Search Results (1,482)

Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, a key acyltransferase in the phenylpropanoid pathway and a canonical member of the BAHD acyltransferase family (BAHD), catalyzes the formation of pivotal intermediates in the biosynthesis of secondary metabolites such as lignin, chlorogenic acid, and flavonoids. These compounds serve indispensable protective functions in terrestrial plants, underpinning their adaptive responses to abiotic stresses such as drought, ultraviolet (UV) radiation, and oxidative damage. Although the role of HCT/HQT in the core phenylpropanoid pathway has been extensively characterized, its precise functional contributions to the flavonoid biosynthetic branch—particularly with respect to substrate selectivity, kinetic regulation, and metabolic channeling—remain incompletely understood. This review systematically analyzes the structural features, spatial conformation, catalytic mechanism, and substrate promiscuity of HCT/HQT to clarify its molecular determinants of activity and specificity. Furthermore, it highlights regulatory factors influencing HCT/HQT gene expression, such as transcription factors (MYB, bHLH, WRKY), phytohormones (GA₃, Eth, MeJA, 6-BA, MT), and abiotic/biotic stressors (temperature, blue light, nitric oxide, nano-selenium). Collectively, these insights illuminate how plants dynamically fine-tune phenylpropanoid metabolism in coordination with developmental programs and environmental challenges. This work provides a foundation for further research on HCT/HQT and supports efforts to develop improved crop varieties through targeted regulation of this central metabolic node. Full article

Tyrosinase promotes excessive deposition of melanin, which may lead to severe skin diseases. Passiflora edulis f. edulis seeds have been reported to be rich in diverse bioactive constituents exhibiting potential tyrosinase inhibitory activity. However, the principal bioactive constituents responsible for tyrosinase inhibitory activity and its underlying mechanisms remain largely unclear. Therefore, this study aimed to: (1) optimize SC-CO₂ extraction of Passiflora edulis f. edulis seed oil (PFSO) for maximum yield and bioactive preservation; (2) comprehensively characterize its physicochemical and phytochemical profile; (3) elucidate the tyrosinase inhibition mechanism through kinetic, spectroscopic, and computational approaches; and (4) validate its safety, antioxidant, and anti-pigmentation efficacy in a zebrafish model. PFSO exhibited a yield of 24.96%, with a high content of unsaturated fatty acids (88.03%, mainly linoleic acid at 74.40%). The oil inhibited tyrosinase via a reversible mixed-type mechanism (IC₅₀ = 1.12 mg/mL). Fluorescence spectroscopy and molecular docking revealed that linoleic acid binds to LYS180 and β-sitosterol binds to TYR78, mainly driven by hydrogen bonding and hydrophobic interaction, which changed the microenvironment of tryptophan residues and indicated static quenching. Further validation experiments revealed that the major constituent, linoleic acid, exhibited only weak inhibitory activity against tyrosinase (IC₅₀ = 29.44 mg/mL), whereas the key component β-sitosterol markedly suppressed tyrosinase activity (IC₅₀ = 46.43 μg/mL). In vitro assays demonstrated PFSO’s significant efficacy in reducing the melanin content and tyrosinase activity in α-MSH-stimulated B16F10 murine melanoma cells. In vivo experiments in zebrafish that received dietary supplementation with PFSO confirmed that PFSO (≤5 mg/mL) reduced ROS production, suppressed melanin deposition, inhibited tyrosinase activity, and downregulated the expression of melanogenesis-related genes (TYR, TYRP1, TYRP2, MITF). This study provides, for the first time, a comprehensive elucidation of PFSO’s potential as a natural tyrosinase inhibitor, integrating extraction optimization, multicomponent characterization, multimodal inhibition analysis, and in vivo validation. Full article

Background: Soluble immune checkpoint molecules, including soluble PD-1 (sPD-1) and soluble PD-L1 (sPD-L1), have emerged as potential minimally invasive biomarkers in non-small cell lung cancer (NSCLC). However, their diagnostic, kinetic, and prognostic significance across different disease settings remains unclear. This prospective study evaluated baseline levels, longitudinal fluctuations, and clinical associations of sPD-1 and sPD-L1 in early- and advanced-stage NSCLC. Methods: Three cohorts were prospectively enrolled: early-stage NSCLC patients undergoing curative surgery (n = 25), advanced-stage NSCLC patients receiving pembrolizumab-based immunotherapy (n = 55), and non-oncological controls (n = 16). Serum sPD-1 and sPD-L1 were measured by ELISA at baseline and at four months post-surgery (early stage) or six months post-treatment (advanced stage). Baseline comparisons, longitudinal changes, correlation with tumor PD-L1 expression (TPS), and associations with recurrence (early stage) or 6-month objective response (advanced stage) were assessed. Results: Baseline sPD-1 and sPD-L1 levels did not differ significantly among controls, early-stage, and advanced-stage cohorts. In early-stage patients, sPD-L1 increased post-operatively (p = 0.006) while sPD-1 decreased (p < 0.001). In advanced-stage disease, sPD-1 declined during immunotherapy (p < 0.001), whereas sPD-L1 remained unchanged (p = 0.37). Baseline levels and continuous percent changes were not predictive of most outcomes. However, a ≥20% postoperative increase in sPD-L1 was strongly associated with recurrence in early-stage NSCLC (OR = 10.29; 95% CI: 1.40–215.20; p = 0.019). No sPD-1/PD-L1 metric predicted response in advanced disease. Baseline sPD-L1 showed no correlation with tumor PD-L1 expression (ρ = −0.09, p = 0.53) in the advanced-stage cohort. Conclusions: sPD-1 and sPD-L1 demonstrate distinct kinetic patterns across NSCLC settings. A postoperative >20% surge in sPD-L1 may identify early-stage patients at elevated risk of recurrence, whereas soluble checkpoints were not predictive of treatment response in advanced disease. These findings support further investigation of soluble checkpoint dynamics as complementary biomarkers in NSCLC management in larger cohorts. Full article

This commentary critically evaluates the translational relevance of a recent study investigating the effects of ozonated saline solution (O₃SS) on microglial and endothelial cell models. While the original research proposes potential antioxidant and anti-inflammatory benefits of low-dose ozone exposure, we identify significant methodological and conceptual flaws that undermine its conclusions. Key concerns include the unjustified assumption that ozone behaves similarly in microwell cultures and clinical infusion settings, despite known physicochemical differences affecting ozone stability and reactivity. The use of immortalized BV2 and HUVEC cells, which lack the complexity of in vivo systems, further limits the study’s applicability. The absence of accurate ozone quantification, proper controls, protein-level validation, and kinetic modeling exacerbates these weaknesses. Our analysis also demonstrates, through differential equation modeling, that ozone rapidly decays in saline solutions, making systemic delivery via infusion chemically implausible as a therapeutic approach. Moreover, the extrapolation of in vitro gene expression data to systemic therapeutic claims lacks scientific justification. We conclude that while the observed cellular responses in vitro are of academic interest, they do not support the efficacy or safety of O₃SS in clinical settings. A more rigorous approach is necessary to substantiate the biomedical potential of ozonated solutions. Full article

Fibroblast growth factor 2 (FGF2) is expressed in retinal Müller glia cells, and its expression increases in response to photoreceptor degeneration. To investigate the physiological relevance of FGF2, we analyzed retinal morphology and cellular responses in Fgf2-deficient (Fgf2^−/−) mice. Loss of FGF2 did not affect photoreceptor survival, retinal vasculature, or retinal pigment epithelium (RPE) integrity. To further understand its role in retinal degeneration, Fgf2^−/− mice were crossed with Pde6b^STOP/STOP mice, a model of retinitis pigmentosa (RP). We then analyzed outer nuclear layer thickness, cone number, rod outer segments length, RPE morphology, and microglia number in Fgf2^−/− Pde6b^STOP/STOP and Pde6b^STOP/STOP mice. Although FGF2 was upregulated in degenerating photoreceptor cells in the Pde6b^STOP/STOP retina, its absence did not accelerate photoreceptor loss in Fgf2^−/− Pde6b^STOP/STOP mice. Interestingly, microglia numbers were significantly changed at early disease stages in Fgf2^−/− Pde6b^STOP/STOP retinas compared with Pde6b^STOP/STOP controls, suggesting that FGF2 modulates inflammatory signaling. Together, these results show that loss of FGF2 does not alter photoreceptor degeneration kinetics or retinal morphology, but may contribute to the regulation of early microglial accumulation during degeneration. Full article

This study aimed to determine the effects of diammonium phosphate (DAP) and yeast autolysates (organic nutrients) added during alcoholic fermentation on the content and profile of aroma compounds in Sauvignon Blanc wines. Sequential additions of either DAP or organic nutrients were applied mainly during the first half of fermentation, increasing yeast assimilable nitrogen (YAN) from an initial 124 mg N/L to final concentrations of 208 and 209 mg N/L for DAP and yeast autolysates, respectively. Control musts were fermented without nutrient supplementation. All treatments were fermented using commercial yeast strain. Varietal thiols, ethyl and acetate esters, higher alcohols, glutathione (GSH), and YAN were monitored at early, mid, and late stages of fermentation, as well as in the final wines. Varietal thiols were formed at early stages of fermentation in all treatments; however, concentrations of both 4-methyl-4-sulfanylpentan-2-one (4MSP) and 3-sulfanylhexan-1-ol (3SH) were higher in wines supplemented with organic nutrients comparing to DAP and control. Compared to the control, DAP and organic nutrient supplementation increased ethyl ester concentrations in wine by 40.2% and 26.9%, respectively. Both nutrient treatments also resulted in higher acetate ester concentrations, while total higher alcohols were reduced by 19.1% with DAP and 12.1% with organic nutrients. No significant differences in GSH concentrations were observed among treatments. Sensory analysis revealed that wines supplemented with DAP achieved the highest scores for tropical aroma, varietal aroma, and overall quality. Overall, sequential supplementation with either inorganic or organic nitrogen positively influenced fermentation kinetics and aroma compound composition, resulting in improved varietal expression of Sauvignon Blanc wines. However, in low-YAN musts, DAP had a greater impact than organic nitrogen sources and should therefore be considered a key strategy for ensuring an adequate yeast nitrogen status. Full article

Although the dissolution of sparingly soluble salts is of interest to many fields, such as material science, dentistry, and geochemistry, the simplicity of these reactions provides its own motivation for study. Three features of these reactions are examined in this paper: (i) the unusual forms of the kinetic expression that have been used to describe their rates of reaction, (ii) the observation that the rate of dissolution is correlated with the potential difference across the solid-solution interface, and (iii) the observation of non-stoichiometric dissolution. Mechanistic descriptions of the kinetics of dissolution in current use do not account for all these factors, while the surface vacancy model does. In this paper, it is shown that linear kinetics arise from a symmetry of the rates of removal and deposition of anions and cations. On the other hand, non-linear kinetics arise from an asymmetry in the rates of removal and deposition of anions and cations. Because the surface vacancy model is an electrochemical model, the influence of potential difference on the rate of reaction is inherent to the model. A transient, or non-stationary state, version of the model is used to explain how non-stoichiometric dissolution arises. Full article

Major depressive disorder (MDD) lacks reliable laboratory tests for diagnosis and treatment monitoring, underscoring the need for robust molecular readouts in blood. Beyond symptom-based classification, MDD can also be viewed as a condition involving impaired homeostatic regulation across stress-responsive, immune, metabolic, and neural systems. Consistent with this perspective, altered intron retention (IR) patterns have been observed in peripheral blood in depression-related and treatment-response contexts, supporting the translational relevance of this RNA-processing layer to mood disorders. A key observation underpinning this review is that IR can function as a reversible, intervention-responsive readout of physiological state. In a pre-symptomatic stress-like state in klotho mutant mice (a premature-aging model), widespread IR increases revert toward a healthy pattern upon treatment, suggesting that IR is embedded in a controllable homeostatic layer. Against the backdrop of limited cross-cohort transferability of differential gene expression (DGE) signatures, we propose that IR provides a mechanistically grounded biomarker layer because it reports regulated RNA processing states rather than context-fragile abundance endpoints. We operationalize IR as a post-transcriptional “throttle” on effective gene output, with increased IR/detained intron (DI) states acting as a reversible brake and decreased IR acting as an accelerator that increases translation-competent mRNA supply. Mechanistic exemplars across immune, metabolic, and neuronal systems (e.g., IFNG, OGT, MAT2A, neuronal activity-triggered intron excision, and intron detention-mediated stemness/differentiation switching in adult neural stem cells) show that defined inputs can switch IR/DI states to tune output kinetics. Integrating these findings, we propose an “Intron Retention Homeostat” (IR-Homeostat) model in which cells sense deviations from physiological set points and implement feedback control of gene output through switchable IR/DI regulation. This framework positions IR not only as a robust state readout for stratification, treatment response prediction, and pharmacodynamic profiling, but also as a tractable entry point to identify the molecular sensors and mediators that couple homeostatic signals to RNA processing control. Full article

Colored potato cultivars are rich in phenolic compounds that confer high antioxidant capacity; however, these beneficial metabolites could be susceptible to oxidation by polyphenol oxidases (PPOs), leading to enzymatic browning and the loss of antioxidant potential. Despite the agronomic relevance of this trade-off, the dynamics of the PPO gene family (StPPOs) gene expression in pigmented potatoes remains poorly characterized. Here, we present an integrated biochemical and molecular analysis of two purple-fleshed Peruvian landraces (Siriñacha and Angashungo), a partially pigmented landrace (Sapa), and non-pigmented cultivars, including the commercial cultivar Desirée. We quantified the total phenolic content, antioxidant capacity, and enzymatic browning index (EBI) using colorimetric and spectrophotometric methods. We also generated gene expression profiles of ten StPPO genes using semi-quantitative and digital PCR. Purple-fleshed cultivars exhibited significantly higher phenolic content and antioxidant capacity but also displayed accelerated browning kinetics compared to non- or partially pigmented genotypes. Expression analysis revealed cultivar-specific StPPO patterns, with StPPO2 and StPPO8 being markedly upregulated in pigmented materials, particularly StPPO8. These findings provide the first integrated biochemical and transcriptional evidence linking specific StPPO isoforms to enzymatic browning in colored potatoes, and highlight their potential for biotechnological applications. Full article

Histone deacetylases (HDACs) 1–3 are key regulators of gene expression and represent important therapeutic targets in cancer, neurodegenerative, and immune disorders. Many potent class I HDAC inhibitors display slow- and tight-binding kinetics, which profoundly influence their efficacy and pharmacodynamics. In particular, their dissociation rate (off-kinetic) is critical, since prolonged target engagement greatly influences drug efficacy in vivo. However, the off-kinetics of HDAC inhibitors are often overlooked in the early stages of drug development. Here, we investigated the dissociation kinetics of tucidinostat, trapoxin A, and TNG260 in comparison to the pan-HDAC inhibitor vorinostat. Using biochemical 100-fold jump dilution assays, NanoBRET assays, and cellular washout experiments, we characterized the dissociation of these compounds from purified proteins and in a cellular context. Tucidinostat showed moderately slow off-kinetics, while the clinical candidate TNG260 demonstrated pronounced tight-binding properties. Trapoxin A displayed remarkable discrepancies between assays, as it showed fast dissociation kinetics in the biochemical assay, but tight-binding properties in a cellular setting. These findings not only address the previously unexplored dissociation kinetics of two clinically relevant inhibitors, but also underscore the importance of comprehensive kinetic profiling of novel HDAC inhibitors in cellular models. Full article

Background: Gene expression and cellular identity are regulated by epigenetics that occurs through chromatin modifications, RNA changes, chromatin accessibility, and three-dimensional genome organization. Although DNA methylation has been the focus of most epigenetics studies in the past, other non-methyl epigenetic processes, including histone post-translational modifications (PTMs), epitranscriptomic marks, and chromatin remodeling, are dynamic, reversible, and context-dependent, and thus are difficult to accurately interrogate using endpoint sequencing-based assays, especially in heterogeneous tissues, developing systems, and therapeutic response environments. Scope and Approach: The present review discusses epigenetic modifications other than DNA methylation regarding sensor-based technologies that can measure live, dynamic, and spatially resolved measurements. Epigenetic sensors include any genetically encoded sensors (GECs) based on resonance energy transfer, CRISPR/dCas-derived sensors, or aptamer-based sensors, and hybrid biochemical/imaging sensors that can be used in live or semi-live settings. It lays emphasis on the technologies, which have been developed recently, that allow real-time kinetic measurements, working in three-dimensional and organoid models, and being applied to disease-relevant perturbations. On these platforms, performance properties such as specificity, sensitivity, spatial and temporal resolution, ability to perform dynamic versus locus-specific interrogation, and perturbed endogenous chromatin states are compared. Key Conclusions and Outlook: Together, these sensing strategies are complementary to the traditional methods of measuring epigenomics in that they show epigenetic dynamics unobservable with static measurements. We list the important technical issues, including specificity, quantitation, multiplexing, and chromatin perturbation, and report the barriers and solutions in development and design. Lastly, we provide a conceptual map of how live epigenetic sensing and multi-omics and translational models can be integrated, and how the two methodologies can be used to develop functional epigenetics and guide disease modeling and drug development. Full article

Progesterone receptor (PR) regulates gene expression through recruiting coregulators and general transcription factors by activation functions AF1 and AF2. AF1 localizes to the non-conserved and disordered N-terminal domain and is believed to facilitate tissue- and gene-specific activity. Our previous proteomic analysis identified three key residues (K464, K481 and R492) in AF1 that are monomethylated. Methylation mimic mutations KKR → FFF created hypoactive PR, whereas the KKR → QQQ mutation generated hyperactive PR in gene reporter assays. The current study used these mutants to determine the roles of AF1 in PR regulation of cellular activities and global gene regulation in breast cancer cells MCF-7. AF1-FFF mutation attenuated PR regulation of cell proliferation and apoptosis in response to progestin, whereas AF1-QQQ mutation enhanced these effects. AF1-FFF mutation attenuated gene regulation by progestin in ~60% of PR target genes, including genes involved in cell proliferation, hypoxia and TNFα signaling. However, the AF1-FFF mutation had little effect on ligand-independent gene regulation, suggesting distinct mechanisms of gene regulation by liganded and unliganded PR. Intriguingly, impaired activity of methylation mimic mutant PRB-FFF is associated with greater chromatin binding in ChIP-Seq analysis, corresponding to a stronger association between PRB-FFF and Steroid Receptor Coactivator-1 (SRC-1), a member of the p160 family of nuclear receptor coactivators, as was previously reported. In conclusion, PR AF1 is important for the core activities of liganded PR in regulating ~half of target genes and cell proliferation. AF1 monomethylation may modulate PR-chromatin interactions through stronger association with coregulators, thereby decelerating chromatin binding kinetics. This is supported by PRODIGY’s prediction of higher binding affinities of monomethylated AF1 and methylation mimic mutant with SRC-1. 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

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

Petroleum hydrocarbons remain major environmental contaminants, and understanding the mechanisms governing their biodegradation is essential for designing effective remediation plans. The strategy in this article is slightly different from other cases in the literature. Such literature models require, for their elaboration, a significant number of experiments; the number of experimental determinations is at least proportional to the square of the number of constants introduced in the mathematical expressions. For this reason, the strategy followed in this article is different—starting from a set of experiments carried out and presented in a coherent and published manner, a simple methodology for building specific and minimal models, which will allow solving specific problems, was effectively developed. This study develops a nonlinear mathematical structure, expressed as a system of coupled differential equations, that simultaneously describes the degradation of petroleum hydrocarbons and the dynamics of hydrocarbon-degrading bacteria and fungi in soil–sludge mixtures. The model was calibrated using experimental data obtained from biopiles prepared with different volumetric ratios of contaminated soil and sewage sludge. Approximate analytical solutions were derived and the distributed constants were evaluated. For a consistent discussion, the analytical solutions were assessed against numerical desk simulations performed with a classical fourth-order Runge–Kutta method, which accurately reproduced the nonlinear behavior of the specific system. This numerical approach was chosen in order to overcome the proper difficulties encountered in this strategy implementation. The results show that the soil–sludge ratio strongly influences biodegradation efficiency, while kinetic parameters determine whether microbial communities evolve toward a stationary regime or accelerated contaminant removal. The combined analytical–numerical framework provides a robust predictive tool for optimizing mixture composition and improving the design of bioremediation treatments for petroleum-contaminated soils. Full article