title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=180 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Evaluating techniques for determining elasmobranch body size: a review of current methodologies link: https://peerj.com/articles/18646 last-modified: 2024-12-23 description: There is global awareness that many species of elasmobranchs (sharks and rays) have life history characteristics that make them susceptible to overexploitation. The study of these animals is critical, as it contributes to increasing knowledge of these specimens and aids in their conservation. In particular, growth rate, age, fecundity, and size at maturity are key parameters for defining management and conservation strategies in elasmobranchs. Biometric data collection allows these parameters to be determined and considered in the evaluation of population demography. Over the last decades, several methodologies for measuring elasmobranch size have evolved, progressing from traditional capture-based methods to sophisticated, non-intrusive photographic techniques. The present review aims to understand and analyse all the existing non-invasive techniques that currently allow the collection of zoometric data in elasmobranchs and, later, to highlight the advantages and limitations of each technique, with comments on their application to fieldwork. To this end, 49 articles were selected, encompassing seven measurement techniques: photogrammetry using distance to the individual, bar photogrammetry, laser photogrammetry, stereo-DOV, stereo-BRUV, stereo-ROV, and aerial photogrammetry. Globally, the last four techniques are excellent alternatives to methods that involve animal capture or death, as they are practical, simple to use, minimally invasive, and potentially highly accurate. Each technique’s requirements related to equipment and cost, limitations, and distinctive features are presented here and summarized to guide researchers on what’s available and how to select the most appropriate for their studies. creator: Ana S. Ferreira creator: Márcia A. Naré creator: Joana I. Robalo creator: Núria D. Baylina uri: https://doi.org/10.7717/peerj.18646 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ferreira et al. title: DNA metabarcoding reveals diet diversity and niche partitioning by two sympatric herbivores in summer link: https://peerj.com/articles/18665 last-modified: 2024-12-23 description: BackgroundFood provides essential nutrients and energy necessary for animals to sustain life activities. Accordingly, dietary niche analysis facilitates the exploration of foraging strategies and interspecific relationships among wildlife. The vegetation succession has reduced understory forage resources (i.e., shrubs and herbs) available to sika deer (Cervus nippon kopschi). Little is known about the summer foraging strategies or the interspecific relationship between sika deer and Reeves’ muntjac (Muntiacus reevesi).MethodsThe present study used high-throughput sequencing and DNA metabarcoding techniques to investigate the feeding habits and interspecific relationships between sika deer and Reeves’ muntjac in our study.ResultsA total of 458 amplicon sequence variants (ASVs) were identified from fecal samples, with 88 ASVs (~19.21%) unique to sika deer and 52 ASVs (~11.35%) unique to Reeves’ muntjac, suggesting the consumption and utilization of specific food items for the two species. The family Rosaceae was the most abundant for both species, especially Rubus spp. and Smilax china. Alpha diversity (local species richness) indicated that the dietary species richness of sika deer was higher than that of Reeves’ muntjac, but the difference was not statistically significant. Sika deer also exhibited a higher evenness index (J′ = 0.514) than Reeves’ muntjac (J′ = 0.442). Linear discriminant effect size analysis revealed significant differences in forage plants between the two herbivores. The niche breadths of sika deer and Reeves’ muntjac were 11.36 and 14.06, respectively, and the dietary niche overlap index was 0.44. Our findings indicate the diet partitioning primarily manifested in the differentiation of food items and the proportion, which ultimately reduces the overlap of nutritional niches and helps avoid conflicts resulting from resource utilization. This study provides a deeper insight into the diversity of foraging strategies and the interspecific relationship of herbivores from the food dimension. creator: Ruofei Li creator: Dandan Wang creator: Zhiming Cao creator: Yuqin Liu creator: Wenguo Wu creator: Wuhua Liu creator: Jianwen Zhan creator: Yongtao Xu uri: https://doi.org/10.7717/peerj.18665 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Identification of the whole genome of alternative splicing and RNA-binding proteins involved in nintedanib-induced apoptosis in gastric cancer cells link: https://peerj.com/articles/18697 last-modified: 2024-12-23 description: BackgroundIt has been demonstrated that nintedanib can inhibit the proliferation of gastric cancer cells, but the specific mechanism of action is unclear.ObjectiveInvestigating the changes of key factors involved in gene transcription and post-transcriptional regulation during the process of treating gastric cancer with nintedanib.MethodsIn this study, we performed transcriptome sequencing on gastric cancer cell groups treated with nintedanib and control groups. The SUVA (Splice sites Usage Variation Analysis) software was used to identify differential alternative splicing (AS) events between the nintedanib-treated group and the control group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were conducted to assess the functional differences and pathways associated with these events. Finally, a co-expression regulatory network of differentially expressed RNA-binding proteins (RBPs) and differentially spliced genes was established. Results: A total of 915 differential AS events were identified between the two groups, and these differential genes were closely related to the apoptosis pathway. Further analysis revealed that differential RBPs (TAGLN2, TAGLN, SRSF6, PKM, SRSF2, NOC2L, IPO4, C1QBP, DHX9) may affect the anti-proliferative effect of nintedanib on gastric cancer cells by regulating downstream genes involved in cell proliferation and angiogenesis (NR4A1, BBC3, IFI27) through alternative splicing.ConclusionThis study systematically identified important changes in alternative splicing and RNA-binding proteins during the process of nintedanib-induced apoptosis in gastric cancer cells. It innovatively revealed the mechanisms of action of nintedanib in gastric cancer cells and expanded the selection of new targets for gastric cancer treatment. creator: Xiaohua Dong creator: Zhilong Liu creator: Miao Yu creator: Xiaojun Yang creator: Hui Cai uri: https://doi.org/10.7717/peerj.18697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Dong et al. title: Quality of life and subjective well-being comparison between traumatic, nontraumatic chronic spinal cord injury, and healthy individuals in China link: https://peerj.com/articles/18709 last-modified: 2024-12-23 description: BackgroundDifferentiating between traumatic and non-traumatic spinal cord injuries (NT-SCI) is critical, as these classifications may significantly impact patients’ health outcomes and overall well-being, potentially resulting in differences in treatment protocols and therapeutic efficacy.ObjectiveThis study aims to compare the quality of life (QoL) and satisfaction with life (SWL) among individuals with traumatic spinal cord injuries (T-SCI), NT-SCI, and the healthy population in China.MethodA quantitative, cross-sectional survey was conducted between July and December 2020 in the Rehabilitation and Physiotherapy Department of Tongji Hospital, Hubei University of Science and Technology. The World Health Organization Quality of Life Brief Version (WHOQOL-BREF) and the Satisfaction with Life Scale (SWLS) were administered to evaluate QoL and subjective well-being (SWB). An independent t-test was performed to assess differences within the SCI population, while Pearson’s correlation coefficient was utilized to explore relationships between the WHOQOL-BREF domains and the SWLS. Multiple linear regression analysis was applied to identify key determinants influencing World Health Organization Quality of Life (WHOQOL) domain scores and overall SWLS score.ResultParticipants with NT-SCI exhibited significant differences in overall health as measured by the WHOQOL-BREF domains compared to those with T-SCI (p < 0.05). Both the NT-SCI and T-SCI groups demonstrated lower mean scores across all four WHOQOL-BREF domains compared to healthy individuals. No significant differences were observed between the NT-SCI and T-SCI groups in the SWLS, although both groups scored lower than the healthy population. Additionally, SWB was moderately positively correlated with QoL (p < 0.01). Collectively, the predictor variables explained 22.28% of the variance in physical health, 6.43% in psychological health, 28.67% in social health, and 25.68% in environmental health. Furthermore, the independent variables accounted for approximately 22.67% of the variance in the SWLS.ConclusionsIndividuals with NT-SCI experience significantly worse overall health outcomes compared to those with T-SCI, although both groups report QoL and life satisfaction than healthy individuals. No significant differences in life satisfaction were found between two groups. Additionally, SWB shows a moderate positive correlation with QoL, highlighting the close relationship between mental and physical health in SCI populations. creator: Ruba Altahla creator: Jamal Alshorman creator: Sayed Zulfiqar Ali-Shah creator: Mohammad Nasb creator: Xu Tao uri: https://doi.org/10.7717/peerj.18709 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Altahla et al. title: Spatial heterogeneity of soil properties in planted mixed forests in the rocky desertification areas of the Wuling Mountain link: https://peerj.com/articles/18724 last-modified: 2024-12-23 description: In this study, experiments were conducted on soil samples collected from depths of 0–15 cm, 15–30 cm, and 30–50 cm at the National Long-term Scientific Research Base for the Comprehensive Management of Rocky Desertification in the Wuling Mountains. The aim was to determine the physicochemical indexes and explore the nature and spatial heterogeneity of the soil of the planted mixed forests within the rocky desertification area of the Wuling Mountain. Various analytical methods were employed, including descriptive statistical analysis, correlation analysis, analysis of variance, principal component analysis, spatial interpolation analysis, and kriging interpolation, to fit the optimal model of the semi-variance function of soil physicochemical properties and analyze the model’s parameters. The results indicated that soil physical and chemical properties varied with depth and were generally correlated. The relationship between soil organic matter and total nitrogen content was the closest. Additionally, there was a certain degree of correlation between soils at different depths in the vertical profile, generally the correlation between layer B (15–30 cm) and layer C (30–50 cm) > that between layer A (0–15 cm) and layer B (15–30 cm) > that between layer A (0–15 cm) and layer C (30–50 cm). The weighting coefficients of the principal components of soil physicochemical properties indicated that soil organic matter, nitrogen, phosphorus, potassium, pH, total porosity, and capillary porosity are key factors in the soil properties of karst desertification areas. The spatial variability of soil physicochemical properties at different depths ranged from 21.91 to 87.59 m, and the abutment ratio (Co/Co+C) of these properties ranged from 12.99% to 89.53%. Using kriging interpolation in ArcGIS, the spatial distribution pattern of soil physical and chemical properties was mapped, revealing that these indicators were distributed with heterogeneous patches of various sizes and shapes. Therefore, the degree of rocky desertification significantly influences the spatial distribution pattern of soil physical and chemical properties. creator: Ziqian Pan creator: Yanyan Dong creator: Gongxiu He creator: Tongtong Guo creator: Ninghua Zhu uri: https://doi.org/10.7717/peerj.18724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Pan et al. title: Malignant behaviors and immune response in melanoma: Epstein-Barr virus induced gene 3 as a therapeutic target based on an in-vitro exploration link: https://peerj.com/articles/18730 last-modified: 2024-12-23 description: BackgroundEpstein-Barr virus induced gene 3 (EBI3), a member of the IL-12 family, is known to be involved in malignant progression in a variety of cancers, but its role in melanoma is unclear. The aim of this study was to explore the effects of EBI3 on the malignant phenotype melanoma to reveal its potential as a therapeutic target.MethodsIn this study, we used bioinformatics to analyze the expression of EBI3 in pan-cancer and verified its expression level in melanoma cells by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Subsequently, the effects of EBI3 knockdown on cell proliferation, migration and invasion were detected using the Cell Counting Kit-8 (CCK-8) and Transwell assays. Changes in immune-related cytokines were detected by ELISA, and macrophage polarization was observed using immunofluorescence. Finally, the phosphorylation levels of signaling pathways such as Smad3, STAT6 and cGAS-STING were analyzed by Western blot.ResultsEBI3 was evidently highly-expressed in melanoma, and silencing of EBI3 could visibly suppress the survival and migration/invasion of melanoma cells, concurrent with the increased levels of BAX and CDH1 and the decreased expressions of BCL2 and CDH2. Meanwhile, EBI3 knockdown diminished the phosphorylation levels of both Smad3 and STAT6 and the levels of immune response-relevant cytokines in melanoma cells, while aggravating the macrophage M1 polarization and the expression of cGAS, p-STING and p-IRE1 α in THP-1 monocyte-derived macrophages co-cultured with EBI3-silenced melanoma cells.ConclusionThis study filled the blank on the involvement of EBI3 in melanoma, hinting the possibility of controlling EBI3 as a therapeutic strategy in the management of melanoma. creator: Ying Zhang creator: Fengrui Cheng creator: Xingrui Cai creator: Jingping Wu uri: https://doi.org/10.7717/peerj.18730 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Enrichment effects on growth, health, and reproduction in a single clone of the asexual Amazon molly, Poecilia formosa link: https://peerj.com/articles/18734 last-modified: 2024-12-23 description: This study examines the impact of two types of environmental enrichment on the growth of the Amazon molly (Poecilia formosa), a clonal fish species. We investigated the effects of two welfare-related enrichment factors: physical enrichment (presence of a halfpipe PVC and gravel substrate, E) and social enrichment (presence of visible neighbor fish, N). Fish were divided into four treatment groups: (1) both physical and social enrichment (EN), (2) no physical enrichment but social enrichment (nEN), (3) physical enrichment without social enrichment (EnN,), and (4) no enrichment (nEnN). Results showed that individuals, which received both types of enrichment, exhibited faster growth rates and lower early life mortality compared to the other groups, indicating improved health and welfare. However, this initial advantage did not persist into adulthood, suggesting that the benefits of enrichment may be stage specific. These findings highlight the importance of environmental factors in promoting welfare in a particular species, especially during early developmental stages. This study may have implications for early life-stage fish research indicating that some environmental factors may play a role in enhancing growth, reproductive competence, and reduced mortality. Enrichment effects on growth, health, and reproduction in a single clone of the asexual Amazon molly, Poecilia formosa. creator: Debbie Cunningham creator: Tyler Reich creator: Theresa E. Rizzi creator: Chance Powell creator: Ingo Schlupp uri: https://doi.org/10.7717/peerj.18734 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Cunningham et al. title: Association of tyrosine kinase 2 polymorphisms with susceptibility to microscopic polyangiitis in a Guangxi population link: https://peerj.com/articles/18735 last-modified: 2024-12-23 description: BackgroundHeredity and epigenetics affect the pathogenesis of microscopic polyangiitis (MPA). Tyrosine kinase 2 (TYK2) polymorphisms (rs2304256C > A, rs280519A > G, and rs12720270G > A) may be potential protective factors against anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). Current research suggests that TYK2 is associated with various autoimmune diseases; however, no study has examined the relationship between TYK2 polymorphisms and AAV. This study assessed the effect of TYK2 polymorphisms on susceptibility to MPA.MethodsOverall, 562 Chinese participants (265 patients with MPA and 297 healthy volunteers) were recruited. Polymerase chain reactions combined with high-throughput sequencing were used to analyze polymorphic loci, while logistic regression analysis was used to assess the relationship between polymorphism of the TYK2 gene and MPA susceptibility.ResultsIn males, individuals with the CA genotype (rs2304256) in the overdominant model showed a significantly reduced risk of MPA (odds ratio (OR) = 0.52; 95% confidence interval (CI) [0.29–0.93]; p = 0.025). Regarding rs280519, male carriers of the AG genotype had a significantly lower risk of developing MPA in both the codominant (OR = 0.51; 95% CI [0.28–0.93]; p = 0.039) and overdominant (OR = 0.48; 95% CI [0.27–0.86]; p = 0.013) models. The GA genotype of rs12720270 was associated with low susceptibility to MPA in males (OR = 0.52; 95% CI [0.29–0.93]; p = 0.027).ConclusionsThis study indicates that mutations in the TYK2 gene (rs2304256, rs280519, and rs12720270) may be associated with a reduced risk of MPA in the male Chinese population in Guangxi. The A allele of single nucleotide polymorphism (SNP) rs2304256 may be a protective factor against MPA, while the G alleles of SNPs rs280519 and rs12720270 are protective factors against MPA. creator: Binglan Yang creator: Liepeng Chu creator: Fei Feng creator: Shurong Lu creator: Chao Xue uri: https://doi.org/10.7717/peerj.18735 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Malignant solid tumor-related spontaneous intracerebral hemorrhage: a propensity score matching study link: https://peerj.com/articles/18737 last-modified: 2024-12-23 description: BackgroundSpontaneous intracerebral hemorrhage (sICH) is a severe event with high mortality. Recently, evidence has emerged suggesting that malignant solid tumors may increase the risk of sICH through unique cancer-related factors. However, the specific risk factors and clinical characteristics of sICH in patients with malignant solid tumor remain poorly understood.ObjectiveThis study aimed to investigate the clinical characteristics of and identify the risk factors associated with sICH in individuals with malignant solid tumors.MethodsThis retrospective study was carried out in patients with active malignant solid tumors and sICH at the First Affiliated Hospital of Guangxi Medical University between January 2010 and December 2020. Patients were separated into control and malignant solid tumor-related spontaneous intracerebral hemorrhage (MST-sICH) groups. The control group consisted of patients presenting with malignant solid tumors alone who were matched to the MST-sICH group using a 1:1 propensity score matching (PSM) approach. Patient clinical data, laboratory findings, and imaging results were collected. Univariate analysis was carried out to determine the risk factors associated with MST-sICH. In addition, a receiver operator characteristic analysis was performed to identify potential predictors for poor prognosis.ResultsDecreased hemoglobin (HGB) levels, together with increased lymphocyte counts (LYCs), and an increased neutrophil-to-lymphocyte ratio (NLR) were found in the MST-sICH group compared to the control group. The results of the multivariate logistic regression analysis indicated a HGB levels (OR: 0.959, 95% CI [0.928–0.992]), an increased in LYCs (OR: 0.095, 95% CI [0.023–0.392]). Furthermore, there was an increased in NLR levels (OR: 2.137, 95% CI [1.427–3.200]). In the receiver operating characteristic (ROC) curve analysis, the area under the curve (AUC) with HGB, LYCs, and NLR as joint predictors was 0.955 (95% CI [0.901–1.000]), with a sensitivity of 100%, a specificity of 82.6%, and a Youden Index of 0.826.ConclusionDecreased HGB levels, elevated LYCs, and a higher NLR were identified as independent risk factors for sICH in patients with active solid malignancies. These markers could assist clinicians in stratifying high-risk patients, facilitating closer monitoring and informing targeted preventive strategies to mitigate the incidence of sICH in this at-risk population. creator: Shuolin Liang creator: Liuyu Liu creator: Bin Qin creator: Shengri Chen creator: Zhijian Liang uri: https://doi.org/10.7717/peerj.18737 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Liang et al. title: Impact of storage and extraction methods on peat soil microbiomes link: https://peerj.com/articles/18745 last-modified: 2024-12-23 description: Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modified PowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations. creator: Dylan Cronin creator: Yueh-Fen Li creator: Paul Evans creator: Gene W. Tyson creator: Ben J. Woodcroft creator: Virginia I. Rich uri: https://doi.org/10.7717/peerj.18745 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Cronin et al.