Search Results (3,267)

Cucumber green mottle mosaic virus (CGMMV) represents a serious threat in the production of watermelon. Small RNAs facilitate a mechanism known as RNA interference (RNAi), which regulates gene expression. RNAi technology employs foreign double-stranded RNAs (dsRNAs) to target and reduce the expression levels of specific genes in plants by interfering with their mRNAs. In this study, watermelon plants were treated with dsRNAs of CGMMV MET, IR, and HEL fragments that had been generated in E. coli HT115. We investigated variations in several factors, including viral accumulation, virus-derived small interfering RNAs (vsiRNAs), and symptom severity. MET-dsRNA, IR-dsRNA and HEL-dsRNA dramatically decreased the symptoms of CGMMV in plants in the growth chamber test. Plants treated with viral-derived dsRNA showed a considerable decrease in both virus titers and vsiRNA levels. We also explored the mobility of spray-on dsRNA-derived long dsRNA and discovered that it could be identified in both inoculated leaves and the systemic leaves. IR-dsRNA outperformed MET-dsRNA and HEL-dsRNA in dsRNA therapy. Illumina sequencing of small RNAs from watermelon plants treated with IR-dsRNA and those that were not treated showed that the decreased accumulation of vsiRNAs was consistent with interference with CGMMV infection in systemic leaves. dsRNA-treated plants showed a higher level of 24-nt viral siRNA and lower level of 22-nt viral siRNA accumulation, while 22-nt viral siRNA predominated in untreated plants, indicating that dsRNA treatment improved DCL3 activity. In conclusion, our research provides deeper insights into the mechanism of antiviral RNA interference and confirms the effectiveness of applying dsRNA locally to enhance plant antiviral activity. Full article

Glioblastoma (GBM) is an aggressive and lethal malignant brain tumor. Cell–cell interactions (CCIs) in the tumor microenvironment, mediated by ligand–receptor (LR) pairs, are known to contribute to its poor prognosis. However, the prognostic influence of CCIs on patients with GBM and the spatial expression profiles of such LR pairs within tumor tissues remain incompletely understood. This study aimed to identify prognostic LR pairs in GBM and their intratumoral localization via multitranscriptomic analysis. The CCIs among GBM cells as well as between GBM and niche cells were comprehensively evaluated using 40,958 cells in single-cell RNA sequencing datasets. They were found to form intercellular networks in GBM by specific LR pairs, which were mainly implicated in extracellular matrix (ECM)-related biological processes. Survival analysis revealed that 13 LR pairs related to ECM biological processes contributed to poor prognosis (p < 0.05, and 95% confidence intervals > 1). Notably, our spatial transcriptomic analysis using three independent GBM cohorts revealed that the identified poor prognostic LR pairs were localized in specific regions within GBM tissues. Although the clinical importance of these LR pairs requires further investigation, our findings suggest potential therapeutic targets for GBM. Full article

As with other non-coding RNAs (ncRNAs), the aberrant expression of long non-coding RNAs (lncRNAs) can be associated with different forms of cancers, including breast cancer (BC). Various lncRNAs may either promote or suppress cell proliferation, metastasis, and other related cancer signaling pathways by interacting with other cellular machinery, thus affecting the expression of BC-related genes. However, lncRNAs are characterized by features that are unlike protein-coding genes, which pose unique challenges when it comes to their study and utility. They are highly diverse and may display contradictory functions depending on factors like the BC subtype, isoform diversity, epigenetic regulation, subcellular localization, interactions with various molecular partners, and the tumor microenvironment (TME), which contributes to the intratumoral heterogeneity and phenotypic plasticity. While lncRNAs have potential clinical utility, their functional heterogeneity coupled with a current paucity of knowledge of their functions present challenges for clinical translation. Strategies to address this heterogeneity include improving classification systems, employing CRISPR/Cas tools for functional studies, utilizing single-cell and spatial sequencing technologies, and prioritizing robust targets for therapeutic development. A comprehensive understanding of the lncRNA functional heterogeneity and context-dependent behavior is crucial for advancing BC research and precision medicine. This review discusses the sources of lncRNA heterogeneity, their implications in BC biology, and approaches to resolve knowledge gaps in order to harness lncRNAs for clinical applications. Full article

Biomphalaria pfeifferi snails serve as the major intermediate host for intestinal schistosomiasis in Sudan. The genetic structure and infection status of 163 B. pfeifferi collected from six localities in Gezira State, Sudan (East Gezira, Greater Wadmedani, Hasahisa, North Umelgura, South Gezira, and Managil) were characterized. Cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) mitochondrial genes were used for B. pfeifferi molecular identification and genetic diversity investigation. Schistosoma mansoni infection was detected using the traditional cercarial shedding and molecular methods (Sm^F/R primers). Five COI haplotypes and ten 16S haplotypes were identified, with haplotype diversity of 0.50 for COI and 0.11 for 16S. High evolutionary divergence was observed between groups (Fst = 0.94) for the COI, and low genetic divergence (Fst = 0.04) for the 16S, indicating genetic divergence among Sudanese B. pfeifferi, with the 16S showing lower divergence than the COI, consistent with a post-bottleneck population expansion. Cercarial shedding detected an overall infection prevalence of 3.6% (8/219), with only two snails from Hasahisa shedding S. mansoni cercariae. The Sm^F/R primers revealed a higher infection prevalence of 7.4% (12/163), with all S. mansoni positive samples found at the Hasahisa site. Findings highlight the value of molecular diagnostic tools for accurate surveillance and emphasize the need for site-specific control strategies. Full article

This study examined the effect of long-term physical activity during the finishing period on meat and fat quality, and metabolic gene expression in obese Alentejano (AL) pigs. From 87.3 to 161.6 kg BW and for 130 days, eighteen pigs were assigned to either individual pens without an exercise area (NE, n = 9) or an outdoor park with an exercise area (WE, n = 9). Both groups received identical commercial diets at 85% ad libitum intake. Loin (Longissimus lumborum—LL), tenderloin (Psoas major—PM), and dorsal subcutaneous fat samples were obtained at slaughter, and analyzed for fatty acid composition and gene expression. Physical activity modulated the fatty acid profile and key metabolic genes in muscle and fat tissues. WE pigs showed higher palmitoleic (p = 0.031) and linolenic (p = 0.022) acids in LL, while Fatty acid synthase and Leptin in LL were downregulated (p = 0.071 and p = 0.018, respectively); Fatty acid binding protein 4 was downregulated (p = 0.003) and Stearoyl-CoA desaturase upregulated (p = 0.020) in the PM of WE pigs, indicating changes in lipid metabolism. Also, Myosin heavy chain 7 was upregulated (p = 0.016) in LL, suggesting oxidative muscle remodeling. These findings suggest that moderate, long-term physical activity during finishing induces modest but favorable metabolic adaptations in muscle and fat tissues without compromising meat quality in AL pigs, supporting its use in traditional rearing systems aimed at balancing animal welfare and product quality in local breeds. Full article

Postpartum uterine diseases such as metritis and endometritis impair reproductive performance and cause substantial economic losses in dairy cows worldwide. The multifactorial etiology, involving polymicrobial infections and complex host immune responses, poses diagnostic and therapeutic challenges. Traditional treatments rely on antibiotics, e.g., cephalosporins like ceftiofur and cephapirin, with broad-spectrum efficacy. However, emerging antimicrobial resistance, biofilm formation by pathogens such as Trueperella pyogenes, Fusobacterium necrophorum, and Escherichia coli, and bacterial virulence factors have reduced effectiveness of conventional therapies. Advances in systems biology, particularly proteomics, metabolomics, and microRNA (miRNA) profiling, have provided unprecedented insights into the molecular mechanisms underpinning uterine disease pathophysiology. Proteomic analyses reveal dynamic changes in inflammatory proteins and immune pathways, whereas metabolomics highlight shifts in energy metabolism and bacterial–host interactions. Furthermore, miRNAs have critical roles in post-transcriptional gene regulation affecting immune modulation, inflammation, and tissue repair, and also in modulating neutrophil function and inflammatory signaling. Uterine inflammation not only disrupts local tissue homeostasis but also compromises early embryo development by altering endometrial receptivity, cytokine milieu, and oocyte quality. Integration of multi-omics approaches, combined with improved diagnostics and adjunct therapies—including micronutrient supplementation and immunomodulators—offers promising avenues for enhancing disease management and fertility in dairy herds. This review synthesizes current knowledge on proteomics, metabolomics, and miRNAs in postpartum uterine diseases and highlights future directions for research and clinical applications. Full article

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease characterized by aberrant fibroblast activation, lysosomal dysfunction, and cellular senescence. Transcriptomic analyses have identified ependymin-related 1 (EPDR1) as a fibroblast-enriched gene in IPF, but its biological function remains unclear. EPDR1 expression was assessed in lung fibroblasts, lung tissues, bronchoalveolar lavage fluid (BALF), and serum from IPF patients and controls using qPCR, Western blotting, ELISA, and immunohistochemistry. Lysosomal function, autophagic flux, and senescence markers were analyzed in primary fibroblasts following siRNA-mediated EPDR1 knockdown. EPDR1 was significantly upregulated in IPF-derived fibroblasts and localized to fibrotic regions enriched with α-SMA⁺, COL1A1⁺, and FN1⁺ myofibroblasts of IPF-derived lung tissues. EPDR1 levels were markedly elevated in the BALF and serum of IPF patients and correlated with increased mortality. IPF fibroblasts exhibited reduced lysosomal acidification and impaired autophagic flux, indicated by p62 and LC3B accumulation. EPDR1 knockdown restored lysosomal function; enhanced autophagic degradation; and reduced senescence markers, including p21, p16, and SA-β-gal activity. EPDR1 drives lysosomal dysfunction and fibroblast senescence in IPF. Its elevated expression in lung tissue and biological fluids, together with its association with prognosis, highlights EPDR1 as a potential biomarker and therapeutic target in IPF. Full article

Background: The human gut microbiome—a diverse ecosystem of trillions of microorganisms—plays an essential role in metabolic, immune, and neurological regulation. However, modern lifestyle factors such as antibiotic overuse, cesarean delivery, reduced breastfeeding, processed and high-sodium diets, alcohol intake, smoking, and exposure to environmental toxins (e.g., glyphosate) significantly reduce microbial diversity. Loss of keystone species like Bifidobacterium infantis (B. infantis) and Lactobacillus reuteri (L. reuteri) contributes to gut dysbiosis, which has been implicated in chronic metabolic, autoimmune, cardiovascular, and neurodegenerative conditions. Materials and Methods: This Qualitative Systematic Review (QualSR) synthesized data from over 547 studies involving human participants and standardized microbiome analysis techniques, including 16S rRNA sequencing and metagenomics. Studies were reviewed for microbial composition, immune and metabolic biomarkers, and clinical outcomes related to microbiome restoration strategies. Results: Multiple cohort studies have consistently reported a 40–60% reduction in microbial diversity among Western populations compared to traditional societies, particularly affecting short-chain fatty acid (SCFA)-producing bacteria. Supplementation with B. infantis is associated with a significant reduction in systemic inflammation—including a 50% decrease in C-reactive protein (CRP) and reduced tumor necrosis factor-alpha (TNF-α) levels—alongside increases in regulatory T cells and anti-inflammatory cytokines interleukin-10 (IL-10) and transforming growth factor-beta 1 (TGF-β1). L. reuteri demonstrates immunomodulatory and neurobehavioral benefits in preclinical models, while both probiotics enhance epithelial barrier integrity in a strain- and context-specific manner. In murine colitis, B. infantis increases ZO-1 expression by ~35%, and L. reuteri improves occludin and claudin-1 localization, suggesting that keystone restoration strengthens barrier function through tight-junction modulation. Conclusions: Together, these findings support keystone species restoration with B. infantis and L. reuteri as a promising adjunctive strategy to reduce systemic inflammation, reinforce gut barrier integrity, and modulate gut–brain axis (GBA) signaling, indicating translational potential in metabolic and neuroimmune disorders. Future research should emphasize personalized microbiome profiling, long-term outcomes, and transgenerational effects of early-life microbial disruption. Full article

Chalcone Synthase (CHS) plays a vital role in flavonoid synthesis, influencing plant growth, development, and responses to both biotic and abiotic stress. In this study, 11 CHS genes were identified in Poncirus trifoliata using bioinformatics methods, with their distribution across five chromosomes and unassigned contigs. Each gene contains 2–3 exons and 3–8 conserved motifs. In silico prediction suggested that the PtrCHS proteins are localized in the cytoplasm. PtrCHS9 and PtrCHS11 share identical protein tertiary structures. Phylogenetic analysis classified the CHS family members into four subgroups. Synteny analysis revealed one set of collinear gene pairs within Poncirus trifoliata. Between Poncirus trifoliata and Arabidopsis thaliana, two sets of collinear gene pairs were identified, while one such set was found between Poncirus trifoliata and Oryza sativa. Promoter element analysis showed the presence of various hormone response and stress response elements within PtrCHS promoters. RNA-Seq data demonstrated tissue-specific expression patterns of PtrCHSs. RT-qPCR results indicated that all CHS genes, except PtrCHS11, respond to salt stress with dynamic, member-specific patterns. Additionally, four PtrCHSs (PtrCHS3, PtrCHS5, PtrCHS7, and PtrCHS10) were significantly upregulated in response to cold treatment. Notably, PtrCHS7 and PtrCHS10 maintained high expression levels at both 6 and 12 h, implying they may be key players in cold stress response in Poncirus trifoliata. Clones of PtrCHS7 and PtrCHS10 were obtained, and overexpression vectors were constructed in preparation for gene transformation. Overall, this study provides a solid foundation for future research into the functions of the PtrCHSs. Full article

Objective: Molecular biology techniques were employed to investigate the effects of thrombospondin-4 (Thbs4) expression in dorsal root ganglion (DRG) on peripheral nerve injury repair and regeneration, as well as to elucidate the underlying molecular mechanisms. Methods: A sciatic nerve transection model in rat was established to analyze Thbs4 expression and localization in DRG tissues after injury. Both siRNA and adeno-associated virus (AAV) were used to knockdown or overexpress Thbs4. The effects of knockdown and overexpression of Thbs4 on axon growth were assessed using immunofluorescence staining. The roles of Thbs4 in peripheral nerve injury repair and regeneration were determined using behavioral assays, electrophysiological recordings, and transmission electron microscopy. Results: Thbs4 was primarily localized in the cell membrane and cytoplasm of DRG neurons but was also found in the intercellular spaces. In vitro experiments demonstrated that Thbs4 overexpression promoted axonal regeneration and reduced neuronal apoptosis. They also showed that Thbs4 overexpression accelerated sciatic nerve regeneration and enhanced the recovery of motor and sensory functions. Conversely, Thbs4 knockdown had the opposite effects. This study also showed that the knockdown or overexpression of Thbs4 significantly altered the expression of NF-κB and ERK signaling pathways, suggesting their involvement in peripheral nerve repair and regeneration. Conclusions: Thbs4 expression in DRG tissues is significantly altered following sciatic nerve injury. The NF-κB and ERK may be involved in regulating the repair and regeneration of the peripheral nerve by Thbs4. Full article

The research interest in the oral microbiome’s role in esophageal cancer is growing, yet a comprehensive synthesis of available evidence is still lacking. This study aimed to explore the effects of oral microbiome on the development of esophageal cancer through a systematic review of existing literature retrieved from the Embase, PubMed, and Web of Science databases. Eighteen studies published between 2015 and 2024 were obtained, involving 1191 cases and 1403 controls, mostly using oral saliva samples and 16S rRNA gene sequencing. Findings on alpha-diversity were inconsistent, while most studies reported significant beta-diversity differences between cases and controls. Notably, several investigations on esophageal squamous cell carcinoma showed higher levels of Prevotella, Porphyromonas, and Fusobacterium, while two studies on esophageal adenocarcinoma reported elevated levels of Actinomyces species. A fixed-effect meta-analysis of two studies showed that individuals with specific oral microbial signatures had significantly higher odds of developing esophageal squamous cell carcinoma (OR = 9.50; 95% CI: 5.89–15.29). Quality assessments highlighted methodological strengths but noted variability in group comparability and local applicability. These results reveal the potential of oral microbiome shift as an early detection biomarker and for developing personalized strategies in treating esophageal cancer, meriting further clinical investigation. Full article

Myocardial infarction (MI) and its sequelae continue to be the leading cause of mortality globally. Following MI, a series of structural pathophysiological changes occur in the myocardium, including sympathetic remodeling. Tyrosine hydroxylase (TH), protein gene product 9.5 (PGP9.5), and synaptophysin (SYN) are recognized as key markers of sympathetic nerves. However, the expression patterns of these biomarkers during sympathetic remodeling, particularly their temporal profiles, remain insufficiently characterized. A cohort of 60 healthy adult male C57BL/6 mice was randomly divided into a control group (n = 12) and four MI groups with postoperative intervals of 2, 5, 7, and 10 days (n = 12/group). MI was induced via permanent ligation of the left anterior descending coronary artery (LAD). Cardiac tissues were subjected to histological analyses (HE and Masson’s trichrome staining), immunohistochemical profiling, and quantitative reverse-transcriptase PCR (qRT-PCR) (TH, PGP9.5, and SYN). Immunohistochemical staining revealed that TH-, PGP9.5-, and SYN-immunopositive sympathetic nerves were present in the epicardium, myocardial interstitium, and the periphery of small blood vessels in normal mice. Normal cardiomyocytes were negative for TH but exhibited focal expression of PGP9.5 and SYN. In the myocardial infarction tissue, TH-positive staining indicated sympathetic nerve proliferation in the epicardium, myocardial infarction border zone, and infarct zone, with peak expression occurring at 7 days post-MI. In contrast to TH, PGP9.5 exhibited prominent immunoreactivity, specifically localized to the infarct core and peri-infarct zone cardiomyocytes, while SYN was primarily located in fibroblast-like cells within the same region. qRT-PCR analyses revealed that the time-dependent trends of TH, PGP9.5, and SYN mRNAs exhibited similarities, peaking between 5 and 7 days post-MI. TH demonstrates higher specificity than PGP9.5 and SYN in sympathetic nerve identification, solidifying its role as the optimal biomarker for post-MI sympathetic remodeling. The ectopic expression of PGP9.5 and SYN in non-neuronal cells within myocardial infarction tissue remains speculative and requires further mechanistic studies for validation. Full article

Subclinical mastitis is an udder infection and inflammation in dairy animals that causes no visible changes in the milk or udder, making it hard to detect. Animal welfare and health are negatively impacted by dairy cow mastitis, which also severely impairs the dairy industry’s financial standing. This study was carried out in the three local Municipalities of Free State Province, South Africa, sought to determine bacterial contamination of raw milk of cows infected with subclinical mastitis using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA Sanger sequencing. From subclinical mastitic samples, our MALDI-TOF results revealed coliform bacteria such as Pseudomonas oryzihabitans with 25/71 (32.21%) as a dominant species, followed by Pseudomonas aeruginosa, Escherichia coli, Pantoea agglomerans and Enterobacter kobei at 9/71 (12.67%), 8/71 (11.27%), 6/71 (8.45%) and 6/71 (8.45%), respectively. Finally, Enterococcus faecalis, Enterococcus faecium, Micrococcus luteus, Routella ornithinolytica were detected at 3/71 (4.22%) each and 1 sample with mixed species of Routella platicola 1/71 (1.40%) and Routella ornithinolytica at 1/71 (1.40%). The most frequent microbes causing dairy cow mastitis can be identified using MALDI-TOF MS, a technique that is strong, quick, and accurate. With the inclusion of new species, the database can be enhanced and expanded over time. Full article

Intercellular junctions are involved in the regulation of epithelial function and remodeling in the female reproductive system; however, their importance in the avian oviduct is poorly known. The aim of this study was: first, to provide information on the expression and localization of key tight (occludin, claudin 1, 4, 5, junctional adhesion molecule [JAM] 2, 3) and adherens (E-cadherin, β-catenin) junction proteins in the hen oviduct, and second, to compare expression and localization of these molecules between laying and subjected to fasting-induced pause in laying hens. Tissue samples from all oviductal segments, i.e., infundibulum, magnum, isthmus, shell gland, and vagina were collected on the sixth day of the experiment from the control hens and hens that had been fasted for five consecutive days. Specific oviductal part-dependent expression patterns of examined genes (by quantitative real-time polymerase chain reaction [qRT-PCR]) and/or proteins (by Western blotting) were found, with the highest mRNA transcript and protein abundances in the infundibulum, shell gland, and vagina, and the lowest in the magnum. Fasting-induced partial regression of the oviduct was accompanied by alterations in mRNA transcript and protein abundances of examined molecules. Reduced staining intensity of immunoreaction (analyzed by immunofluorescence) for occludin, E-cadherin, and β-catenin proteins was observed in the oviduct of non-laying hens. Our results indicate the potential involvement of these proteins in controlling intercellular communication, cell signaling, paracellular permeability, and mucosal barrier functionality, which impact the functioning of the hen oviduct. Furthermore, our observations provide novel insights into the molecular composition of tight and adherens junctions and its contribution to the remodeling of the oviduct during its regression induced by fasting. Full article

Human papillomavirus (HPV) is common in both sexes and is also detected in male urine and semen. However, its exact origin and its etiological role in the male genital tract remain unclear. A total of 157 formalin-fixed paraffin-embedded tissues from 156 primary prostate cancer lesions and one metastatic lesion were analyzed. HPV-DNA was detected using a nested PCR, and HPV genotyping was performed using flow-through hybridization for positive cases. In situ hybridization (ISH) was used to localize HPV-DNA, whereas HPV-E6/E7 mRNA ISH and p16^INK4a immunohistochemistry were conducted on high-risk (HR) HPV-positive samples. A nested PCR analysis demonstrated that HPV-DNA was detected in 9.6% of prostate cancers and 0% of seminal vesicles. HR-HPV was observed in 4.5% of the samples. Unknown type was the most common genotype. Of the genotypes which could be identified in the genotyping assay, HPV44 was the most prevalent. HPV prevalence was significantly higher in patients with high-grade groups. Among 15 HPV-positive cases, HPV-DNA was found in 9 cancerous and 10 non-cancerous lesions. E6/E7 mRNA was expressed in 6 of 7 HR-HPV-positive cases, while p16^INK4a expression was weak or absent in all cases. HPV can infect prostate tissue and may contribute to carcinogenesis in some cases, but p16^INK4a was not a consistent surrogate for E7 expression. Full article