Search Results (3,010)

Carotenoids are a class of C40 isoprenoid-derived fat-soluble pigments that play vital roles in plant physiology and human health and serve as precursors for several biologically critical regulatory molecules. Carotenoid cleavage dioxygenases (CCDs) are key enzymes that catalyze the selective oxidative cleavage of carotenoids into apocarotenoids, thereby significantly influencing plant development and responses to abiotic stress. Although extensive research has been conducted on many model species, comprehensive studies on the StCCD gene family in potato remain limited. In this study, we conducted a genome-wide analysis to identify and characterize the CCD gene family in potato. Phylogenetic and structural analyses classified the 17 StCCD genes into six distinct subfamilies, which are distributed across five chromosomes of the genome. Analysis of cis-acting regulatory elements revealed that the promoters of most StCCD genes contain various elements associated with light responsiveness, stress signaling, and phytohormone regulation. Molecular docking analysis indicated that CCD proteins exhibit distinct substrate specificity in their binding to carotenoids and intermediate products. The expression profiling of StCCD genes uncovered pronounced specificity in their expression, which was evident across tissues, throughout tuber maturation, and following exposure to abiotic stresses and hormonal applications. This specificity strongly implicates these genes in the regulation of developmental processes and stress adaptation mechanisms. This study provides a comprehensive genomic and transcriptomic overview of the CCD gene family in potato, establishing a foundation for functional characterization of individual genes in the future. Full article

Tea plants are frequently threatened by insect pests, resulting in substantial yield and quality losses. Methyl jasmonate (MeJA) is a key defense signaling molecule in plants; however, its integrated effects on tea plant growth, resistance, and quality-related traits remain poorly understood. In this study, field experiments were conducted to evaluate the effects of exogenous MeJA at different concentration (0.02–20 mM) on growth traits, quality components, and resistance to the tea green leafhopper and tea orange gall mite in Camellia sinensis ‘Zhongcha 108’, and transcriptome analysis was further integrated to elucidate the underlying molecular mechanisms. The results showed that appropriate MeJA concentrations (0.2–2 mM) significantly optimized bud morphology, characterized by shortened internodes, thicker stems, and reduced leaf insertion angles. Importantly, these treatments did not significantly alter the measured quality-related biochemical components, such as free amino acids and soluble sugars, within the evaluated time frame. Collectively, this study provides the first field-based evidence defining an effective MeJA concentration window that balances pest resistance induction, growth modulation, and processing suitability for flat-type green tea, offering practical guidance for the rational application of MeJA in tea plantation management. Full article

Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent synovitis, in which fibroblast-like synoviocytes (FLSs) serve as the primary effector cells that drive the destruction of joints. Baicalin has previously demonstrated efficacy in significantly ameliorating joint symptoms in rats with CIA. As such, this study aims to investigate its underlying molecular mechanisms and impact on the FLSs of rats with CIA through an integrated proteomics and transcriptomics analysis. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted based on two datasets; it revealed that the retrograde endocannabinoid signaling pathway—associated with susceptibility to RA—is the only one involved in both the signaling and metabolic processes modulated by baicalin. Nineteen differentially expressed proteins (DEPs) downregulated by baicalin comprise seventeen subunits of NADH dehydrogenase and two receptors, glutamate receptor 2 (GRIA2) and γ-aminobutyric acid receptor subunit alpha-5 (GABRA5). Three differential metabolites (DMs) were also affected by baicalin: γ-aminobutyric acid (GABA) and phosphatidylcholine (PC) were upregulated and phosphatidylethanolamine (PE) was downregulated. Our findings suggest that the baicalin-mediated alleviation of joint synovitis is closely related to the upregulation of GABA and PC; downregulation of GRIA2, GABRA5, and PE; and preservation of mitochondrial homeostasis within the retrograde endocannabinoid signaling pathway in FLSs. Full article

Background/Objectives: Skin photoaging represents a predominant form of extrinsic aging, characterized by structural and functional impairment of the skin barrier. In severe cases, it may precipitate dermatological diseases and even tumors. Given the prevalence and detrimental effects of skin photoaging, strategies for its effective prevention and mitigation have garnered significant research interest. Chrysanthemum morifolium Ramat cv. ‘Hangju’ contains diverse bioactive compounds, including flavonoids, phenylpropanoids, phenolic acids, and polysaccharides, which have been proven to exhibit antioxidant and anti-inflammatory effects. Methods: This study employed a UVB-induced mouse model of skin photoaging to evaluate the potential of dietary supplementation with Chrysanthemum morifolium Ramat cv. ‘Hangju’ flower extract (CME) in vivo. Results: In the photoaged skin of female SKH-1 hairless mice, dietary supplementation with CME significantly increased skin moisture content, reduced wrinkle formation, suppressed epidermal hyperplasia, enhanced collagen density, and suppressed the senescence marker expression and DNA damage marker expression. Analysis of the skin transcriptome suggested that CME could alter gene expression patterns and potentially modulate critical signaling pathways involved in skin homeostasis. Moreover, 16S rRNA sequencing indicated that CME mitigated UVB-induced gut microbiota dysbiosis. Conclusions: These preclinical findings reveal the anti-photoaging property of dietary CME supplementation and point to its potential application as a functional dietary supplement for promoting skin health. Full article

Significant differences in reproductive performance exist between meat-type ducks (e.g., Qiangying Duck, QD) and laying-type ducks (e.g., Shaoxing Duck, SD). The molecular mechanisms underlying these differences, particularly concerning ovarian development and function, remain incompletely understood. This study aimed to comprehensively characterize the ovarian transcriptomes of these two duck types, focusing on differential gene expression and post-transcriptional regulatory events. We performed an integrated full-length transcriptome analysis of ovarian tissues from these two breeds using PacBio SMRT and Illumina sequencing. Bioinformatic analyses, including functional annotation, differential expression analysis, and the identification of APA events, were used. We discovered substantial breed-specific differences in alternative polyadenylation (APA), with SD ducks exhibiting significant 3′UTR shortening in 3799 genes and 3′UTR lengthening in 1626 genes compared to QD. The integrated analysis of differential gene expression and APA events highlighted key genes related to steroid hormone synthesis (HMGCS1, DHCR24), lipid metabolism (SCD), signal transduction (HRAS), and antioxidant defense (SOD1). The functional enrichment implicated critical pathways such as mitochondrial energy metabolism, oxidative phosphorylation, and fatty acid degradation. Our study provides a comprehensive atlas of post-transcriptional regulation in the duck ovary and reveals APA as a crucial process of gene regulation. APA may contribute to the differential ovarian function and egg-laying capacity between meat and laying ducks, thus offering valuable targets for genetic selection. Full article

Rice blast, caused by the fungus Magnaporthe oryzae, is a devastating disease that threatens global food security, causing annual yield losses of 10–30%. Consequently, novel control strategies beyond conventional fungicides are urgently needed. Tetramycin, a polyene macrolide antibiotic, is known for its broad-spectrum antifungal activity. However, the specific mechanisms underlying its efficacy against rice blast remain to be fully elucidated. In this study, we demonstrate that tetramycin confers resistance through a dual mode of action. First, in vitro assays revealed that tetramycin directly inhibits M. oryzae mycelial growth. Second, and more critically, it functions as a potent immune elicitor in Oryza sativa. Transcriptome analysis coupled with physiological assays showed that tetramycin treatment triggers a rapid oxidative burst, characterized by significantly elevated activities of key defense enzymes, including superoxide dismutase, peroxidase, phenylalanine ammonia lyase, and polyphenol oxidase (PPO). This oxidative response is further orchestrated through the simultaneous activation of the jasmonic acid (JA) and salicylic acid (SA) signaling pathways, as evidenced by the distinct upregulation of their respective biosynthetic genes and hormone levels. Collectively, these findings indicate that tetramycin not only acts as a direct fungicide but also primes the rice innate immune system via a synergistic reactive oxygen species-JA-SA signaling network, offering a sustainable strategy for rice blast management. Full article

Recurrent endometrial cancer (EC) has limited therapeutic options beyond platinum-based chemotherapy, highlighting the need to identify exploitable molecular vulnerabilities. Tumors with high genomic instability, including microsatellite instability-high (MSI-h) or copy-number-high (CNH) ECs, rely on the ATR-CHK1 signaling pathway to tolerate replication stress and maintain genome integrity, making this pathway an attractive therapeutic target. However, acquired resistance to ATR and CHK1 inhibitors (ATRi/CHK1i) often develops, and the transcriptomic basis of this resistance in EC remains unknown. Here, we established isogenic ATRi- and CHK1i-resistant cell line models from MSI-h (HEC1A) and CNH (ARK2) EC lineages and performed baseline transcriptomic profiling to characterize stable resistance-associated states. MSI-h-derived resistant clones adopted a unified transcriptional state enriched for epithelial-mesenchymal transition, cytokine signaling, and interferon responses, while ATRi-resistant models showing additional enrichment of developmental and KRAS/Notch-associated pathways. In contrast, CNH-derived resistant clones diverged by inhibitor class, with ATRi resistance preferentially enriching proliferation-associated pathways and CHK1i resistance inducing interferon signaling. Notably, THBS1, EDN1, and TENM2 were consistently upregulated across all resistant models relative to parental lines. Together, these findings demonstrate that acquired resistance to ATRi and CHK1i in EC is shaped by both lineage and inhibitor class and provide a transcriptomic framework that may inform future biomarker development and therapeutic strategies. Full article

Endometriosis (EM) is a chronic inflammatory disease characterized by the growth of endometrial-like tissue outside the uterus, yet its molecular mechanisms remain poorly understood. This study investigated the expression of mucins (MUC1, MUC2, MUC5AC, MUC6, MUC16) and their O-glycans in endometriotic lesions, given their roles in epithelial protection, adhesion, and immune modulation. Using immunohistochemistry, Western blotting, lectin profiling, histochemical staining, and transcriptomic analysis, we compared mucin levels and glycosylation patterns in eutopic and ectopic tissues from women with and without endometriosis and measured mucin-derived tumor markers in serum (CA 125/MUC16 and CA 15-3/MUC1) and peritoneal fluid (CA 125/MUC16). The results showed significant upregulation of all mucins in EM biopsies, with increased MUC1 transcript levels, while MUC6 and MUC16 protein levels did not always align with transcripts. Yet, tumor markers CA 125 and CA 15-3 showed no significant differences between groups. Looking at mucin distribution in biopsies of peritoneal (pEM), deep infiltrating and ovarian EM, MUC1 was significantly overexpressed in lesions of all EM forms, while MUC5AC was significantly elevated in pEM. Lectin analysis revealed specific glycan changes, including elevated core-1 O-glycans and α(1-2)-linked fucosylation, while sialylation remained unchanged. These findings demonstrate consistent mucin dysregulation and glycan alterations, implicating their roles in epithelial adhesion, immune evasion, and lesion persistence. Mucin biology thus emerges as a promising target for diagnostic and therapeutic strategies in endometriosis. Full article

Pigs are a major source of animal protein for humans and serve as valuable biomedical models. Compared to Western commercial pig breeds, Jinhua pigs are characterized by superior meat quality due to dynamic muscle development and fat deposition. However, studies investigating dynamic transcriptional regulation of swine meat quality traits across developmental stages remain limited. In this work, we collected longissimus dorsi muscle tissue from three Jinhua and three Landrace × Yorkshire pigs at 1, 90, and 180 days of age, respectively. We have uncovered differentially expressed genes and transcripts, alternative splicing events, and gene fusion events across development stages utilizing RNA sequencing data. CKM exhibited consistent breed-specific alternative splicing and gene fusion events across all three stages, representing a stable regulator of muscle development in Jinhua pigs. On the other hand, our findings highlight day 90 as a critical “window phase” for muscle development and meat quality differences between Jinhua and Landrace × Yorkshire pigs at this stage, exhibiting the greatest number of inter-breed differences in transcriptomic genetic regulation. Additionally, time series analysis revealed that genes with peak expression at day 90 were significantly enriched in pathways associated with muscle development and function. Finally, we identified PFKM, PRKAG3, and CKM as candidate genes with age-specific expression and post-transcriptional regulation that likely influence muscle development. This study advances understanding of transcriptional regulation in pig muscle with implications for meat quality improvement. Full article

Drought stress severely restricts plant growth and substantially reduces crop productivity. Although drought-response mechanisms have been extensively characterized within individual plant species, the conserved metabolic strategies shared across species remain insufficiently understood. To elucidate both conserved and species-specific metabolic mechanisms underlying drought adaptation, we performed an integrated transcriptomic and metabolomic analysis in rice, maize, and tomato. Profiling of 543 annotated metabolites revealed strikingly divergent baseline metabolic landscapes: tomato leaves were enriched in triglycerides and anthocyanins, whereas maize and rice accumulated higher levels of glycerophospholipids, tricin-derived flavonoids, and B vitamins. Under drought conditions, these differences were further reflected in the distinct sets of differentially accumulated metabolites (DAMs) detected in tomato (121), rice (98), and maize (94). Despite these species-specific signatures, we identified a conserved drought-responsive module consisting of five phenolamides that were consistently induced across all three species. Reconstruction of the associated regulatory network uncovered divergent enzymatic control strategies governing phenolamide biosynthesis: the drought-induced BAHD acyltransferases OsPHT4 in rice and SlPHT3 in tomato exhibited broad-spectrum catalytic activities, whereas the maize homolog ZmPHT4 fulfilled a similar biosynthetic role through constitutive, non-drought-inducible activity. Together, this study provides a comprehensive metabolic framework for plant drought response and demonstrates that extensive species-specific metabolic architectures and transcriptional regulatory divergence coexist beneath a conserved core metabolomic response, offering promising targets for the precise genetic enhancement of crop drought tolerance. Full article

Delayed harvesting of grapes can alter fruit quality and plays an important role in alleviating the problem of market saturation during peak seasons, as well as in regulating the supply period of grapes. In this study, by conducting a comparative analysis of fruit quality, metabolomics (aroma compounds) and transcriptome sequencing of ‘Shine Muscat’ grapes harvested at six different on-tree ripening stages after maturity, we found that: (1) delayed harvesting led to dramatic variation in berry color change (light green to yellow) with a significant increase in soluble solids (19.5 to 20.89 Brix); (2) A total of 25 volatile aroma compounds was identified in collected berry samples, while trans-2-hexenal and hexanal exhibited the highest concentrations in all samples, marking them as key volatile compounds in ‘Shine Muscat’ grapes. Notable variation in the concentrations of linalool, n-butanol, benzyl alcohol, phenylethanol, β-citronellol, and propionic anhydride were recorded in selected harvest periods. OAV analysis results show that linalool has the largest OAV among the detected compounds, and its OAV proportion increased from 53% to 95% during the six sampling periods of ‘Shine Muscat’; (3) Transcriptome sequencing of selected samples demonstrated a positive correlation between eight terpene-synthesis-related genes and linalool accumulation. Furthermore, genes within the MEP pathway (specifically VvTPS55, VvTPS59) and several transcription factors were associated with terpenoids metabolism. Based on soluble solids and OAV results, T18–T22 period (18–22 weeks post-flowering) can become good quality on-vine storge berries. The gene expression profile and developmental patterns of metabolites in MEP pathway may helpful in functional characterization of candidate genes related to terpenoid metabolism in future studies. Full article

WRKY transcription factors play critical roles in plant growth, development, metabolism, and stress responses. In this study, we performed the first genome-wide characterization of the WRKY gene family in Bupleurum chinense, using a T2T-level assembly of the autotetraploid genome. A total of 303 BcWRKY genes were identified and found to be unevenly distributed across four subgenomes. Phylogenetic and structural analyses revealed that segmental duplications after polyploidization drove lineage-specific expansion of the family. Meta-transcriptome analysis demonstrated that BcWRKY genes exhibited tissue-specific expression patterns and dynamic responses to stress, suggesting functional diversification. Under drought, waterlogging, methyl jasmonate, and ABA treatments, the contents of saikosaponins A and D significantly increased. This increase was accompanied by transcriptional activation of multiple BcWRKY genes. Correlation analysis between ten BcWRKYs and ten saikosaponins biosynthetic associated genes (BcBASs, BcCYPs, and BcUGTs) identified BcWRKY22, BcWRKY33, and BcWRKY46 as potential regulators of saikosaponin metabolism under stress conditions. Our study provided a comprehensive framework for understanding BcWRKY gene evolution and secondary metabolic regulation in polyploid medicinal plants. It also offered candidate genes for breeding B. chinense cultivars with high saikosaponin content. Full article

High-grade serous ovarian cancer (HGSOC) is the most prevalent and aggressive form of epithelial ovarian cancer and is characterized by high recurrence rates and poor clinical outcomes. In this study, we identify molecular signatures associated with recurrence by conducting integrative transcriptomic and proteomic analyses on paired primary and recurrent HGSOC tissues from 34 patients. RNA sequencing and proteomic profiling revealed 185 differentially expressed genes (DEGs) and 36 differentially expressed proteins (DEPs) linked to recurrence. Pathway enrichment and Ingenuity pathway analyses highlighted the involvement of immune cell trafficking, cell signaling, and MAPK pathway activation in recurrent tumors. A survival analysis identified seven DEGs that correlated significantly with recurrence-free survival; among them, IL7R, IRF8, and PTPRC were upregulated in recurrent tumors and associated with poor prognosis, and NSG1 was downregulated and linked to favorable outcomes. Immunohistochemistry validated the differential expression of these markers at the protein level. The proteomic analysis demonstrated that recurrent tumor-specific DEGs are functionally linked to MAPK signaling. Co-expression analyses revealed dynamic regulatory interactions between the DEGs and DEPs, suggesting context-dependent molecular shifts during recurrence. This integrative multi-omics approach reveals that key molecular alterations underlie HGSOC recurrence and identifies IL7R, IRF8, PTPRC, and NSG1 as potential prognostic biomarkers and therapeutic targets. Our findings provide a foundation for targeted strategies to improve outcomes for patients with recurrent HGSOC. Full article

Plant organic cation transporters (OCTs) are involved in a variety of beneficial biological processes, such as cadaverine transfer in plants and soil, and play an active role in the formation of plant stress resistance. In this study, 52 OCT family genes were identified in tomato, and comprehensive bioinformatics analyses of these numbers, such as promoter cis-acting elements, gene mapping and collinearity, protein characterization and phylogenetic analysis. By analyzing the expression of tomato OCT family genes under cold and salt stresses using transcriptome data and qRT-PCR experiments, a key gene regulating cold stress tolerance, SlOCT20, was identified. Subcellular localization experiments indicated that SlOCT20 was mainly localized in the cell membrane. When the SlOCT20 gene was silenced in tomato, the tolerance to cold stress was significantly reduced and oxidative stress was aggravated, indicating that this gene positively regulates the tolerance to cold stress in tomato. Full article

Background: Honeybees sustain vital ecological roles through foraging behavior, which provides pollination services and is likely regulated by dopamine signaling coupled to brain energy metabolism. However, the genetic and metabolic mechanisms underlying this regulation remain unclear. Methods: We treated honeybee workers with the dopamine receptor agonist bromocriptine and employed an integrative approach, combining liquid chromatography–mass spectrometry (LC–MS) metabolomics with single-nucleus RNA sequencing (snRNA-seq). Results: Metabolomics revealed increased levels of N6-carboxymethyllysine (CML) and a coordinated shift in central carbon metabolites, including higher glucose, pyruvate, and lactate within glycolysis, and ribose-5-phosphate in the pentose phosphate pathway (PPP). Integration with transcriptomics showed heterogeneous responses: glial cells exhibited higher glycolysis pathway scores and upregulated hexokinase expression compared to neurons, whereas major PPP enzymes were upregulated in both glial and neuronal subsets. Conclusions: These findings suggest that dopamine receptor activation is associated with altered whole-brain metabolic profiles and concurrent, cell-type-specific upregulation of glycolytic and PPP enzyme genes, particularly in glia. This study characterizes these neuro-metabolic associations, offering insights into the cellular and metabolic basis of foraging behavior in worker bees. Full article