Search Results (181)

Myocardial ischemia–reperfusion (I/R) injury is a frequent complication of acute myocardial infarction (AMI), yet clinical biomarkers and targets remain limited. Although tRNA-derived small RNAs (tsRNAs) are emerging cardiovascular regulators, their roles in I/R injury are not fully elucidated. We identified tsRNA-3025a via sequencing in mouse I/R models and validated its clinical significance. Circulating tsRNA-3025a was significantly upregulated in AMI and unstable angina patients, independently predicting adverse events within 30 days. Functionally, tsRNA-3025a exacerbated apoptosis and mitochondrial dysfunction in vitro, while its in vivo silencing reduced infarct size, improved cardiac function and increased the proportion of Ki67- and pH3-positive cardiomyocytes. Mechanistically, tsRNA-3025a aggravated injury by targeting PIK3C2A, thereby suppressing autophagosome formation and impairing protective autophagic flux during reperfusion. In conclusion, circulating tsRNA-3025a serves as a prognostic biomarker for post-PCI patients. Targeting tsRNA-3025a attenuates myocardial I/R injury and restores myocardial regeneration and repair by regulating PIK3C2A-mediated protective autophagy flux. Full article

Pneumocystis is an opportunistic fungal pathogen that causes severe Pneumocystis pneumonia (PCP) in immunocompromised individuals and laboratory animals. Three host-specific species—Pneumocystis murina (P. murina), Pneumocystis carinii (P. carinii), and Pneumocystis jirovecii (P. jirovecii)—are closely associated with infections in humans and laboratory animals. However, the conventional method, microscopic staining, suffers from low sensitivity, operator-dependent subjectivity, and inability to differentiate species, highlighting the urgent need for a multiplex qPCR assay. In this study, we established a multiplex qPCR method targeting the mtLSUrRNA gene of P. murina, the TS gene of P. carinii, and the mtSSUrRNA gene of P. jirovecii. Primers and probes were designed and optimized using a matrix approach. The method was systematically evaluated for sensitivity, specificity, and reproducibility using recombinant plasmid standards and laboratory animal samples. Validation was performed on 260 mouse lung samples, 30 P. murina-positive samples, 25 rat lung samples, 6 rat bronchoalveolar lavage fluid (BALF) samples, and 8 P. carinii-positive samples. Results were compared with single-plex qPCR and staining microscopy (performed on 68 mouse lung samples, 38 Pneumocystis-positive samples). The limits of detection (LOD) were 5 copies/μL for P. murina, 6 copies/μL for P. carinii, and 8 copies/μL for P. jirovecii. Standard curves showed excellent linearity (R² ≥ 0.999) with amplification efficiencies of 90–110%. No non-specific reactions were observed with 22 common pathogens, and intra-/inter-group coefficients of variation (CV%) were below 1%. Moreover, interference testing revealed minimal matrix effects on the amplification system and no mutual interference among the primers and probes. The multiplex qPCR detected all 38 positive samples (100%), showing 100% concordance with single-plex qPCR, whereas Giemsa staining detected none (0%) and toluidine blue staining only 60% (3/5) of the tested positives, suggesting that the multiplex qPCR achieved higher detection rates than staining microscopy. In conclusion, this novel multiplex qPCR method offers high sensitivity, specificity, and reproducibility, providing a sensitive and specific tool for laboratory animal health monitoring and epidemiological surveillance. Its clinical application for human PCP diagnosis requires further validation with authentic human specimens. Full article

The rumen epithelium of Tibetan sheep plays a critical role in energy metabolism and immune defense; however, its post-transcriptional regulatory mechanisms under high-altitude hypoxia stress remain unclear. In this study, we employed integrated mRNA and miRNA transcriptome sequencing to analyze the adaptive strategies of the rumen epithelium in Tibetan sheep at different altitudes. A total of 2183 differentially expressed genes (DEGs) and 135 differentially expressed miRNAs (DEmiRNAs) were identified. Functional enrichment analysis revealed that DEGs and their target genes were significantly enriched in immune-related pathways such as the NF-κB signaling pathway and cytokine–cytokine receptor interaction, as well as metabolic pathways including oxidative phosphorylation and branched-chain amino acid degradation. Integrated network analysis highlighted key regulatory pairs, including oar-miR-370-3p targeting PCK2 and IL1R2, and novel-miR-781 regulating PIK3R5, suggesting coordinated modulation between mitochondrial homeostasis and immune responses. Specifically, the upregulation of immune genes (CCL19, MADCAM1) and heat shock proteins at TS4500m indicates enhanced mucosal immunity and stress tolerance, while altered expression of metabolic genes reflects a shift in energy substrate utilization. These findings elucidate a complex mRNA-miRNA regulatory network that enables Tibetan sheep to maintain rumen epithelial integrity and energy balance under extreme high-altitude conditions, providing novel insights into the molecular basis of hypoxia adaptation in ruminants. Full article

As a representative form of extreme weather, typhoons inflict widespread and systemic damage, posing a severe threat to the livestock industry. The stress they induce, typhoon stress (TS), is an unavoidable and complex environmental challenge that severely disrupts the ovarian function of Wenchang chickens. In this preliminary study, we employed a two-group comparison design (n = 6 per group) integrating behavioral observations, serum biochemical assays, histopathological examinations, and molecular analyses (qPCR, 16S rDNA sequencing, and transcriptome sequencing) to explore the role of the microbiota–gut–brain–ovarian axis (MGBOA) in this process. The findings revealed that TS markedly reduced water intake and locomotor activity, while it elevated serum corticosterone (CORT) and oxidative stress markers. It also induced shifts in gut microbiota composition, including a decrease in Bacteroides and an increase in Escherichia–Shigella. Furthermore, TS compromises duodenal intestinal barrier integrity, as evidenced by downregulation of the tight junction proteins TJP1 and CLDN1, structural damage to intestinal villi, and a reduced villus-to-crypt ratio. In the hypothalamus, VIP mRNA expression was upregulated, while GHSR expression was downregulated; the expression of the tight junction protein CLDN5 was also reduced. In the ovary, reproductive potential was suppressed, manifested by a reduction in follicle number and downregulation of STAR expression. Ovarian transcriptome analysis highlighted enrichments in pathways associated with inflammation (e.g., Toll-like receptor signaling) and lipid metabolism (e.g., PPAR signaling). These results support the hypothesis that TS impairs egg production via the MGBOA, providing preliminary mechanistic insights into how environmental stressors might disrupt animal productivity through MGBOA-mediated pathways. Full article

This study investigated the synergistic effects of liquid fermentation of rapeseed meal (RSM) on feed microbiota, growth performance, and muscle development in growing pigs. RSM was fermented using four compound probiotics and eleven enzyme preparations, and microbial changes were analyzed using 16S rRNA sequencing. Seventy-two Duroc × Jingfen White pigs were randomly assigned to three groups: soybean meal (Ctrl), RSM, and fermented RSM (FRSM). FRSM showed higher trichloroacetic acid-soluble protein (TCA-sp) content and significantly lower neutral detergent fiber (NDF), acid detergent fiber (ADF), anti-nutritional factors (ANFs), and toxins (TS) (p < 0.01). Fermentation increased microbial diversity, with higher abundances of Lactobacillus and Pediococcus. Compared with Ctrl and RSM, the feed-to-gain ratio (F/G) decreased in the FRSM group (p < 0.01). FRSM also improved serum antioxidant capacity, enhanced intestinal villus height (VH)and villus height/crypt depth ratio (VH/CD), and upregulated the expression of tight junction proteins (ZO-1, occludin) and the anti-inflammatory factor IL-10 (p < 0.01). FRSM group also increased myofiber diameter and cross-sectional area in the longissimus dorsi and elevated MyoD, MyoG and Myf5 expression (p < 0.01). RNA-seq revealed 2094 differentially expressed genes enriched in metabolic pathways. Overall, FRSM improved growth performance, intestinal health, and muscle development in growing pigs, which may guide the development of protein resource utilization technologies. Full article

Radiation-responsive promoters represent a functionally distinct class of transcriptional regulatory elements that translate genotoxic stress signals into quantifiable gene expression outputs. These promoters occupy a unique mechanistic position within the broader radiation biomarker landscape: rather than directly measuring molecular damage products, they report the cellular interpretation of radiation-induced stress through coordinated gene regulatory networks. This review provides a systematic analysis of five major classes of radiation-responsive promoters—microRNA (miRNA) promoters, tRNA-derived small RNA (tsRNA) promoters, acute-phase protein gene promoters, DNA repair gene promoters, and long non-coding RNA (lncRNA) promoters—with emphasis on their regulatory logic, dose-response characteristics, and current evidence for clinical deployment. We further describe four complementary screening strategies: homology-based conservation analysis, functional genomics and transcriptomics, epigenetic modification profiling, and synthetic biology promoter engineering. Applications spanning biosensor development, biological dosimetry, treatment response prediction, and radiation-guided gene therapy are evaluated within a two-track framework that distinguishes biomarker-oriented applications (Track A) from tool-oriented reporter gene systems (Track B). Critical appraisal of current limitations—including insufficient clinical-grade validation, absence of standardized dose-response curves, and reproducibility deficits—is integrated throughout. Future priorities include multi-center prospective validation studies, FAIR-compliant data infrastructure, AI-driven multi-omics integration, and point-of-care detection platforms. Radiation-responsive promoter biology holds significant potential for advancing precision radiotherapy and nuclear emergency medical response, contingent upon systematic closure of the current evidence gap relative to established gold-standard cytogenetic methods. Full article

Background: Accurate estimation of the postmortem interval (PMI), the time elapsed between death and body discovery, is a critical challenge in forensic science due to the complex interplay of factors affecting decomposition. Traditional methods based on macroscopic changes often lack precision, especially in later postmortem stages. Methods: This study aimed to develop a novel PMI estimation framework by integrating the dynamics of endogenous small non-coding RNAs (sncRNAs) and exogenous bacterial-derived small RNAs (sRNAs) using sRNA transcriptomics and machine learning. Results: Cardiac RNA degradation strongly correlated with PMI, with a random forest (RF) model achieving high accuracy (coefficient of determination (R²) = 0.939, mean absolute error (MAE) = 2.987 h). Employing PANDORA-seq, we profiled temporal changes in sncRNAs (miRNAs, tsRNAs and piRNAs) in postmortem cardiac tissue within 30 h in a mouse model, while simultaneously assessing RNA integrity (RIN) across eight organs. PANDORA-seq revealed stable sncRNA landscapes with specific dynamic shifts, leading to the identification of seven novel biomarkers (four tsRNAs, three piRNAs) for PMI prediction (R² = 0.760, MAE = 158.990 min). Bacterial-derived sRNAs, predominantly from Staphylococcus aureus, were upregulated at 30 h postmortem, suggesting complementary biomarker potential. Bioinformatics analysis indicated that host miRNAs may target bacterial mRNAs, hinting at cross-kingdom interactions. Conclusion: These findings highlight the potential of integrated endogenous and exogenous sRNA analysis in PMI estimation, providing a high-precision, rapid diagnostic tool and revealing complex postmortem molecular processes. Full article

Background: Norovirus is the leading cause of viral gastroenteritis globally, with environmental persistence contributing significantly to transmission dynamics. Despite the recognized burden in the Middle East, systematic environmental surveillance data from restaurant settings remain critically limited, particularly regarding the role of cleaning materials as reservoirs for viruses. Middle East region. Methods: A cross-sectional environmental surveillance study was conducted across 20 restaurants in Muscat and A’Sharqiyah regions, Oman (September 2020–August 2021). Forty environmental samples comprising 20 dishcloths and 20 tabletop swabs were collected from diverse restaurant types. Viral RNA was extracted using QIA amp Viral RNA MiniKit and analyzed using real-time RT-PCR following ISO/TS 15216-1:2017 protocols with genogroup-specific primers. Results: Norovirus RNA was detected in 4 of 40 samples (10%, 95% CI: 2.8–23.7%) with higher prevalence on dishcloths (3/20, 15%, 95% CI: 3.2–37.9%) versus tabletops (1/20, 5%, 95% CI: 0.1–24.9%). All positive samples were genogrouped II with cycle threshold values of 31.8–36.2. Positive samples originated from three restaurants in high-traffic urban areas, with fast-food establishments showing the highest contamination. Field observations revealed substandard 41 sanitation practices, including frequent dishcloth reuse without disinfection. Conclusions: This paper fills a gap in the current body of knowledge by offering initial systematized evidence on norovirus contamination of the environment in restaurants within the Gulf region. The results indicate that cleaning things, especially the dishwasher cloths, are the main viral reservoirs, and the contamination rates are three times higher than food-containing surfaces. These results underscore the urgent need for enhanced sanitation protocols that specifically target cleaning implements rather than surfaces alone and emphasize the importance of routine environmental surveillance in understanding and interrupting norovirus transmission dynamics in food service settings. Full article

Male infertility, a global health issue marked by spermatogenic failure, hinges on selenium (Se) as a key element for normal spermatogenesis. Among different Se species, Se-methylselenocysteine (MeSeCys) has been developed as a natural organic Se supplement with potent antioxidant and anti-inflammatory properties, but its direct effects on male reproduction need to be further explored. This study investigated the effect of MeSeCys on GC-1 spg (GC-1) and GC-2 spd (ts) (GC-2) cell lines, which mimic early stages. Treatment with 75 μmol/L MeSeCys for 24 h markedly enhanced the viability of both cell lines, with a more pronounced effect observed in GC-1 than in GC-2 cells. Moreover, this study demonstrated that MeSeCys enters cells through SLC7A11 or LRP8 channels and elevates intracellular Se levels in both GC-1 and GC-2 cells, with higher levels observed in GC-1 cells. RNA sequencing (RNA-seq) and bioinformatics analysis revealed that MeSeCys may regulate selenocompound metabolism and the glutathione metabolism pathway in both cell lines, increasing their intracellular glutathione (GSH) levels. Importantly, in GC-1 cells, MeSeCys specifically modulates the mTOR pathway, which further modulates glutathione metabolism and intracellular redox balance. This finding provides novel insights into the beneficial effects of MeSeCys on male reproductive cells, highlighting its potential as a nutritional supplement for male reproductive health. Full article

Transfer RNA-derived small RNAs (tsRNAs) represent an emerging category of small non-coding RNAs generated through specific cleavage of precursor or mature tRNAs. Increasingly recognized as pivotal players in the pathogenesis of complex malignancies, tsRNAs not only regulate cancer progression but also hold promising clinical potential for cancer diagnosis and treatment. This review highlights recent advances in the application of high-throughput sequencing technologies in the systematic identification of tsRNAs, with a focus on their roles in cancer diagnosis, prognostic assessment, and targeted therapy. Delving into the translational medicine dimensions of tsRNAs may provide novel strategies for molecular diagnosis and therapeutic interventions in oncology. Full article

Transport stress (TS) significantly impacts immune function and infection, of which the cellular and molecular mechanisms remain elusive. In this study, we investigated the effects of TS on immune responses and its role in exacerbating Mycobacterium tuberculosis (Mtb) infection. TS induced anxiety-like behaviors, disrupted hypothalamic–pituitary–adrenal (HPA) axis homeostasis, altered hormone secretion patterns, and led to dysregulation of stress response genes in mice. Single-cell RNA sequencing of the spleen revealed severe immune dysfunction upon TS, characterized by inhibition of Th17 differentiation, IL-17 signaling, and antigen presentation. Importantly, TS affects the crosstalk between the HPA axis and the spleen through ligand–receptor interactions. Furthermore, TS exacerbated the severity of Mtb infection and disturbed infection-induced gene regulation. TS impairs Th1/Th2 differentiation through neuroendocrine immune dysregulation, and also compromises macrophage immune function, further weakening host defense. These findings could greatly contribute to understanding TS-induced neuroendocrine immune regulation and deteriorated infection. Full article

The role of extracellular vesicle non-coding RNAs in host–parasite interactions remains poorly understood, particularly for human liver flukes. Although tRNA-derived small RNAs (tsRNAs) are emerging as new regulatory molecules in parasite exosomes, they have not yet been characterized for the liver flukes. We performed small RNA sequencing to profile tsRNAs in the exosome-like vesicles derived from the liver fluke Opisthorchis felineus. Transcriptomic data from human cholangiocytes were analyzed to assess the enrichment of the predicted target genes among differentially expressed genes. We identified 247 functional tRNA genes in the O. felineus genome. Exosome-like vesicles were highly enriched for particular tsRNAs: derived from tRNA-Asp-GTC, tRNA-Ile-AAT, tRNA-Lys, tRNA-His, and tRNA-Tyr. This enrichment was independent of both genomic tRNA copy number and the amino acid composition of the trematode proteome. In silico prediction revealed that these tsRNAs target human genes involved in cell cycle, migration, and proliferation. Notably, these predicted target genes were significantly enriched among the differentially expressed genes in treated cholangiocytes. Our study provides the first evidence that O. felineus exosomes carry a specific repertoire of tsRNAs with the potential to regulate host gene networks. We propose that tsRNAs may contribute to host cell manipulation during O. felineus infection. Full article

Background: Pulmonary fibrosis (PF) is an irreversible interstitial lung disease in which the TGF-β/SMAD signaling pathway plays a critical role in its pathogenesis. Due to the anti-inflammatory and antioxidant properties of Thymus species, it is hypothesized that they may suppress pulmonary fibrosis by modulating the TGF-β/SMAD pathway. This study aimed to investigate the potential antifibrotic effects of Thymus syriacus essential oil (TS) on the TGF-β/SMAD pathway in bleomycin-induced PF. Methods: PF was induced with bleomycin, and TS was administered at concentrations of 50 and 100 mg/mL for 28 days. mRNA and protein levels of TGF-β1, SMAD2, COL1, and α-SMA in lung tissues isolated were analyzed using real-time PCR and ELISA. TNF-α levels in BALF were measured by ELISA. ROS and MDA levels in lung issues were determined using 2,7-DHCFDA and TBARS tests, respectively. Histopathological evaluation was performed using Hematoxylin–Eosin and Masson’s trichrome staining. Blood samples were analyzed for kidney, liver, and cardiac toxicity markers. The chemical composition of TS was determined by GC–MS. Results: TS significantly reduced levels of TGF-β1, SMAD2, COL1, α-SMA, TNF-α, ROS and MDA compared to the BLM group. PF alterations were markedly attenuated by TS treatment. Thymol, p-cymene and carvacrol were identified as major constituents of TS. Conclusion: Overall, TS alleviates pulmonary fibrosis by suppressing the TGF-β/SMAD2 signaling pathway. Full article

Oncolytic coxsackievirus B3 (oCVB3) strain PD-H has shown potent oncolytic efficacy and a remarkable safety profile in the treatment of colorectal cancer in vivo after intratumoral (i.t.) injection. In this study, we investigated the safety and efficiency of PD-H following intravenous (i.v.) virus administration. When injected i.v. into Balb/C mice bearing subcutaneous Colon-26 tumors, PD-H led to slightly reduced tumor progression and a significant increase in animal survival, but it also caused multi-organ infection and tissue damage. To improve the safety profile of PD-H, we inserted microRNA target sites (miR-TS) of the heart-specific miR-1, pancreas-specific miR-375, liver-specific miR-122, and brain-specific miR-124 or the tumor-suppressor miR-145 into the genome of PD-H and generated the viruses PD-622TS and PD-145TS. Both viruses replicated similarly and induced cytotoxicity comparable to that of PD-H in the colorectal carcinoma cell lines Colon-26 and CT-26Luc. Their replication was inhibited in HEK293T cells transiently transfected with the cognate microRNAs. In vivo, i.v. administration of PD-145TS and PD-622TS to healthy Balb/C mouse resulted in significantly lower viral titers in the organs of mice and led to significantly less-intense pathological alterations compared to PD-H. PD-622TS injected i.v. into Balb/C mice with CT-26Luc-induced peritoneal carcinomatosis did not induce off-target alterations in normal organs, but it failed to induce a therapeutic effect. These data indicate that PD-H or microRNA-regulated PD derivatives exhibit only limited therapeutic efficacy following i.v. injection in colorectal tumor-bearing mice. However, the newly engineered microRNA-regulated PD-H variants demonstrate improved safety profiles. Full article

Neurodevelopmental disorders (NDDs) such as autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and intellectual disability (ID) arise from disruptions of molecular programmes that coordinate neurogenesis, synaptogenesis, and circuit maturation. While genomic studies have identified numerous susceptibility loci, genetic variation alone accounts for only part of disease heritability, underscoring the importance of post-transcriptional and epigenetic regulation. Among these regulatory layers, non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), PIWI-interacting RNAs (piRNAs), and transfer RNA-derived small RNAs (tsRNAs), have emerged as central modulators of neural differentiation, synaptic plasticity, and intercellular signalling. Recent multi-omics and single-cell studies reveal that ncRNAs fine-tune chromatin accessibility, transcriptional output, and translation through tightly integrated regulatory networks. miRNAs shape neurogenic transitions and circuit refinement; lncRNAs and circRNAs couple chromatin architecture to activity-dependent transcription; and tsRNAs and piRNAs extend this regulation by linking translational control to epigenetic memory and environmental responsiveness. Spatial transcriptomics further maps ncRNA expression to vulnerable neuronal and glial subtypes across cortical and subcortical regions. Clinically, circulating ncRNAs, especially those packaged in extracellular vesicles, exhibit stable, disease-associated signatures, supporting their potential as minimally invasive biomarkers for early diagnosis and patient stratification. Parallel advances in RNA interference, antisense oligonucleotides, CRISPR-based editing, and vesicle-mediated delivery highlight emerging therapeutic opportunities. These developments position ncRNAs as both mechanistic determinants and translational targets in NDDs, offering a unifying framework that links genome regulation, environmental cues, and neural plasticity, and paving the way for next-generation RNA-guided diagnostics and therapeutics. Full article