Search Results (1,339)

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder primarily characterized by memory loss and cognitive decline, which significantly impacts patients’ quality of life and imposes substantial emotional, practical, and economic burdens on their families. As the most common cause of senile dementia, AD currently affects approximately 50 million people worldwide, with projections indicating a threefold increase by 2050 due to rising life expectancy and an aging global population. Diagnosis of AD remains challenging. Neuroimaging techniques reveal atrophy in critical brain regions, particularly in the cortex, hippocampus, and limbic system, which are essential substrates for memory, personality changes, and other cognitive functions. The hallmark molecular changes associated with AD include the accumulation of β-amyloid plaques and the formation of tau protein tangles. Several underlying mechanisms contribute to neuron loss, such as oxidative stress, neuroinflammation, microbial dysbiosis, and insulin resistance. In this context, exosomes—small extracellular vesicles that facilitate cell communication—transport proteins, DNA, mRNA, and non-coding RNA (ncRNA), all of which play a significant role in the neurobiology of AD. Furthermore, emerging research indicates that exosomal ncRNAs may serve as promising biomarkers for AD, offering the possibility of improved diagnostic precision. This review explores the potential of exosomal ncRNAs—specifically circular RNAs and microRNAS—as non-invasive biomarkers for AD, highlighting recent advances and future directions in translational studies. Full article

Tomato brown rugose fruit virus (ToBRFV) has been causing severe agricultural damage worldwide since its recent discovery. While related to tobacco mosaic virus, its properties and infection mechanisms are poorly understood. To uncover their structure and nanomechanics, we carried out atomic force microscopy (AFM) measurements on individual ToBRFV particles. The virions are rod-shaped with a height and width of 9 and 30 nm, respectively. Length is widely distributed (5–1000 nm), with a mode at 30 nm. ToBRFV rods displayed a 22.4 nm axial periodicity related to structural units. Force spectroscopy revealed a Young’s modulus of 8.7 MPa, a spring constant of 0.25 N/m, and a rupture force of 1.7 nN. In the force curves a step was seen at a height of 3.3 nm, which is related to virion wall thickness. Wall thickness was also estimated by predicting coat protein structure with AlphaFold, yielding a protein with a length of 7.3 nm. Accordingly, the structural element of ToBRFv is a right circular cylinder with an equal height and diameter of ~22 nm and a wall thickness between 3.3 and 7.3 nm. Thus, at least four to nine serially linked units are required to encapsidate a single, helically organized RNA genome. Fragmentation of ToBRFV into these cylindrical structural units may result in a facilitated release of the genome and thus efficient infection. Full article

Chicken meat represents the most widely consumed source of animal protein globally. The identification of non-coding RNAs (ncRNAs) that affect muscle development provides new selection targets for poultry breeding. In this study, muscle samples from high- and low-breast-weight chickens were collected and sequenced for long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and mRNAs. Using weighted gene co-expression network analysis, we found 95 lncRNAs and 46 circRNAs that were significantly associated with breast muscle traits. Subsequently, 51 candidate lncRNAs and 22 candidate circRNAs were screened through differential expression analysis. Finally, by constructing an ncRNA–mRNA regulatory network and performing pathway enrichment analysis, we identified four lncRNAs (e.g., MSTRG.9172.1) and seven circRNAs (e.g., novel_circ_009419) as key regulatory molecules. Functional analysis revealed that these molecules modulate genes such as CD28, CCND2, TIAM1, and RRM2 through pathways including the actin cytoskeleton, p53 signaling pathway, and other pathways. In conclusion, this study provides clearer insight into the epigenetic regulatory network involved in chicken breast muscle development and offers important molecular markers for chicken genetic selection. Full article

Coffee pulp, the primary residue generated during the wet processing of Coffea arabica L., is frequently applied directly to fields as a crude soil amendment. However, this practice often lacks proper microbial stabilization, limiting its agronomic potential and posing risks due to the presence of phytotoxic compounds. In Colombia, disease-resistant varieties such as Coffea arabica L. var. Castillo and var. Cenicafé 1, developed by the National Coffee Research Center (Cenicafé), are the amongst the most widely cultivated varieties in the country; however, despite their widespread adoption, the microbial ecology of postharvest residues from these varieties remains poorly characterized. This study aimed to isolate and functionally characterize native microbial communities from the pulp of Coffea arabica var. Castillo and var. Cenicafé 1, and to evaluate their role in postharvest processing and organic waste management. Fresh pulp samples were collected from a wet-processing facility located in tropical mid-elevation zones. A total of 53 microbial isolates were recovered using culture-dependent techniques on selective media targeting yeasts, lactic acid bacteria (LAB), and filamentous fungi. Amplicon sequencing of the 16S rRNA gene (V3–V4 region) and ITS1 region was conducted to profile bacterial and fungal communities, revealing diverse microbial consortia dominated by Aspergillus, Lactobacillus, Leuconostoc, Pichia, and Saccharomyces species. Enzymatic screening indicated high pectinolytic and cellulolytic activity. Composting trials using inoculated pulp showed a ~40% reduction in composting time and improved nutrient content. These findings support the use of native microbiota to enhance composting efficiency and postharvest valorization, contributing to more sustainable and circular coffee systems. Full article

Heterobasidion root rot fungi represent a major threat to conifer forest stands, and virocontrol (biocontrol) has been proposed as an alternative strategy of disease management in recent years. Here, we investigated the occurrence of RNA viruses and viroid-like genomes in Heterobasidion annosum sensu lato in near-natural forests of Bosnia and Herzegovina (Dinaric Alps), a region previously unexplored in this regard. Seventeen H. annosum s.l. isolates were screened for virus presence by RNA Sequencing and bioinformatic analyses. In total, 32 distinct mycoviruses were discovered in the datasets, 26 of which were previously unknown. The detected viruses represent two dsRNA (Partitiviridae and Curvulaviridae), six linear ssRNA (Mitoviridae, Narnaviridae, Botourmiaviridae, Virgaviridae, Benyviridae, and Deltaflexiviridae) and three circular ssRNA (Dumbiviridae, Quambiviridae, and Trimbiviridae) virus families. In addition to the known circular ambiviruses with their hammerhead (HHRz) and hairpin (HPRz) ribozymes, two other smaller non-coding circular RNAs of ca. 910 bp each were identified encoding HHRz and deltavirus (DVRz) ribozymes in both polarities of their genomes. This study documents the first report of a putative viroid-like RNA agent in Heterobasidion, along with beny-like and deltaflexivirus-like viruses in Heterobasidion abietinum, and expands the known virosphere of Heterobasidion species in Southeastern European forests. Full article

Heart failure with preserved ejection fraction (HFpEF) represents a growing global public health challenge, now accounting for approximately half of all heart failure cases and often linked to a systemic pathophysiological process in older adults with multiple comorbidities. Despite increasing recognition of the vascular contributions to HFpEF, the precise molecular mechanisms, particularly the role of noncoding Ribonucleic Acids (ncRNAs) in mediating vascular aging and subsequent cardiac dysfunction, remain incompletely understood. This review provides a comprehensive overview of the mechanistic link between vascular aging and HFpEF, with a specific focus on the pivotal roles of ncRNAs in this complex interplay. We delineate the classification of vascular aging, its cellular hallmarks, including endothelial senescence, vascular smooth muscle cell phenotypic switching, and extracellular matrix remodeling, and its systemic implications, such as inflammaging, oxidative stress, and reduced nitric oxide bioavailability. We then detail how these vascular alterations, including increased ventricular afterload and impaired myocardial perfusion due to coronary microvascular dysfunction, contribute to HFpEF pathophysiology. The review extensively discusses recent findings on how diverse classes of ncRNAs, notably microRNAs, long noncoding RNAs, and circular RNAs, along with emerging evidence for PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and tRNA-derived small RNAs, regulate these vascular aging processes and serve as molecular bridges connecting vascular dysfunction to heart failure. In conclusion, understanding the regulatory landscape of ncRNAs in vascular aging may reveal novel biomarkers and therapeutic avenues, offering new strategies for precision medicine in HFpEF. Full article

Hippophae rhamnoides ssp. sinensis Rousi a species of significant ecological and economic value that is native to the Qinghai–Tibet Plateau and arid/semi-arid regions. Investigating the mitochondrial genome can elucidate stress adaptation mechanisms, population genetic structure, and hybrid evolutionary history, offering molecular insights for ecological restoration and species conservation. However, the genetic information and evolutionary mechanisms of its mitochondrial genome remain poorly understood. This study aimed to assemble the complete mitochondrial genome of H. rhamnoides L. ssp. sinensis using Illumina sequencing, uncovering its structural features, evolutionary pressures, and environmental adaptability and addressing the research gap regarding mitochondrial genomes within the Hippophae genus. The study assembled a 454,444 bp circular mitochondrial genome of H. rhamnoides ssp. sinensis, with a GC content of 44.86%. A total of 73 genes and 3 pseudogenes were annotated, with the notable absence of the rps2 gene, which is present in related species. The genome exhibits significant codon usage bias, particularly with high-frequency use of the alanine codon GCU and the isoleucine codon AUU. Additionally, 449 repetitive sequences, potentially driving genome recombination, were identified. Our evolutionary pressure analysis revealed that most genes are under purifying selection, while genes such as atp4 and nad4 exhibit positive selection. A nucleotide diversity analysis revealed that the sdh4 gene exhibits the highest variation, whereas rrn5 is the most conserved. Meanwhile, phylogenetic analysis showed that H. rhamnoides ssp. sinensis from China is most closely related to Hippophae tibetana, with extensive homologous sequences (49.72% of the chloroplast genome) being identified between the chloroplast and mitochondrial genomes, indicating active inter-organellar gene transfer. Furthermore, 539 RNA editing sites, primarily involving hydrophilic-to-hydrophobic amino acid conversions, were predicted, potentially regulating mitochondrial protein function. Our findings establish a foundation for genetic improvement and research on adaptive evolutionary mechanisms in the Hippophae genus, offering a novel case study for plant mitochondrial genome evolution theory. Full article

Adipose tissue development plays a critical role in determining carcass quality and meat production efficiency in swine; however, the regulatory mechanisms governing fat deposition remain incompletely understood. Circular RNAs (circRNAs), characterized by high stability and resistance to RNase R degradation, have emerged as important epigenetic regulators of livestock traits. This study investigated the regulatory role of circIDH2 in adipogenic differentiation of porcine preadipocytes and the underlying molecular mechanisms. Functional assays revealed that silencing circIDH2 markedly promoted preadipocyte proliferation while inhibiting differentiation and lipid accumulation; conversely, circIDH2 overexpression produced the opposite effects. Mechanistically, circIDH2 acted as a molecular sponge for miR-193a-5p through complementary base pairing, thereby relieving the repression of its target gene RASGRP4, a positive regulator of adipogenesis. Furthermore, this study demonstrated that miR-193a-5p promoted proliferation but suppressed the differentiation of porcine preadipocytes, whereas RASGRP4 inhibited proliferation while promoting adipogenic differentiation. Rescue experiments further confirmed the regulatory relationship among circIDH2, miR-193a-5p, and RASGRP4. In summary, the findings indicated that circIDH2 functioned as a key regulator of adipogenesis by modulating the miR-193a-5p/RASGRP4 axis, thereby suppressing preadipocyte proliferation and promoting adipogenic differentiation. These results provide a theoretical foundation for future investigations into the regulatory mechanisms of adipose tissue development. Full article

Background: Centella asiatica, a medicinally important species that is rich in bioactive compounds, lacks a characterized mitochondrial genome, despite nuclear and chloroplast assemblies. We sequenced and annotated its mitochondrial genome to elucidate its genetic foundations and evolutionary mechanisms. Methods: Assembly using Illumina short-reads and Nanopore long-reads was used to characterize the mitochondrial genome. Analyses included structural characterization, codon usage bias, repetitive sequences, horizontal gene transfer (HGT), collinearity, and phylogeny. The resulting tissue-specific (root, stem, and leaf) long non-coding RNA (lncRNA) profiles identified RNA editing sites. Results: The complete mitochondrial genome (249,777 bp, 45.5% GC) comprises three circular contigs encoding 51 genes (33 protein-coding, 15 tRNA, and 3 rRNA). Comparative genomics revealed synteny with the Apiaceae family of plants and evidence of HGT. Phylogenetic analysis resolved taxonomic relationships within Apiales. We predicted that 547 RNA editing sites would be identified in its protein-coding genes. Tissue profiling identified 725 (root), 711 (stem), and 668 (leaf) editing sites, with >71% concordance to predictions. RNA editing-generated cryptic promoters/terminators occur in mitochondrial core function genes (e.g., ATP synthase, cytochrome c reductase/oxidase, ribosome large subunit, and cytochrome c biogenesis), exhibiting a lower frequency in the leaves compared to the roots and stems. Conclusions: We provide the first complete mitochondrial genome assembly for C. asiatica, delineating its complex structure, tissue-modulated RNA editing, and evolutionary trajectory. This high-quality genomic resource establishes a foundation for molecular evolutionary studies and enhances the genomic toolkit for this pharmacologically significant species. Full article

The T-2 toxin is one of the most toxic mycotoxins, to which the population is exposed through the diet. T-2 toxins are especially found in cereals and cereal-based products. To deepen our understanding of the mechanisms of T-2 toxin action, the morphological changes, oxidative stress, and inflammatory response of this mycotoxin have been evaluated in HepG2 cells. The mRNA and protein expression levels of inflammatory cytokines such as IL-1β, IL-6, and TNF-α and proteins such as Nrf2 and HO-1 were analyzed after T-2 exposure (7.5, 15, and 30 nM) by qPCR and Western blot assays. Firstly, changes in the morphology of HepG2 cells after T-2 exposure from circular to elongated shape were observed in a concentration-dependent manner by indirect immunofluorescence. These alterations may reflect early signs of cell stress. The results revealed an upregulation of the mRNA of IL-1β, IL-6, and TNF-α after T-2 exposure, with the highest increase in TNF-α after 30 nM T-2, suggesting a proinflammatory effect. Regarding the oxidative response, HO-1 at the lowest T-2 concentration was upregulated. However, the Nrf2 at all T-2 concentrations tested was downregulated. These findings were corroborated by Western blot analysis. These results confirm that T-2 hepatotoxicity produces an increase in key inflammatory cytokines, modulates the Nrf2/HO-1 pathway, and produces morphological changes in HepG2 cells. The next step would be to test whether a co-exposure of natural antioxidants with T-2 exerts a cytoprotective effect. Full article

Chronic infection with the hepatitis B virus (HBV) results in over 1 million deaths annually. Although currently licensed treatments, including pegylated interferon-α and nucleoside/nucleotide analogs, can inhibit viral replication, they rarely eradicate covalently closed circular DNA (cccDNA) reservoirs. Moreover, vaccination does not offer therapeutic benefit to already infected individuals or non-responders. Consequently, chronic infection is maintained by the persistence of cccDNA in infected hepatocytes. For this reason, novel therapeutic strategies that permanently inactivate cccDNA are a priority. Obligate heterodimeric transcription activator-like effector nucleases (TALENs) provide the precise gene-editing needed to disable cccDNA. To develop this strategy using a therapeutically relevant approach, TALEN-encoding mRNA targeting viral core and surface genes was synthesized using in vitro transcription with co-transcriptional capping. TALENs reduced hepatitis B surface antigen (HBsAg) by 80% in a liver-derived mammalian cell culture model of infection. In a stringent HBV transgenic murine model, a single dose of hepatotropic lipid nanoparticle-encapsulated TALEN mRNA lowered HBsAg by 63% and reduced viral particle equivalents by more than 99%, without evidence of toxicity. A surveyor assay demonstrated mean in vivo HBV DNA mutation rates of approximately 16% and 15% for Core and Surface TALENs, respectively. This study presents the first evidence of the therapeutic potential of TALEN-encoding mRNA to inactivate HBV replication permanently. Full article

Liquid biopsy has emerged as a valuable tool for the detection and monitoring of colorectal cancer (CRC), providing minimally invasive insights into tumor biology through circulating biomarkers such as circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additional biomarkers, including tumor-educated platelets (TEPs) and exosomal RNAs, offer further potential for early detection and prognostic role, although ongoing clinical validation is still needed. This review summarizes the current evidence on the diagnostic, prognostic, and predictive capabilities of liquid biopsy in both metastatic and non-metastatic CRC. In the non-metastatic setting, liquid biopsy is gaining traction in early detection through screening and in identifying minimal residual disease (MRD), potentially guiding adjuvant treatment and reducing overtreatment. In contrast, liquid biopsy is more established in metastatic CRC for monitoring treatment responses, clonal evolution, and mechanisms of resistance. The integration of ctDNA-guided treatment algorithms into clinical practice could optimize therapeutic strategies and minimize unnecessary interventions. Despite promising advances, challenges remain in assay standardization, early-stage sensitivity, and the integration of multi-omic data for comprehensive tumor profiling. Future efforts should focus on enhancing the sensitivity of liquid biopsy platforms, validating emerging biomarkers, and expanding multi-omic approaches to support more targeted and personalized treatment strategies across CRC stages. Full article

Background: Polycystic ovary syndrome (PCOS) is a complex and multifactorial disorder affecting reproductive, endocrine, and metabolic functions in women of reproductive age. While environmental and lifestyle factors play a role, increasing evidence highlights the contribution of genetic and epigenetic mechanisms to its pathogenesis. Objective: This narrative review aims to provide an updated overview of the current evidence regarding the role of genetic variants, gene expression patterns, and epigenetic modifications in the etiopathogenesis of PCOS, with a focus on their impact on ovarian function, fertility, and systemic alterations. Methods: A comprehensive search was conducted across MEDLINE, EMBASE, PubMed, Web of Science, and the Cochrane Library using MeSH terms including “PCOS”, “Genes involved in PCOS”, and “Etiopathogenesis of PCOS” from January 2015 to June 2025. The selection process followed the SANRA quality criteria for narrative reviews. Seventeen studies published in English were included, focusing on original data regarding gene expression, polymorphisms, and epigenetic changes associated with PCOS. Results: The studies analyzed revealed a wide array of molecular alterations in PCOS, including the dysregulation of SIRT and estrogen receptor genes, altered transcriptome profiles in cumulus cells, and the involvement of long non-coding RNAs and circular RNAs in granulosa cell function and endometrial receptivity. Epigenetic mechanisms such as the DNA methylation of TGF-β1 and inflammation-related signaling pathways (e.g., TLR4/NF-κB/NLRP3) were also implicated. Some genetic variants—particularly in DENND1A, THADA, and MTNR1B—exhibit signs of positive evolutionary selection, suggesting possible ancestral adaptive roles. Conclusions: PCOS is increasingly recognized as a syndrome with a strong genetic and epigenetic background. The identification of specific molecular signatures holds promise for the development of personalized diagnostic markers and therapeutic targets. Future research should focus on large-scale genomic studies and functional validation to better understand gene–environment interactions and their influence on phenotypic variability in PCOS. Full article

Stress granule formation is a type of liquid–liquid phase separation in the cytoplasm, leading to RNA–protein condensates that are associated with various cellular stress responses and implicated in numerous pathologies, including cancer, neurodegeneration, inflammation, and cellular senescence. One of the key components of mammalian stress granules is the DEAD-box RNA helicase DDX3, which unwinds RNA in an ATP-dependent manner. DDX3 is involved in multiple steps of RNA metabolism, facilitating gene transcription, splicing, and nuclear export and regulating cytoplasmic translation. In this study, we investigate the role of the RNA helicase DDX3’s enzymatic activity in shaping the RNA content of ribonucleoprotein (RNP) condensates formed during arsenite-induced stress by inhibiting DDX3 activity with RK-33, a small molecule previously shown to be effective in cancer clinical studies. Using the human osteosarcoma U2OS cell line, we purified the RNP granule fraction and performed RNA sequencing to assess changes in the RNA pool. Our results reveal that RK-33 treatment alters the composition of non-coding RNAs within the RNP granule fraction. We observed a DDX3-dependent increase in circular RNA (circRNA) content and alterations in the granule-associated intronic RNAs, suggesting a novel role for DDX3 in regulating the cytoplasmic redistribution of non-coding RNAs. Full article

Acute myeloid leukemia (AML) is a malignant hematological tumor with a high prevalence in elderly people, and circular RNA (circRNA) plays an important role in age-related diseases. Induction of cancer cell senescence is a highly promising therapeutic strategy; however, the presence of senescence-associated circRNAs in AML remains to be elucidated. Here, we show that the expression patterns of circRNAs differed between elderly AML patients and healthy volunteers. circSATB1 was significantly overexpressed in elderly patients and AML cells. Knockdown of circSATB1 resulted in the inhibition of proliferation and arrest of the cell cycle in the G0/G1 phase; no effect on apoptosis or DNA integrity was observed, and precocious cellular senescence was promoted, characterized by no change in telomere length. Database analysis revealed that there may be two miRNA and nine RNA-binding proteins (RBPs) involved in regulating the cellular functions of circSATB1. Our observations uncover circSATB1-orchestrated cell senescence in AML, which provides clues for finding more modest therapeutic targets for AML. Full article