Search Results (502)

Group II introns are catalytic RNAs that combine self-splicing ribozyme activity with mobility and have played major roles in shaping organellar genome evolution. In green macroalgae of the genus Ulva, organellar genomes are highly compact, yet they harbor unusually diverse and dynamic repertoires of group II introns. To understand how organellar group II introns diversify and persist within compact organellar genomes, we performed a comparative analysis of mitochondrial and chloroplast group II introns across Ulva, integrating secondary structure reconstruction, intron occurrence patterns, and phylogenetic inference based on both conserved intron RNA regions and intron-encoded proteins (IEPs), including reverse transcriptase/maturase (RT/M) and LAGLIDADG homing endonuclease (LHE). A total of 168 mitochondrial and 123 chloroplast introns were identified and classified into 32 families belonging to seven major subgroups (IIA1-RT/M, IIA2-RT/M, IIB1-RT/M, IIB1-LHE, IIB2-RT/M, IIB2-LHE, and IIB-like). Most intron families retain the canonical six-domain architecture (DI–DVI), but four mitochondrial IIA families display a seven-domain configuration generated by the lineage-specific insertion of an additional stem-loop structure (DIIIa). Phylogenetic analyses revealed a high degree of congruence, supporting persistent coevolution between RNA scaffolds and their IEPs. Notably, the LHE-encoding families were scattered across distinct IIB lineages instead of forming a single clade, suggesting that at least two independent invasion events occurred within the IIB1 and IIB2 lineages. Analysis of intron occurrence frequency revealed an evolutionary continuum ranging from structurally intact and broadly distributed families to lineage-specific families exhibiting progressive scaffold degeneration, with the chloroplast infA-62 family representing a stably inherited lineage maintained through vertical transmission. These results suggest that organellar group II introns in Ulva evolve through coordinated scaffold remodeling, enzymatic replacement, and differential distribution patterns across genomic compartments, highlighting Ulva organellar genomes as a valuable comparative model for investigating the long-term evolution of mobile ribozymes within compact genomic environments. Full article

Cancer is a heterogeneous systemic disease that is strongly influenced by dynamic interactions with the tumour microenvironment (TME). Despite major advances in understanding spatial and molecular tumour heterogeneity, the temporal dynamics of tumours have received far less attention. Growing evidence has linked circadian clocks to cancer risk, progression, and treatment response, including in breast cancer. However, temporal regulation has yet to be recognized as a cancer hallmark, and its interaction with the TME remains poorly understood. This review examines how circadian rhythms organize breast cancer biology through bidirectional interactions with the TME. Circadian clocks coordinate proliferation, DNA damage responses, metabolism, and immune surveillance. Ageing, chronic stress, and obesity, all of which are established breast cancer risk modifiers, disrupt these rhythms and are reciprocally exacerbated by circadian dysfunction, establishing feed-forward loops that accelerate disease. Within the TME, the extracellular matrix (ECM) plays a central role in mediating this bidirectional control. Stiffened fibrotic stroma dampens epithelial clock amplitude, while circadian rhythms in turn shape collagen turnover and ECM remodelling. These dynamics can foster inflammation, stem cell expansion, and metastatic dissemination, including time-of-day-dependent release of circulating breast tumour cells. Systemically, circadian clocks gate immune cell trafficking, creating predictable windows of immunosurveillance and therapeutic vulnerability. By integrating insights from mechanobiology, metabolism, immune regulation, and ageing, we position circadian timing as a unifying layer that connects cell-intrinsic programmes with the evolving breast TME. Understanding these connections opens new opportunities for chronotherapeutic strategies in which treatment timing is aligned with circadian rhythms to improve outcomes. Full article

Artificial intelligence (AI), including machine learning (ML) and deep learning (DL), is increasingly transforming the study, manufacturing, and clinical translation of adipose-derived stem/stromal cells (ADSCs). ADSC-based therapies face persistent challenges related to donor variability, heterogeneous cell populations, limited standardization of culture protocols, and the need for robust quality control (QC) and potency assessment under Good Manufacturing Practice (GMP) conditions. This review discusses how AI-driven approaches can support the ADSC pipeline from donor and tissue pre-screening, through isolation and expansion, to differentiation and batch release decisions. We highlight major methodological advances in computer vision and label-free imaging for monitoring morphology, confluency, proliferation, senescence, and contamination, as well as AI-assisted optimization strategies for culture parameters and differentiation protocols. In addition, we examine the growing role of multi-omics integration (transcriptomics, proteomics, metabolomics, and secretomics) combined with ML to predict functional potency, stratify donors, and identify biomarkers associated with therapeutic efficacy. Finally, we address current limitations, including data scarcity, inter-laboratory variability, model interpretability, and regulatory requirements, and outline future perspectives such as closed-loop bioprocess control, foundation models, and federated learning frameworks. Overall, AI offers a powerful toolkit to improve the reproducibility, safety, and scalability of ADSC manufacturing and to accelerate the development of standardized, data-driven regenerative medicine products. Full article

R-loops, three-stranded nucleic acid structures formed by an RNA-DNA hybrid, have emerged as important regulators of transcription and genome stability. Although advances in high-throughput sequencing have revealed widespread R-loop landscapes, platform-specific biases hinder the identification of conserved R-loops in specific cell types. Mouse embryonic stem cells, which are transcriptionally active, provide an ideal system for investigating the potential roles of stable R-loops in RNA biology. Here, we integrated 13 independent R-loop profiling datasets from four experimental platforms to define 27,950 Common R-loop regions in mouse embryonic stem cells and characterized their chromatin environment and associated biological functions. Common R-loop regions were reproducibly detected across methods and were preferentially localized to promoter-proximal and genic regions enriched in CpG islands. Genes associated with Common R-loops were highly and stably expressed, showing strong functional enrichment in RNA metabolic processes such as mRNA processing, RNA splicing, and ribonucleoprotein complex biogenesis. Chromatin state analysis revealed that Common R-loops are enriched in transcriptionally active and regulatory contexts. Sequence feature analysis further identified GC skew as a prominent signature of Common R-loops, particularly within transcribed chromatin states. Transcription factor motif analyses have identified distinct regulatory environments in Common R-loop regions, including pluripotency-associated OCT4-SOX2-TCF-NANOG motifs in enhancers, CTCF motifs in open chromatin, and YY1 motifs in promoters. Together, this study provides the first integrated analysis of conserved R-loop regions in mouse embryonic stem cells, revealing their preferential localization at regulatory loci linked to RNA metabolism and highlighting R-loops as structural and functional nodes in RNA biology. Full article

Hepatocellular carcinoma (HCC) exhibits a striking male predominance, particularly in Hepatitis B Virus (HBV) endemic regions. While lifestyle factors and estrogen protection are traditional explanations, they fail to fully account for this disparity. This review elucidates the molecular mechanisms driving this gender gap, focusing on the interplay between the Androgen Receptor (AR), viral replication, and the suppression of NKG2D-mediated immune surveillance. We synthesized experimental and clinical findings linking AR signaling, the viral protein HBx, and the regulation of NKG2D ligands (MICA/MICB). Current evidence identifies a positive feedback loop where AR enhances HBV replication, while HBx amplifies AR activity. Crucially, this axis systematically dismantles innate immunity: AR signaling represses MICA/B transcription via miRNA networks and upregulates ADAM metalloproteases, leading to ligand shedding and the release of soluble MICA (sMICA), effectively blinding Natural Killer (NK) cells. We propose that historical failures of anti-androgen monotherapy likely stemmed from ignoring this immune modulation. Consequently, targeting the AR-NKG2D axis represents a promising strategy to sensitize tumors to immunotherapy, suggesting that future therapeutic approaches should combine AR modulation with immune checkpoint inhibitors or shedding-blockade. Full article

Epigenetic dysregulation is a central driver of cancer progression, therapeutic resistance, and phenotypic plasticity. Among epigenetic mechanisms, microRNAs (miRNAs) and DNA methyltransferases (DNMTs) engage in reciprocal regulatory interactions that extend beyond transient gene control. Emerging evidence indicates that DNMT–miRNA feedback loops function as epigenetic memory units, stabilizing malignant cell states and enabling durable phenotypic inheritance even after removal of initiating stimuli under conditions shaped by persistent redox and stress signaling cues. In this review, we synthesize mechanistic, computational, and translational studies demonstrating how double-negative DNMT–miRNA feedback architectures generate bistable regulatory circuits that lock cancer cells into epithelial–mesenchymal transition, stem-like, and therapy-resistant states through redox-sensitive regulatory thresholds rather than static epigenetic alterations. This framework provides a unifying explanation for why transient environmental or therapeutic cues can induce long-lasting epigenetic reprogramming and why conventional single-target epigenetic inhibitors often fail to achieve durable clinical responses. Building on this concept, we propose that herbal medicines and plant-derived phytochemicals act as epigenetic reset signals capable of destabilizing pathological epigenetic attractor states encoded by DNMT–miRNA memory circuits by modulating intracellular redox balance and redox-responsive signaling pathways. Owing to their multi-component and systems-level regulatory properties, herbal interventions modulate miRNA expression, DNMT activity, and upstream stress-responsive pathways in a coordinated manner, facilitating transitions from memory-dominated states toward renewed epigenetic plasticity. We further discuss the translational implications of combining miRNA-based therapies with herbal medicine as a strategy for epigenetic reprogramming rather than transient suppression within a redox-guided therapeutic framework. Finally, we address key challenges and clinical feasibility considerations, including delivery, heterogeneity, and safety, and outline future directions for biomarker-guided and systems-informed epigenetic therapies that incorporate redox state as a functional determinant of epigenetic responsiveness. By reframing DNMT–miRNA interactions through the lens of epigenetic memory, this review highlights miRNA–herbal combination strategies as a forward-looking approach for overcoming therapeutic resistance and achieving durable reprogramming in cancer through selective manipulation of redox-sensitive epigenetic signaling circuits. Full article

The vascular cambium serves as the fundamental meristem for wood formation. It determines wood biomass and structural properties by balancing self-renewal with the bidirectional production of xylem and phloem. This process is controlled by a complex network of peptides, transcription factors, and phytohormones. These regulatory networks coordinate cambial stem cell activity, balancing cell division and differentiation. Additionally, layers of regulation such as chromatin state, protein stability, and non-coding RNAs add significant complexity to these networks. Emerging single-cell and spatial transcriptomics, together with quantitative modeling, now resolve cambial heterogeneity, predicting the dynamic characteristics of wood formation. This review synthesizes current knowledge of cambial regulation, highlighting how feedback loops, spatial gradients, and dynamic signaling networks collectively orchestrate the predictive potential for improving cambial activity and wood formation. Full article

High-temperature Daqu (HTD)’s quality determines the characteristics and yield of the Chinese sauce-aroma baijiu. However, winter production frequently encounters challenges such as fermentation instability and metabolic fluctuations, primarily stemming from complex, unmonitored microenvironmental changes within the HTD pile. This study established a closed-loop system linking the microenvironment, HTD quality, microbiome, and metabolome. Through continuous monitoring of the winter fermentation pile’s microenvironmental conditions and integrating multi-omics analyses, we revealed that CO₂ concentration within fermentation piles is the core factor causing quality variations in HTD. By breaking the respiratory bottleneck formed by carbon dioxide (CO₂) accumulation through the turning anaerobic stress can be alleviated, thereby driving metabolic succession. The study found that vertical CO₂ concentration heterogeneity severely restricts the enrichment of aerobic core functional microbial communities such as the Bacillus species. This directly blocks key metabolic pathways including amino acid metabolism and energy supply via ABC transporters. Moreover, the specific accumulation of Amadori products further confirms that this low-temperature environment under CO₂ stress causes the Maillard reaction to stall at intermediate stages. Consequently, this study proposes a steady-state control strategy centered on oxygen and CO₂ gas characteristics. By actively regulating the gaseous microenvironment to eliminate metabolic heterogeneity, it provides theoretical support for standardizing traditional fermentation processes. Full article

Offspring of hypertensive disorders of pregnancies (HDP) exhibit early-life endothelial dysfunction and have an elevated susceptibility to hypertension during adulthood which is potentially mediated by microRNA (miRNA), a key regulator of gene expression. RNA sequencing showed that miR-196a-5p was significantly upregulated in HUVEC exposed to HDP and may regulate angiogenesis in endothelial cells. Therefore, this study aims to elucidate the role of miR-196a-5p in regulating angiogenesis in HUVEC exposed to HDP. miR-196a-5p expression was validated by stem-loop RT-qPCR. Predicted target genes were identified using four algorithms, miRWalk, miRDB, TargetScan, and DIANA-microT-CDS, focusing on angiogenesis-related genes. Protein expression was confirmed through ELISA. Stem-loop RT-qPCR showed that miR-196a-5p expression was significantly upregulated in HDP HUVEC. Bioinformatic analysis revealed that the PDGFRA gene, a key regulator for angiogenesis, was significantly enriched. Overexpression of miR-196a-5p significantly downregulated PDGFRA, VEGF, and bFGF in HDP HUVEC, whereas its suppression upregulated these genes significantly. The ELISA result confirmed the corresponding changes at the protein level. However, PDGFRA protein levels increased with miR-196a-5p overexpression and decreased with its inhibition. Collectively, the results indicate that miR-196a-5p may have a regulatory effect on PDGFRA, VEGF, and bFGF that is associated with angiogenesis, and the modifications could be beneficial in future epigenetic targeted therapy. Full article

Extracellular matrix (ECM) stiffening is a defining biophysical feature of solid tumors that reshape gene regulation through mechanotransduction. Increased collagen crosslinking and stromal remodeling enhance integrin engagement, focal-adhesion signaling and force transmission to the nucleus, where key hubs such as lysyl oxidase (LOX), focal adhesion kinase (FAK) and the Hippo co-activators YAP1 and TAZ (WWTR1) promote proliferation, invasion, stemness and therapy resistance. Here, we synthesize evidence that quantitative changes in matrix stiffness remodel the miRNome and lncRNome in both tumor and stromal compartments, including extracellular vesicle cargo that reprograms metastatic niches. To address heterogeneity in experimental support, we classify mechanosensitive ncRNAs into studies directly validated by stiffness manipulation (e.g., tunable hydrogels/AFM) versus indirect associations based on mechanosensitive signaling, and we summarize physiological versus pathophysiological stiffness ranges across tissues discussed. We further review competing endogenous RNA (ceRNA) networks converging on mechanotransduction nodes and ECM remodeling enzymes, and discuss translational opportunities and challenges, including targeting mechanosensitive ncRNAs, combining ncRNA modulation with anti-stiffening strategies, delivery barriers in dense tumors, and the potential of circulating/exosomal ncRNAs as biomarkers. Overall, integrating ECM mechanics with ncRNA regulatory circuits provides a framework to identify feed-forward loops sustaining aggressive phenotypes in rigid microenvironments and highlights priorities for validation in physiologically relevant models. Full article

This study presents the implementation of a project-based learning (PjBL) methodology in Science, Technology, Engineering, and Mathematics (STEM) disciplines to enhance experiential and collaborative learning within an introductory engineering course. The primary objective was to deepen students’ understanding of electrical energy storage principles, with a particular focus on charging processes and energy conservation, through the emulation of an electrochemical supercapacitor. Engineering students at Tecnológico de Monterrey designed, modeled, and analyzed a double-loop RC equivalent circuit comprising two capacitors, utilizing both computer simulations and laboratory experiments. The PjBL methodology was structured into three phases: engagement, which contextualizes the problem and emphasizes the significance of supercapacitors; research, which encompasses system design, mathematical modeling, and simulation; and action, which entails circuit assembly and the resolution of differential equations using Kirchhoff’s laws. The results indicate that this approach effectively integrates theoretical and practical knowledge, develops technical skills, and promotes collaboration. Furthermore, it aligns learning outcomes with explicit assessment criteria, illustrating compatibility with outcome-based pedagogical frameworks such as Outcome-Based Education (OBE). Full article

Dengue virus is an important human pathogen that infects over 400 million people each year. Despite its global health significance, several essential aspects of the viral replication mechanism remain poorly understood. Flaviviruses carry out asymmetric viral RNA synthesis, wherein positive-strand RNA is synthesized in excess over negative-strand RNA. The template for positive-strand synthesis is the negative strand in a double-stranded RNA intermediate, yet little is known about how positive-strand RNA synthesis is initiated. Orthoflaviviruses, including dengue virus, require an RNA promoter, stem–loop A (SLA) at the 5′ end of the viral genome for negative-strand RNA synthesis. Consequently, a complementary stem–loop structure is predicted at the 3′ end of the negative strand (3′SLA), where positive-strand synthesis is initiated. To understand the functional role of 3′SLA, we investigated its structure and examined its interaction with the viral replication proteins NS5 polymerase and NS3 helicase. NS5 and NS3 differentially recognize the stem–loop structures of the positive and negative strands (5′SLA and 3′SLA, respectively), yet NS5 polymerase efficiently synthesizes RNA from both 5′SLA- and 3′SLA-containing templates. We further show that the stable 5′ and 3′SLA elements readily form a duplex that mimics the replication intermediate under our in vitro conditions. Both NS5 and NS3 showed reduced binding to this dsRNA intermediate and NS3 was unable to unwind it, suggesting that additional factors may be required to regulate viral replication in infected cells. Full article

Background/objectives: Grapevine (Vitis vinifera L.) is one of the most economically and culturally important fruit crops worldwide and hosts more than 100 viruses. Viral infections can cause severe yield losses, but plants can adapt to infection through changes in miRNA-mediated regulatory pathways. MicroRNAs are key regulators of plant development and stress responses. Several prediction tools are available for miRNA detection from small RNA sequencing data, each relying on different algorithms. The aim of this study was to compare miRNA predictions generated by three widely used tools (miRador, ShortStack, and miRDeep2) and to evaluate how viral coinfections influence miRNA expression in grapevine. Methods: Two grapevine cultivars, Refošk (“Terrano”) and Zeleni Sauvignon (“Sauvignon Vert”), were analyzed. Small RNA sequencing was performed on virus-free plants and plants coinfected with grapevine Pinot gris virus (GPGV), grapevine rupestris stem pitting-associated virus (GRSPaV), and grapevine rupestris vein feathering virus (GRVFV). Three miRNA prediction tools were used to identify miRNAs annotated in public databases. Differential expression analysis was performed separately for each tool and by using an integrated approach that combined all three datasets. The expression of selected miRNAs was further evaluated using stem-loop RT-qPCR. Results: The three prediction tools detected markedly different numbers of miRNAs, resulting in largely distinct sets of differentially expressed miRNAs and limited overlap between individual analyses. The integrated approach yielded a separate set of differentially expressed miRNAs, most of which overlapped with at least one individual dataset. Stem-loop RT-qPCR analysis supported the differential expression of several selected miRNAs. Conclusions: This study provides new insight into miRNA expression in grapevine under mixed-virus infection and demonstrates that miRNA profiling outcomes are strongly influenced by the choice of bioinformatic prediction tool. Our results highlight the importance of integrated analytical strategies combined with experimental validation to obtain robust and biologically meaningful interpretations of miRNA expression in plants. Full article

Distinct from the traditional Modular Multilevel Converter (MMC) which focuses on fundamental frequency operation, the Static Var and Filter (SVF) within the Multi-Source Line-Commutated Converter (SLCC) system is tasked with the core function of high-frequency harmonic filtering. This paper reveals a unique engineering reliability issue stemming from this functional difference: to satisfy the Nyquist sampling theorem for precise tracking and elimination of high-frequency harmonics, the update frequency of the capacitor voltage balancing algorithm in the SLCC-SVF system is forced to increase significantly. Mathematical modeling and quantitative analysis demonstrate that this strong coupling between harmonic tracking demands and the voltage sorting strategy directly drives an abnormal surge in the average switching frequency (reaching over five times that of the fundamental condition), severely threatening device safety. To address this, an optimized adaptive hybrid modulation strategy is proposed. The system operates under Nearest Level Modulation (NLM) in normal conditions and automatically transitions to Carrier Phase-Shifted PWM (CPS-PWM)—leveraging its closed-loop balancing capability—when switching frequency or junction temperature exceeds safety thresholds. Furthermore, a non-integer frequency ratio optimization theory for low-modulation indices is constructed specifically for SVF conditions to prevent low-frequency oscillations. PLECS simulation results validate the theoretical analysis, showing that the proposed strategy effectively reduces the average switching frequency by approximately 20% under complex harmonic conditions, significantly enhancing thermal stability and operational reliability while guaranteeing filtering performance. Full article

This study examines the pricing efficiency of the Mint Gold Certificate (ALTINS1) traded on Borsa Istanbul and its relationship with the underlying asset (gram gold), focusing on the structural break identified in the data. Analyses conducted using Mann–Kendall trend analysis, the Pettitt structural break test, Rolling Window regression, and the Threshold Error Correction Model (Threshold ECM) reveal that certificate prices have systematically decoupled from the underlying asset, creating a persistent premium exceeding 16%. The findings indicate that the risk structure of the certificate has diverged from the underlying asset, the market has become desensitized to high premium levels (asymmetric threshold effect), and prices move independently of fundamental value through a speculative feedback loop (Granger causality). The study argues that the root cause of this anomaly lies in the “Limits to Arbitrage” problem stemming from supply constraints and short-sale bans, offering new evidence on the pricing efficiency of financial innovations in emerging markets. Full article