Search Results (4,178)

Background: Freeze tolerance is an uncommon but highly effective strategy that allows certain vertebrates to survive prolonged exposure to subzero temperatures in a frozen, ischemic state. While past studies have characterized the metabolic and biochemical adaptations involved, including cryoprotectant accumulation and metabolic rate suppression, the contribution of post-transcriptional gene regulation by microRNAs (miRNAs) remains largely unexplored. This study investigated freeze-responsive miRNAs in cardiac tissue of the gray tree frog, Dryophytes versicolor, to better understand the molecular mechanisms that support ischemic survival and tissue preservation. Methods: Adult frogs were subjected to controlled freezing at −2.5 °C, and cardiac tissue was collected from frozen and control animals. Total RNA was extracted and analyzed via small RNA sequencing to identify differentially expressed miRNAs, followed by target gene prediction and KEGG pathway enrichment analysis. Results: A total of 3 miRNAs were differentially expressed during freezing, with significant upregulation of miR-93-5p and let-7b-5p and downregulation of miR-4485-3p. Predicted targets of upregulated miRNAs included genes involved in immune signaling pathways (e.g., cytokine–cytokine receptor interaction), steroid hormone biosynthesis, and neuroactive ligand–receptor interaction, suggesting suppression of energetically costly signaling processes. Downregulation of miRNAs targeting cell cycle, insulin signaling, and WNT pathways indicates possible selective preservation of cytoprotective and repair functions. Conclusion: Overall, these results suggest that D. versicolor employs miRNA-mediated regulatory networks to support metabolic suppression, maintain essential signaling, and prevent damage during prolonged cardiac arrest. This work expands our understanding of freeze tolerance at the molecular level and may offer insights into biomedical strategies for cryopreservation and ischemia–reperfusion injury. Full article

Chlorophyll biosynthesis is essential for photosynthesis and plant development. Disruptions in this pathway often manifest as pigment-deficient phenotypes. This study characterizes the morphological, anatomical, and physiological consequences of a chlorophyll-deficient rice mutant (yellow seedling, YS) caused by a loss-of-function mutation in the OsCHLI gene, which encodes the ATPase subunit of magnesium chelatase. Comparative analyses between YSs and wild-type green seedlings (GSs) revealed that YSs exhibited severe growth retardation, altered mesophyll structure, reduced xylem and bulliform cell areas, and higher stomatal and papillae density. These phenotypes were strongly light-dependent, indicating that OsCHLI plays a crucial role in light-mediated chloroplast development and growth. Transcriptome analysis further revealed global down-regulation of photosynthesis-, TCA cycle-, and cell wall-related genes, alongside selective up-regulation of redox-related pathways. These results suggest that chlorophyll deficiency induces systemic metabolic reprogramming, prioritizing stress responses over growth. This study highlights the multifaceted role of OsCHLI in plastid maturation, retrograde signaling, and developmental regulation, providing new insights for improving photosynthetic efficiency and stress resilience in rice. Full article

Intrauterine growth restriction (IUGR) severely hinders the development of the livestock industry and impacts economic efficiency. MicroRNAs (miRNAs) participate in the epigenetic regulation of animal growth and development. Using IUGR pigs as a model, this study analyzed transcriptomic data from IUGR piglets to investigate the miRNA-mRNA regulatory network in their testes. Compared with NBW pigs, IUGR pigs exhibited reduced testicular volume, decreased weight, and abnormal testicular development. A total of 4945 differentially expressed mRNAs and 53 differentially expressed miRNAs were identified in IUGR testicular tissues, including 1748 downregulated and 3197 upregulated mRNAs, as well as 41 upregulated and 12 downregulated miRNAs. The integrated analysis of differentially expressed genes, miRNA target genes, and the miRNA-mRNA network revealed that IUGR may impair testicular development by disrupting cell cycle progression and apoptotic pathways, thereby hindering normal testicular cell growth. Furthermore, analysis of the miRNA-mRNA network indicated that miRNAs such as ssc-miR-23a, ssc-miR-29c, ssc-miR-193a-3p, and ssc-miR-574-3p could serve as potential marker miRNAs for IUGR testes, while YWHAZ, YWHAB, and PPP2CA may function as core target genes within this regulatory network. In conclusion, this study enhances our understanding of male reproduction in IUGR pigs and provides a theoretical foundation for preventing and treating IUGR-induced male reproductive disorders. Full article

Survivin, a pivotal member of the inhibitor of apoptosis proteins (IAP) family, plays critical roles in cell cycle regulation and division. Survivin is overexpressed in most malignancies, making it an attractive therapeutic target. Due to its high specificity and potency, siRNA-based RNA interference (RNAi) has emerged as a powerful therapeutic strategy for effectively downregulating disease-related genes such as survivin in cancer therapy. However, naked siRNA suffers from rapid enzymatic degradation, poor cellular uptake, and off-target effects, severely limiting its therapeutic efficacy in vivo. Development of polymer-based nanocarriers for tumor-targeted delivery of survivin siRNA (siSurvivin) holds great potential to address these challenges. In this review, we first described the structure and function of survivin and summarized the survivin-targeted therapeutic strategy. Then, the siRNA delivery systems, particularly the polymeric nanocarriers, were introduced. Furthermore, a plethora of polymer-based nanocarriers for tumor-targeted siSurvivin delivery, including synthetic polymers (branched polymers, dendritic polymers, polymeric micelles), natural polymers (polysaccharides, proteins, and others), lipid-polymer hybrid nanoparticles, and polymer composite nanoparticles, were elaborated. Promising results underscore the potential of polymer-based nanocarriers for survivin siRNA delivery to enhance cancer therapy, providing a roadmap for future clinical translation. Full article

Pseudorabies virus (PRV), a highly pathogenic alphaherpesvirus, poses a potential threat to public health and safety due to its broad host range and risk of cross-species transmission. Viruses have evolved multiple strategies to exploit host factors for entry into and survival in host cells. Drebrin is an actin-binding protein that restricts rotavirus entry by inhibiting dynamin-mediated endocytosis. However, its role and mechanism in DNA virus infection, particularly in herpesviruses, remain unexplored. In this study, we investigated the role of Drebrin in PRV infection using pharmacological inhibition (BTP−2) and CRISPR-Cas9-mediated gene knockout. Both the Drebrin inhibitor BTP−2 and gene knockout significantly suppressed PRV replication. Intriguingly, Drebrin exhibited stage-specific effects on the viral life cycle: its inhibition enhanced viral internalization during early infection but impaired viral replication at later stages, suggesting that Drebrin plays a complex role in the regulation of PRV infection. PRV infection partially disrupted actin stress fibers and caused an increase in cell size. Drebrin knockout also altered the host-cell morphology, reduced the cell surface area, and induced actin cytoskeleton rearrangement, which was further modulated in PRV-infected cells. In summary, our data demonstrate that Drebrin functions as a critical host factor governing the entire PRV life cycle by regulating actin cytoskeleton reorganization. Full article

Exosomes have been shown to play an important role in embryo implantation, but the mechanism is still unclear. This study aimed to investigate the functional roles of lncRNAs in intrauterine exosomes in goat pregnancy. We used RNA-seq to identify the lncRNA profiles of exosomes obtained from goat uterine rinsing fluid at 5, 15, and 18 days of gestation. In addition, we performed weighted gene co-expression network analysis based on differentially expressed mRNAs (DEMs) and lncRNAs (DELs). Functional enrichment analyses of gene modules were conducted using Gene Ontology classification (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. A lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) regulatory network was constructed based on predictive interaction derived from miRTarBase, miRDB and RNAhybrid databases. Altogether, 831 DELs were identified. GO and KEGG analysis showed that the target genes were enriched in processes associated with embryo implantation, such as signaling receptor activity, binding and immune response. Nine functional co-expression modules were enriched in various biological processes, such as metabolic pathways, protein transport, cell cycle and VEGF signaling pathway. Additionally, 12 lncRNA-mediated ceRNA networks were constructed. Our results demonstrate that exosomal lncRNAs in uterine flushing fluid exhibit dynamic changes across gestational stages and play an important role in regulating the uterine microenvironment during embryo implantation. These findings provide a foundational basis for screening exosome-derived lncRNAs that influence embryo implantation and contribute to elucidating the mechanistic roles of lncRNAs in exosome-mediated processes during early pregnancy. Full article

Environmental pollution with microplastics (MPs) can have a negative impact on human health. Certain findings point to the relationship between MP and the development of inflammatory bowel diseases (IBD). We investigated the effect of MP consumption on the severity of chronic colitis in male C57BL/6 mice. The MP effect was modeled by drinking water consumption with a suspension of 5 μm PS particles at a concentration of 10 mg/L replacement for 12 weeks. Chronic colitis was induced by three seven-day cycles of 1% DSS consumption (starting from the 8th, 29th and 50th days of the experiment). We investigated inflammatory infiltration, the goblet cell volume fraction and the highly sulfated and neutral mucins content in them, the endocrine cell number, the ulcerative-inflammatory process prevalence, changes in the gene’s expression encoding tight junction proteins, glycocalyx components proapoptotic factor Bax and proliferation marker Mki67 in the colon, and TNFα, IL-1β, IL-6 and IL-10 cytokines content in the serum. In healthy mice, MP did not cause pathological changes in the colon; however, indirect data indicate an increase in colon permeability. In chronic colitis, MP leads to higher prevalence of all pathological changes in general, and ulcers in particular, in a greater number of crypt abscesses and enteroendocrine cells. MP consumption leads to a more severe chronic colitis course. Full article

Colorectal cancer (CRC) remains a major cause of cancer-related mortality. Cetuximab improves survival by combining EGFR inhibition with immune activation. This study evaluated the influence of killer cell immunoglobulin-like receptor (KIR)-mediated immune responses on cetuximab efficacy in 124 metastatic CRC patients: 55 with wild-type (WT) KRAS and 69 with KRAS mutations. Peripheral blood was genotyped for 19 KIR genes and relevant HLA alleles, focusing on key KIR–HLA interactions (2DL1–C2, 3DL1–Bw4, 3DS1–Bw4). KRAS-WT patients showed better outcomes, receiving more treatment cycles (median: 17 vs. 4) and showing slower disease progression (60% vs. 92.8% at 12 months). WT patients had higher frequencies of inhibitory KIRs and the Bw4 allele, with KIR3DS1–Bw4 heterozygosity linked to longer survival (p = 0.013). In KRAS-mutant patients, heterozygous KIR genotypes (AB) and mixed A/B semi-haplotypes were associated with improved survival (p = 0.002). Multivariate analysis confirmed KIR3DS1–Bw4 as a favorable factor in WT patients and AB genotypes as beneficial in KRAS-mutants. In conclusion, KIR–HLA interactions significantly impact cetuximab efficacy in metastatic CRC, with distinct immunogenetic profiles in WT and KRAS-mutant patients. These results highlight the potential of KIR–HLA profiling to guide personalized treatment strategies. Full article

Developmental dysplasia of the hip (DDH) is a congenital disorder influenced by genetic and epigenetic factors. This study aimed to elucidate the molecular pathogenesis of DDH through a comprehensive transcriptomic analysis, identifying differentially expressed genes (DEGs) and long non-coding RNAs (lncRNAs) in hip joint capsules from DDH patients and healthy controls. RNA sequencing data from 12 samples (6 DDH, 6 controls) were retrieved from the NCBI database. Functional annotation was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses via the DAVID tool. A protein–protein interaction (PPI) network of DEGs was constructed using STRING with medium confidence settings. Among 78,930 transcripts, 4.3% were significantly differentially expressed, according to DESeq2 analysis. A total of 3425 DEGs were identified (FDR < 0.05, |log2 FC| > 2), including 1008 upregulated and 2417 downregulated transcripts in DDH samples. Additionally, 1656 lncRNAs were detected among the DEGs. These findings enhance our understanding of the genetic and epigenetic landscape of DDH and highlight the involvement of key biological pathways such as cell cycle regulation and Wnt signaling. This study provides a foundation for future molecular research into the pathogenesis of DDH. Full article

Drought stress significantly limits crop growth and yield, and the mechanisms underlying genotypic variation in drought tolerance remain unclear. This study investigated the growth and transcriptomic responses of two sorghum varieties, drought-sensitive Jinza 35 (V1) and drought-tolerant Longza 24 (V2), under drought conditions. Comparative transcriptomic analysis, along with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, revealed distinct molecular mechanisms between the two varieties. Both varieties exhibited drought-responsive changes in photosynthesis-related pathways. However, the drought-tolerant V2 showed significant enrichment in phenylpropanoid biosynthesis, starch-sucrose metabolism, and plant hormone signaling pathways, suggesting enhanced metabolic flexibility under stress. In contrast, V1 primarily activated ribosome metabolism and cell cycle regulation pathways, indicating a less adaptive response focused on basic cellular processes. These findings highlight key metabolic and regulatory differences underlying drought tolerance in sorghum. The study provides valuable molecular insights and candidate pathways for future functional studies and the breeding of drought-resistant sorghum varieties. Full article

Chk1, a highly conserved serine/threonine protein kinase, functions as a critical regulator of fungal cell cycle progression, mitotic fidelity, and DNA damage response. In this study, we characterized an orthologous Chk1 (AoChk1) in a ubiquitous nematode-trapping fungus, Arthrobotrys oligospora, through targeted gene knockout coupled with integrated phenotypic, metabolomic, and transcriptomic analyses. This study aims to elucidate the function and potential regulatory networks of AoChk1 in A. oligospora. Deletion of Aochk1 leads to significant reductions in nucleus number, hyphal cell length, conidial production, and trap formation, but an increase in the accumulation of lipid droplets and autophagy. In addition, transcriptomics data indicate that AoChk1 plays an important role in cell cycle and division, nuclear architecture and organelle dynamics, protein homeostasis maintenance, and membrane systems. In addition, the inactivation of the Aochk1 exhibited remarkably reduced metabolite abundance relative to the WT strain. In conclusion, our results identify AoChk1 as an important regulator of asexual development, pathogenicity, and metabolic processes in A. oligospora. Full article

Background/Objectives: The clinical, histopathological, and dermoscopic features may be associated with melanoma mutational status. The aims of the study were to assess the clinical, histopathological, and dermoscopic features of melanoma to identify their correlation with BRAF, NRAS, and cell cycle genes’ mutational status in melanoma. Methods: The clinical, histopathological information, dermoscopic images, and genomic DNA of 55 histopathologically diagnosed primary cutaneous melanomas were retrospectively analyzed. Next-generation sequencing (NGS) assays were conducted on the Ion GeneStudio S5 platform (Thermo Fisher Scientific, Waltham, MA, USA), using the Ion AmpliSeq™ Italian Melanoma Intergroup Somatic Panel. Results: Overall, 55 melanomas, including 30 superficial spreading, 24 nodular, and 1 naevoid, were analyzed. BRAF mutation was more frequently observed in ulcerated melanoma (16/23; 69.6%), with mitotic rate ≥ 5 n/mm² (8/11; 72.7%), while NRAS mutation was more common in amelanotic/hypomelanotic (8/17; 70.0%) and nodular melanoma (10/24; 41.7%). Dermoscopically, shiny white structures (OR = 3.50; 95% confidence interval: 1.13–10.84) were associated with BRAF-mutated melanomas, whereas a homogeneous disorganized pattern was associated with NRAS-mutated melanomas (OR = 6.96; 1.49–32.53). The risk of diagnosing cell cycle gene-mutated melanomas was significantly increased in presence of vascular patterns (OR = 4.50; 1.33–15.20), linear irregular (OR = 3.75; 1.18–11.92), polymorphous vessels (OR = 4.05; 1.27–12.97), and milky red globules/areas (OR = 3.14; 1.00–9.89). The blue-white veil was significantly associated with P53 mutation (OR = 35.84; 2.01–640.2). Conclusions: Conversely to Wild Type, BRAF, NRAS, and cell cycle gene-mutated melanomas were significantly associated with clinical and dermoscopic features underlying a more aggressive melanoma phenotype. The vascular pattern, linear irregular, polymorphous vessels, and milky-red globules/areas may be considered predictors of cell cycle mutated melanomas. Full article

Background: This study investigates the expression of microRNAs (miRNAs) in the semitendinosus muscle of cattle breeds with varying intramuscular fat (IMF) deposition to identify key miRNA regulators of beef marbling, utilizing Hereford (HER; higher IMF) and Holstein-Friesian (HF; moderate IMF) bulls, and Limousin (LIM; low IMF) bulls with lower IMF in the semitendinosus muscle. Methods: MicroRNA profiling used custom bovine microarrays and the Agilent software. The selected miRNAs, miR-34a, miR-149-5p, miR-208b, miR-499, miR-660, and miR-1343-5p, were chosen for validation using real-time PCR, confirming their differential expression. Target prediction utilized miRWalk, while functional and pathway analyses were conducted using the DAVID database to interpret biological relevance. Results: Microarray analysis identified 51 differentially expressed miRNAs. Among these, 24 exhibited consistent expression patterns in high-marbling breeds compared to the low-marbling LIM breed. Bioinformatic analysis of the 4941 predicted target genes of these 24 miRNAs revealed significant enrichment in pathways crucial for marbling, including the adipocytokine, AMPK, MAPK, and PI3K-Akt signaling pathways, as well as biological processes such as cell differentiation and lipid homeostasis. Notably, miR-34a and miR-149-5p emerged as significant regulators, with miR-34a targeting genes like SIRT1, HMGA2, PTPN11, VEGFA, FGF1, FGF2, and BRAF, and miR-149-5p influencing adipogenesis and lipid metabolism through its association with crucial KEGG pathways such as PI3K–Akt, MAPK, PPAR, TGF-β, cAMP, and Wnt signaling, all of which collectively influence adipocyte differentiation, lipid metabolism, cell cycle control, and angiogenesis. Conclusions: The findings underscore identified miRNAs’ possible coordinated regulatory role, particularly miR-34a and miR-149-5p, in the complex molecular mechanisms governing IMF deposition in cattle, providing potential targets for improving beef quality. Full article

Persistent RNA virus infections (PI) are often characterized by extended viral shedding and maintained cycles of inflammation. The innate immune Complement (C′) pathways can recognize acute infected (AI) cells and result in their lysis, but the relative sensitivity of PI cells to C′-directed killing is incompletely understood. Here, we extended our previous studies on the interactions of C′ with parainfluenza virus AI and PI A549 cells to two additional respiratory tract cell lines. AI Hep2 and H1975 cells infected with Parainfluenza virus 5 (PIV5) were found to be highly sensitive to C′ lysis. By contrast, PIV5 PI cells were highly resistant to killing by C″. Surface deposition of membrane attack complex (MAC) and C3 was also greatly reduced on the surface of PI cells compared to AI cells. PI cells had lower levels of surface viral glycoprotein expression compared to AI cells. Treatment of AI cells with ribavirin (RBV) showed a dose-dependent decrease in both viral glycoprotein expression and sensitivity to C′-mediated lysis. When surface viral glycoprotein levels were reduced in AI cells to those in PI cells, AI cells became similarly resistant to C′. While sialic acid levels on PI cell surfaces matched that of naïve cells, enzymatic removal of this sialic acid did not increase sensitivity to C′-mediated lysis. Despite their varying profiles of C′ activation and deposition, these studies indicate downregulation of viral gene expression as a common mechanism of C′ resistance across various parainfluenza virus PI cell lines. Full article

Human DEAD-box helicase 3 (DDX3) is a multifunctional RNA helicase implicated in mRNA unwinding and the regulation of gene expression. While DDX3 has been extensively studied in the context of RNA virus replication, its role in DNA virus replication remains less understood. In this study, we explore the involvement of DDX3 in the life cycle of Herpes Simplex Virus type 2 (HSV-2), a double-stranded DNA virus. Silencing of DDX3 expression with siRNA significantly impaired HSV-2 replication, indicating that DDX3 supports viral propagation. Unexpectedly, HSV-2 infection led to a marked reduction in cellular DDX3 protein levels during in vitro replication in human cells, particularly at 24 h post-infection, corresponding to the peak of viral production. Notably, this decrease was not accompanied by a reduction in DDX3 mRNA levels, nor was it prevented by proteasome inhibition, suggesting an alternative mechanism of DDX3 depletion. Further analysis revealed substantial amounts of DDX3 protein within HSV-2 virions, supporting the hypothesis that DDX3 is packaged into viral particles during replication. We propose that HSV-2 exploits host DDX3 by incorporating it into progeny virions to facilitate early stages of infection in newly infected cells. However, no evidence linking DDX3 to the assembly process of HSV-2 particles was found. These findings expand the known functional repertoire of DDX3 and highlight its potential as a host factor co-opted by DNA viruses, suggesting a broader relevance in antiviral strategies. Full article