Search Results (14,519)

Background: Managing neuropathic pain (NP) is particularly challenging in the context of opioid use, and the mechanisms behind chronic pain remain unclear. Objective: This study evaluated the impact of turmeric bioactive compounds on brain regions including frontal cortex (FC), hippocampus (HPC), and hypothalamus (HPT) in the spinal nerve ligation (SNL) in a rat model of NP. Methods: Twenty-four SD rats were assigned to four groups (N = 6 per group), namely sham+vehicle (Sham-V), SNL+vehicle (SNL-V), SNL + 100 mg/kg curcumin (SNL+100CUR), and SNL + 50 mg/kg bisdemethoxycurcumin (SNL+50BDMC), treated daily for four weeks via oral gavage. Gene expression levels related to neuroinflammation, oxidative stress, and mitochondrial homeostasis were measured using qRT-PCR. Protein-level or functional mitochondrial assays were not performed due to limited sample availability. Results: In the FC, SNL decreased the expression level of NRF1 and OPA1, but only OPA1 was increased by BDMC. In the HPC, SNL increased CD11b, NRF2, and MFN1; BDMC decreased CD11b and increased IBA1, NRF1, TFAM, PGC1α and Complex I; and CUR increased NRF1, TFAM, DRP1 and Complex I levels. In the HPT, SNL decreased GFAP and MFN1, with CUR and BDMC further decreasing GFAP but not affecting MFN1. Additionally, CUR and BDMC decreased the expression of several key markers of neuroimmune signaling and mitochondrial homeostasis, including IBA1, CD11b, NFkB, NRF1/2, DRP1, OPA1, PGC1α, TFAM, and PINK1. Conclusions: CUR and BDMC induced region-specific transcriptional remodeling of mitochondrial homeostasis across FC, HPC, and HPT in SNL rats, with somewhat limited effects in the FC, mixed effects in the HPC, and broader downregulation in the HPT. Full article

Background: Bacterial adaptation to environmental and chemical stress involves coordinated, system-level responses collectively described as perturbome. Understanding conserved elements within core perturbomes may reveal strategic vulnerabilities for antimicrobial development. Methods: In this study, we implemented an integrative framework combining functional and comparative genomics, drug–target interactions and molecular docking to prioritize conserved stress-response targets in Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Results: A total of 147 genes from previously defined core perturbomes were analyzed through interactome reconstruction and functional enrichment. Interactome and functional analyses revealed significant connectivity and functional clustering, primarily associated with molecule biosynthesis, translation, transcriptional regulation, and energy metabolism. Orthology-based comparative genomics identified six conserved orthogroups shared across at least two species, representing key stress-adaptive nodes including fatty acid synthesis initiation, metabolic stress buffering, transcription termination (Rho), ATP synthesis, peptidoglycan remodeling, and UDP-glucose-mediated envelope biosynthesis. Drug–target interaction analyses suggested that these conserved proteins are modulated by enzymatic inhibitors, metabolite analogs, or active-site competitors. Structural and docking analyses focused on a selected protein, FabF (β-ketoacyl-ACP synthase II) and confirmed catalytically coherent binding of cerulenin within the active site, with high concordance between experimentally resolved and AlphaFold-predicted structures, supporting the reliability of structure-based prioritization. Conclusions: Overall, the results demonstrate that bacterial stress responses converge on evolutionarily conserved metabolic and regulatory elements essential for homeostasis and tolerance to perturbations, being the first work integrating core perturbome data from different microorganisms. The proposed perturbome-informed framework provides a rational strategy to identify robust, broad-spectrum antimicrobial targets and highlights opportunities for drug repurposing and future experimental validation. Full article

Background/Aims: While pathogenic germline variants play a critical role in pediatric cancer susceptibility, traditional clinical genetics primarily focuses on single-gene interpretations. Transitioning to a systems-level analysis of inherited variation can uncover shared biological vulnerabilities, informing genetic counseling, surveillance, and targeted therapeutics. This study aims to implement an unsupervised machine learning framework to identify and characterize Germline Mutation Signatures (GMS) across diverse pediatric malignancies, elucidating latent genomic patterns that reveal shared oncogenic mechanisms. Methods: We analyzed germline whole-exome and whole-genome sequencing (WES/WGS) data from a retrospective cohort of 420 pediatric cancer patients and matched non-cancer controls. Variants were deeply annotated to capture multi-dimensional features, including predicted pathogenicity, splice-site disruption, regulatory impact, population frequency, and sequence context. To enable robust modeling, we integrated an augmented feature set encompassing evolutionary constraint, loss-of-function intolerance, and compositionally normalized substitution spectra. These high-dimensional annotations were processed using a deep autoencoder for non-linear representation learning, followed by Gaussian Mixture Modeling (GMM) of the latent space. Results: The framework delineated 13 signatures (GMS1–GMS13), yielding an optimal Davies–Bouldin index of 1.051. These signatures map to fundamental biological processes, including DNA repair deficiencies, transcription-coupled damage, replication stress, and aberrant RNA regulation. Crucially, these GMSs transcend traditional tissue-of-origin classifications, manifesting across multiple distinct cancer types. This observation indicates convergent germline etiologies and suggests potential shared susceptibilities to pathway-directed therapies. Conclusions: The discovery of these cross-cancer signatures provides a scalable, biologically interpretable framework for decoding inherited pediatric cancer risk. While the therapeutic mapping networks identified are currently exploratory and serve as a hypothesis-generating foundation, this deep learning-driven paradigm establishes a robust basis for stratified precision medicine. Pending prospective clinical validation, this approach holds significant translational potential to move beyond single-gene paradigms toward unified, systems-level precision oncology strategies. Full article

Background/Objectives: Managing bone diseases demands novel, natural compounds to bypass the heavy side effects of current therapies. Honey is well-known for its therapeutic traits, yet we know very little about how specific floral varieties impact bone tissue. This study confronts this gap by comparing how acacia, chestnut, and coriander honeys drive human osteoblast behavior in vitro. Methods: After mapping the phenolic/flavonoid profiles and antioxidant capacities of these honeys, we tested them on hFOB 1.19 human osteoblasts. We tracked cell migration via scratch assays and validated osteogenic maturation through Alkaline Phosphatase (ALP) activity and Alizarin Red (AR) mineralization over 7 days. Confocal time-lapse imaging with pharmacological inhibitors monitored intracellular calcium dynamics, while gene shifts were analyzed via qRT-PCR. Results: Coriander honey (CH) packed the highest polyphenol levels and antioxidant power. Biologically, while all honeys accelerated scratch closure, CH drove cell motility most potently. Remarkably, a 7-day treatment with these honeys sparked a significant and robust increase in ALP activity and mineralization, surpassing the osteogenic induction observed with standard osteoinductive media. Mechanistically, CH triggered a sharp [Ca²⁺] spike, relying on external calcium entry and IP3-dependent internal release via PLC activation. qRT-PCR confirmed this anabolic shift via OPG and OPN upregulation. Conclusions: Honey exerts pronounced multi-level osteopromotive effects at both the functional and transcriptional levels, tightly linked to its botanical source. Among the variants, coriander honey stands out for its exceptional ability to fast-track osteoblast migration, differentiation, and early mineral deposition. Therefore coriander honey represents a promising in vitro candidate that warrants further preclinical evaluation for bone repair applications. Full article

Candidozyma auris (formerly known as Candida auris) has emerged as a formidable clinical fungal pathogen as a result of its multidrug resistance and persistent colonization capabilities. In this study, three clinical C. auris strains (namely C. auris strain 01, C. auris strain 03, and C. auris strain 13) with distinct origins were characterized to investigate their phenotypic variations and mechanisms of azole resistance. Comprehensive profiling revealed significant inter-strain differences in biofilm formation, cell surface hydrophobicity, adhesion capacity, and phospholipase activity. Testing for antifungal susceptibility showed that the three clinical strains exhibited different minimum inhibitory concentrations for multiple azoles (fluconazole, voriconazole, and itraconazole) and echinocandins (anidulafungin and micafungin). Sequencing identified Y132F mutations in the ERG11 gene of the three clinical strains. Mechanistic investigations demonstrated that fluconazole exposure significantly upregulated the expression of efflux pump genes (CDR1 and CDR2) and the genes encoding their transcriptional regulators (MDR1 and TAC1b). In a murine skin colonization model, comparing data from the standard strain C. auris strain CBS12766 and clinical strains of C. auris strain 03 and C. auris strain 13 exhibited a significantly higher fungal burden of tissue, whereas strain C. auris strain 01 showed an intermediate level. Host immunity response analysis revealed that expression of the IL-1β gene was significantly elevated in C. auris strain CBS12766-infected mice, while expression of IL-6 and CXCL-1 genes was predominantly increased in the C. auris strain 01, with TNF-α gene expression levels being comparable across all strains. Histopathological examination confirmed local infiltration of inflammatory cells and mild epidermal edema, indicating active host immune engagement. Overall, our findings highlighted substantial phenotypic heterogeneity, different colonization capacities, and differences in expression of inflammatory cytokines among the C. auris strains. Further investigations into fluconazole-response mechanisms identified enhanced efflux pump activity, along with ERG11 gene Y132F mutations and transcription factor modulation among these clinical strains. Full article

Background/Objectives: Immune surveillance is increasingly recognized as a modifier of myeloproliferative neoplasm (MPN) initiation and evolution, yet the contribution of the NKG2D receptor and its ligands MICA/MICB to CALR-mutated disease remains unclear. Methods: We performed high-resolution next-generation sequencing genotyping of MICA and MICB in 43 patients with CALR-mutated MPN (WHO 2022 criteria) and compared the allele and haplotype distributions with those of 156 healthy Bulgarian controls and 85 patients with JAK2 V617F-positive MPN. Associations were tested using age- and sex-adjusted additive generalized linear models; bi-locus haplotypes were evaluated using haplotype score methods. In a genotyped subgroup (35 CALR-mutated MPN patients and 105 controls), functional KLRK1 (NKG2D) polymorphisms were analyzed for haplotype-level associations. We also performed 700 ns molecular dynamics simulations of selected MICA variants in complex with NKG2D and reanalyzed publicly available single-cell RNA-sequencing data (GSE117826) and RNA-sequencing data from CRISPR/Cas9-edited CALR-mutant iPSC-derived megakaryocytes to evaluate MICA/MICB expression. Results: MICA*004:001 was significantly associated with CALR-mutated MPN versus controls (p = 0.004; Bonferroni-adjusted p = 0.047), while MICB*008:001 showed only nominal association. Exploratory haplotype analyses identified a MICA*009:01-MICB*004:001 haplotype associated with CALR-mutated status (p = 0.008) and a KLRK1 G-A-G-T haplotype (rs1049174-rs2617160-rs2246809-rs2617170) associated with increased CALR-mutated MPN risk (OR = 3.61; p = 0.029). Transcriptomic reanalysis indicated a higher fraction of CALR-mutant stem and progenitor cells expressing detectable MICA/MICB transcripts, and heterozygous CALR-mutant megakaryocytes exhibited higher MICA expression than the wild type. Conclusions: Together, these data support an exploratory immunogenetic and transcriptomic link between the NKG2D-MICA/MICB axis and CALR-mutated MPN, but direct protein-level and functional studies are required before mechanistic or therapeutic conclusions can be drawn. Full article

Palmatine chloride (berbericinine, C₂₁H₂₂ClNO₄) is a protoberberine alkaloid found in several plants, including Rhizoma Coptidis, Cortex Phellodendri, Rhizoma Corydalis, Guduchi (Tinospora cordifolia), and Tinospora sagittata roots. Palmatine chloride (PA) is known as an inhibitor of dopamine generation. However, its effect on endoplasmic reticulum (ER) stress-related macrophage activation caused by endotoxin (lipopolysaccharide) is not yet well known. In this study, the effects of PA on pyroptotic responses of mouse macrophages (RAW 264.7) activated by endotoxin were investigated using Griess reagent assay for nitric oxide (NO) production, fluo-4 assay for cytosolic calcium release, dihydrorhodamine 123 assay for hydrogen peroxide production, multiple cytokine assay for cytokine production, real-time PCR for inflammatory gene transcriptions, and flow cytometry assay for p38 MAPK activation. Preliminary experiments using THP-1 human monocytic cells demonstrated that PA was not cytotoxic and significantly reduced basal NO production. Results revealed that PA significantly reduced excessive production levels of NO, hydrogen peroxide, pro-inflammatory cytokines (such as interleukin (IL)-6, CCL3 (MIP-1α), and CSF2 (GM-CSF)), and cytosolic calcium release in endotoxin-stimulated RAW 264.7, but significantly increased the production of anti-inflammatory cytokine IL-10. PA inhibited endotoxin-induced transcripts of Chop, Stat1, Fas, and c-Fos in activated RAW 264.7. It also decreased p38 MAPK phosphorylation and level of Fas in RAW 264.7 stimulated by endotoxin. To further interpret these findings, a network pharmacology-informed analysis based on large-scale literature mining was performed, supporting the multi-target regulatory role of PA in ER stress-related pathways. Briefly, PA exerts anti-inflammatory effects on endotoxin-stimulated RAW 264.7 via the calcium-CHOP pathway, consequently reducing endotoxin-induced production of pro-inflammatory mediators (NO, cytokines, etc.) and relieving ER stress-related pyroptotic cascade. Full article

Antibiotic-resistant bacteria are widely distributed and threaten public health. Photocatalytic antimicrobial technology can effectively inactivate multidrug-resistant bacteria without readily inducing resistance. We previously showed that oxygen-rich vacancy Bi₂MoO₆ (OBM) exhibits excellent activity against methicillin-resistant Staphylococcus aureus (MRSA), but the underlying molecular mechanisms remain poorly understood. Here, we employed integrated transcriptomics and metabolomics, with qRT-PCR validation, to systematically elucidate the antibacterial mechanism of OBM against MRSA. OBM treatment induced profound transcriptional and metabolic alterations: 231 differentially expressed genes and 206 differentially abundant metabolites were identified. Functional enrichment analysis revealed cooperative involvement in multiple critical pathways, including inhibition of amino acid biosynthesis and protein translation, disruption of cell wall and membrane integrity, induction of oxidative stress, collapse of energy metabolism (suppression of oxidative phosphorylation and impaired ATP synthesis), and imbalance in nucleotide metabolism (down-regulation of DNA helicase and mismatch repair genes, dysregulation of purine/pyrimidine metabolism). These findings demonstrate that OBM photocatalytically inactivates MRSA through a multi-target systemic attack at both the transcriptional and metabolic levels, providing a novel theoretical foundation for the development of photocatalytic materials aimed at controlling MRSA and other drug-resistant bacteria. Full article

Pepper (Capsicum annuum L.) is an important horticultural crop whose growth, development, and yield formation are severely constrained by heat stress. The Mediator complex is a key transcriptional co-regulator in plants and plays important roles in developmental processes and stress responses. However, the MED gene family and its functions in heat stress responses remain largely unexplored in pepper. Using the chromosome-level reference genome of the cultivated pepper (Capsicum annuum var. annuum) cultivar Zhangshugang, a total of 49 CaMED genes were identified and classified into four conserved Mediator modules, namely the head, middle, tail, and kinase modules. Comprehensive bioinformatic analyses showed that CaMED genes are evolutionarily conserved across species, whereas differences in gene structure and sequence characteristics among family members may contribute to their functional diversification. Promoter analysis further showed that these genes contain abundant cis-acting elements related to light, phytohormone, and stress responses. Transcriptome analysis of the 49 identified CaMED genes showed distinct tissue-specific expression patterns, with many members showing preferential expression during early flower development and late placenta development. Furthermore, expression profiling of all CaMED genes using publicly available transcriptome datasets under 42 °C heat-stress conditions, followed by RT-qPCR validation of selected candidates, showed that CaMED25a displayed a relatively stable heat-responsive expression pattern. Virus-induced gene silencing of CaMED25a compromised heat tolerance in pepper plants under heat stress, as evidenced by increased H₂O₂ accumulation and significantly reduced expression of heat defense-related genes, including CaHSP18, CaHSP25.9, and CaHSP70.1. Taken together, this study provides an integrated analysis of the pepper CaMED gene family and reveals the positive contribution of CaMED25a to heat stress tolerance. These findings lay the groundwork for subsequent studies on CaMED gene function and the molecular regulation of high-temperature responses in pepper. Full article

Hepatocellular carcinoma (HCC) is a lethal malignancy requiring novel therapeutic interventions. While Polyporus umbellatus exhibits anti-tumor properties, its specific bioactive pharmacophores and molecular mechanisms remain elusive. This study integrated network pharmacology, computational simulation, and experimental validation to decipher the anti-HCC efficacy of Polyporus umbellatus. Screening identified 11 bioactive sterols, with intersection analysis revealing 63 core targets. Clinical data stratified Checkpoint Kinase 1 (CHEK1) as a critical high-risk oncogene associated with poor prognosis. Molecular dynamics simulations (100 ns) demonstrated that polyporusterone E, a key constituent, forms a thermodynamically stable complex with CHEK1 via high-affinity hydrogen bonding. In vitro assays in HepG2 and HuH-7 cells confirmed that CHEK1 overexpression drives proliferation and metastasis, while its silencing reverses these phenotypes. Crucially, treatment with Polyporus umbellatus extract and purified polyporusterone E significantly compromised HCC cell viability and downregulated CHEK1 expression at transcriptional and translational levels. These findings suggest that polyporusterone E may downregulate CHEK1 expression and modulate CHEK1-associated signaling in HCC cells, providing preliminary evidence for the molecular basis of Polyporus umbellatus and highlighting its potential as a complementary therapeutic strategy for HCC management. Full article

Reverse transcription quantitative real-time PCR (RT-qPCR) is a highly efficient and sensitive technique for quantifying gene transcript levels. The accuracy of gene expression analysis depends critically on the selection of appropriate reference genes for normalization, which is essential to minimize technical variation arising from differences in RNA quality, reverse transcription efficiency, and sample handling. Schisandra chinensis is a medicinally important plant with a long history of use in traditional Chinese medicine and has gained increasing global recognition. In recent years, a growing number of studies have employed molecular biology approaches to investigate the molecular mechanisms underlying secondary metabolite biosynthesis in S. chinensis. However, systematically validated reference genes for RT-qPCR analysis in this species have not yet been established. In the present study, the expression stability of eleven candidate reference genes was evaluated across different tissues and under various abiotic stress conditions in S. chinensis using four statistical algorithms: geNorm, NormFinder, BestKeeper, and RefFinder. Comprehensive analysis revealed that PP2A15 and UBC2 were the optimal reference gene combination for leaves; UBC2 and UBC11 for stems; RPL6 and PP2A15 for roots; RPL21 and RPL6 for fruits; and RPL6 and UBC11 as the best-performing pair across all tissue types. Under abiotic stress conditions, UBC11 and UBC2 exhibited the highest stability in both leaves and roots under salt stress; UBC2 and GPN1 proved most stable under alkaline stress; UBC2 and RPL6 were identified as the most suitable combination under drought stress; and UBC2 and UBQ12 demonstrated consistently stable expression across all three abiotic stress treatments. The reliability of these reference gene combinations was further validated by examining the expression profiles of three target genes. Collectively, these findings establish a validated reference gene toolkit for future gene expression studies in S. chinensis, particularly for the functional characterization of genes involved in lignan biosynthesis and abiotic stress responses. Full article

Endometriosis is a long-term gynecological condition marked by the growth of endometrial-like tissue outside the uterus, which undergoes proliferation, bleeding, and regeneration. This disease is associated with disrupted steroid hormone signaling, notably progesterone (P4) resistance and estradiol (E2) dominance. P4 resistance has been associated with impaired activation of the progesterone receptor (PR) and reduced transcription of P4 target genes, while elevated E2 levels induce estrogen receptor (ER)-mediated signaling, enhancing estrogen-dependent lesion growth. This hormonal imbalance contributes to a pro-inflammatory microenvironment, chronic pelvic pain, infertility, and enhanced neuroangiogenesis. Emerging evidence indicates that the coordinated regulation of neurotrophins and sex hormones promotes nerve fibers and blood vessel growth and invasion within endometriotic lesions. P4 and E2 have been shown to modulate the expression of key neurotrophins, including nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF). This review presents current evidence on the interplay between neurotrophins and ovarian steroids in endometriosis, with a specific focus on their contribution to neuroangiogenesis and pain pathophysiology. The review includes articles in English containing the Medical Subject Headings (MeSH) terms: “endometriosis”, “neurotrophins”, “nerve growth factor”, “brain-derived neurotrophic factor”, “neuroangiogenesis”, “progesterone”, and “estradiol”, found in the PubMed database published between 2000 and 24 May 2026. This review included a range of original research articles, systematic reviews, meta-analyses, prospective observational studies, case–control studies, and review papers, for a total of 122 articles. Full article

Circadian rhythms impose temporal organization on immune function, shaping host responses to infection, injury, and chronic disease. While transcriptional control by core clock components such as CLOCK and BMAL1 has been extensively characterized, this paradigm alone cannot explain the rapid and dynamic nature of immune signaling. Emerging evidence identifies post-translational modifications (PTMs)—including phosphorylation, ubiquitination, and acetylation—as critical regulators that confer speed, reversibility, and specificity to inflammatory pathways. Here, we propose the concept of a “Chrono-PTM axis,” in which circadian timing and PTM-dependent signaling are functionally integrated to govern immune activation thresholds. We discuss how PTMs not only regulate core clock machinery but also temporally gate key innate immune pathways, including NF-κB signaling and inflammasome activation, thereby controlling cytokine production at multiple levels. Furthermore, we highlight the role of immunometabolism in supplying essential cofactors that couple cellular energetic states to PTM dynamics, linking metabolic oscillations to inflammatory outputs. Disruption of this axis contributes to the pathogenesis of autoimmune diseases, cancer, and tissue-specific inflammatory disorders. Finally, we outline emerging therapeutic opportunities targeting the Chrono-PTM axis, including chronotherapy and PTM-directed interventions, and identify critical gaps in temporal proteomics and translational studies. Elucidating the integration of circadian and post-translational regulation will provide a unifying framework for understanding immune homeostasis and may enable time-informed precision immunotherapy. Full article

Interferons (IFNs) play vital roles in antiviral immunity, yet the functional diversity of type I IFNs in teleosts remains incompletely characterized. In this study, we identified and characterized a group II type I interferon, designated IFNc (MsIFNc), from largemouth bass (Micropterus salmoides). The cDNA sequence of MsIFNc is 660 bp in length, encoding a 184-amino-acid polypeptide containing a signal peptide and four conserved cysteines predicted to form two disulfide bonds. Phylogenetic analysis confirmed its classification within the teleost IFNc subgroup. Tissue expression profiling revealed constitutive MsIFNc transcription in all examined tissues, with the highest levels in the liver, intestine, and spleen. Moreover, MsIFNc expression was significantly upregulated in the spleen following polyinosinic–polycytidylic acid (polyI:C) stimulation. Recombinant MsIFNc (rMsIFNc) was successfully expressed in Pichia pastoris and significantly enhanced the viability of primary hepatocytes infected with Micropterus salmoides rhabdovirus (MSRV). These results demonstrate that IFNc is an important component of the immune response in largemouth bass, providing a basis for understanding the function of fish IFNc. Full article

Cyanobacteria, the only prokaryotic oxygenic phototrophs, rely on sophisticated regulatory networks, including those mediated by small RNAs (sRNAs) to cope with environmental fluctuations. Here, we delineate the sRNA landscape of Synechocystis sp. PCC 6803 under short- and long-term ammonium stress, revealing a significant proportion of antisense RNAs (asRNAs). Functional characterization identified three asRNAs (sll0312-as, sll0873-as, and slr1667-as) as key regulators of ammonium stress tolerance, implicating their targets (sll0312, sll0873, and slr1667) as new players in nitrogen fluctuation acclimation. The sll0944-as and sll1515-as were also identified, revealing an additional regulatory layer targeting known carbon/nitrogen metabolism regulators. Mechanistically, we characterized the ammonium-induced asRNA ssr0692-as, demonstrating that it represses pirA translation via direct 5′UTR interaction. This finding, integrated with the known role of the nitrogen limitation-responsive sRNA NsiR4 targeting the same region, supports a synergistic model wherein these two sRNAs precisely modulate PirA protein levels—and thus the downstream nitrogen flux—across varying nitrogen availability. Together, our findings expand the functional repertoire of cyanobacterial sRNAs and elucidate a dynamic post-transcriptional mechanism to fine-tune nitrogen metabolism in response to fluctuating nutrient conditions. Full article