Search Results (2,210)

Background/Objectives: Vitamin B₁₂ (cobalamin) and folate (vitamin B₉) are essential cofactors in one-carbon metabolism required for DNA synthesis, methylation, and genomic stability. Deficiencies in these nutrients can cause megaloblastic anemia, neurological dysfunction, and hyperhomocysteinemia, linking micronutrient imbalance to cardiovascular and neurocognitive outcomes. Population-based surveillance of these biomarkers provides insight into nutritional trends and supports analytical standardization. Methods: This retrospective study included all routine plasma (P) vitamin B₁₂ and folate measurements performed at Uppsala University Hospital from 2005 to 2024 (n = 647,302 and 578,509, respectively). Data were extracted from the laboratory information system and summarized using annual medians, percentile distributions, and coefficients of variation (CV). Linear regression was used to validate the method comparison and assess the impact of the 2021 transition from the Abbott Architect to the Roche cobas platform. Descriptive statistics summarized the temporal and seasonal patterns of P-vitamin B₁₂ and P-folate. Results: Median P-vitamin B₁₂ concentrations remained stable (340–370 pmol/L; median CV = 4.6%), while P-folate increased from 10.5 to 15.5 nmol/L (median CV = 12.9%) from 2005 to 2024. Low P-folate (<7 nmol/L) was observed in 7.1% of measurements and low or borderline P-vitamin B₁₂ (<250 pmol/L) in 22.6%. Females exhibited slightly higher concentrations of both analytes. Although no clear seasonal pattern was observed, small biological effects cannot be excluded. Sample volumes decreased during the summer. The transition to Roche assays introduced measurable methodological shifts, particularly for P-folate. Conclusions: Levels of P-vitamin B₁₂ remained stable over two decades, while P-folate status increased modestly. This reflects both dietary influences and assay-related differences following the 2021 platform transition. Continuous surveillance of biomarker medians provides a sensitive tool for detecting analytical drift and for monitoring long-term nutritional trends in clinical populations. Full article

Thyroid hormones (THs) regulate metabolism, proliferation, and genomic stability. Clinical studies have linked levothyroxine therapy with higher Oncotype DX Recurrence Scores in breast cancer (BC), suggesting a potential effect of thyroid hormone signaling on genomic risk. Here, we investigated the impact of triiodothyronine (T3) on DNA damage and repair pathways in estrogen receptor-positive T47D breast cancer and non-tumorigenic MCF10A cells. RNA sequencing revealed significant upregulation of RAD51 and enrichment of DNA repair pathways following 24 h T3 exposure. Consistently, T3 increased γH2AX and 53BP1 nuclear foci, indicating transient activation of the DNA damage response (DDR). These effects were transient, returning to baseline after 48 h, suggesting cellular adaptation. T3 also enhanced proliferation at 10 μM but inhibited growth at higher concentrations. Our findings indicate that acute exposure to T3 induces transient genomic stress, providing a potential mechanistic basis for the observed association between thyroid hormone therapy and increased BC recurrence risk. Full article

Human zinc finger Ran-binding protein 3 (ZRANB3) is crucial for DNA damage tolerance (DDT), as it prevents excessive damage, restores fork progression, and ultimately maintains genome stability. This unique and ancient architecture mainly exerts its function during replication fork reversal (RFR) and within the p53/Polι axis; thus, ZRANB3 is considered a tumour suppressor. However, possible additional roles in DNA synthesis and cell metabolism have been proposed. In tumour cells, ZRANB3 gene expression is deregulated, a condition that is frequently associated with poor survival and adverse clinical outcomes. ZRANB3 can be altered by functional mutations, gene copy number alterations, and a combination of the two. Although its mRNA levels typically correlate with p53 expression, this correlation breaks down in the context of p53 mutations and high proliferative activity. This comprehensive review integrates the currently available yet fragmented literature on ZRANB3, both at the gene and protein levels, examines its regulation in cancer development, and discusses the evidence supporting its role as a tumour suppressor and prognostic biomarker. Full article

Mitochondria not only generate ATP and metabolites essential for nuclear and cytoplasmic processes but also actively shape nuclear epigenetic regulation. Conversely, the nucleus encodes most of the proteins required for mitochondrial functions, and intriguingly, certain nuclear-encoded epigenetic factors—such as DNA and histone modifiers—also localize to mitochondria, where they modulate mitochondria genome stability, gene expression, metabolic flux, and organelle integrity. This reciprocal interplay defines mitochondria as both a source and a target of epigenetic regulation, integrating energy metabolism with gene expression and cellular homeostasis. This review highlights emerging mechanisms that link mitochondrial metabolism to chromatin remodeling, DNA and histone modifications, and transcriptional control, as well as how nuclear epigenetic enzymes translocate into mitochondria and regulates their functions. We also briefly introduce recent methodological advances that enable spatially selective depletion of mitochondrial proteins, offering new tools to dissect this bidirectional communication. Together, these insights underscore mitochondria’s central role as an energetic and epigenetic hub coordinating nuclear function, development, and disease. 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

Breast cancer subtypes are known to have important pathobiological and clinical features. For example, triple-negative breast cancer (TNBC) remains one of the most aggressive and treatment-resistant breast cancer subtypes, lacking hormone and HER2 targets. Increasing evidence suggests that circular RNAs (circRNAs) and their N6-methyladenosine (m⁶A) modifications play critical roles in cancer biology through the regulation of gene expression, stability, and signaling networks. This study aimed to identify m⁶A methylation patterns in circRNAs among breast cancer subtypes, explore their potential biological functions, and assess their diagnostic and prognostic relevance compared with luminal breast cancer subtypes. Genome-wide profiling of m⁶A-modified circRNAs was conducted in TNBC and luminal breast tumor samples using methylated RNA immunoprecipitation followed by microarray analysis. Differential methylation and expression analyses were integrated with pathway enrichment, survival correlation, and receiver operating characteristic (ROC) curve assessments to identify subtype-specific and clinically relevant circRNA candidates. Distinct m⁶A circRNA methylation signatures were identified across breast cancer subtypes, with TNBC showing enrichment in pathways related to Wnt/β-catenin, CDC42 GTPase signaling, and cytoskeletal remodeling. Several circRNAs, including those derived from ZBTB16, DOCK1, METTL8, and VAV3, exhibited significant hypermethylation and high diagnostic accuracy (AUC > 0.80). Survival analyses revealed associations between circRNAs from key host genes and overall or relapse-free survival, suggesting prognostic potential. These findings uncover subtype-specific m⁶A circRNA methylation landscapes that may contribute to tumor aggressiveness and heterogeneity. Identified circRNAs represent candidates for investigation as biomarkers for subtype classification and prognosis and may inform future research into epigenetic and post-transcriptional therapeutic targets in breast cancer. Full article

With the rapid growth of the population and the economy, environmental and health issues caused by animal protein consumption have received increasing attention. The world urgently needs alternative proteins as a way out, and microbial proteins have tremendous potential as sustainable protein sources. In this study, Neurospora intermedia FF171 was isolated and identified from Pu-erh fermented tea. FF171 can rapidly produce substantial mycelial biomass using a sugar byproduct as a carbon source. The combination of sugarcane molasses and corn gluten meal as carbon and nitrogen sources, respectively, resulted in a dry biomass of 9.10 ± 0.20 g/L and a protein yield of 6.16 ± 0.11 g/L (67.48% protein content). FF171 exhibits genetic stability, and no mycotoxins were detected in the biomass. Furthermore, the strain’s genome was sequenced and annotated. Bioinformatics analysis, including comparison of specific sequences with reference strains in the GRAS (Generally Recognized as Safe) database, was conducted to assess potential toxicity, allergenicity, and antimicrobial resistance. The results revealed no virulence or pathogenic factors and no antibiotic resistance genes, while the risk of triggering allergic reactions was minimal. Taken together, these findings suggest that Neurospora intermedia FF171 is a safe and promising candidate for mycoprotein production, with strong potential as a future alternative protein source. 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

As a monophyletic group, bryophytes—mosses, liverworts, and hornworts—represent some of the earliest land plants, evolving under harsh terrestrial conditions that prompted major morphological, physiological, and molecular changes. Limited water availability, extreme temperatures, and osmotic stresses often caused cellular desiccation in these pioneering plants. Because bryophytes occupy a key position in land-plant evolution and are closely related to streptophyte algae, their desiccation-tolerance strategies hold significant evolutionary importance. Early adaptations included changes in growth patterns and the formation of specialized vegetative structures. Bryophytes also survive extreme habitats by regulating physiological and biochemical traits such as photosynthetic pigment maintenance, osmotic adjustment, membrane stability, redox balance, and the accumulation of compatible solutes and stress-responsive proteins. Advances in molecular biology and whole-genome sequencing of model mosses and liverworts have further revealed that they possess diverse stress-responsive signaling components, including phytohormones, receptor proteins, protein kinases, and key transcription factors that control stress-related gene expression. However, a comprehensive synthesis of these molecular mechanisms is still lacking. This review aims to provide an updated overview of how mosses and liverworts use plant growth regulators, stress-responsive proteins, compatible solutes, antioxidants, and integrated signaling networks to survive in dry terrestrial environments. Full article

This review explores strategies to enhance meat quality in poultry, focusing on both management and genetic methods. Poultry meat quality is influenced by many factors, including rearing conditions, nutrition, animal welfare, and post-slaughter processing. Key management factors such as stocking density, ventilation, temperature, and humidity are emphasized for their significant impact on bird welfare and the resulting meat texture, color, and microbial stability. Welfare-enhancing practices like gentle handling, environmental enrichment, and thermal comfort are highlighted for their direct effects on stress levels and meat properties such as water-holding capacity and pH. Innovations in slaughtering and chilling techniques, including electrical and gas stunning and rapid chilling, are shown to preserve meat quality and prevent common defects like pale, soft, and exudative (PSE) or dark, firm, and dry (DFD) meat. The review also underscores the importance of hygiene protocols, hazard analysis and critical control points (HACCP) systems, and traceability technologies to ensure food safety and foster consumer trust. On the genetic front, it discusses conventional selection, marker-assisted selection (MAS), and genomic selection (GS) as tools for breeding birds with better meat quality traits, including tenderness, intramuscular fat, and resistance to conditions like woody breast. Functional genomics and gene editing are identified as the leading edge of future advances. Ultimately, the review advocates for an integrated approach that balances productivity, quality, animal welfare, and sustainability. As consumer expectations increase, the poultry industry must adopt precise, science-based strategies across the entire production process to reliably deliver high-quality meat products. Full article

Fishes are frequently exposed to hypoxic stress, yet their tolerance to hypoxia varies significantly among species. The association between this variation and alterations in the hypoxia-inducible factor (HIF) pathway remains unclear. We discovered that otomorphs generally retain two Hif-1α paralogs (Hif-1αa and Hif-1αb), resulting from the teleost-specific genome duplication (TGD), whereas most euteleosts possess only a single Hif-1αa copy. In otomorphs, key mutations disrupt one conserved Leu-X-X-Leu-Ala-Pro (LXXLAP) motif in the oxygen-dependent degradation (ODD) domain of the Hif-1αa proteins. Molecular dynamics simulations revealed that these mutations impede the recognition of the critical proline residue by prolyl hydroxylase domain protein 2 (PHD2), suggesting enhanced normoxic stability of Hif-1αa. We also investigated the expression profiles of hif-1α and downstream genes in four fish species (two otomorphs and two euteleosts). In otomorphs, the hif-1αa genes were highly expressed specifically in the heart; concomitantly, two critical downstream genes, ldha and mct4, exhibited relatively high expression levels in vital tissues such as the heart, brain, and muscle. This coordinated expression pattern promotes a heightened glycolytic capacity and facilitates lactate shuttling in these tissues, thereby ensuring energy supply during hypoxic stress. Our integrated computational analyses indicate that otomorphs achieve enhanced hypoxia tolerance through the subfunctionalization of Hif-1α paralogs. Full article

The calmodulin-binding protein 60 (CBP60) family comprises essential Ca²⁺-responsive transcription factors that orchestrate salicylic acid (SA)-mediated immunity and broader stress responses. Despite being extensively characterized in model species, the CBP60 family remains poorly understood in watermelon (Citrullus lanatus), a globally significant cucurbit crop highly susceptible to aphid infestation and fusarium wilt. In this study, we performed a comprehensive genome-wide identification and characterization of the CBP60 gene family in watermelon, identifying 16 putative ClaCBP60 members, all of which harbor the conserved calmodulin-binding domain. These genes are non-randomly distributed across chromosomes, featuring a prominent cluster of 10 members on chromosome 3. Phylogenetic analysis across seven cucurbit species categorized the CBP60 proteins into four distinct subfamilies, revealing both evolutionary conservation and lineage-specific diversification. Gene structure and conserved motif analyses revealed shared core domains with subfamily-specific variations, indicative of functional divergence. Furthermore, synteny analysis showed strong collinearity with cucumber and melon, reflecting the evolutionary stability of key CBP60 loci. Transcriptional profiling under F. oxysporum infection and aphid infestation revealed dynamic expression patterns, with ClaCBP60_01 and ClaCBP60_16 exhibiting rapid and robust induction during the early stages of both stresses. These findings indicated that ClaCBP60 genes operate in a coordinated yet diversified manner to modulate defense signaling against F. oxysporum and aphid attack. This study provides a systematic insight into CBP60 family members in watermelon, establishing a foundation for validation and molecular breeding aimed at enhancing biotic tolerance. Full article

ARID1A, a key subunit of the SWI/SNF chromatin remodeling complex, plays a context-dependent function in cancer, acting both as a tumor suppressor and, in certain conditions, as an oncogene. ARID1A, as a tumor suppressor, maintains transcriptional regulation, genomic stability, and cellular differentiation. In breast cancer, ARID1A loss-of-function leads to dysregulation of cell cycle checkpoints and impaired DNA repair and promotes epithelial-to-mesenchymal transition (EMT), jointly accelerating tumor proliferation and increasing therapeutic resistance. Notably, context-dependent ARID1A loss-of-function often concurs with activation of the PI3K/AKT signaling pathway and corresponds with poor prognosis. On the contrary, aberrant ARID1A overexpression can provoke oxidative stress and agitate the cytochrome P450 system, potentially facilitating early tumorigenesis. Consequently, understanding ARID1A’s dual and context-dependent role highlights its potential as a biomarker and therapeutic target in precision oncology. Full article

Temozolomide (TMZ) remains foundational in the management of adult-type diffuse gliomas in general, and glioblastoma specifically. However, its efficacy harbors an evolutionary trade-off. TMZ drives its cytotoxicity through generating O⁶-methylguanine lesions, especially active in MGMT-silenced, mismatch repair (MMR)-proficient tumors. By selecting for acquired MMR-deficient subclones, often via MSH6 inactivation, this process escalates into a hypermutator phenotype, generating thousands of de novo alterations. This is a hallmark of the mutational signature known as SBS11, characterized by C>T transitions, which is associated with TMZ treatment. The hypermutator phenotype drives heterogeneity, therapeutic resistance, spatial diversification, and distant recurrence. Despite harboring a mutational burden comparable to melanoma and lung cancer, TMZ-induced hypermutation does not sensitize gliomas to immune checkpoint blockade. This resistance reflects the profoundly immunosuppressive brain microenvironment, impaired antigen presentation, marked transcriptional plasticity, and perhaps also the frequent use of corticosteroids. Emerging strategies aim to exploit vulnerabilities created by TMZ-mediated genomic instability, including PARP, ATR, WEE1, and AURKA inhibition; alternative alkylators; metabolic rewiring; and G-quadruplex stabilization. Notably, the real-time detection of evolving mutational signatures via CSF-based liquid biopsies may enable adaptive therapy before radiographic progression. By reframing TMZ as a potent evolutionary agent rather than a conventional chemotherapy, this review synthesizes recent mechanistic insights and translational opportunities to guide a next-generation, evolution-informed treatment paradigm for glioma. Full article

Background/Objectives: The selection and validation of species-specific housekeeping genes (HKGs) have become increasingly common in functional genomics, with application of quantitative Polymerase Chain Reaction (qPCR) or cDNA-based qPCR (RT-qPCR). Despite the Macrobrachium amazonicum having RNA-seq studies available, there are still no data on the most stable and consistent HKGs for use in relative gene expression analyses. Therefore, the present study aimed to identify and validate seven HKGs in M. amazonicum: Eukaryotic Translation Initiation Factor (EIF), 18S ribosomal RNA (18S), Ribosomal Protein L18 (RPL18), β-actin, α-tubulin (α-tub), Elongation Factor 1-α (EF-1α), and Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH). Methods: The HKGs were identified in the M. amazonicum transcriptome, characterized for identity confirmation, and compared against public databases. Subsequently, RT-qPCR assays were prepared using muscle, hepatopancreas, gills, testis, androgenic gland, and ovary to assess the stability of the HKG markers, employing the comparative ∆Ct, BestKeeper, NormFinder, and GeNorm methods. Results: All candidate HKGs identified showed high similarity with other decapods. Reactions performed with these markers demonstrated high specificity, PCR efficiency, and elevated coefficients of determination. The comprehensive ranking, indicated that no single HKG was stable across all tissues, with HKGs showing the best stability being tissue-specific. The most stable HKGs were RPL18 and 18S. GAPDH, historically used as an HKG, showed the poorest performance in stability ranking for most tissues tested, whereas β-actin was most suitable only for ovarian. Conclusions: These data reinforce the need for species-specific HKG validation and provide an appropriate panel of reference markers for gene expression studies in the M. amazonicum. Full article