Search Results (9,757)

Rice grain quality is strongly influenced by starch composition and structure, which differ between the two major cultivated Oryza sativa subspecies, indica and japonica. Although allelic variation in several key genes has been linked to these differences, it remains unclear whether subspecies divergence in starch metabolism is more strongly reflected in gene repertoire, structural organization, promoter composition, or transcriptional regulation. Here, we identified 52 starch metabolism-related genes representing 26 orthologous gene pairs in indica and japonica rice and compared their gene structures, predicted promoter cis-regulatory elements, and grain-filling expression patterns. The analyzed gene set was largely conserved between the two subspecies, with limited structural variation among orthologs. Although promoter analysis revealed differences in predicted cis-regulatory element composition, the strongest divergence was observed at the transcriptional level during grain filling. At 10 days after flowering (DAFs), RNA-seq profiling revealed relatively higher expression of several starch biosynthesis genes, including SSI, SSIIa, and BEI, in japonica than in indica. qRT-PCR further confirmed higher expression of SSI, SSIIa, BEIIb, and GBSSI in japonica, whereas AGPS2b was more highly expressed in indica during early grain filling. By 30 DAFs, expression of most tested genes had declined markedly in both subspecies. These findings indicate that divergence between indica and japonica is more clearly associated with transcriptional regulation during grain filling than with major differences in core starch metabolism gene content or structural organization. Full article

Background: Lung cancer remains the leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) accounting for approximately 85% of all cases. Isorhamnetin (ISO), a natural dietary flavonoid, has demonstrated potent anti-lung cancer activity in cell models. However, its precise mechanism of action within the complex landscape of NSCLC remains to be fully elucidated. Methods: The effects of ISO on NSCLC cell viability, apoptosis, and cell cycle distribution were assessed in A549 and H1650 cells using the MTT assay, Annexin V-FITC/PI staining, and flow cytometry. Wound healing and Transwell assays were employed to evaluate the isorhamnetin impact on cell migration, invasion, and adhesion. To investigate the underlying molecular mechanisms, RNA sequencing (RNA-seq) was performed, followed by validation of key target genes and proteins using qRT-PCR and Western blot analysis. Results: ISO treatment elicited a significant, dose- and time-dependent inhibition of NSCLC cell viability, which coincided with a marked induction of apoptosis. Cell cycle analysis revealed that ISO triggered an S-phase arrest. Transcriptomic profiling identified ELFN1 and TMEM186 as significantly upregulated genes, while SETDB1 was downregulated in a concentration-dependent manner; this was accompanied by a concomitant upregulation of FGFBP1 protein expression. Functionally, ISO effectively suppressed the migratory, invasive, and adhesive capabilities of both cell lines. Conclusions: Our findings demonstrate that ISO exerts a potent anti-proliferative and anti-metastatic effect on NSCLC cells. The underlying mechanism is multifaceted, involving the induction of apoptosis and cell cycle arrest, coupled with the modulation of a novel regulatory network centered on ELFN1, TMEM186, SETDB1, and FGFBP1. These results provide new mechanistic insights into the anti-tumor pharmacology of isorhamnetin and highlight its potential as a therapeutic agent targeting both cancer cells and their supporting microenvironments. Full article

High-quality genomic DNA extraction remains a major bottleneck for fungal genomics, particularly for worldwide aerobic and non-photosynthetic mushroom species that rely on their rigid cell walls, interference between metabolites, polysaccharides, etc., and complex genomes. This study systematically compares five DNA extraction protocols involving four distinct sample preparation procedures (fresh (A), filtered (B), frozen (C) and cryogenic mycelium (D)) across mycelial cultures of eight Tunisian fungal strains representing Ascomycota and Basidiomycota to identify the optimal combination for genomic DNA extraction from mycelium. The eight phylogenetically diverse fungal species were analyzed using short-read (MiSeq and NextSeq550) and/or long-read (MinION Mk1C) sequencing technologies, giving a depth coverage between 3.7× and 83×. The generation and quality of the assemblies were assessed within the Galaxy platform, which revealed a gap percentage of 0–0.509%. Taxonomic characterization and phylogenetic inference were performed with SANGER technology using the Internal Transcribed Spacer (ITS) and D1/D2 region of the 26S rRNA gene, assigning the species to our eight different strains: Clitopilus baronii (BS6), Porostereum spadiceum (BS200), Trametes versicolor (BS22-9), Schizophyllum commune (BS23-13), Gloeophyllum abietinum (BS23-14), Irpex laceratus (BS100), Trichoderma asperellum (GC9) and Trichoderma harzianum (S3). The optimized DNeasy Plant Pro Kit protocol with cryogenic biomass treatment presents a safe and cost-effective method for fungal genome sequencing and taxonomic resolution. This integrated comparative evaluation of extraction for sequencing identifies an optimal Qiagen-based extraction strategy combined with cryogenic treatment for eight diverse Tunisian fungal species, guiding method selection based on specific cell wall characteristics rather than proposing a universal protocol limited by unequal replication and strain numbers. Full article

Pseudomonas aeruginosa is a versatile opportunistic pathogen that thrives in hostile environments by tightly regulating zinc (Zn) homeostasis. The CzcRS two-component system is pivotal for Zn resistance, primarily by activating the CzcCBA efflux pump, yet its basal activity and full regulon remain poorly defined. Here, we analyzed putative CzcR targets under zinc sufficiency (ZS) and zinc excess (ZE) conditions in P. aeruginosa PAO1 using ChIP-seq. Under ZE, we identified 32 CzcR binding sites, potentially regulating 39 genes, many of which are linked to virulence, antibiotic resistance, and stress response. Under ZS, 10 binding sites were detected, revealing distinct CzcR targets. Considering the presence of a CzcR binding motif close to the peaks summit and RNA-seq data, we identified seven and four novel CzcR-regulated genes under ZE and ZS conditions, respectively, mostly implicated in bacterial virulence. Our findings highlight that CzcR may exhibit different functionalities depending on Zn concentration: its basal activity maintains physiological robustness, while its activated form orchestrates Zn detoxification and virulence modulation. This study expands our understanding of how P. aeruginosa integrates metal sensing with clinically relevant phenotypes, highlighting CzcR as a key regulator at the intersection of metal homeostasis and pathogenicity. Full article

The maturation of oocytes is a critical step in mammalian reproduction, involving dynamic regulation of gene expression. Therefore, investigating how gene expression varies during different stages of oocyte maturation is highly important. This study employed single-cell RNA sequencing (scRNA-seq) to analyze bovine oocytes at the germinal vesicle (GV) and metaphase II (MII) stages. The results identified 1787 differentially expressed genes (DEGs) between the two stages, with 1556 genes upregulated and 231 downregulated in the GV stage. Further investigation using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that the upregulated genes are mainly involved in mitochondrial functions and energy metabolism, whereas the downregulated genes are primarily associated with signaling pathways. Validation through RT-qPCR confirmed that COA4, TKT and GPX4 were significantly higher in GV-stage oocytes, while ISG15, MAP1LC3C and ZEB2 were notably downregulated. This study highlights significant gene expression differences between GV and MII bovine oocytes, underscoring the vital roles of genes related to energy metabolism and signaling during oocyte maturation. The expression patterns of these genes provide important molecular markers for further elucidating the mechanisms underlying oocyte maturation. Full article

Glioblastoma (GBM) is characterized by hypoxia-driven metabolic adaptation and profound therapeutic resistance. Ferroptosis, an iron-dependent lipid peroxidation-related cell death process, has emerged as a potential vulnerability; however, its relationship with hypoxia signaling remains incompletely defined. In this study, we performed integrative transcriptomic and single-cell RNA sequencing analyses to investigate the relationship between hypoxia signaling and ferroptosis-related gene signatures in GBM. Intersection analysis of hypoxia-associated differentially expressed genes and curated ferroptosis-related gene sets identified 29 core candidate genes. FerroScore stratification revealed that tumors with higher ferroptosis-related transcriptional signatures were significantly associated with poor overall survival. Among these genes, HILPDA emerged as a hypoxia-associated gene consistently linked to ferroptosis-related gene expression patterns and immune-related transcriptional programs. HILPDA expression showed significant correlations with iron-ROS axis components, including HMOX1, NOX4, and STEAP3, and was associated with immune microenvironment changes characterized by T cell depletion and inflammatory infiltration. Single-cell RNA-seq analysis further supported the cellular-level association between HILPDA expression and hypoxia-related transcriptional states. Structural equation modeling suggested that the relationship between HILPDA expression and ferroptosis-related gene signatures may be mediated through hypoxia-related pathways. Collectively, these findings indicate a transcriptomic association between hypoxia signaling and ferroptosis-related gene signatures in GBM and identify HILPDA as a candidate gene associated with this axis. Full article

Human T-cell leukemia virus type 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a chronic inflammatory disease driven by HTLV-1-infected CD4⁺ T cells; however, the phenotypic and functional characteristics of disease-associated T-cell subsets remain incompletely understood. We analyzed samples using flow cytometry (n = 3–5 per group) and RNA-seq (n = 13), focusing on CADM1^highCD4⁺ T cells enriched for HTLV-1-infected cells to evaluate a transferrin receptor (TfR)-expressing subset. TfR⁺CADM1^highCD4⁺ T cells were detected in both asymptomatic carriers and patients with HAM, but their frequency among CD4⁺ T cells was higher in HAM patients. These cells exhibited a Treg-like phenotype with higher Foxp3 and CTLA-4 expression than TfR⁻ cells and showed increased Ki-67 positivity, consistent with proliferation. Despite this phenotype, they produced interferon-γ, indicating inflammatory potential, while Foxp3 expression was lower in HAM patients than in asymptomatic carriers, suggesting a more inflammatory phenotype. Furthermore, TfR transcript levels (RNA-seq TPM) correlated with clinical indicators of disease activity, including neopterin and CXCL10 protein levels, and the Osame motor disability score. Collectively, these findings suggest that TfR identifies a proliferative, Foxp3-low, Treg-like inflammatory CD4⁺ T-cell subset that is associated with disease activity in HAM. Full article

Background: Bone metastasis is a major determinant of morbidity and therapeutic failure in advanced prostate cancer (PCa); however, the transcriptional programs and tumor microenvironmental alterations driving metastatic progression remain incompletely understood. This study aimed to systematically characterize transcriptomic differences between non-metastatic and bone-metastatic PCa and to identify key microenvironmental signaling pathways involved in tumor survival and chemoresistance. Methods: Bulk RNA sequencing was performed on 49 non-metastatic and 28 bone-metastatic PCa specimens. Differential expression analysis was integrated with weighted gene co-expression network analysis (WGCNA), gene set enrichment analysis, and immune/stromal deconvolution. Key findings were validated using in vitro functional assays, including Transwell co-culture models, small interfering RNA (siRNA)-mediated gene silencing, cell viability, apoptosis, and docetaxel resistance analyses. Results: Transcriptomic profiling identified 574 differentially expressed genes. Bone-metastatic tumors were enriched in ribosome-related and translational pathways, whereas non-metastatic tumors displayed immune-associated signatures, including natural killer (NK) cell-mediated cytotoxicity and cytokine signaling. WGCNA revealed immune-related gene modules preferentially enriched in non-metastatic disease. Immune deconvolution demonstrated significantly higher infiltration of NK cells and endothelial cells in non-metastatic tumors. Chemokine-receptor analysis highlighted upregulation of the CXCL10-CXCR3 axis in non-metastatic PCa. In vitro, PCa cells expressed CXCR3, while endothelial cells markedly increased CXCL10 expression upon co-culture. Functional assays showed that endothelial-derived CXCL10 promoted PCa cell survival, suppressed apoptosis, and conferred resistance to docetaxel via CXCR3-dependent signaling; these effects were reversed by CXCL10 or CXCR3 knockdown. Conclusions: These findings uncover a context-dependent endothelial-immune chemokine network distinguishing non-metastatic from bone-metastatic PCa and identify the CXCL10-CXCR3 axis as a critical mediator of tumor survival and chemoresistance, suggesting a potential therapeutic vulnerability in advanced prostate cancer. Full article

Pathogen manipulation of host behavior is a widespread evolutionary strategy to enhance its transmission, yet whether different pathogens elicit distinct behavioral and molecular responses in the same host remains poorly understood. We performed parallel behavioral assays and comparative transcriptomic analyses on third-instar Lymantria dispar larvae infected with Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV, virus), Staphylococcus aureus (bacterium) and Metarhizium anisopliae (fungus). Climbing height was recorded over 72 h post-infection, and gene expression pattern was profiled using RNA-seq at 72 h. Only LdMNPV infection induced significant, sustained upward climbing behavior among the three pathogen infection groups. All three pathogens activated Toll and IMD immune pathways, but LdMNPV triggered substantially broader transcriptomic reprogramming. Notably, the virus specifically upregulated multiple energy metabolism pathways (nicotinate/nicotinamide metabolism, pyruvate metabolism, TCA cycle and oxidative phosphorylation) and the neuroactive ligand-receptor interaction pathway—a pattern absent in bacterial and fungal infections. LdMNPV drove tree-top disease through a virus-specific, multi-system manipulation strategy that couples metabolic activation with neural signaling modulation. This comparative study reveals fundamental differences in behavioral manipulation across pathogen kingdoms and provides candidate pathways for functional validation. Full article

Peritoneal dialysis (PD) is limited by insufficient phosphate removal, leading to adverse cardiovascular outcomes in patients with chronic kidney disease. To advance the understanding of the molecular mechanisms of peritoneal phosphate transport, RNAseq data of phosphate transporters in four PD-relevant cell lines were analyzed. The expression and localization of the respective proteins were validated by immunostaining in these cells. The transcriptomics of omental arterioles from children on PD were analyzed. In vitro Transwell models of an immortalized mesothelial cell line (MeT-5A) and human umbilical vein endothelial cells (HUVECs) and respective co-cultures were established, enabling quantification of phosphate transport across mesothelial and endothelial monolayers. Sodium phosphonoformate tribasic hexahydrate (PFA) and Tenapanor were used to inhibit transcellular and paracellular transport pathways. Cell viability and integrity markers were measured over the experimental periods. SLC20A1 and SLC20A2 were expressed across all studied cell types, while SLC34A2 and SLC34A3 were mesothelial cell-specific. Omental arterioles of children on low-glucose-degradation-product (GDP) PD showed higher SLC20A1 expression vs. stage 5 chronic kidney disease (CKD5) and healthy controls. Permeability for phosphate was lower across MeT-5A compared with HUVEC monolayers and was not further reduced in co-culture. Inhibitors reduced both transcellular and paracellular transport to 75% in MeT-5A and 65% in co-cultures, while no effects were observed in HUVEC alone, suggesting the mesothelial cell layer as a significant barrier for phosphate transport. Our studies provide first analyses combining findings on molecular phosphate transporters in peritoneal cells and arterioles and introducing a Transwell model for quantitative studies of phosphate kinetics. Full article

Salt stress is a major abiotic factor that significantly limits crop yields worldwide. Late embryogenesis abundant (LEA) proteins, which are widely present across diverse organisms, play critical and multifaceted roles in plant responses to abiotic stress. However, only a few salt tolerance-related HvLEA genes have been identified in barley. In this study, we characterized 107 HvLEA proteins in barley, which were classified into eight groups and found to be distributed across all seven chromosomes. RNA-Seq analysis of root and leaf tissues from the cultivar “Golden Promise” at 12, 48, and 120 h after salt stress treatment identified 69 differentially expressed HvLEA genes across both tissues. Among these, 41 HvLEA genes were commonly differentially expressed in leaves and roots. Six genes (HvDHN2, HvDHN5, HvDHN10, HvLEA1.1, HvLEA1.6, and HvSMP2) were extremely up-regulated after salt stress in both roots and leaves, with log2FC values exceeding 10, indicating their potential key roles in salt stress response. qPCR validation of selected genes confirmed expression trends consistent with the RNA-Seq data. Database predictions and co-expression network analysis suggested that, in addition to potential protein interactions within the same family, these genes may interact with partners such as cysteine-rich receptor kinases, zinc finger proteins, calcium-binding EF-hand family proteins, NAC domain-containing proteins, and glycosyltransferases. This study identified key HvLEA genes involved in salt stress response and provided valuable genetic resources for improving barley tolerance through molecular breeding. Full article

Background: Among primary intracranial neoplasms in adults, glioblastoma multiforme stands out for both its prevalence and its exceptionally invasive character. Uric acid-related genes (UARGs) may enhance tumor cell invasiveness and drug resistance by promoting oxidative stress responses. This study aimed to elucidate uric acid-driven mechanisms in glioblastoma, focusing on risk stratification and therapeutic vulnerability. Methods: Transcriptomic profiles of GBM were retrieved from TCGA and GEO repositories, followed by performing differentially expressed analysis, univariate Cox and LASSO regression, in order to screen prognostic UARGs and construct a risk model. Then, prognostic analyses were expanded by performing immune microenvironment analysis, drug sensitivity analysis, tumor mutation analysis, independent prognostic analysis, and nomogram construction. Additionally, dataset GSE162631 was interrogated to pinpoint pivotal cell subsets and to map intercellular communication as well as pseudo-time analysis. Results: A risk model incorporating six prognostic UARGs (TIMP1, PLAUR, CTSB, KLF10, RARRES2, and PTPRN) was constructed and identified as a favorable prognostic signature. Resting dendritic cells and drugs (including acetalax and trametinib) were found to be associated with GBM patients’ risk stratification. Low-risk patients showed relatively higher mutation rates of PTEN and TP53. A nomogram was developed based on RARRES2 and PTPRN, which exhibited favorable predictive performance for GBM prognosis. Furthermore, scRNA-seq profiling identified dendritic cells (DCs), macrophages, and T cells as key populations in the tumor microenvironment. Intercellular communication inference indicated relatively strong DCs-macrophage crosstalk, and pseudo-time analysis linked prognostic UARG expression to the differentiation trajectory of critical cell subsets. Conclusions: This study identified uric acid-related genes as potential independent indicators of clinical outcomes in glioblastoma progression. A novel prognostic UARG-associated signature was developed and validated, which showed potential in predicting GBM patient outcomes. Full article

Intramuscular fat (IMF) marbling is a key determinant of beef quality, yet predicting how breed-specific gene expression translates into tissue-scale fat patterning remains a major challenge. Using a small public transcriptomic dataset (n = 3 per breed), this study presents a proof-of-concept omics-to-tissue modeling framework that converts RNA-seq data into biophysically interpretable parameters governing intramuscular adipogenesis. Using transcriptomic profiles from GSE161967 (Japanese Black Wagyu versus Chinese Red Steppes), we derived composite indices capturing the adipogenic commitment (φ) and lipid droplet capacity (ψ) from curated gene modules. These indices were mapped via calibrated linear functions to a Cellular Potts Model (CPM), parameterizing the fibro-adipogenic progenitor (FAP) differentiation probability, lipogenesis rate, adipocyte cohesion, and progenitor abundance. The gene-derived parameters placed Wagyu in a high-adipogenic regime ($p_{F\to A}^{\mathrm{base}}$ = 0.65; $k_{lipogenesis}$ = 0.12), while Chinese Red Steppes resided in a low-adipogenic regime (0.25; 0.04). The CPM simulations revealed a sharp, predictive threshold at $p_{F\to A}^{\mathrm{base}}$ ≈ 0.55, below which IMF remained negligible and above which stable adipocyte clusters and 8–9% IMF emerged. Without post hoc tuning, the gene-derived parameters correctly predicted robust marbling in Wagyu and a lean phenotype in Chinese Red Steppes. A sensitivity analysis identified the adipogenic commitment as the primary control parameter, with lipogenesis acting as an amplifier. Together, these results demonstrate that transcriptomic measurements can quantitatively predict emergent marbling phenotypes through a small set of interpretable biophysical parameters, establishing a generalizable framework for forecasting complex tissue traits from omics data. Full article

Infection of the large yellow croaker (Larimichthys crocea) embryo cell line YCE1 with megalocytivirus strain FD201807 leads to accumulation of capsid-deficient viral intermediates within intracellular vesicles at 48 h post-infection (a phenotype associated with non-lytic egress), which coincides with the initial peak of viral genomic copies. To characterize the host molecular response during this critical stage, we performed time-course RNA sequencing at 24, 48, 96, and 144 hpi. Integrated analysis identified 6661 differentially expressed genes (DEGs) and 1138 differential alternative splicing (DAS) events affecting 892 genes, with DAS event abundance peaking at 48 h. DAS genes in autophagy and Golgi vesicle transport pathways, both integral to animal innate immunity, were significantly enriched exclusively at this timepoint, featuring novel mutually exclusive exon (MXE) isoforms in gopc (Golgi-associated PDZ and coiled-coil motif containing) and rint1 (RAD50 interactor 1). Weighted gene co-expression network analysis (WGCNA) of DEGs identified mapk9 (mitogen-activated protein kinase 9) and map1lc3a (microtubule-associated protein 1 light chain 3 alpha) as hub genes within modules enriched for autophagy-related functions. Separate co-expression analysis of DAS genes revealed rnf5, rimoc1, and golga4 as hub genes, with gopc exhibiting only a single linkage to rnf5. These findings implied concurrent transcriptional and virus-induced host splicing regulation of vesicle-associated innate defense pathways and suggest that splicing-derived features may serve as potential candidates for diagnostics or prevention against megalocytivirus disease in L. crocea. Full article

Ischemic stroke promotes monocyte recruitment to the injured brain and their differentiation into monocyte-derived macrophages (MDMs). These cells contribute to debris clearance but may also exacerbate neuroinflammation. However, the heterogeneity of MDM subsets and the phenotypic transitions that shape MDM functional states during the subacute phase of stroke remain incompletely characterized. To address this, we first performed single-cell RNA sequencing (scRNA-seq) to define the transcriptional landscape of the mouse brain 48 h after transient middle cerebral artery occlusion/reperfusion compared with sham controls. Reclustering of macrophage-lineage cells identified multiple MDM subsets, including a distinct Cd68^hi/Ctsd^hi MDM subset enriched for lysosomal and lipid-processing gene expression programs. Cell trajectory inference supported a transition from early recruited MDMs toward the Cd68^hi/Ctsd^hi state, accompanied by induction of transcriptomic networks that drive MDM function to favor a clearance-competent phenotype in response to ischemic stroke. Complementary single-cell ATAC sequencing (scATAC-seq) demonstrated cell type-specific chromatin remodeling after stroke and revealed MDM subclusters with accessibility at key loci regulating lysosomal function and lipid metabolism. Together, our findings define a cellular and regulatory framework of the subacute post-stroke brain and identify a lysosome-enriched Cd68^hi/Ctsd^hi MDM trajectory, highlighting endolysosomal and lipid-processing programs during early stroke recovery. Full article