in vitro experiments demonstrated that silencing HKDC1 resulted in a marked reduction in the proliferation, migration, and invasion capabilities of neoplasm cells.ConclusionOur initial pan-cancer analysis provided a comprehensive understanding of the oncogenic roles of HKDC1 across diverse cancer types. Moreover, HKDC1 has the potential to serve as a significant prognostic biomarker. creator: Zhi Liang creator: Tianhao Zhang creator: Jiajia Huang creator: Zhixin Huang creator: Zeyu Zhao creator: Shirong Cai creator: Jinping Ma uri: https://doi.org/10.7717/peerj.19083 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Liang et al. title: TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis link: https://peerj.com/articles/19072 last-modified: 2025-03-19 description: BackgroundCervical cancer (CC) is a prevalent female malignancy strongly influenced by the tumor microenvironment (TME). This study focuses on the role of TGF-β signaling in cancer-associated fibroblasts (CAFs) and its interaction with immune cells, aiming to elucidate its impact on CC progression.MethodsThe TME of CC patients was analyzed using scRNA-seq data and we identified the major cell types in the TME with a focus on the activation of the TGF-β signaling pathway in fibroblasts. Gene modules related to the TGF-β signaling pathway were identified by Weighted correlation network analysis (WGCNA). Using The Cancer Genome Atlas Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA-CESC) dataset, a prognostic gene model was constructed by univariate Cox, LASSO Cox and multivariate Cox regression analyses. For cellular validation, the mRNA level of prognostic model-related genes was tested via quantitative real-time real-time polymerase chain reaction (PCR). Thereafter, the following assays, including cell counting kit-8, scratch and wound healing assays, were applied to assess the viability, migration and invasion of CC cells.ResultsAnalysis at single-cell resolution identified nine major cell types in the TME, and significant activation of the TGF-β signaling pathway in fibroblasts was correlated with tumor proliferation and differentiation. Strong TGF-β signaling communication between fibroblasts and macrophages and NK/T cells suggested a crucial role in the shaping of the immunosuppressive microenvironment. WGCNA analysis identified gene modules significantly associated with the TGF-β signaling pathway. The prognostic model constructed based on three genes, ITGA5, SHF and SNRPN, demonstrated good predictive ability in multiple datasets, validating its potential for clinical application. Meanwhile, the cellular validation assays have revealed the higher expression of ITGA5 and SNRPN and lower expression of SHF in CC cells. Further, ITGA5 knockdown suppressed the viability, migration and invasion of CC cells.ConclusionThis study confirmed the important role of the TGF-β signaling pathway in CC, especially in fibroblasts on tumor microenvironment and tumor progression. The current model could effectively evaluate the prognosis of CC, providing a theoretical foundation for developing CC therapies according to the TGF-β signaling pathway. The present results provide new perspectives for further research on the pathological mechanisms and clinical management of CC. creator: Haina Qu creator: Jing Zhao creator: Xia Zuo creator: Hongyue He creator: Xiaohan Wang creator: Huiyan Li creator: Kun Zhang uri: https://doi.org/10.7717/peerj.19072 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Qu et al. title: Assessing morphological variations in the seagrass genus Halodule (Cymodoceaceae) along the Brazilian coast through genetic analyses link: https://peerj.com/articles/19038 last-modified: 2025-03-19 description: BackgroundSeagrass meadows are distributed globally and provide critical ecological functions and ecosystem services, but seagrasses are still poorly studied compared with other coastal and marine foundation species. Species taxonomy is uncertain in various seagrass genera, such as the genus Halodule. Until recently, the morphological characteristics of leaves were the major criteria for species identification. In Brazil, three species of Halodule are recognized and separated solely using leaf morphology criteria by some authors; however, the leaves present high variability and plasticity, resulting in great uncertainty about species diversity. A review of seagrass species validation using both morphological and phylogenetic methods is needed. This includes examining the genus Halodule with the aim of better understanding its diversity and spatial distribution and consequently supporting management and conservation goals.MethodsPlant samples with the morphological forms of H. beaudettei and H. wrightii were collected at five sites across three Brazilian marine ecoregions. Leaf tip format and leaf width and length were compared among all the sites and between the two populations with different leaf tip forms. Molecular diversity and divergence indices and analyses were used to estimate the genetic distance between H. wrightii and H. beaudettei populations. To determine the phylogenetic relationship between the two morphologies, we sequenced two molecular markers, the internal transcribed spacer (ITS) fragment and the rbcL gene, to construct phylogenetic trees using Bayesian inference.ResultsWe identified H. beaudettei morphology at two sites in Northeast Brazil, while H. wrightii was found in all the ecoregions in the remaining areas, distinguished by the leaf tip shape that occurred at each site. Leaf width and length varied across the five sites, and leaf length differed between H. wrightii and H. beaudettei, with higher values observed in H. beaudettei. Variations in morphological measurements may be related to habitat conditions at each site studied. No divergence was observed for the DNA sequences of two molecular markers, except for a single base in the ITS region, resulting in the Brazilian specimens merging at a single node in the phylogenetic trees. AMOVA and genetic distance analysis revealed low genetic variation but high structuring within populations. The ITS marker showed insufficient genetic variance to delineate the two morphologies as different species which indicating H. wrightii and H. beaudettei are closely related. A genomic approach is needed to fully resolve this issue. This study represents the first step toward the complete determination of the Halodule genus on the Brazilian coast. creator: Virgínia Eduarda de Sousa creator: Maria Cristina F. da Silva Cortinhas creator: Joel C. Creed creator: Maria Gardênia S. Batista creator: Maira C. Proietti creator: Margareth Copertino uri: https://doi.org/10.7717/peerj.19038 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Sousa et al. title: Fatty acid biomarkers reveal the interaction between two highly migratory species in the Southern Humboldt System: the swordfish and its prey, the jumbo squid link: https://peerj.com/articles/19129 last-modified: 2025-03-18 description: Marine trophodynamics refer to the transfer of energy from prey to predators. In marine invertebrates and fishes, the nutrients obtained through the consumption of food and/or prey are stored as energy reserves in certain tissues and/or organs including the liver, muscle, or gonads, and that these are subsequently used as bioenergetic fuel for highly energy-demanding fundamental physiological processes. In the southern Humboldt Current System, the interaction between two highly migratory resources and top species has been observed: the swordfish (Xiphias gladius) and its prey the jumbo squid (Dosidicus gigas). Because of this trophic interaction, these species store large amounts of energy (as lipids and fatty acids) in their main organs. However, how the fatty acid profile varies in the various organs of the predator and its prey is still unknown, as is its potential use as trophic biomarkers and the ecophysiological role it plays. Our results showed a moderate similarity between the fatty acid profile of the digestive gland of D. gigas with the profiles of the liver, gonad, and muscle of X. gladius, particularly with fatty acids: palmitic (C16:0), stearic (C18:0), oleic (C18:1n9), gadoleic (C20:1), EPA (C20:5n3), and DHA (C22:6n3). Our findings on the use of fatty acids as biomarkers of the interaction between two highly migratory species in the southern Humboldt System may reveal the degree of preference swordfish have for preying on jumbo squid, particularly through the consumption of the digestive gland. In both species, a high bioenergetic fuel content characterized by a predominance of saturated, monounsaturated, and polyunsaturated fatty acids may be necessary to sustain the high energy costs involved in their migratory and reproductive processes in the Humboldt Current system. creator: Marco Quispe-Machaca creator: Fabián Guzmán-Rivas creator: Patricio Barría Martínez creator: Christian Ibáñez creator: Ángel Urzúa uri: https://doi.org/10.7717/peerj.19129 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Quispe-Machaca et al.