PeerJ最新文献

Accurately predicting coding genes from metagenomic samples containing a high proportion of eukaryotic content remains a significant challenge. Novel and reliable methods for the simultaneous prediction of prokaryotic and eukaryotic microbial genes are crucial to address this. We evaluated gene prediction accuracy of MetaGeneMark and MetaEuk using representative genomes from diverse organisms. Based on these findings, we developed an innovative analytical workflow. This approach involves an initial prediction of eukaryotic genes using MetaEuk, followed by the masking of these predicted eukaryotic genes and any co-identified partial prokaryotic genes using a custom Perl script. Remaining prokaryotic genes are then predicted from the masked metagenome using MetaGeneMark or metaProdigal. This integrated strategy achieved similar quantities and average lengths of eukaryotic genes compared to using MetaEuk alone. Notably, the quantity of predicted prokaryotic genes and viral genes using the new workflow was 14-18% higher than that obtained with standalone prokaryotic predictors. Furthermore, validation on a mixed prokaryotic-eukaryotic metagenome demonstrated that our workflow yielded genes with significantly higher average lengths, indicating reduced fragmentation and improved gene integrity. This novel workflow effectively enables the rapid and comprehensive retrieval of high-quality prokaryotic and eukaryotic coding sequences from diverse metagenomes.

Background: Colostomy is a surgical intervention that affects physical and psychological health and can cause difficulties in areas such as personal care, hygiene, nutrition, mobility, and social interactions.

Purpose: To determine the severity of difficulties encountered in daily living activities by individuals with colostomy and to examine in which activities they experience the most difficulty.

Methods: The research was conducted with 94 patients using a cross-sectional and descriptive design based on the Model of Living. Data were collected using the "Patient Identification Information Form" and the "Daily Living Activities Difficulty Level Assessment Form" In the first stage, the "Patient Identification Information Form" was administered to the patients, and the "Daily Living Activities Difficulty Level Assessment Form" was introduced. In the second stage, patients were contacted by telephone 15 days after discharge, and the difficulties they experienced in daily living activities were evaluated within the framework of the Daily Living Model using scores ranging from 0 to 10.

Results: Patients experienced the most difficulty in areas such as excretion (8.0 ± 0.9) and anxieties about death and the future, quality of life, and meeting spiritual needs (7.0 ± 0.6), while activities with moderate difficulty were eating and drinking (4.0 ± 0.8), personal hygiene (6.0 ± 0.7), and sleep-rest (6.0 ± 0.5). The activities with the least difficulty were determined to be respiration (1.0 ± 0.4) and maintaining body temperature (2.0 ± 0.6). Patients with a higher level of education experienced less difficulty in sexual life activities. Single patients experienced less difficulty in providing a safe environment and engaging in work-leisure activities compared to married patients. Patients with temporary stomas reported experiencing less difficulty in eating and drinking activities compared to those with permanent stomas.

Conclusion: The study found that the daily living activities of patients with colostomy are affected at different levels. These findings emphasize the importance of a holistic care approach addressing the physical and psychosocial needs of individuals with stomas. Future research should evaluate specific interventions aimed at improving the quality of life of these individuals.

The utility of eDNA for fish species and community monitoring is well-established using targeted amplification (i.e., qPCR and ddPCR) and sequencing approaches (i.e., metabarcoding). However, the lack of optimized and standardized methods across the eDNA workflow reduces the sensitivity of eDNA surveys and precludes the reliable comparison of findings across studies, respectively. DNA extraction is a prime target for optimization efforts because the extraction method is highly variable across eDNA studies despite being one of the most influential factors in detection efficiency across the entire post-collection workflow. Sequence analysis is arguably the least standardized step in the workflow, with new bioinformatics pipelines frequently emerging in the literature and being implemented with innumerable unique combinations of parameter values. The current study aimed to support the optimization and standardization of eDNA methods for fish detection by assessing two commercial DNA extraction kits. The kits, manufactured by Qiagen and Macherey-Nagel, were evaluated based on cost, time, and performance specifications and the success of brook trout detection by metabarcoding across three bioinformatics pipelines, qPCR, and ddPCR. Our protocols were effective in detecting brook trout in all 20 samples analyzed. Brook trout eDNA was detected by ddPCR in nine (90%) Qiagen extracts but only seven (70%) Macherey-Nagel extracts. The concentration of target DNA determined by ddPCR was significantly greater in Qiagen extracts. In comparison, detection success was equal across the two extraction kits using qPCR (70%) and metabarcoding (100% across all three bioinformatics pipelines). The concentration of target DNA determined by qPCR was not significantly different between Qiagen extracts and Macherey-Nagel extracts; however, the number of target DNA reads determined by metabarcoding was significantly greater in Qiagen extracts using MetaWorks, but no significant difference was found using the MiFish Pipeline. Under our experimental conditions, the Qiagen kit was selected as the preferred kit; while slightly more time-intensive, performance was equal or superior across all analysis methods at a substantially lower cost than the Macherey-Nagel kit. We present this method optimization as a case study which can be applied as a framework for eDNA practitioners to facilitate the evaluation of novel eDNA extraction kits as they become available, against established methods in the field.

Background: Benign prostatic hyperplasia (BPH) is a common urinary system disease in elderly men, and transurethral resection of the prostate (TURP) is the gold standard for treating BPH. However, this surgery often leads to intraoperative and postoperative bleeding. Tranexamic acid (TXA) is an antifibrinolytic drug commonly used for hemostasis. This study aims to investigate the hemostatic effect of tranexamic acid in TURP surgery.

Aim: Evaluate the efficacy of tranexamic acid in TURP surgery.

Methods: We systematically searched the PubMed, Embase, EBSCO, Cochrane Library, and Web of Science databases for randomized controlled trials (RCTs) on TXA treatment for bleeding during transurethral resection of the prostate (TURP), published up to December 2025. Data analysis and management were performed using Review Manager version 5.3.

Result: After applying the predefined inclusion and exclusion criteria, a total of eight studies involving 611 patients were included in our meta-analysis. The results of our analysis indicated that the TXA group significantly outperformed the control group in three outcomes: intraoperative blood loss (P = 0.04), postoperative 24-hour hemoglobin levels (P < 0.001), and postoperative 24-hour hemoglobin difference (P = 0.02). However, no significant differences were observed between the TXA and control groups regarding surgical time (P = 0.28) and length of hospital stay (P = 0.08).

Conclusions: Compared to the control group, TXA significantly reduces intraoperative and postoperative bleeding in TURP surgery, making it valuable for anemic patients and in reducing surgical complications.

Background: While gut microbiota dysbiosis is a hallmark of inflammatory bowel disease (IBD), the causal microbial drivers and their host-mediated mechanisms remain elusive. This study leverages an integrated multi-omics approach, combining Mendelian randomization (MR) and transcriptome analysis, to bridge the gap from microbial causality to host molecular pathways.

Methods: We performed a two-sample MR analysis using large-scale genome-wide association study (GWAS) data to identify specific gut microbiota taxa with a causal effect on IBD risk. Subsequently, we conducted a multi-level bioinformatic analysis of IBD patient transcriptomes to elucidate the downstream host genes, regulatory networks, and immune cell interactions modulated by these causal microbes.

Results: Our MR analysis established a robust causal protective effect of the family Bifidobacteriaceae against IBD. Integrating this finding with transcriptomic data, we identified three key host genes as potential mediators acting through distinct mechanisms: LCT, whose regulation may foster a protective prebiotic niche; MCM6, which appears to function as a hub driving the proliferation of pathogenic immune infiltrates; and UBXN4, a critical regulator of cellular proteostasis, the failure of which can precipitate inflammatory stress.

Conclusions: This study moves beyond association to delineate a causal protective role for Bifidobacteriaceae in IBD and pinpoints specific host genes (LCT, MCM6, UBXN4) through which this effect is likely orchestrated. These findings provide a novel mechanistic framework for host-microbiota interactions and highlight new pathways for therapeutic intervention in IBD.

Fatigue-related changes in running technique may depend on a runner's preferred style. Understanding these changes can inform targeted training to enhance performance. In previous work, we identified two technique-based clusters of runners: the "neutral pelvis" and the "tilted pelvis" clusters. This follow-up study examined whether fatigue induces cluster-specific technique adaptations. Sixty runners (neutral pelvis, n = 32; tilted pelvis, n = 28) completed a treadmill run to exhaustion at 5% above their individual lactate threshold speed. Stride frequency, duty factor, trunk and lower limb kinematics were compared between clusters at the start, middle, and end of the run using a 2-way repeated measures analysis of variance (ANOVA). All runners reached exhaustion in ∼20 minutes, covering ∼5 km. Runners from the tilted pelvis cluster consistently showed greater trunk-to-pelvis extension, more pelvic anterior tilt and greater hip flexion, and a smaller duty factor compared with the neutral pelvis cluster throughout the run. Fatigue-related adaptations were similar across clusters: reduced stride frequency, increased duty factor, greater trunk flexion during stance, increased plantar flexion, and higher coordination variability (trunk-to-pelvis-hip, hip-knee, knee-ankle) during swing. Although fatigue affected both groups similarly, the underlying technique differences suggest these adaptations may have distinct mechanical or performance consequences. Understanding such cluster-specific responses can help coaches tailor training and fatigue management strategies to individual running styles.

Background: Various associations between adipose tissue and atherosclerosis (AS) have been revealed. This study aims to identify biomarkers in the epididymal adipose tissue of AS mice and to explore their effects on adipose tissue inflammation and adipogenesis.

Methods: The gene expression profiles of epididymal adipose tissue (GSE57659 and GSE76812) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEG) screened by Limma R package and genes searched by weighted gene correlation network analysis (WGCNA) were performed to classify common genes associated with AS. The Protein-Protein interaction (PPI) network was constructed by Cytoscape software, and hub genes were eventually determined by the Cytohubba plugin. Finally, one of these hub genes was selected. The cell proliferation ability was assessed using the CCK8 assay. Oil Red O staining and Western blot were employed to evaluate the lipid content in adipocytes. The extent of the inflammatory response in adipocytes was determined by Enzyme-Linked Immunosorbent Assay (ELISA).

Results: A total of 125 DEGs were identified between the control group and the atherosclerosis group. Among these, 34 genes were selected based on two key modules identified through WGCNA. Subsequently, five key nodes were identified, namely Capg, Timp1, Lgals3, Agt, and Mmp9. Capg was selected as the primary gene of interest for further investigation. Following the transfection of 3T3-L1 cells with lentivirus, Capg was overexpressed. Capping actin protein, gelsolin like (CAPG) significantly enhanced preadipocyte proliferation, as demonstrated by CCK-8 and upregulated expression of the Cyclin D1. Furthermore, Oil Red O staining revealed a marked elevation in intracellular lipid accumulation upon CAPG overexpression. Western blot analysis showed increased protein levels of PPAR γ and adiponectin. Furthermore, CAPG in 3T3-L1 cells resulted in a marked upregulation of IL-6 and MCP-1.

Conclusion: CAPG promotes the proliferation and differentiation of adipocyte precursor cells. Additionally, CAPG enhances the inflammatory response in adipocytes, potentially serving as a key molecule mediating obesity-related atherosclerosis.

Background: Basil (Ocimum basilicum L.), a widely cultivated culinary and medicinal herb in the Lamiaceae family, is particularly vulnerable to various environmental stressors. This study examines how water deficit and elevated nutrient-solution electrical conductivity (EC) affect the photosynthetic efficiency of basil plants grown in an nutrient film technique (NFT) hydroponic system.

Methods: Chlorophyll fluorescence was assessed using both continuous-excitation and modulated pulse-amplitude-modulated (PAM) techniques. Fluorescence parameters were monitored in plants at two developmental stages, immature and mature, under drought and high-electrical-conductivity (EC) stress.

Results: Both stressors altered Photosystem II (PSII)-related fluorescence parameters, but high EC stress caused a wider spectrum of changes. In mature plants, those alterations were less pronounced, indicating enhanced tolerance likely due to more efficient electron transport and greater structural stability of the photosynthetic apparatus. The obtained results supported our hypothesis, that drought and high-EC stress would differentially impair photosynthetic efficiency, with drought imposing stronger osmotic limitations on photochemistry and high EC introducing additional ionic constraints. These stresses generated distinct physiological response patterns detectable by chlorophyll fluorescence measurements.

Background: It is well known that the main vector of invasion by land flatworms has been the export of potted plants from their countries of origin to the invaded country. Within the invaded country, transport to garden centres where the plants are sold, and transport to the buyer's garden, are also carried out by humans. However, it is less clear how flatworms can then invade neighbouring gardens, given their slow movement rates.

Methods: We re-examined citizen science reports in metropolitan France received over more than 12 years (2013-2025), searching the 6500 original emails for keywords suggesting transport by pets.

Results: We found 15 citizen science observations of cats (13) or dogs (2) with flatworms stuck to their fur. Surprisingly, all reports concerned the species Caenoplana variegata, the two-tone planarian, even though this species is not the most abundant in gardens in France. Over the period 2020-2024, observations of C. variegata on dogs and cats represented 7.3% (10/137) of reports.

Discussion: We suspect that transport by domestic animals is a significant factor favouring invasion by C. variegata, which possesses a particularly sticky mucus adapted to arthropod predation. This is compounded by the fact that the species reproduces asexually in Europe, and therefore the transport of a single individual may be sufficient to facilitate an invasion. We calculated a conservative estimate of the distances travelled outdoors by all the dogs and cats in France, which was 18 billion km/year; if only a tiny proportion of these journeys involve pets carrying flatworms, this transport as a dispersal factor becomes entirely plausible.

Conclusions: We believe that animal transport is a significant factor favouring land flatworm invasion, but that this does not apply to all species. A citizen science initiative could provide a better understanding of the extent and importance of animal transport as a factor for land flatworm invasions in other countries.

Purpose: This study investigates metabolic profiles in follicular fluid of patients with endometriosis (EM), polycystic ovary syndrome (PCOS), tubal blockage (TB), and unexplained infertility (UEI), assessing their associations with follicular development and in vitro fertilization (IVF) outcomes. It aims to identify metabolic alterations and potential biomarkers for EM diagnosis and personalized reproductive strategies.

Methods: Follicular fluid samples were collected from 12 infertility patients (3 EM, 3 PCOS, 3 TB, and 3 UEI) undergoing IVF. Metabolomic profiling was performed using liquid chromatography-mass spectrometry (LC-MS), followed by pathway enrichment analysis to identify key metabolic pathways. Statistical analyses were conducted to compare metabolic profiles across groups, assess correlations with follicular development rate (FDR), and evaluate potential biomarkers for EM diagnosis.

Results: EM patients showed significant metabolic changes, including reduced steroid biosynthesis and elevated thiamine metabolism metabolites, linked to lower FDR. Oxidative stress markers (3-chloro-L-tyrosine, 8-oxoerythraline) were elevated and negatively correlated with FDR. A predictive model identified D-mannosamine, D-galacturonic acid, and 3-chloro-L-tyrosine as potential EM biomarkers with high diagnostic accuracy.

Conclusion: This study reveals distinct metabolic disruptions in the follicular fluid of EM patients, particularly in steroid biosynthesis and thiamine metabolism pathways, which are linked to impaired follicular development. The identification of specific metabolites as potential biomarkers for EM provides a foundation for developing diagnostic approaches that minimize the need for additional invasive procedures and support personalized assisted reproductive technology (ART) strategies. This pilot study requires further validation to confirm these findings and translate them into clinical practice.