Search Results (136,465)

The microbial production of 1,5-pentanediol (1,5-PDO), a versatile platform chemical with extensive industrial applications, remains limited by suboptimal fermentation titers and incomplete understanding of metabolic bottlenecks. To address these challenges, this study employed comparative transcriptomics to systematically identify novel genetic targets capable of enhancing 1,5-PDO biosynthesis in engineered Escherichia coli. Transcriptomic profiling of the 1,5-PDO-producing strain relative to the parental E. coli W3110, conducted at both exponential (24 h) and stationary (96 h) growth phases, revealed 1384 significantly differentially expressed genes, including 851 upregulated and 533 downregulated genes. From these, 20 candidate metabolic genes associated with 1,5-PDO synthesis were selected for functional validation through plasmid-based overexpression or CRISPR interference (CRISPRi)-mediated repression. Reverse engineering confirmed that overexpression of fecA (encoding an iron(III)-citrate transporter) and deletion of gadA (encoding glutamate decarboxylase) significantly enhanced 1,5-PDO production. Subsequent chromosomal integration of fecA at the neutral ilvG locus and deletion of gadA generated the optimized strain S7, which achieved a 1,5-PDO titer of 1.7 g/L in shake flask cultures, representing a 13.3% increase over the parental strain, with a concomitant 50% improvement in glucose yield (0.18 mol/mol). In fed-batch fermentation at the 5 L bioreactor scale, strain S7 attained a titer of 12.45 g/L and a glucose yield of 0.26 mol/mol, marking a 15.6% enhancement in carbon conversion efficiency relative to the parental strain (0.225 mol/mol), while concurrently improving biomass accumulation by 7.6%. These findings demonstrate that transcriptomics-guided reverse engineering constitutes an effective strategy for elucidating nonobvious metabolic determinants and optimizing microbial cell factories for efficient 1,5-PDO production. The identification of fecA and gadA as beneficial targets provides valuable insights into the metabolic rewiring underlying enhanced 1,5-PDO biosynthesis and establishes a foundation for further strain improvement through systems metabolic engineering. Full article

Background:Apocynum venetum L., a saline–alkali-tolerant plant, is a valuable resource for forage, textile, and medicinal purposes. This study aimed to identify the AQP gene family in A. venetum genome-wide and explore their potential functions under abiotic stress. Methods: Gene identification, phylogenetic relationships, structural features, and evolutionary patterns were analyzed, along with gene expression patterns and correlations with physiological traits. Results: Phylogenetic analysis classified the 25 candidate AvAQP genes into five distinct subgroups, with members exhibiting conserved gene structures, motifs, and phosphorylation patterns. Subcellular localization predictions indicate targeting primarily to the plasma membrane or the vacuole, with one isoform (AvTIP5;1) predicted to localize to both. Synteny analysis revealed three intraspecific and multiple interspecific gene pairs (26 with Arabidopsis thaliana and 34 with Medicago truncatula). In silico promoter analysis identified 49 cis-regulatory elements associated with phytohormone response, stress signaling, and development, providing preliminary clues for their possible involvement in diverse biological processes. qPCR profiling under abiotic stress demonstrated tissue-specific expression patterns among AvAQP members under different stress conditions. Correlation analyses between gene expression and physiological indicators (growth- and water-related traits) were predominantly positive, with only a few negative correlations under stress conditions, suggesting that AvAQP expression may be associated with plant physiological status. Conclusions: This study presents a comprehensive analysis of the AQP family in A. venetum providing a foundation for further functional characterization of these genes in response to abiotic stress. Full article

Chronic non-communicable diseases rarely occur in isolation; cardiovascular, metabolic, neurodegenerative, malignant, and age-associated disorders share upstream drivers including oxidative stress, chronic inflammation, mitochondrial dysfunction, and metabolic imbalance. This narrative review synthesizes epidemiological, interventional, and mechanistic studies identified through targeted literature searches to examine redox biology as a shared mechanistic hub linking these conditions. We evaluate antioxidant-rich dietary patterns, selected nutraceuticals, myocardial ischemia–reperfusion injury as a clinical exemplar, rare redox-imbalance disorders as mechanistic stress models, and emerging gene-based reinforcement of endogenous antioxidant systems. Rather than proposing clinical targets, we present an integrative, hypothesis-generating framework illustrating how coordinated lifestyle-driven modulation of redox balance may simultaneously influence multiple disease trajectories. Collectively, the evidence supports a unified redox framework for multi-disease prevention for multi-disease prevention and future intervention design. Full article

Adeno-associated viruses (AAVs) are a promising gene therapy technology, but major technical challenges remain. One problem is that commonly used AAVs have a low efficiency in penetrating the blood–brain barrier (BBB) and the blood–retina barrier (BRB). Consequently, gene delivery to the nervous system has limitations. Another problem is that AAVs induce immune reactions that cause serious side effects. To avoid immune reactions, the AAV dose must be reduced to lower levels that may result in insufficient gene delivery. Researchers have been modifying viral capsid protein sequences and searching for effective peptide sequences to solve these problems. As a result, Cell-Penetrating Penta-Peptides (CPP5s) have been shown to be effective in improving the BBB/BRB penetration of AAVs and suppressing immune reactions against AAVs. CPP5s were originally developed from peptide sequences of the Bax (a pro-apoptotic protein) binding domain of Ku70 (a DNA repair protein) and from negative control cell-penetrating peptides without Bax-binding activity. This article will discuss the background science of CPP5s and future directions of CPP5s for AAV-mediated gene delivery to the nervous system as well as other organs. Full article

Cannabidiol is a non-psychoactive compound originating from Cannabis sativa L., with a promising therapeutic profile that influences numerous cellular processes. A major area of interest is its impact on mitochondria, organelles essential for cellular metabolism, ATP production, calcium homeostasis, and stress response. This article explores the available data on contribution of CBD effect on mitochondria to its therapeutic potential in treatment of various pathologies: cancer, cardiovascular, lung, neurological, gastrointestinal and liver disease, and muscle pathologies. Regarding cancer, the cytotoxic effects of cannabidiol on glioma, leukaemia, non-Hodgkin lymphoma, prostate, gastric, and breast cancer are analysed. In the case of cardiomyopathies and heart failure, cannabidiol plays an important role in reducing oxidative stress and promoting mitochondrial biogenesis. In lung diseases, cannabidiol reduces the expression of mitochondrial fission genes and increases the expression of fusion genes. When it comes to neurological pathologies, cannabidiol protects neurons and exhibits a strong antioxidant effect, while in gastrointestinal and liver diseases, cannabidiol stabilises mitochondrial membrane potential, increases ATP production, and reduces oxidative stress. In muscle affections, cannabidiol improves mitochondrial function by inhibiting excessive mitophagy. Although modern formulations may improve the low bioavailability of CBD, its potential non-selective cytotoxicity toward non-malignant cells remains an important concern that warrants further investigation. Nevertheless, cannabidiol possesses a remarkable therapeutic potential, and its effects on mitochondria open new perspectives in the treatment of numerous diseases. Full article

Gene transcription is inherently stochastic, and promoter-switching-induced transcriptional bursting generates substantial cell-to-cell variability in mRNA abundance. Such variability is commonly characterized by the mean and variance; however, these low-order statistics fail to capture the geometric features of mRNA copy number distributions and may obscure mechanistic differences in promoter dynamics. In this work, we analyze a two-state stochastic gene transcription model and derive explicit analytical expressions for higher-order moments of mRNA abundance. We show that skewness and kurtosis provide mechanistically informative signatures of transcriptional bursting, explicitly depending on promoter switching kinetics and burst size. Our results demonstrate that distinct promoter dynamics can produce identical mean expression levels and variances while exhibiting markedly different skewness and kurtosis. The explicit analytical expressions derived here reveal how higher-order moments encode mechanistically informative signatures of transcriptional bursting through distributional asymmetry and heavy-tailed behavior. These results demonstrate that higher-order moments encode mechanistic information beyond mean–variance statistics and provide a powerful framework for distinguishing between different promoter-switching mechanisms in stochastic gene transcription. Full article

Vitamin B6 is an essential micronutrient whose biologically active form, pyridoxal 5′-phosphate (PLP), acts as a cofactor in metabolic reactions linked to tumorigenesis and also functions as an antioxidant. Low plasma PLP levels are consistently associated with cancer, but studies on dietary intake have yielded conflicting results. Overall, evidence suggests that the effects of vitamin B6 deficiency on cancer are context-dependent, varying with cell type and tumor stage. Accordingly, high expression of PDXK and PNPO, two key genes involved in PLP biosynthesis, is associated with tumor progression in some malignancies, whereas it correlates with improved outcomes in others. This review explores Drosophila melanogaster as a useful model to investigate underlying mechanisms, bypassing the limitations of human studies. Research in Drosophila demonstrates that PLP deficiency promotes cancer by triggering genomic instability. Furthermore, a critical PLP-SHMT gene–nutrient interaction impacting oncogenesis has been established in flies, offering significant therapeutic implications. Finally, studies in Drosophila have shown that PLP deficiency can promote tumor development by also triggering the loss of heterozygosity (LOH). These findings highlight Drosophila as a powerful tool to elucidate the molecular pathways linking vitamin B6 deficiency to cancer. Full article

The hypothalamic–pituitary–adrenal (HPA) axis coordinates metabolic, immune, and behavioral responses to a changing environment. Its molecular effectors are the nuclear receptors for glucocorticoids and mineralocorticoids (the GRs/MRs), encoded by nr3c1/nr3c2. The MR serves as the high-affinity sensor of basal hormone concentrations, whereas the GR amplifies the stress response and mediates negative feedback. Despite their shared domain architecture, the receptors have diverged functionally: isoform composition, post-translational modifications, and the complement of co-regulators together determine which genes are activated or repressed in a given tissue at a given time. The regulation of the HPA axis activity is a major determinant of embryonic development. Pregnancy adds a placental control layer that meters maternal signals: 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2) in the syncytiotrophoblast inactivates cortisol, whereas 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) can regenerate it, and systemic buffering by transcortin (cortisol-binding globulin, CBG) limits the free hormone fraction. Under stress, inflammation, or hypoxia, this barrier weakens, exposing the fetus to stronger glucocorticoid pulses during windows of heightened vulnerability for brain and immune development. Such overexposure not only reshapes ongoing transcription but is also epigenetically inscribed: the methylation of alternative nr3c1 promoters, the remodeling of histones, and the shifts in ncRNA profiles recalibrate the axis sensitivity for the long term. At the phenotypic level, this manifests as variability in stress reactivity, cognitive and affective trajectories, and an immune and metabolic risk across later ontogeny. In this review, we integrate evidence on the structure and functions of the GR, the mechanisms of its post-translational and epigenetic regulation, and the role of the placenta, to provide a coherent framework for understanding the multifaceted consequences of prenatal stress and to identify potential targets for early prevention. Full article

Long-term nutritional excess causes hepatic steatosis, endoplasmic reticulum (ER) stress, hyperglycemia, and hyperlipidemia. Mitogen-activated protein kinase phosphatase-3 (MKP-3) is a well-established stress-regulated protein and a regulator of gluconeogenesis. Our previous study revealed that acute ER stress reduced gluconeogenesis and MKP-3 protein stability. However, the expression of MKP-3 and its regulatory mechanisms in chronic ER stress remain unclear. The aim of this study was to investigate the effects of chronic ER stress on hepatic MKP-3 expression and its role in the regulation of gluconeogenesis. The results show that long-term administration of thapsigargin (Tg) or palmitic acid promoted gene expression of Mkp-3 and gluconeogenic genes Pepck, G6pc, and Pgc1α in primary mouse hepatocytes. In addition, a long-term high-fat diet (HFD) or Tg administration significantly increased hepatic ER stress and blood glucose level in mice, while inducing the expression of Mkp-3 and hepatic gluconeogenic genes Pepck, G6pc and Pgc1α. Further study revealed that liver-specific Mkp-3 knockout (Mkp-3 LKO) reversed the blood glucose level and expression levels of gluconeogenic genes those were induced by long-term HFD in mice. Moreover, activation of the PKR-like ER kinase (PERK) by its agonist increased hepatic Mkp-3 expression, whereas inhibitor of PERK suppressed the expression of Mkp-3 under Tg administration. These results suggest that chronic high-fat diet might promote hepatic gluconeogenesis via the PERK/MKP-3 pathway. Consequently, this study identified a potential therapeutic target for treating obesity-related hyperglycemia. Full article

The global prevalence of obesity continues to rise, posing serious risks to human health largely because obesity itself leads to metabolic disorders of carbohydrate and lipids. Currently, effective and healthy interventions for lowering blood glucose, reducing blood lipids, and promoting weight loss remain limited due to the complexity of obesity development. Lactobacillus plantarum (GDMCC 1.140) was shown to promote catabolic processes and reduce hepatic lipid accumulation in largemouth bass fed with high-starch feed (HSF) in our previous study; however, molecular mechanisms underlying the function of this probiotic remain unclear. Here, we evaluated the effects of L-carnosine, one of metabolites produced by Lactobacillus plantarum, on carbohydrate and lipid metabolisms in an obesity model of zebrafish, which was induced by HSF. Histopathological analyses of livers from different groups indicated that a dietary supplement with L-carnosine can alleviate hepatic impairment and reduce lipid accumulation in the hepatocytes of obese zebrafish. Transcriptomic analyses revealed that L-carnosine supplementation can reverse the expression of about 70 HSF-induced genes, mainly gene-specific transcription regulators and metabolite interconversion enzymes. Furthermore, approximately 250 HSF-inhibited genes were found to be up-regulated by L-carnosine, reaching levels comparable to those in normal-starch feed (NSF) zebrafish. These genes, targeted by L-carnosine and inhibited by HSF, are highly enriched in GO terms such as lipid metabolic process, small molecule metabolic process, and cellular response to chemical stimulus, with monocarboxylic acid metabolic process, modified amino acid metabolic process and aldehyde metabolic process following, and in KEGG pathways of carbohydrate, lipid and amino acid metabolisms, such as pentose and glucuronate interconversions, glycolysis/gluconeogenesis, glycerolipid metabolism, pentose phosphate pathways, fatty acid degradation, beta-alanine metabolism and arginine and proline metabolism. These findings provide functional and molecular evidence that L-carnosine can ameliorate HSF-induced disorders of carbohydrate and lipid metabolisms. Full article

Rheumatoid arthritis (RA) is a chronic autoimmune rheumatic disease of unknown etiolgy, characterized by erosive polyarthritis that leads to joint destruction and systemic inflammatory lesions in internal organs. Pain is a primary symptom of RA and a major contributor to psychological disturbances, which influence patients’ subjective evaluation of their condition. These psychological issues may stem from disruptions in central pain regulation mechanisms, such as central sensitization (CS), which can also affect central metabolic processes. The objective was to investigate how the severity of central sensitization, measured by the Central Sensitization Inventory (CSI) questionnaire (Part 1), impacts clinical and neuropsychiatric parameters, as well as the expression of genes related to inflammation, tissue destruction, carbohydrate metabolism, and fatty acid metabolism in peripheral blood mononuclear cells (PBMCs) in patients with RA. Methods involved collecting blood samples from 59 RA patients (mean age 52.0 years). Clinical status was assessed using the DAS28 index and serum levels of CRP, ASPA, and RF. Neuropsychiatric parameters were evaluated through questionnaires measuring CS severity score (CSI), pain intensity (VAS, BPI), neuropathic pain (PainDETECT), anxiety and depression (HADS), fatigue (FSS, FACIT-F), fibromyalgia symptoms (FIRST), and pain catastrophizing. Protein expression in PBMCs was measured by ELISA, while gene expression was analyzed using quantitative real-time RT-PCR. All patients exhibited moderate to high disease activity. Participants were divided into four subgroups according to their CSI scores: subclinical (0–29 points), mild (30–39 points), moderate (40–49 points), and severe/extreme (50–100 points). Higher CSI scores correlated with significant increases in neuropsychiatric symptoms and a notable decrease in vitality. However, clinical parameters showed no significant differences among the subgroups. Gene expression analysis revealed upregulation of genes involved in the pentose phosphate pathway (G6PD), antioxidant defense (SOD1), fatty acid metabolism (FASN, CPT1B), apoptosis (CASP3), and tissue destruction and hypernociception (MMP-9) compared to healthy controls. The pro-inflammatory cytokine IL-1β expression was comparable to controls, while TNFα expression was elevated only in patients with severe/extreme CS scores. These findings suggest that CS-related disturbances may contribute to increased disease severity in RA, even in patients receiving active antirheumatic treatment. At the cellular level, disease severity appears linked to dysregulated expression of genes governing central metabolic processes, despite low expression of pro-inflammatory cytokine genes. Full article

Background: Main risk factors associated with the development of sarcopenia (coexistence of muscle mass loss and dysfunction) are a sedentary lifestyle coupled with obesity. Associated mitochondrial dysfunction leads to energy deficits and perturbations in the balance between protein synthesis and degradation, thereby triggering muscle dysfunction or atrophy. Aside from exercise, which is challenging to implement and maintain, particularly in women, treatments for diminishing sarcopenia are scarce. The objective of the present study was to evaluate the effect of the flavanol (−)-epicatechin (EC) in a hypercaloric diet-induced obese female rat model. Muscle strength and endurance, as well as relative mitochondrial DNA content in skeletal muscle, were assessed. Methods: Female rats were fed a hypercaloric diet to induce obesity, as evidenced by increases in body weight, Lee index, and lipid profile alterations, and by abdominal fat accumulation, and to promote a sarcopenic phenotype. Functional tests of grip strength and mobility (treadmill) were performed. Mitochondrial relative content was evaluated by measuring the ratio of mtDNA/nuclear DNA, and the expression of genes related to mitochondrial biogenesis (Pgc1-α, Tfam), fusion (Mfn1 and Opa1), fission (Drp1 and Fis1), and mitophagy (Pink1 and Pkn), and function; citrate synthase and Ucp3 were also evaluated. Results: A significant decrease in mobility and strength was observed in obese female rats, accompanied by reduced mitochondrial numbers, activity, and dynamics, but not by changes in muscle size or weight. Treatment with EC induced mitochondrial biogenesis and positive changes in mitochondrial dynamics (fission and fusion) and activity, as measured indirectly by changes in citrate synthase and Ucp3 expression. Discussion: Results reinforce the potential of EC as a modulator of mitochondrial function in dysfunctional conditions associated with obesity, thereby attenuating the mechanisms underlying sarcopenia. Full article

Background: Urothelial bladder cancer (UBC) is a molecularly heterogeneous disease, and most sequencing studies have relied on bladder-specific or solid tumor-restricted panels. Whether broader pan-cancer assays provide additional clinically relevant information remains unclear. Methods: We performed targeted next-generation sequencing using an extended gene panel on tumor samples from 100 patients with UBC treated at a tertiary center. Somatic single-nucleotide variants, small insertions/deletions, copy-number alterations, and gene co-occurrence patterns were analyzed and correlated with clinicopathological features, disease-free survival (DFS), and overall survival (OS). Results: Recurrent alterations were identified in FGFR3 (≈50%), TP53 (≈35%), STAG2 (≈25%), and PIK3CA (≈20%), consistent with established molecular pathways in UBC. Less frequent but potentially actionable alterations, including mutations in BRCA1 and ALK, were also detected, reflecting the extended coverage of the panel. TP53 mutations were independently associated with worse OS, whereas STAG2 alterations were associated with improved OS, particularly in tumors without concurrent TP53 mutations. FGFR3 mutations showed a favorable but non-independent trend. No gene retained independent prognostic significance for DFS. Co-occurrence analysis revealed an FGFR3/PIK3CA-associated pathway and relative mutual exclusivity between FGFR3 and TP53. Copy-number alterations were modest overall. Comparison with TCGA data demonstrated a higher frequency of FGFR3 alterations in our cohort, likely reflecting the larger proportion of non–muscle-invasive tumors. Conclusions: Pan-cancer targeted sequencing provided a comprehensive genomic landscape of UBC, capturing canonical drivers and additional alterations that may be overlooked by bladder-restricted assays. The identification of TP53 and STAG2 as prognostic markers highlights the potential value of broader genomic profiling for biologically informed risk stratification in urothelial bladder cancer. Full article

Antimicrobial resistance (AMR) emerges and circulates across interconnected human, animal, food, and environmental reservoirs; however, food fermentation systems remain underexplored as indicators of local AMR pressure, even though artisanal dairy fermentations may function as natural sentinels of AMR. In this study, we used an artisanal dairy fermentation chain as a One Health model to investigate whether environmentally exposed lactobacilli can reflect stage-associated shifts in resistance. A total of 1.085 isolates representing 16 Lactobacillus species were recovered from the same artisanal dairy matrix at two fermentation stages: day 5 (“Tyrovolia”; n = 518) and day 30 (“Kopanisti”; n = 567). Susceptibility to 14 antibiotics was evaluated by broth micro-dilution, and L. acidophilus was further screened for selected resistance genes. Overall resistance increased significantly from 69.88% (362/518) at day 5 to 77.25% (438/567) at day 30 (p = 0.0059), while multidrug resistance rose from 37.57% to 60.73% of resistant isolates (p < 0.001). Across the 224 species–antibiotic combinations examined, 129 (57.58%) showed an increased upper MIC limit at day 30, and resistance increased significantly for 9 of the 14 antibiotics tested, with the largest rises observed for metronidazole (RR = 7.67), chloramphenicol (RR = 5.74), quinupristin/dalfopristin (RR = 4.11), vancomycin (RR = 2.78), and trimethoprim (RR = 2.43). In contrast, erythromycin and oxytetracycline resistance declined significantly at the ripened stage. In L. acidophilus, 21 resistance genes were detected in 14/70 day-5 isolates and 19 genes in 13/71 day-30 isolates, but marked genotype–phenotype discordance was observed, including matrix-dependent expression patterns for tetM, ermB, and blaTEM. Collectively, these findings show that environmentally exposed artisanal dairy fermentations can enrich resistance phenotypes and may serve as sensitive sentinels of AMR dynamics at the human–animal–environment interface. Full article

The SERPINE1 gene encodes the serine protease inhibitor plasminogen activator inhibitor type-1 (PAI-1), a major negative regulator of the plasmin-dependent pericellular proteolytic cascade and a crucial determinant in the program of stromal remodeling. Recent omics approaches confirmed that high tumor SERPINE1 levels are prognostic for poor disease outcomes and shorter disease-free survival in various malignancies. Kinetic analysis of biomarkers of cell cycle transit in growth-synchronized p53 dual mutant human keratinocytes confirmed that PAI-1 transcription occurred early after growth activation of quiescent (G₀) cells and prior to G1 entry. Previous evidence has confirmed that differential residence of USF family members (USF1→USF2 switch) at the PE2 region hexanucleotide E box motif (CACGTG) in the SERPINE1 proximal promoter characterizes the G₀→G₁ transition period and the transcriptional status of the SERPINE1 gene. A consensus PE2 E box motif (5′-CACGTG-3′) at nucleotides −566 to −561 is required for USF occupancy of the PE2 E box and serum-stimulated SERPINE1 transcription. Interference with USF2 occupancy of the PE2 E Box site by a double-stranded PE2 “decoy”, or induced expression of a dominant-negative USF (A-USF) construct, attenuate serum- and TGF-β1-stimulated SERPINE1 synthesis. Tet-Off activation of an A-USF insert reduced both PAI-1 and PAI-2 transcripts while increasing the fraction of proliferating (Ki-67⁺ cells). Conversely, overexpression of USF2 or adenoviral delivery of a PAI-1 vector inhibited HaCaT colony expansion. These findings are discussed in this review and collectively suggest that the USF1→USF2 transition at the PE2 E box site and subsequent SERPINE1 transcription impact serum-stimulated keratinocyte growth and, likely, cell cycle progression. Full article