Search Results (291)

The global rise in antimicrobial resistance (AMR) demands innovative strategies beyond traditional antibiotics. Peptide Nucleic Acids (PNAs), synthetic DNA analogues with peptide-like backbones, act as thermically, chemically, and enzymatically stable sequence-specific agents capable of silencing essential bacterial genes. Through antisense mechanisms, PNAs bind bacterial mRNA or rRNA, blocking translation or ribosome assembly and thereby inducing species-specific growth inhibition. Their programmable design enables precise targeting of multidrug-resistant pathogens while sparing commensal microbiota. Recent advances, including γ-modified backbones, cationic substitutions, and delivery platforms such as cell-penetrating peptides (CPPs), dendron conjugates, and nanoparticles, have improved solubility, stability, and cellular uptake. Studies show promising in vitro and, albeit less frequently, in vivo efficacy against both Gram-positive and Gram-negative bacteria, often with synergistic activity when combined with conventional antibiotics. Although challenges remain in delivery and large-scale production, PNAs represent a promising class of antimicrobials to combat AMR through targeted gene inhibition. Full article

Background/Objectives: Coenzyme Q10 (CoQ10) is crucial for mitochondrial bioenergetics and redox balance and has been studied in hearing disorders. Its clinical use ranges from genetic mitochondrial deafness to acquired hearing loss associated with oxidative stress. This review aimed to map human clinical evidence on CoQ10 in hearing issues and differentiate its therapeutic roles based on underlying causes. Methods: This review was conducted following the PRISMA Extension for Scoping Reviews (PRISMA-ScR). A systematic search of PubMed, Europe PubMed Central, the Directory of Open Access Journals (DOAJ), and ClinicalTrials.gov was performed. Human clinical studies evaluating CoQ10 or water-soluble CoQ10 formulations with hearing-related outcomes were included and synthesized descriptively. Results: Fourteen studies met the inclusion criteria, including randomized controlled trials, non-randomized clinical studies, case series, and case reports. Two distinct therapeutic roles of CoQ10 emerged: in primary mitochondrial hearing disorders caused by defects in mitochondrial DNA or CoQ10 biosynthesis pathways, CoQ10 acted as a replacement therapy and was consistently linked to stabilization or prevention of progressive sensorineural hearing loss. Conversely, in acquired or age-related conditions—including presbycusis, noise-induced hearing loss, ototoxicity, tinnitus, and sudden sensorineural hearing loss—CoQ10 was used as an antioxidant or neuroprotective supplement, with outcomes showing functional preservation, symptom reduction, or decreased cochlear injury. Internal validity varied across studies: most evidence for replacement therapy was derived from observational designs, and antioxidant applications were mainly supported by small or preliminary clinical trials. Conclusions: The available evidence suggests two distinct clinical roles of CoQ10 in hearing disorders: (i) replacement therapy in genetically defined mitochondrial deafness and (ii) adjunctive antioxidant/neuroprotective use in acquired conditions. Given heterogeneity and limited study quality, further well-designed trials are needed before broad clinical recommendations can be made. Full article

Background: The present study set out to identify key miRNAs, TFs and signaling pathways associated with bladder cancer, with a view to elucidating the networks of miRNA-TF-gene interactions that may serve as potential molecular biomarkers for disease diagnosis. Methods: An integrative analysis was conducted using the publicly available microarray dataset GSE130598. Expression profanalyzede analyzed from 42 muscle-invasive bladder cancer (MIBC) tissues and 42 matched adjacent normal bladder tissues. After data preprocessing and normalization, differentially expressed genes (DEGs) were identified. To identify the associated biological processes and signaling pathways, functional enrichment analyses were conducted using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Protein–protein interaction (PPI) network analysis was then employed to identify hub genes and key molecular interaction modules associated with bladder cancer. Results: MYC, TP53, SP1, E2F1, E2F3, NFKB1, and TWIST1 were identified as central transcriptional regulators, indicating their roles in controlling genes involved in cell cycle regulation, DNA damage response, and tumor progression. Several miRNA families, including miR-200, miR-17, miR-29, miR-141, and miR-548, have been identified as key post-transcriptional regulators, suggesting their involvement in oncogenic signaling and cellular differentiation. PPI network analysis revealed MAPK3, AKT1, CHEK1, CDK1, AURKA, and AURKB as hub genes associated with cell proliferation, mitotic control, and intracellular signaling. Conclusions: Fundamental molecular processes underlying bladder cancer pathogenesis include cell cycle control, signal transduction, and genomic stability. These findings provide insight into the molecular regulatory landscape of MIBC and highlight potential targets for diagnostic and prognostic applications. Full article

Silage is a core roughage resource for ruminant production, but aerobic deterioration caused by microorganisms severely reduces its nutritional value and increases microbial risk. This study aimed to isolate and identify specific spoilage organisms (SSOs) from Napier grass silages during aerobic deterioration and evaluate their spoilage capability. Based on morphological observation, physiological and biochemical tests, and ITS rDNA sequence analysis, four SSOs were obtained as Trichosporon asahii (TA32), Nakaseomyces glabratus (NG38), Candida tropicalis (CT39), and Pichia kudriavzevii (PK41) with high lactate-assimilating and spoilage capacity. All four strains were facultative anaerobic yeast and exhibited robust growth within the range of 25–40 °C and pH 3.5–6.5. To verify their spoilage capability, these purified strains were inoculated into Napier grass silage and exposed to air. Fermentation and chemical parameters were monitored at 0, 2, 5, and 9 days. Results showed that silages inoculated with PK41 or TA32 exhibited the lowest aerobic stability with most rapid increase in pH (p < 0.05), while the control (CON) remained the highest aerobic stability (p < 0.05). These results provide a theoretical basis for developing targeted preservation technologies to extend the shelf-life of silage. Full article

Background: Keratoconus (KC) is a progressive corneal ectasia and a leading cause of corneal transplantation in young adults. Once regarded as a biomechanical disorder, KC is now recognized as a complex disease driven by genetic predisposition, epigenetic modulation, and environmental triggers. Advances in genomics and transcriptomics have begun to elucidate the molecular mechanisms underlying corneal thinning and ectasia. Objectives: This review synthesizes two decades of evidence on the genetic and epigenetic architecture of keratoconus, highlights key molecular pathways implicated by these findings, and discusses translational implications for early diagnosis, risk prediction, and novel therapeutic strategies. Methods: A narrative review was conducted of peer-reviewed human, animal, and in vitro studies published from 2000 to 2025, with emphasis on genome-wide association studies (GWAS), sequencing data, methylation profiling, and non-coding RNA analyses. Findings were integrated with functional studies linking genetic variation to molecular and biomechanical phenotypes. Results: Genetic studies consistently implicate loci such as ZNF469, COL5A1, LOX, HGF, FOXO1, and WNT10A, alongside rare variants in Mendelian syndromes (e.g., brittle cornea syndrome, Ehlers–Danlos spectrum). Epigenetic research demonstrates altered DNA methylation, dysregulated microRNAs (e.g., MIR184, miR-143, miR-182), and aberrant lncRNA networks influencing extracellular matrix remodeling, collagen cross-linking, oxidative stress, and inflammatory signaling. Gene–environment interactions, particularly with eye rubbing and atopy, further shape disease expression. Translational progress includes polygenic risk scores, tear-based biomarkers, and early preclinical studies using RNA-based approaches (including siRNA and antisense oligonucleotides targeting matrix-degrading and profibrotic pathways) and proof-of-concept gene-editing strategies demonstrated in corneal cell and ex vivo models. Conclusions: Keratoconus arises from the convergence of inherited genomic risk, epigenetic dysregulation, and environmental stressors. Integrating multi-omic insights into clinical practice holds promise for earlier detection, precision risk stratification, and development of targeted therapies that move beyond biomechanical stabilization to disease modification. Full article

The CRISPR–Cas9 system has significantly advanced genome editing but remains constrained by its requirement for specific protospacer adjacent motifs (PAMs). To overcome this limitation, PAM-relaxed nucleases, including the novel near-PAMless chimeric SpRYc, have been developed. Here, we evaluated SpRYc editing activity across multiple experimental systems, including human HEK293 and CEM-R5 cells, as well as Drosophila melanogaster S2 cells and embryos. In HEK293 cells, SpRYc exhibited broad PAM compatibility, enabling editing at non-canonical PAMs, albeit with reduced and variable efficiency at canonical NGG sites compared to SpCas9. This context dependency was more pronounced in CEM-R5 T cells, where SpRYc activity at endogenous CXCR4 and B2M loci was largely restricted to NGG PAMs. In contrast, unlike SpCas9, SpRYc displayed negligible genome-editing activity in Drosophila embryos in vivo. Notably, the transcriptional activator dSpRYc-VPR showed robust activity in Drosophila S2 cells at both canonical and non-canonical PAMs. Reduced chromatin occupancy of dSpRYc-VPR suggests a balance between expanded PAM recognition and DNA-binding stability, providing a mechanistic explanation for context-dependent performance of SpRYc. Overall, our results highlight that expanded targeting flexibility comes at the cost of variable efficiency, underscoring the need for extensive locus- and context-specific validation of PAM-relaxed genome-editing tools. Full article

The oral microbiome has become an emerging focus of oral cancer research, with growing evidence linking microbial communities to disease development, progression, and prognosis. However, there is limited consensus on optimal sampling strategies, storage methods, and analytical approaches. This narrative review critically evaluates current strategies for sampling, preservation, DNA extraction, sequencing, and data analysis in oral microbiome research related to oral cancer. We compared commonly used sampling methods, including saliva, oral rinse, swab, brush, and tissue biopsy, and reviewed preservation conditions, extraction kits, sequencing platforms, and analytical pipelines reported in recent oral microbiome studies. Sampling approaches affect microbial yield and site specificity. Saliva and oral rinse samples are convenient and noninvasive but may dilute lesion-specific microbial signals, whereas lesion-directed swabbing or brushing yields greater microbial biomass and biological relevance. Preservation media and storage temperature significantly influence microbial stability, and DNA extraction methods vary in their ability to remove host DNA. Although 16S rRNA gene sequencing remains the most common approach, shotgun metagenomics offers higher resolution and function insights but is still limited by clinical applicability. Differences in data pre- and post-processing models and normalization strategies further contribute to inconsistent microbial profiles. Given that oral mucosal sites differ markedly in structure and microenvironment, careful consideration is required to ensure that collected samples accurately represent the biological question being addressed. Methodological consistency across all workflow stages—from collection to analysis—is essential to generate reproducible, high-quality data and to enable reliable translation of oral microbiome research into clinical applications for cancer detection and risk assessment. Together, these insights provide a framework to guide future study design and support the development of clinically applicable microbiome-based biomarkers. Full article

×Trititrigia cziczinii Tzvelev is a promising crop developed through distant hybridization between Elytrigia intermedia (Host) Nevski (=Thinopyrum intermedium (Host) Barkworth & D.R. Dewey) and Triticum aestivum L., followed by backcrossing with wheat. This study elucidates the genomic composition of this hybrid and its parental taxa using molecular phylogenetic analysis of nuclear (ITS, ETS) and chloroplast (trnK–rps16, ndhF) DNA markers, complemented by Next-Generation Sequencing (NGS) of the 18S–ITS1–5.8S rDNA region. Results from Sanger sequencing revealed that the primary nuclear ribosomal DNA (rDNA) of the hybrid originates from Triticum aestivum; a finding strongly supported by both Bayesian inference and Maximum Likelihood analyses. Chloroplast DNA data unequivocally indicate maternal inheritance from T. aestivum. In contrast, ETS sequence analysis showed phylogenetic affinity to Elytrigia intermedia, suggesting complex genomic reorganization or chimeric sequence formation in the hybrid. NGS data corroborate the dominance of T. aestivum-like ribotypes in the hybrid’s rDNA pool, with only a minor fraction identical to the main ribotype of E. intermedia. Genetic structure analysis further revealed geographic heterogeneity in the genomic composition of E. intermedia populations. The predominance of the wheat genome in ×T. cziczinii is likely a consequence of stabilizing backcrosses and illustrates a case of rDNA elimination from one parental genome during hybridization. This research underscores the complex genomic dynamics in artificial hybrids and the utility of multi-marker phylogenetic approaches for clarifying their origins. Full article

Background/Objectives: Cervical cancer is a leading cause of cancer-related mortality among women, primarily driven by persistent infections with high-risk human papillomavirus (HPV), particularly HPV-16. Vaccines based on plasmid DNA encoding the viral oncogenes E6 and E7 represent a promising immunotherapeutic strategy, but their efficacy remains limited due to poor cellular uptake. Cell-penetrating peptides such as RALA improve intracellular delivery, and functionalization with octa-arginine peptide conjugated to mannose (R8M) further enhances targeting of antigen-presenting cells (APCs). This study aimed to obtain the minicircle DNA (mcDNA) encoding mutant HPV-16 E6 and/or E7 antigens, and optimize its complexation with mannosylated RALA-based nanoparticles to improve vector delivery and consequently antigen presentation. Methods: Nanoparticles were formulated at different concentrations of RALA, with and without R8M functionalization. Their characterization included hydrodynamic diameter, polydispersity index, zeta potential, complexation efficiency (CE), stability, morphology, and Fourier-Transform Infrared Spectroscopy. In vitro assays in JAWS II dendritic cells (DCs) assessed biocompatibility, transfection efficiency and target gene expression. Results: Optimal conditions were obtained at 72.5 µg/mL of RALA, producing nanoparticles smaller than 150 nm with high CE (>97%) and uniform size distribution. Functionalization with R8M at 58 µg/mL preserved these characteristics when complexed with all mcDNA vectors. The formulations were biocompatible and effectively transfected DCs. Mannosylated formulations enhanced antigenic expression compared to non-mannosylated counterparts, evidencing a mannose-receptor-mediated uptake, while increasing the production of pro-inflammatory cytokines. Conclusions: Nanoparticles based on the RALA peptide and functionalized with R8M significantly improved mcDNA transfection and gene expression in APCs. These findings support further investigation of this system as a targeted DNA vector delivery platform against HPV-16. Full article

The peptidylarginine deiminase (PAD) family includes five isozymes (PAD1–4 and PAD6) with unique tissue distributions and substrate specificities. These enzymes facilitate citrullination, a post-translational modification where positively charged arginine residues are converted into neutral citrulline residues in the presence of calcium ions. This process significantly changes protein properties, affecting molecular interactions, structural stability, and biological functions. Over the past six years (2019–2025), there has been significant progress in understanding PAD activity mechanisms and their therapeutic potential. Recent discoveries include the regulated nuclear translocation of PAD2, PAD4’s specific role in forming cancer extracellular chromatin networks (CECNs), and the development of next-generation inhibitors with greatly improved pharmacological profiles. PAD4 is crucial in forming neutrophil extracellular traps (NETs). Citrullination of histones H3 and H4 by PAD4 destabilizes chromatin, helping release DNA-protein networks as an antibacterial defense. However, excessive NET formation can contribute to autoimmune diseases and thrombosis. Similarly, the bacterial peptidylarginine deiminase from Porphyromonas gingivalis (PPAD)—the only known prokaryotic citrullinating enzyme—plays a key role. Working with R-gingipains, PPAD triggers pathological citrullination of host proteins, leading to immune tolerance breakdown and linking periodontal disease with systemic autoimmune disorders such as rheumatoid arthritis, atherosclerosis, and Alzheimer’s disease. Once thought to be a rare post-translational modification, citrullination is now understood as a vital regulatory mechanism in both normal physiology and disease, involving both internal processes of homeostasis and external mechanisms of bacterial pathogenesis. Full article

Ultraviolet radiation B (UVB) radiation can induce oxidative stress, DNA damage, and inflammation, leading to skin wrinkling, impaired barrier function, and an increased risk of cancer. Addressing or preventing photoaging may provide a promising therapeutic avenue for these conditions. Hyperoside (HY), a compound abundantly found in medicinal plants including Hypericum perforatum and Crataegus, has been reported to have various pharmacological activities such as antioxidant, anti-inflammatory, cytoprotective, and antitumor effects; however, there are currently no studies systematically exploring the potential and mechanisms of HY in alleviating skin damage caused by ultraviolet (UV) rays. We investigated the inhibitory effects of HY on oxidative stress responses, reducing keratinocyte aging. HY can also exert these effects by mediating the PI3K/AKT/mTOR signaling pathway through miR-361-5p, maintaining mitochondrial dynamic stability, alleviating mitochondrial dysfunction, and enhancing mitophagy. Additionally, in vivo, HY was able to significantly improve skin wrinkles in mice while reducing changes in thickness and aging of the epidermis and dermis. Full article

Studies of the genomic stability of Ewing sarcoma (EwS) have produced contradictory findings. While they are generally characterized by low mutation rates of individual genes, several cases exhibit genomic alterations that manifest as chromosomal gains and losses. Taken together, these alterations represent independent biomarkers for EwS, such as loss of heterozygosity (LOH) or an altered genome. Patients with primary EwS tumors with fewer than three copy number alterations (CNAs) have a better prognosis than those with more CNAs. The functional mechanisms underlying this chromosomal instability are not yet clear. However, there are indications that this may be directly caused by the EWSR1::ETS translocations that are characteristic of EwS. The transcriptional behavior of the chimeric transcription factor EWSR1-FLI1 leads to the formation of R-loop DNA–RNA hybrids that form when RNA binds back to DNA during transcription and increased replication stress, which may result in structural chromosomal changes. Additionally, the formation of EWSR1 fusion genes in EwS results in the loss of one or both wild-type EWSR1 alleles in sarcoma cells. As chromosome segregation has been observed under loss of wild-type EWSR1, EWSR1 loss has been proposed as a potential source of LOH. So, it is highly probable that a chromosomal translocation and the subsequent formation of the EWSR1-ETS fusion protein cause the genomic alterations in EwS. This indicates that targeted therapy should be directed against the CNA and LOH biology caused by the fusion protein. Full article

Post-mortem interval (PMI) analysis plays a crucial role in forensic investigations, providing essential insights into the time since death. This study examined histological changes and ribonucleic acid (RNA) quantification across major organs to identify molecular indicators for PMI estimation. Because RNA gradually degrades after death, understanding its stability under different tissue, temperature, and PMI conditions provides valuable forensic insights. We analyzed post-mortem changes in total RNA from the heart, kidney, liver, and lung tissues of Sprague Dawley rats stored at 4 °C and 26 °C. Tissue samples were collected at various PMIs and evaluated histologically for cellular integrity. Total RNA concentration and purity were measured, and complementary DNA (cDNA) was synthesized for molecular analysis. Expression levels of 5S rRNA, B2m, Gapdh, and Sort1 were quantified using reverse transcription quantitative PCR (RT-qPCR). The results showed that PMI and organ type significantly affected total RNA concentration, whereas temperature exerted only a minor effect. Among the four target genes, 5S rRNA exhibited the lowest Ct values, indicating the highest stability. Notably, RNA degradation patterns varied with temperature, particularly in kidney and liver tissues. These findings suggest that RNA-based molecular markers, particularly 5S rRNA, may serve as promising indicators for accurate PMI estimation. Full article

In the context of climate change, Rhododendron species are pivotal in sustaining the stability of alpine ecosystems. Within alpine tundra (elevation > 2200 m) and timberline (elevation ~ 2000 m) regions of Changbai Mountain, the three studied Rhododendron species (Rhododendron aureum, Rhododendron lapponicum, and Rhododendron redowskianum) are prevalent; their mechanisms of adaptation to high-altitude environments remain insufficiently understood. This study employed an integrative approach, combining soil chemical analysis, physiological assessments, and molecular evolutionary analysis, to investigate phenotypic plasticity and genetic adaptation of these Rhododendron species. Both habitats demonstrated oligotrophic characteristics, with no significant differences (p > 0.05) observed in the concentrations of soil total organic carbon (TOC), ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃⁻-N), and available phosphorus (AP). Nonetheless, soil nutrient variability was more marked in timberline. Physiological traits, including malondialdehyde (MDA), soluble sugar, proline, and soluble protein, exhibited species-specific patterns; for example, R. redowskianum displayed elevated proline content in the timberline habitat, although no consistent inter-habitat trends were identified. From a total of 1995 orthogroups analysed, we identified 279 positively selected genes (PSGs, dN/dS > 1). These genes were found to be enriched in GO terms associated with DNA replication, amino acid transport, and pathway of nucleocytoplasmic transport. The study highlights tissue development and reproduction as primary evolutionary trajectories, while identifying cold stress as a significant environmental selection pressure. This research elucidates Rhododendron’s alpine adaptability and provides insights into alpine plant adaptation mechanisms and species conservation under climate change. Full article

R-loops are three-stranded nucleic acid structures implicated in genome regulation and stability. In Arabidopsis thaliana, the chloroplast-localized RNase H1 enzyme (AtRNH1C) is important for chloroplast development and genome integrity; however, its molecular activity has not been experimentally verified. In the present study, we characterized the enzymatic activity of recombinant AtRNH1C toward model R-loops of various structures. Using a set of synthetic R-loop substrates, we demonstrate that AtRNH1C cleaves the RNA within DNA/RNA hybrids with a strong preference for purine-rich sequences, most notably at G↓X dinucleotides. Kinetic assays showed that the enzyme’s efficiency is highly dependent on the length of the hybrid duplex but is not affected by a G-quadruplex structure in the single-stranded DNA flap of the R-loop. The most rapid degradation was observed for an R-loop with an 11 nt DNA/RNA hybrid region. This study provides a comparative analysis of chloroplast-localized RNase H1 activity and elucidates its substrate preferences, suggesting that an R-loop with a heteroduplex length closest to the native size found in transcription elongation complexes is the most efficient substrate. These findings suggest that the enzymatic activity of AtRNH1C is sufficient to perform its function in maintaining chloroplast genome stability by the degradation of R-loops in DNA. Full article