Search Results (16,267)

Retrotransposons exhibit increased activity in cancer cells. One possible approach to anticancer therapy is to use this activity to influence the energy balance in cells. Abnormal distribution of retrotransposons in the genome requires additional energy consumption, which can lead to a significant decrease in the total amount of free ATP molecules in the cell. A decrease in ATP levels below a certain threshold can in turn trigger a cell death program. To investigate the possibility of such a scenario, we developed a mathematical model of the cellular energy balance that describes the dynamics of energy consumption by the main cellular processes, including costs of retrotransposon activity. The model considers changes in the concentrations of ATP, active retrotransposons (LINE-1 and SINE) in the human genome, as well as mRNAs and proteins that are expression products of retrotransposon and constitutive genes. We estimated the parameter values in the model based on literature data and numerical optimization. We found a single stable stationary solution, characterized by low retrotransposon activity, and used it as the reference steady state for further analysis. Parametric sensitivity analysis revealed the parameters whose changes had the greatest impact on cellular ATP levels. The LINE-1 deactivation rate constant and the maximum LINE-1 transcription rate were the most sensitive among the transposon-related parameters. Perturbation of these parameters led to a decrease in the number of free ATP to 30% of the reference value and below. Transcription of retrotransposons under perturbed parameters became comparable to the translation of constitutive genes in terms of energy costs. The presented results indicate that cancer cell death can be initiated by increasing the load on the energy balance due to the activation of transposons. Full article

Background/Objectives: Therapeutic strategies for Neurofibromatosis Type I (NF1) that correct the underlying pathogenic NF1 variant hold promise for restoring neurofibromin function, reducing tumor burden, and improving patient outcomes by addressing the root cause of the disease rather than its symptoms. Beyond gene editing, transcript reprogramming via RNA trans-splicing has gained attention, particularly with the recent FDA approval of two trans-splicing-based drugs for IND phase 1/2a trials. This study tests whether trans-splicing group I intron ribozymes from Tetrahymena thermophila can be used to repair pathogenic variants of NF1 (pre-)mRNA by 3′-tail replacement. Methods: Splice sites on the NF1 mRNA were identified computationally and validated biochemically, and an efficiency-enhancing Extended Guide Sequence (EGS) of the corresponding ribozyme was identified in a combinatorial experiment. Results: The correct trans-splicing product of this ribozyme was validated in HEK293 NF1−/− cells expressing mNf1. Conclusions: This study established a splice site and activity-enhancing extended guide sequences for the repair of NF1 mRNA. Further optimization of the ribozyme, as well as improved delivery methods, may establish ribozyme-based RNA repair as a viable strategy for NF1 treatment. Full article

Drought stress poses a significant threat to tree growth, making the development of drought-resistant species essential for ecological restoration. WRKY transcription factors are critical regulators of plant drought responses; however, the role of WRKY22 in the woody species Populus ussuriensis K. remains unclear. In this study, the PuWRKY22 gene was cloned from P. ussuriensis via homologous cloning and was found to be highly expressed in leaves and responsive to abscisic acid (ABA) signaling. Subcellular localization confirmed that PuWRKY22 is a nuclear protein. Using fluorescein enzyme complementation assays, PuWRKY22 was shown to bind specifically to W-box cis-elements, indicating its function as a transcriptional regulator. Under ABA and osmotic (sorbitol) stress, the seed germination rate, root growth, and biomass of tobacco and Populus davidiana × Populus bolleana strains overexpressing PuWRKY22 were significantly increased. Additionally, these overexpressed strains exhibited a reduction in reactive oxygen species (ROS) accumulation and a decrease in membrane lipid peroxidation. Transcriptomic analyses revealed that PuWRKY22 activates expression of the ABA receptor gene Ptr.PYL4 (Potri.006G104100.v4.1), which regulates stomatal closure to minimize water loss. Consistent with this, stomatal observations and photosynthetic measurements demonstrated that PuWRKY22 enhances drought tolerance by protecting photosystem II and preserving chlorophyll content. Collectively, this study elucidates the molecular mechanism by which PuWRKY22 enhances drought resistance in woody plants through ABA signaling, providing a foundation for breeding drought-tolerant forest species. Full article

The extensive utilization of amorphous silica nanoparticles (SiNPs) has raised concerns regarding the potential health risks. Previous studies have indicated that SiNPs could trigger both the activation of heat shock proteins (HSPs) and epithelial–mesenchymal transition (EMT) in BEAS-2B cells; however, the underlying mechanisms require further elucidation. This study aimed to investigate how SiNPs activate the heat shock response (HSR) in BEAS-2B cells, which subsequently triggers EMT. Firstly, we observed that SiNPs were internalized by BEAS-2B cells and localized in the endoplasmic reticulum (ER), inducing ER stress. The ER stress led to the activation of SIRT1 by phosphorylation, which enhanced the nuclear transcriptional activity of HSF1 via deacetylation. HSF1 was found to upregulate the levels of HSP70 and HSP27 proteins, which further affected EMT-related genes and, ultimately, induced EMT. Additionally, 4-phenylbutyric acid (4-PBA) inhibited ER stress, which attenuated the SIRT1/HSF1 signaling pathway. The knockdown of SIRT1 and HSF1 using siRNA effectively suppressed the EMT progression. In summary, these results suggested that SiNPs activated the SIRT1/HSF1/HSPs pathway through ER stress, thereby triggering EMT in BEAS-2B cells. The present study identified a novel mechanism of SiNP-induced EMT, which has provided valuable insights for future toxicity studies and risk assessments of SiNPs. Full article

Rubella is typically a mild viral illness, but it can lead to severe complications when contracted during pregnancy, such as pregnancy loss or developmental defects in the fetus (congenital rubella syndrome). Therefore, it is crucial to develop and maintain protective immunity in women of childbearing age. In this study, we assessed the transcriptional factors associated with rubella-specific immune outcomes (IgG binding antibody and avidity, neutralizing antibody, and memory B cell ELISpot response) following a third MMR vaccine dose in women of reproductive age to identify key factors/signatures impacting the immune response. We identified baseline (Day 0) and differentially expressed (Day 28–Day 0) genes associated with several RV-specific immune outcomes, including the transferrin receptor 2 (TFR2), which is an important factor regulating iron homeostasis and macrophage functional activity, and a close functional homolog of TFR1, the cellular receptor of the New World hemorrhagic fever arenaviruses. We also identified enriched KEGG pathways, “cell adhesion molecules”, “antigen processing and presentation”, “natural killer cell-mediated cytotoxicity”, and “immune network for IgA production”, relevant to immune response priming and immune activation to be associated with RV-specific immune outcomes. This study provides novel insights into potential biomarkers of rubella-specific immunity in women of childbearing age. Full article

Previous studies revealed that low expression of Selenoprotein S (SELS) could enhance osteogenic differentiation, but the underlying mechanisms remain unclear. In this study, we aimed to elucidate the role of SELS and its transcription-factor-based regulatory mechanism during osteogenic differentiation. In comparison with 12-week-old mice, which represent the stage of stable osteogenic differentiation, 3-week-old mice, representing the active ossification stage, showed significantly higher levels of SELS in the mandible. Transcriptomic analysis revealed that SELS is primarily associated with extracellular matrix organization and collagen biosynthesis during mandibular development. In bone marrow mesenchymal stem cells (BMSCs) with SELS knockdown, SP7 levels were elevated after 7 days of osteogenic induction in vitro. Consistently, immunohistochemical and immunofluorescence staining confirmed increased SP7 expression in the mandibles of 7-week-old Sels knockout mice. Dual-luciferase reporter assays and chromatin immunoprecipitation (ChIP) analysis demonstrated that SP7 directly binds to the heat shock protein 47 (HSP47) promoter and negatively regulates its transcription. Consequently, upregulation of SP7 following SELS knockdown led to downregulation of HSP47 and concurrent upregulation of the SP7 downstream targets, collagen type I alpha 1 chain (COL1A1) and Secreted protein acidic and rich in cysteine (SPARC). SELS expression is upregulated during active osteogenesis. Low expression of SELS regulates osteogenic differentiation in a bidirectional and fine-tuned manner through the SP7–HSP47/COL1A1/SPARC axis. Full article

Talaromyces pinophilus is a filamentous fungus with notable lignocellulose-degrading capacity based on enzyme activities and protein secretion potential, making it a compelling candidate for industrial biotechnology applications. In this study, we present the genomic characterization of the highly cellulolytic strain Y117, a domesticated variant of T. pinophilus, based on whole-genome sequencing and comparative genomic analysis with eleven related strains. Comprehensive analysis of CAZymes, transcription factors, and secondary metabolite diversity in T. pinophilus strains revealed that the exceptional lignocellulose degradation capacity of Y117 is driven by its unique genomic architecture. Key genomic features that distinguish Y117 include (1) significant expansion of glycoside hydrolase (GH) and carbohydrate-binding module (CBM) families, (2) loss of fungal-RiPP-like clusters, and (3) absence of the developmental regulator BrlA. These genomic adaptations could indicate a metabolic trade-off favoring hydrolytic enzyme production over secondary metabolism and sporulation. Our findings provide fundamental insights into fungal lignocellulose degradation mechanisms while establishing Y117 as a promising chassis for metabolic engineering applications in industrial enzyme production and heterologous protein expression. Full article

Copper ions serve as essential cofactors for many enzymes but exhibit toxicity at elevated concentrations. In Gram-negative bacteria, the Cop system, typically encoded by copABCD, plays a crucial role in maintaining copper homeostasis and detoxification. The chromosome of Pseudomonas putida harbors two copAB clusters but lacks copCD, along with two copR-copS clusters that encode the cognate two-component system. Here, the roles of these Cop components in countering copper toxicity were studied. We found that copAB2 was essential for full resistance to Cu²⁺ in P. putida, while copAB1 made only a minor contribution, partially due to its low expression. The two-component systems CopRS1 and CopRS2 both played significant regulatory roles in copper resistance. Although they could compensate for the absence of each other to mediate copper resistance, they exhibited distinct regulatory effects. CopR1 bound to all four cop promoters and activated their transcription under copper stress. In contrast, though CopR2 bound to the same sites as CopR1 in each cop promoter, it significantly activated only copAB2 and copRS2 expression. Its competitive binding at the copAB1 and copRS1 promoters likely impeded CopR1-mediated activation of these genes. Overall, this study reveals the distinct contributions of the two Cop systems to copper resistance and their regulatory interplay in P. putida. Full article

Glucose functions as both an essential energy source and a critical signaling molecule, playing pivotal roles in regulating plant growth, development, and stress responses. Here, we report that AtCHYR1, a previously characterized RING-type ubiquitin E3 ligase involved in drought tolerance, also participates in glucose signaling. Exposure to high glucose levels significantly inhibits AtCHYR1 expression, particularly in root tips, while low glucose conditions, such as osmotic stress, sugar starvation, and dark conditions, induce its expression. Importantly, analysis of chyr1 mutants and plants overexpressing AtCHYR1 revealed that AtCHYR1 positively regulated the high glucose-mediated inhibition of germination and root growth, as well as starvation-induced growth retardation, through enhanced reactive oxygen species (ROS) accumulation in root tips. Additionally, transcriptional levels of glucose-activated pathogenesis-related (PR) and defense-related genes were reduced, while hypoxia-associated and ROS-inducing genes were significantly upregulated in AtCHYR1-overexpressing plants. Collectively, our findings provide novel insights into the role of AtCHYR1 in plant responses to fluctuating sugar availability and its control of ROS homeostasis during seed germination and plant growth. Full article

Chronic, low-grade inflammation is a key contributor to the development of numerous non-communicable diseases (NCDs), including cardiovascular, metabolic, and neurodegenerative disorders. Conventional anti-inflammatory drugs, such as nonsteroidal anti-inflammatory drugs (NSAIDs) and corticosteroids, often present safety concerns with prolonged use, highlighting the need for safer, multi-targeted therapeutic options. Iridoids, a class of monoterpenoid compounds abundant in several medicinal plants, have emerged as promising bioactive agents with diverse pharmacological properties. They exert anti-inflammatory and metabolic regulatory effects by modulating key signaling pathways, including nuclear factor kappa B (NF-κB), mitogen-activated protein kinase (MAPK), Janus kinase/signal transducer and activator of transcription (JAK/STAT), adenosine monophosphate-activated protein kinase (AMPK), and peroxisome proliferator-activated receptor (PPAR) pathways. This review provides a comprehensive summary of the major iridoid metabolites derived from ten Bulgarian medicinal plant species, along with mechanistic insights from in vitro and in vivo studies. Documented biological activities include anti-inflammatory, antioxidant, immunomodulatory, antifibrotic, organoprotective, antibacterial, antiviral, analgesic, and metabolic effects. By exploring their phytochemical profiles and pharmacodynamics, we underscore the therapeutic potential of iridoid-rich Bulgarian flora in managing inflammation-related and metabolic diseases. These findings support the relevance of iridoids as complementary or alternative agents to conventional therapies and highlight the need for further translational and clinical research. Full article

We previously demonstrated that the activation of FGFR signaling in GIST may be a mechanism of GIST resistance to imatinib mesylate (IM). We show here that IM-resistant GIST cells lacking secondary KIT mutations overexpress claudin-1 on both transcriptional and translational levels. In contrast, a knockdown of CLDN1 or inhibition of its activity by PDS-0330 effectively restored GIST’s sensitivity to IM both in vitro and in vivo. This was evidenced by the increased expression of apoptotic markers (e.g., cleaved PARP and caspase-3) and the decreased proliferation rate of IM-resistant GIST T-1R cells treated with a combination of IM and PDS-0330 (or siRNA CLDN1). In concordance with these findings, a significant synergy was observed between IM and PDS-0330 in GIST T-1R cells. Importantly, decreased tumor size and weight were observed in IM-resistant GIST xenografts treated with a combination of IM and PDS-0330. Furthermore, the combined treatment of IM-resistant tumors induced an increase in intratumoral apoptosis and other changes, as defined by the histopathologic response rate. Based on the co-immunoprecipitation and immunofluorescence microscopy data, we also demonstrated the strong interaction pattern between CLDN1 and FGFR2. Of note, the inhibition or knockdown of CLDN1 effectively decreased the phosphorylation of FGFR2 and FRS-2, a well-known FGFR adaptor protein, thereby illustrating CLDN1’s ability to regulate FGFR-signaling and thereby promote FGFR-mediated survival in KIT-inhibited GIST. Consequently, CLDN1 inhibition in GIST effectively disrupted the FGFR-mediated pathway and re-sensitized tumor cells to IM. In concordance with these data, molecular profiling of CLDN1-inhibited GIST T-1R cells illustrated a significant decrease in the majority of FGFR transcripts, including FGFR2, 3, and 4. Additionally, several FGFR ligands (e.g., FGF14, -19, and -23) were also down-regulated in PDS-0330-treated GIST. Notably, exogenous FGF-2 increased CLDN1 expression in a time-dependent manner. In contrast, pan-FGFR inhibitors effectively reduced CLDN1 levels in IM-resistant GIST T-1R cells, thereby illustrating a cross-talk between CLDN1- and FGFR-mediated pathways in IM-resistant GIST. Based on subcellular fractionation and immunofluorescence microscopy data, we also observed partial relocalization of CLDN1 into the cytoplasm in IM-resistant GIST. Notably, PDS-0330 effectively abrogated this relocalization, suggesting that changes in CLDN1 subcellular distribution might also impact GIST resistance to IM. Lastly, based on our small cohort clinical study (n = 24), we observed the increased expression of CLDN1 in most “high-risk” primary GIST known to be associated with poor prognosis and aggressive behavior, thereby illustrating the prognostic value of increased CLDN1 expression in GIST and providing a further rationale to evaluate the effectiveness of CLDN1 inhibition for GIST therapy. Full article

Nuclear factors of activated T cells (NFATs) are pivotal regulatory factors of immune responses, primarily by modulating T cell activity and regulating inflammatory cytokine gene transcription. The grass carp reovirus (GCRV) triggers a serious hemorrhagic condition, posing a significant threat to sustainable grass carp (Ctenopharyngodon idella) aquaculture. However, the precise function of NFAT in the host’s defense against GCRV infection is mostly undefined. This study comprehensively identified and characterized the NFAT genetic family in grass carp, cloned grass carp NFAT1 (CiNFAT1), and investigated its expression and function during GCRV infection. Eight NFAT genes encoding seventeen isoforms have been detected within the grass carp’s genomic sequence, distributed across six different chromosomes. Comparative analysis revealed homology with zebrafish NFATs. CiNFAT1 possesses a 2697 bp open reading frame, encoding 898 amino acids, and contains conserved Rel homology domain (RHD) and NFAT-homology (IPT) domains. Quantitative PCR (qPCR) revealed ubiquitous CiNFAT1 expression in healthy grass carp tissues, with the highest expression in gills and skin and the lowest in liver. Following GCRV challenge in vivo, CiNFAT1 expression in immune tissues (liver, spleen, kidney, gill, intestine) showed dynamic changes over time. In vitro experiments in CIK cells demonstrated that CiNFAT1 expression peaked at 12 h post-GCRV infection. Further functional studies revealed that overexpression of CiNFAT1 significantly reduced GCRV replication at 36 h post-infection. This reduction was accompanied by elevated expression of type I interferon (IFN-I) and interferon regulatory factor 7 (IRF7) at 24 and 36 h, respectively, as well as modulated IL-2, IL-8, and IL-10. Conversely, RNA interference-mediated knockdown of CiNFAT1 enhanced GCRV VP5 and VP7 mRNA levels and suppressed IL-2 and IL-8 expression. These results suggest that CiNFAT1 contributes to anti-GCRV immunity by promoting antiviral and inflammatory cytokine responses, thereby inhibiting viral replication. This study provides a foundational understanding of the NFAT genetic family in grass carp and highlights an important role of CiNFAT1 in mediating the body’s inherent defense mechanism against GCRV infection, offering insights for disease control strategies in aquaculture. Full article

Peach (Prunus persica) leaves, usually discarded in traditional Chinese medicine, were explored as a source of laxative agents. Using zebrafish larvae for bioactivity-guided fractionation, we isolated a single active flavanone that was identified by NMR and HR-MS as Sakuranetin. In vivo assays demonstrated that Sakuranetin (10–25 µM) accelerated intestinal transit in a dose-dependent fashion; at 25 µM, 64.8% of the fluorescent intestinal content was expelled. Untargeted LC-MS metabolomic analysis revealed significant perturbations in serine biosynthesis and N-glycan precursor biosynthesis, suggesting energetic rewiring of enterocytes. RNA-Seq analysis highlighted gnat1 as the most responsive gene, and molecular docking predicted a stable Sakuranetin–Gnat1 complex with a binding free energy of −8.7 kcal/mol. Concurrent down-regulation of rho transcripts indicated suppression of inflammatory signaling that often accompanies constipation. Our findings identified Sakuranetin as a potent promoter of gut motility and position the otherwise wasted peach leaves as an untapped botanical resource for developing anti-constipation therapeutics. Full article

Sensory heritage encompasses culturally valued practices, rituals, and everyday activities experienced through the senses. While sight often dominates, hearing and smelling are generally more immersive and pervasive. Soundscape research is a well-established field within urban studies; however, smellscape remains insufficiently recognised. This study is part of Multimodal Hong Kong, a project aimed at documenting sensory cultural heritage across the city by capturing the complex interplay between soundscape, smellscape, urban experiences, everyday activities, and memory. We investigated the multisensory environment at Wong Tai Sin Temple through acoustic measurements and perceptual ratings of soundscape and smellscape across 197 locations within and around the site. Additionally, semi-structured interviews were conducted with visitors (N = 54, 15,015 words of transcript), which were analysed using content analysis and natural language processing. The results indicate that elevated noise levels mainly arise from human voices and pipe music within the temple compound, as well as traffic noise in the surrounding area. The smell of incense dominates near the temple altars, whereas natural, grassy odours prevail in the adjacent park. Interview responses confirm that incense burning constitutes a traditional religious practice forming a distinctive olfactory marker for Chinese temples, but it is also perceived as having adverse health implications. This study contributes to the growing body of sensory heritage research, underscoring the importance of both soundscape and smellscape in fostering culturally inclusive, vibrant, and sustainable urban environments. Full article

Upon transferal from plastic to Matrigel, melanoma cells demonstrate growth in three dimensions and form de novo vascular networks—known as vasculogenic mimicry—that are characteristic of the stemness phenotype of aggressive tumors. It has been reported that during malignant transformation, stress, or differentiation, the long-range inter-chromosomal interactions between numerous developmental genes and nucleoli are changed. The aim of this work was to study the potential mechanisms behind the development of the vasculogenic mimicry phenotype in melanoma cells and whether the formation of these 3D structures is connected with the reorganization of inter-chromosomal contacts of rDNA clusters. Here, we show that after 15 h of growth on Matrigel, and following the formation of the vasculogenic mimicry phenotype, dramatic changes occur in Mel Z cells in rDNA contacts with different genomic regions that possess mainly developmental genes. Approximately 400 genes that retained stable contacts with nucleoli were co-expressed with different lincRNAs and were highly associated with H3K27me3 marks and simultaneously regulated by different transcription factors. These genes are involved in development and cell adhesion and may control the basic stage of differentiation. The genes that acquired or increased contacts with rDNA clusters during growth on Matrigel are associated with cell morphogenesis, cell junctions, and the cytoskeleton. Here, we present the first evidence that nucleoli may be involved in both the activation and repression of particular groups of developmental rDNA-contacting genes in melanoma cells forming the vasculogenic mimicry phenotype. We conclude that the inter-chromosomal interactions between developmental genes and rDNA clusters are dynamic, and that nucleoli play an important role in the development of vasculogenic mimicry and stemness phenotypes in aggressive tumor genes. Full article