Search Results (170)

The intrinsic weakness of the budding yeast Saccharomyces cerevisiae in xylose utilization limits its application in biological manufacturing using lignocellulosic biomass. Although the natural yeast strain S. cerevisiae YB-2625 exhibits superior innate xylose-fermenting capability, the underlying mechanisms remain largely unexplored. Here, we employed comparative multi-omics to systematically dissect the molecular basis of its high stress tolerance and superior xylose consumption. Comparative genomics revealed 73,842 single nucleotide polymorphisms (SNPs) and 5191 small insertions/deletions (InDels) in YB-2625 relative to S288C, with significant enrichment in genes associated with chromatin remodeling, transcriptional regulation, and stress signaling. Integration of genomic and transcriptomic data identified candidate variants in key regulators. Functional validation further demonstrated that Tra1, a component of the SAGA, SLIK, and NuA4 histone acetyltransferase complexes, acts as a global regulator with growth-coupled effects on stress tolerance and xylose metabolism. Deletion of TRA1 significantly reduced the final biomass in xylose medium. Moreover, deletion of RTT109 specifically impaired growth on xylose without affecting any of the tested stress tolerance phenotypes. We further examined global chromatin accessibility changes upon deletion of the histone acetyltransferase gene NGG1, a manipulation previously shown to substantially enhance xylose utilization in the engineered YB-2625 background. ATAC-seq analysis revealed that loss of Ngg1 alters chromatin accessibility at loci governing carbohydrate metabolism and stress responses, thereby establishing a direct link between epigenetic remodeling and the superior phenotype of YB-2625. Our findings provide a basis for deciphering the regulatory circuitry governing xylose utilization in recombinant yeast and for the rational engineering of robust strains for lignocellulosic bioconversion. Full article

Predicting CRISPR-Cas9 guide RNA efficiency and off-target activity is a precondition for precise genome editing. Computational models have progressively incorporated chromatin accessibility and epigenetic descriptors into their feature sets, yet synthesising findings from independently published studies—especially when those studies contradict one another—remains an unresolved methodological gap. Large Language Models (LLMs) have been proposed as a route to automate cross-study synthesis, but their utility depends on a constraint that receives less attention than model architecture: how much of the source text actually reaches the model at inference time. Cloud-based models process 48,000-token corpora without hardware limitations, but at the cost of data leaving the local environment and with limited reproducibility across API versions. Local RAG systems avoid the cloud dependency while fragmenting the input, discarding the global context needed to link biological arguments that are distributed across separate papers. We benchmark these strategies using a corpus of four CRISPR-Cas9 efficiency prediction studies and apply the Reduced Interaction Sampling (RIS) engine—a local sparse attention method—to retain the full sequence within the memory envelope of a laboratory server. Preserving that context uncovers three latent inconsistencies. The static epigenetic markers used in DeepCRISPR (CTCF, DNase I) show near-zero Spearman correlations with off-target cleavage ($\rho \le 0.07$), while nucleosome positioning scores from the Block Decomposition Method reach $\rho =0.388$–$0.423$. The sequence-only Apindel model was published in June 2022 without incorporating nucleosome descriptors reported in the concurrent literature. The benchmark review by Konstantakos et al. attributed 10–20% of rank correlation to epigenetics—a figure that reflects the weak feature subset evaluated, not a ceiling on chromatin influence. These discrepancies are invisible when papers are read individually or retrieved as chunks; they become traceable only when the full corpus is processed as a single context window. An independent empirical analysis of 2000 CRISPR-Cas9 off-target cleavage events provides evidence consistent with this pattern: static epigenetic markers yield $\left|\rho \right|\le 0.11$, whereas computed NuPoP Affinity descriptors reach $r=-0.622$ ($p<{10}^{-210}$). On a 30-question cross-study synthesis benchmark (5 independent seeds), baseline accuracy is 53.33%, RAG 60.00%, and RIS (30 seeds, 3% density) 70.00% ($p<0.0001$, t-test vs. RAG, $\sigma =0.00\%$ for all configurations). Full article

DNA methylation has long been regarded as a stable, maintenance-based epigenetic marker. However, this classical binary model struggles to fully explain the dynamic and situational dependence of methylation regulation at the multi-biological level. This review defines DNA methylation as a programmable information layer that systematically integrates the latest advances in three interrelated dimensions of molecular coding, disease status indication, and epigenomic engineering. At the molecular level, this paper describes how the chemical diversity of cytosine modification, the writing–erasing enzyme network, and the three-dimensional structure of chromatin jointly construct a methylated polymorphic coding system and evaluates the performance of emerging sequencing technologies in DNA integrity, reading length, modification resolution, and analytical complexity through a multidimensional scoring framework. At the cellular and clinical levels, this paper comprehensively demonstrates methylation as a quantifiable indicator of cell identity, biological aging and disease status, covering circulating free DNA biomarkers and spatial heterogeneity analysis. Critically, this paper evaluates how the clustered regularly interspaced short palindromic repeats (CRISPR)-based epigenome editing platform achieves causal inference and promotes the transformation of methylation from related biomarkers to functional therapeutic targets. At the same time, persistent challenges such as off-target specificity, in vivo delivery, and spatiotemporal regulation encountered in epigenetic gene editing are discussed. This review reveals the paradigm shift of DNA methylation from passive observation markers to actively engineered regulatory parameters, which has direct therapeutic application prospects. Full article

Metabolic reprogramming constitutes a fundamental hallmark of malignancy, orchestrating a hostile tumor microenvironment (TME) that severely compromises anti-tumor immunity. Despite the transformative success of immune checkpoint blockade and adoptive cell therapies, clinical efficacy is frequently curtailed by the metabolic barriers imposed by the TME. This review systematically elucidates the complex metabolic interplay between tumor cells and infiltrating T cells, highlighting two defining mechanisms driving immune evasion: the competitive sequestration of essential nutrients and the accumulation of immunosuppressive oncometabolites. We detail how the depletion of glucose and critical amino acids (glutamine, arginine, methionine, etc.) imposes a state of “metabolic siege” on T cells, impairing their bioenergetics and effector functions. Concurrently, we explore how accumulated metabolites—such as lactate, succinate, 2-hydroxyglutarate, kynurenine, and lipids—function as non-canonical signaling molecules to subvert immune surveillance via epigenetic remodeling and oxidative stress. Furthermore, we synthesize emerging therapeutic strategies designed to dismantle this metabolic barrier, including targeting metabolic enzymes (IDO1 and FASN) and transporters, repurposing metabolic waste, and genetically engineering T cells with enhanced metabolic fitness and resilience. By integrating the latest insights into the “metabolism–epigenetics–immunity” axis, this review provides a theoretical foundation for developing next-generation immunotherapies that target metabolic vulnerabilities to overcome resistance in cancer treatment. Full article

Cereal crops including wheat, rice, maize, barley, and sorghum collectively supply most global caloric and protein requirements, yet their productivity is increasingly constrained by combined abiotic stresses that co-occur under field conditions. Simultaneous drought, heat, salinity, and cold impose yield losses that consistently exceed those caused by individual stresses and elicit molecular responses that are qualitatively distinct from single-stress reactions and cannot be inferred from them. Despite this agronomic reality, the molecular mechanisms governing combined stress responses in cereals remain poorly resolved, and no integrated framework connecting the transcriptional, epigenetic, and genome-editing dimensions of combined stress tolerance has previously been articulated for this crop group. This review proposes a three-tier integrated framework for understanding and engineering combined abiotic stress tolerance in major cereals. The first tier encompasses transcription factor networks, including bZIP, WRKY, NAC, AP2/ERF, DREB, MYB, and HSF families, that translate combined stress signals into transcriptional reprogramming through ABA-dependent and ABA-independent pathways, hormonal crosstalk, and osmoprotectant and antioxidant defence systems. The second tier addresses the epigenetic regulatory layer, encompassing DNA methylation, histone modifications, and non-coding RNA pathways that gate TF binding site accessibility and encode stress memory in cereals. The third tier examines CRISPR-based tools, including multiplexed Cas9 editing and dCas9-based epigenome editing, that engineer validated targets from both tiers, while confronting polyploid off-target effects, growth penalties, and a laboratory-to-field validation gap. The three tiers are mechanistically coupled, with TF activity shaping epigenetic landscapes, epigenetic states gating TF access, and both providing precision engineering targets. Critical gaps include the absence of combined-stress epigenomic datasets, limited characterisation in barley and sorghum, and early-stage combined-stress-specific strategies. Full article

Depression and anxiety are increasingly understood to involve systemic biological processes, where chronic stress, immune dysregulation, and vascular dysfunction converge on brain-relevant symptoms. Fermented foods are widely studied as psychobiotic candidates, yet results remain inconsistent because products vary in chemistry, viability, sodium, and biogenic amines, and trials often rely on broad symptom outcomes without exposure verification. A major gap is the lack of a reusable, mechanism-first framework that links what a product delivers to barrier, endothelial, and neurovascular target engagement. As a narrative and conceptual review rather than a systematic review, the article integrates mechanistic evidence into a conceptual framework rather than undertaking quantitative evidence synthesis. It addresses that gap by treating fermented vegetables, dairy, soy, and selected Brazilian cassava ferments and artisanal cheeses as metabolite-engineering platforms mapped onto a tri-barrier remodeling axis from gut epithelium to endothelium and platelets to the blood–brain barrier. We synthesize dosing-resolved metabolite modules, including short-chain fatty acids, tryptophan-derived indoles, bile acids, neuroactive small molecules, and peptide and exopolysaccharide fingerprints, and align them with interpretable readouts for permeability, endotoxemia proxies, endothelial activation, immunothrombosis, and epigenetic aging pace. Here we highlight how this modular framework converts heterogeneous food studies into testable exposure hypotheses, guides comparator design and phenotype stratification, and clarifies why null results can be informative. To maintain a focused scope, the review uses selected fermented-food families as representative test platforms rather than attempting a complete survey of global fermented foods. The emphasis is therefore placed on mechanisms, exposure verification, and trial-design principles that can be transferred to other products. Full article

Plant tissue culture is a crucial part of biotechnology that supports crop improvement, plant conservation, and other related fields. Although tissue culture has been successfully used in many plants, low regeneration and transformation rates still exist in some species. Agrobacterium-mediated transformation is commonly used in genetic engineering, but its effectiveness depends heavily on establishing a reliable in vitro regeneration system through organogenesis or somatic embryogenesis. Over the past decade, substantial progress has been made in understanding the molecular basis of regeneration; however, most reviews have focused on individual aspects such as hormone regulation or transcription factor networks in isolation. In contrast, this review provides a comprehensive and integrated framework that systematically links four critical layers—wound signaling, hormonal regulation, developmental regulators, and epigenetic modifications—into a unified regulatory network governing plant regeneration. Furthermore, we highlight recent cutting-edge advances, including artificial intelligence-assisted prediction, single-cell and spatial transcriptomics, epigenome editing, and CRISPR-based activation systems, and we discuss their transformative potential in overcoming genotype-dependent recalcitrance. By synthesizing classical regulatory mechanisms with emerging technologies, this review offers a forward-looking perspective that distinguishes it from earlier publications and provides both theoretical foundations and practical strategies for improving plant regeneration and genetic transformation. Full article

The detection of RASSF1A (Ras-associated domain family 1 isoform A) promoter methylation in body fluids can offer a powerful tool for the early diagnosis of bladder cancer. Zinc finger proteins (ZFPs) serve as sequence-specific recognition elements for targeting double-stranded DNA sequences. Here, we report a cyclic olefin copolymer (COC) chip-integrated ZFP array-based molecular sensor that bypasses the need for bisulfite conversion and PCR amplification to recognize the specific site of DNA methylation in the RASSF1A promoter. Building upon the SEER-LAC (SEquence-Enabled Reassembly of β-Lactamase) framework, we engineered a dual-recognition split-enzyme system in which a COC chip-immobilized ZFP array confers sequence specificity while a co-recruited methyl-binding domain (MBD) enforces methylation-dependent gating, together driving the proximity-induced reconstitution of functional β-lactamase at methylated target loci. Accordingly, this sensor specifically reassembles and restores enzymatic activity only in the presence of specific methylated DNA in the RASSF1A promoter region. We demonstrate that this dual-component array effectively differentiates methylation status with high specificity. Given its rapid turnaround and non-PCR-based mechanism, this system can be well-suited for developing diagnostic assays for bladder cancer, offering a potential alternative to conventional epigenetic screening methods. Full article

Increasingly frequent and severe drought events restrict global agricultural productivity. As sessile organisms, cereal crops have evolved phenotypic plasticity, drawing on drought escape (DE) and drought avoidance (DA) strategies to balance survival and reproduction. While the mechanisms governing photoperiodic flowering and drought responses are well characterized individually, their molecular intersection remains poorly understood. This review summarizes recent advances in the crosstalk between these two pathways. We highlight the divergent roles of core genetic hubs, such as florigen regulation, GIGANTEA (GI), DELLA proteins, and dual-function transcription factors (e.g., ZmCCT, Ghd7, Ppd-H1), and the breeding-selected alleles, including Green Revolution variants, that can partly uncouple stress tolerance from developmental penalties, though trade-offs often remain. Furthermore, we examine the internal networks driving this crosstalk, including circadian clock phase shifts, sugar and energy signaling through the trehalose-6-phosphate (T6P)-SNF1-related protein kinase 1 (SnRK1) module, and the antagonistic balance within phytohormone networks centered on abscisic acid (ABA). Finally, we propose that integrating epigenetic stress memory, systemic root-to-shoot signaling, and targeted CRISPR/Cas promoter engineering provides a useful conceptual framework for breeding climate-resilient, yield-stable crops. Full article

Autoimmune endocrine diseases constitute a group of disorders characterized by immune-mediated destruction or dysfunction of hormone-producing glands. The pathogenesis of these diseases reflects a breakdown of immune tolerance in which regulatory T cells (Tregs) play a key role. The transcription factor forkhead box P3 (FOXP3) is a master regulator of Treg differentiation and suppressive function. Also, it is central to maintaining self-tolerance. Genetic mutations in FOXP3, including those responsible for immune dysregulation, polyendocrinopathy, enteropathy X-linked (IPEX) syndrome, highlight the critical role of FOXP3 in endocrine immune tolerance. Emerging evidence suggests that autoimmune endocrine disorders may reflect organ-specific destabilization of FOXP3 expression rather than complete Treg deficiency. The reversibility or irreversible loss of FOXP3 gene expression represents a key determinant of Treg plasticity and the persistence of autoimmune inflammation. This review proposes an integrated genetic–epigenetic model of FOXP3 instability and examines how the endocrine microenvironment shapes Treg plasticity. Genetic or epigenetic alterations affecting FOXP3 expression can impair Treg activity and precipitate endocrine organ-specific autoimmunity. Epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNA-mediated regulation that modulate FOXP3 transcriptional activity are discussed. From a translational perspective, the potential of FOXP3 as a biomarker for endocrine disease susceptibility and progression was summarized. Furthermore, therapeutic strategies employed for expanding or engineering functional FOXP3⁺ Tregs using antigen-specific vaccines, chimeric antigen receptors (CAR)-Tregs, gene therapy, or low-dose interleukin-2 (IL-2) were described. Full article

Background/Objectives: Stem cells with the ability to differentiate into other cell types and self-renewal afford a powerful apparatus for the healthcare system to replace and rejuvenate damaged tissues and organs in the treatment of various diseases. For the last few decades, stem cell therapy (SCT) has evolved from being an experimental approach to a recognized clinical treatment. SCT and regenerative medicine have garnered tremendous attention and become prominent tools, especially in treating chronic and acute disease and addressing organ failures, and in their repair and replacement, which are directly associated with human health, life, and longevity. Methods: In this review, after providing a brief history and need for the SCT, the employed delivery techniques utilizing various biomaterials, as well as recent developments in nanotechnological methods, are presented. It is focused on the current literature for the recent progress of stem cell therapy and tissue engineering for the application fields in neurological, ophthalmological, cardiovascular, orthopedic, and oncology, followed by the challenges associated with their applications. Results: In addition to safety concerns, challenges such as uncontrollable differentiations, genetic and epigenetic instability, limited cell survival and integration, immunological rejections, scaling and manufacturing drawbacks, as well as unpredictable behaviors and clinical limitations were reviewed. Conclusions: Future aspects with respect to regenerative medicine and tissue engineering, gene editing and personalized therapies, immunomodulation and anti-inflammatory applications, as well as neuroregeneration and treatment of neurodegenerative disorders are reflected. Full article

Nervonic acid (NA, C24:1 Δ15) is a vital extra-long-chain monounsaturated fatty acid essential for neural development, myelin sheath formation, and neurological health. As the most abundant natural source of NA, Malania oleifera Chun & S.K.Lee has become a key model for studying NA biosynthesis and regulation. This review systematically summarizes the metabolic pathways of nervonic acid biosynthesis in M. oleifera, including plastidial de novo fatty acid synthesis, endoplasmic reticulum (ER)-based very-long-chain fatty acid elongation, and Δ15 desaturation. We focus on the catalytic mechanisms and rate-limiting roles of the elongase complex (KCS, KCR, HCD, ECR) and Δ15 desaturase. Additionally, we integrate recent multi-omics data to analyze key enzyme KCS gene families, their phylogenetic relationships, and syntenic distribution patterns. Furthermore, transcriptional regulatory networks (MYB, bZIP, WRI1, ABI3, FUS3) and epigenetic regulation underlying NA accumulation are also discussed. Finally, we highlight advances, challenges, and prospects in metabolic engineering and synthetic biology for sustainable NA production. This review provides a theoretical basis for the conservation, molecular breeding, and biotechnological utilization of M. oleifera. Full article

Anthocyanin-rich dark pigmentation is increasingly recognized as more than a simple consequence of flavonoid accumulation. Here, we define the anthocyanin-driven dark phenotype (ADP) as a coordinated stress-responsive state characterized by intense anthocyanin accumulation coupled with cellular and regulatory reprogramming. Recent studies show that reactive oxygen species, sugar signaling, temperature stress, and hormonal crosstalk converge on MYB–bHLH–WD40-centered regulatory networks that integrate pigment biosynthesis with vacuolar organization, transport activity, and stress adaptation. Epigenetic remodeling, chromatin dynamics, and post-transcriptional regulation further influence pigment intensity and persistence. Importantly, ADPs do not represent an alternative biosynthetic pathway or merely pigment abundance, but instead reflect a systems-level regulatory state governed by coordinated transcriptional, hormonal, and epigenetic control of the canonical anthocyanin machinery. However, several important questions remain unresolved, including how plants retain phenotypic stability under various environmental and developmental settings, whether ADPs contribute to long-term stress memory, and how anthocyanin accumulation is balanced with growth and energy expenditures. To translate ADP-associated features into crop development techniques, these gaps must be filled. We also emphasize spatial omics and CRISPR-based engineering as new methods for analyzing and modifying stress-resilient phenotypes. Full article

Neuroblastoma (NB), the most common extracranial solid tumor of childhood, exemplifies one of the most formidable paradigms of tumor immune evasion (TIME) in pediatric oncology. Despite significant advances in multimodal therapy and the clinical integration of immunotherapeutic strategies, high-risk NB (HR-NB) remains largely refractory to durable immune control. This failure reflects not an absence of immune engagement, but the presence of a highly evolved and developmentally wired immune escape architecture. In this review, we synthesize emerging insights from single-cell, multi-omics, and functional studies to define how developmental lineage, cellular plasticity, metabolic rewiring, epigenetic regulation, and therapy-induced adaptation converge to engineer immune blindness in NB. We discuss how NB’s neural crest origin establishes a baseline of low immunogenicity, which is subsequently reinforced through coordinated suppression of antigen presentation, dominance of immune checkpoint signaling, and profound dysfunction of cytotoxic T and natural killer cells within an immunosuppressive tumor microenvironment. Central to this process is tumor-intrinsic plasticity, whereby lineage instability and dedifferentiation, exacerbated by therapeutic pressure, embed immune silence as a stable tumor state. We highlight evidence positioning RD3 as a master upstream regulator linking cellular identity to immune visibility, governing antigen presentation, innate immune sensing, checkpoint expression, and cytotoxic lymphocyte engagement. Beyond tumor-intrinsic mechanisms, we examine the roles of immunosuppressive myeloid populations, tumor-derived exosomes, metabolic stress, hypoxia, and ferroptosis-associated pathways in reinforcing immune paralysis. Finally, we outline emerging therapeutic strategies aimed at dismantling this architecture, including combinatorial checkpoint blockade, metabolic and epigenetic reprogramming, exosome-targeted interventions, and next-generation immune engineering platforms. Together, this review reframes TIME in NB as a programmable, developmentally rooted process and provides a mechanistic roadmap for restoring immune competence and therapeutic susceptibility in HR disease. Full article

Prophages are bacteriophage genomes that are part of bacterial chromosomes. They are not just dormant passengers; they actively shape pathogen biology. For example, in skin-infecting pathogens such as Staphylococcus aureus, Streptococcus pyogenes, and Pseudomonas aeruginosa, prophages carry important virulence factors, cytotoxins, superantigens, immune evasion clusters, and epigenetic regulators that directly affect the course of skin and soft tissue infections. This same prophage biology provides a therapeutic strategy: prophage-derived molecules, including endolysins, holins, spanins, and polysaccharide depolymerases, demonstrate potent antimicrobial and antibiofilm activity against drug-resistant skin pathogens, with several candidates now in clinical development. Engineered chimeric lysins, CRISPR-encoded prophage delivery systems, and the systematic mining of the skin microbiome phageome collectively enhance the translational potential of this biology. This review integrates mechanistic insights into prophage-mediated virulence. It assesses the translational landscape of prophage-derived therapeutics, delineating the conceptual and clinical frontiers that characterize the forthcoming chapter in this domain. Full article