Search Results (21,774)

Sugar transporters play a pivotal role in photoassimilate partitioning and biomass accumulation in plants. However, how whole-genome duplication (WGD) has reshaped the evolutionary trajectory of the sugar transport system in Bambusoideae remains elusive. Here, we systematically identified and characterized the SUT (Sucrose Transporters) and MST (Monosaccharide Transporters) gene families across 14 bamboo genomes representing four major lineages: herbaceous, temperate woody, neotropical woody and paleotropical woody bamboos. Our results suggest that WGD acted as the primary driving force behind the expansion of these gene families, with woody bamboos possessing significantly higher gene counts than herbaceous bamboos. Notably, extensive gene loss was observed in hexaploid lineages, aligning with the gene dosage balance hypothesis. Phylogenetic and sequence analyses demonstrated that core genes were subjected to purifying selection. Intriguingly, 21 groups of identical protein sequences across species were identified in paleotropical woody bamboos, suggesting high sequence conservation. Transcriptomic and syntenic analyses further unveiled the mechanisms of post-polyploidization expression divergence: homeologs exhibited marked expression asymmetry across subgenomes. Distinct from the broad expression pattern in herbaceous bamboos, which rely on SUT5 and a few STP (Sugar Transporter Protein) genes, woody bamboos have achieved fine-tuned expression partitioning and tissue-specific specialization during different culm developmental stages through significantly expanded SUT and STP family members. This study reveals an evolutionary pattern characterized by “WGD-driven expansion, post-polyploid fractionation, and subgenome expression divergence.” This pattern suggests a potential link to the enhanced sugar allocation efficiency required for the explosive growth of woody bamboos, offering valuable gene resources and a foundation for future functional studies in Poaceae crops. Full article

Efficient nitrogen acquisition and utilization are essential for sustainable wheat production in contrasting management systems. However, little is known about how genotype × management interactions are associated with tissue-specific expression of nitrogen (N)-related genes in durum wheat under organic and conventional field conditions. This study evaluated the agronomic, physiological, and molecular responses of 12 durum wheat genotypes (Triticum turgidum L. subsp. durum) grown under organic and conventional management during the 2022–2023 and 2023–2024 growing seasons. Six genotypes, comprising four higher-performing and two lower-performing genotypes, were selected for molecular analysis. The expression of ten genes involved in nitrate and ammonium transport and N assimilation was analyzed using reverse transcription quantitative polymerase chain reaction (RT-qPCR) in leaf, stem, and root tissues. The mean grain yield was 4078.29 kg ha⁻¹ under organic management and 3997.35 kg ha⁻¹ under conventional management. Thus, mean grain yield was approximately 2.0% higher under organic management. Genotypic responses differed between the two systems: AYM-6 had the highest grain yield under conventional management (5201.92 kg ha⁻¹), whereas AYM-3 had the highest grain yield under organic management (5059.72 kg ha⁻¹). Among the ten genes, NRT2.1 and GS1 had higher transcript abundance under conventional management, whereas the other eight had higher transcript abundance under organic management. GS1 generally had the highest transcript abundance, while NRT1 had the lowest. Gene expression was strongly tissue-dependent, with leaves generally showing the highest transcript levels. Gene–trait analysis further revealed a positive relationship between leaf NRT2.1 expression and grain yield under conventional management (R² = 0.78, p = 0.020) and a negative relationship between root NRT1.1 expression and grain yield under organic management (R² = 0.68, p = 0.043). The results showed management- and genotype-specific agronomic responses, while selected N-related gene-expression patterns were associated with grain yield in a tissue- and management-dependent manner. These findings support the evaluation and selection of durum wheat genotypes directly within the target management system. Full article

Background: Hereditary hemorrhagic telangiectasia (HHT) is a rare autosomal dominant vascular disorder primarily caused by pathogenic variants in the ENG and ACVRL1 genes. Although genotype–phenotype correlations are well established at the population level, the degree of phenotypic similarity among relatives sharing the same variant is poorly characterized. Objective: to explore differences in expressivity and quantify the degree of phenotypic variability among individuals with HHT carrying the same pathogenic variant. Methods: We evaluated 60 patients from a reference center with recurrent ENG and ACVRL1 variants, to quantify intra-familial phenotypic heterogeneity using Shannon entropy indices, Jaccard distances, and a latent variable liability-threshold approach. Results: There was substantial phenotypic variability among individuals and families, with cutaneous telangiectasia being the most frequent manifestation. Shannon entropy and Jaccard analyses indicated broadly high variability. The shared variant accounted for only 3.3% of total variance. Age was significantly associated with disease manifestations (β = 0.027, p = 0.002; OR = 1.028, 95% CI 1.010–1.045), with each additional year increasing the odds of severe symptoms by 2.7%, particularly bleeding severity and skin telangiectasias. Conclusions: These findings suggest that the variable expressivity in HHT is predominantly driven by individual-level factors other than the specific pathogenic variant carried by each patient. Full article

Uremia is the most common pathophysiological symptom in chronic kidney disease (CKD) patients, particularly in end-stage kidney disease (ESKD) patients. Uremia can lead to several vein-specific vascular diseases, such as renal vein thrombosis (RVT), deep vein thrombosis (DVT) and dialysis access-induced venous stenosis. One of our previous studies demonstrated that uremic serum exposure induced different cellular responses in pig venous smooth muscle cells (vSMCs) compared with arterial smooth muscle cells (aSMCs). To explore the underlying mechanisms responsible for vein-specific cellular responses, bulk RNA sequencing was utilized to examine differential gene expression in porcine vSMCs after uremic serum exposure. Differentially expressed genes (DEG) analysis revealed that 408 genes were upregulated, and 387 genes were downregulated after uremic serum treatment. Gene Ontology Biological Process analysis demonstrated that uremic serum exposure led to transcriptomic downregulation of cellular energy expenditure activities, such as the Cell Cycle, and positive transcriptomic enrichment of Cellular Response to Endoplasmic Reticulum (ER) stress, unfolded protein response and hypoxia. Both Gene Set Enrichment Analysis (GSEA) and Overrepresentation Analysis (ORA) obtained similar results. ORA revealed additional signaling pathways predicted to be transcriptomically downregulated, such as the Hippo signaling pathway and Focal Adhesion and Cytoskeletal Structure Regulating pathways. ORA also predicted several positively enriched signaling pathways related to cellular stress responses and waste disposal. To precisely identify vSMC-specific alterations, an interaction-based KEGG GSEA was performed. The analysis revealed several significantly different responses between vSMCs and aSMCs, such as Protein Processing in the Endoplasmic Reticulum, Integrated Stress Response signaling pathway and Mitophagy, which showed more positive responses in vSMCs, while oxidative phosphorylation showed a more positive response in aSMCs. These altered signaling pathways may be responsible for vein-specific clinical symptoms, such as venous segment stenosis in arteriovenous fistula, observed in CKD/ESKD patients. Full article

Selecting and validating appropriate reference genes is a prerequisite for accurate gene expression analysis by means of quantitative real-time PCR (qRT-PCR), particularly in plant species with limited molecular research. Elsholtzia stauntonii is an economically important ornamental, medicinal, and aromatic plant. Although it exhibits a good tolerance to cold and drought, it is notably susceptible to waterlogging stress. To date, systematic investigations into its gene expression in different tissues and under waterlogging stress have not been extensively performed. In the present study, eight candidate reference genes, including GAPDH, ACT, UBQ, UBC, TUA, TUB, EF1-α, and eIF3K, were investigated using qRT-PCR in 13 samples from two distinct groups. The expression stability of these candidate genes was comprehensively assessed using the most commonly adopted algorithms: geNorm, NormFinder, Comparative ΔCt, BestKeeper, and RefFinder. The results demonstrated that UBC and EF1-α were the most suitable reference genes for different tissue samples, whereas ACT, GAPDH, and UBQ exhibited optimal reference genes for leaves under waterlogging stress. In contrast, eIF3K and TUB were identified as the least stable reference genes in different tissue samples and waterlogged leaves, respectively. To validate the suitability of the selected reference genes, the expression patterns of phenylalanine ammonia-lyase gene 1 (ElstPAL1) were analyzed. Comprehensive consideration of reference gene performance and the validation results confirmed that GAPDH and ACT were applicable and accurate for qRT-PCR normalization for different tissues of E. stauntonii, while ACT, GAPDH, and UBQ were effective for waterlogging-stressed leaves. These findings establish a solid foundation for future gene expression studies in E. stauntonii samples from different tissues and subjected to waterlogging stress and will facilitate future molecular studies in this economically important species. Full article

Tilapia species differ markedly in salinity tolerance, providing a useful system for investigating the molecular basis of osmotic adaptation. The solute carrier family 12 (SLC12) encodes cation–chloride cotransporters that play central roles in ion homeostasis and osmoregulation. Here, we compared the SLC12 gene family among Nile tilapia (Oreochromis niloticus), Mozambique tilapia (O. mossambicus), and blue tilapia (O. aureus) using comparative genomic, phylogenetic, protein-structural, and chromosomal analyses. Separately, we re-analyzed a published long-term salinity RNA-seq dataset from GIFT Nile tilapia maintained for 3.5 months at 0, 17, or 27 ppt, focusing on SLC12 expression in the gill, intestine, and skin. All three tilapia species contained 17 SLC12 loci with identical subfamily copy numbers and broadly conserved chromosomal distributions. In the Nile tilapia transcriptomic dataset, paralogous SLC12A2, SLC12A7, and SLC12A10 copies displayed distinct tissue- and salinity-dependent expression patterns. SLC12A8 also showed salinity-responsive expression in Nile tilapia, prompting further comparative sequence and structural analysis. The three SLC12A8 orthologs were broadly similar in sequence and predicted structure, although several species-specific residue differences were observed. These findings reveal overall conservation of the SLC12 family among tilapias, identify salinity-responsive expression differences among paralogous members in Nile tilapia and interspecific sequence variation in SLC12A8, and provide candidate features for further functional investigation. Full article

Quantitative real-time PCR (qRT-PCR) is a widely used technique for quantifying gene expression. However, accurate data normalization requires stable reference genes that exhibit constant expression levels across different experimental conditions. To date, no suitable reference genes have been validated for atemoya fruits (Annona cherimola Mill × A. squamosa L.). This study aimed to evaluate the expression stability of candidate reference genes in atemoya across distinct tissues, postharvest storage stages, and various treatment conditions. To this end, we designed specific primers for six reference genes: ubiquitin carrier-like protein (UBC), actin 7 (ACT7), actin 11 (ACT11), elongation factor 1α (EF1α), 18S ribosomal RNA (18S), and β-tubulin (TUB). Total RNA was extracted from atemoya tissues (e.g., petals, young fruits, and roots), for pulp across three post-harvest time points (0, 2, and 4 days) and under different conditions: 28 °C, 15 °C, ethylene, or 1-MCP treatment. The geNorm tool was subsequently used to identify the most stable reference transcripts under each experimental condition. ACT7 was the most stable reference gene across atemoya tissues, while UBC ranked first under all postharvest conditions tested (28 °C storage, 15 °C cold storage, ethylene, and 1-MCP). Furthermore, the suitability of these reference genes under ethylene and 1-MCP treatments was validated by examining the expression patterns of AaPG and AaERF. Collectively, the combined use of ACT7, UBC, and 18S proved to be the most reliable normalization strategy across all experimental conditions. This validated multi-gene approach provides a robust foundation for future investigations into gene expression and the postharvest ripening mechanisms of atemoya. Full article

Environmental conditions have an impact on animals’ immune systems. Neutrophils, as key components of innate immunity, rapidly respond to bacterial stimuli through the activation of inflammatory and migratory pathways. This study evaluated the transcriptional and functional responses of neutrophils derived from dogs living under different housing environments following in vitro lipopolysaccharide (LPS) stimulation. Distinct transcriptional profiles were observed among groups in genes associated with leukocyte adhesion (CD11b), chemokine signaling (CXCR1, CXCR2, and CXCL8), and cytokines (TNF-α, IL-1β, and IL-6). Additional cytokine analyses confirmed neutrophil activation and revealed differences in the magnitude and duration of cytokine secretion between groups. These findings indicate that environmental background may be associated with differences in both transcriptional responsiveness and cytokine production in canine neutrophils. Dogs originating from different housing conditions exhibited distinct patterns of inflammatory activation. The combined assessment of gene expression and cytokine secretion provides valuable insight into innate immune adaptation and might represent a useful approach for monitoring immune status in dogs. Full article

Polystyrene nanoplastics (PS-NPs; nominal diameter, 100 nm; unmodified and negatively charged) and imidacloprid (IMI) are common freshwater contaminants, but little is known about their combined toxicity in benthic fish. In this study, loaches (Misgurnus anguillicaudatus) were exposed for 21 days to clean water, 100 μg/L PS-NPs, 78 μg/L IMI, or 78 μg/L IMI combined with 25, 50, or 100 μg/L PS-NPs. Each treatment contained 90 fish distributed among three replicate tanks. Survival, hepatic oxidative-stress indices, inflammatory gene expression, histopathology, and intestinal transcriptomic and metabolomic profiles were evaluated. Survival decreased across the co-exposure groups, with a significant overall difference among treatments (log-rank test, p = 0.0027). Hepatic CAT, SOD, and GSH levels decreased, whereas MDA increased, with the strongest changes observed in the higher PS-NP co-exposure groups. Pro-inflammatory genes, including IL-1β, IL-6, IL-8, and TNF-α, were upregulated, whereas IL-4 and IL-10 were downregulated. Histopathological injury of the gill, intestine, and liver was most pronounced in the NIH group. Transcriptomic analysis identified changes in pathways related to digestion, cell-cycle regulation, cholesterol metabolism, and lipid metabolism, while metabolomic analysis revealed alterations in glycerophospholipid, sphingolipid, fatty-acid, and carbohydrate metabolism. HMGCS1, CEL, CYP8B1, APOB, and APOC1 showed treatment-associated expression changes, with APOB displaying a non-linear response across the co-exposure groups. Overall, PS-NP co-exposure was associated with stronger IMI-related adverse responses under the tested conditions and substantial disruption of intestinal lipid homeostasis. Full article

Background: Lung adenocarcinoma (LUAD) is the most common subtype of non-small-cell lung cancer and is one of the leading causes of cancer-related deaths globally. Despite current developments, reliable biomarkers for effective diagnosis, prognosis, and patient stratification are still lacking. Methods: We analyzed publicly available TCGA-LUAD and GEO datasets using integrative bioinformatics approaches, including differential gene expression, weighted gene co-expression network analysis (WGCNA), survival modeling, mutation profiling, immune cell infiltration scores, machine learning, and bulk-RNA and single-cell RNA sequencing. Results: A total of 5581 deregulated genes were identified, with the turquoise module (298 genes) showing strong correlation with LUAD (Corr = −0.79, p < 2.2 × 10⁻³⁰⁸). The integration of two analyses yielded 281 overlapping genes, out of which nine candidates (ANO2, CHIAP2, CPED1, DNASE1L3, GSTM5, HTR3C, PRKCE, SLC14A1, and WNT3A) were selected via LASSO Cox regression to build a prognostic risk model. High-risk patients have significantly worse survival (log-rank p = 0.0027). CPED1 exhibited the highest mutation frequency, with 41% of TCGA-LUAD samples harboring mutations. Among all CPED1 mutation events, missense mutations were the most common (47%). GSEA and KEGG analysis revealed significant enrichment of pathways such as nucleocytoplasmic transport, oxidative phosphorylation, protein processing in the endoplasmic reticulum, ribosome, and ribosome biogenesis in high-risk patients. Immune infiltration analysis indicated differences in immune cell infiltration scores between high- and low-immune-score groups, with M1 macrophages showing strong statistical correlation with aDC, monocytes, and CD4⁺ naïve T cells. Machine learning confirmed that the combined Enet+PLS model predicted CPED1 as a core predictor, and CPED1 was successfully validated in independent GEO datasets (GSE43458 and GSE31210), showing strong diagnostic accuracy (AUCs up to 0.98). Finally, single-cell RNA sequencing revealed that CPED1 was mostly expressed in fibroblasts and myeloid cells, with CPED1 significantly downregulated in LUAD compared with normal samples. Conclusions: This study integrates multi-omics and machine learning to highlight CPED1 as a promising candidate biomarker, with potential diagnostic and prognostic relevance in LUAD. The nine-gene risk signature stratified patients by survival outcomes in the TCGA cohort. Genomic and immune analyses revealed features associated with the high-immune-score group. As the study is entirely computational and the prognostic model lacks external survival validation, these findings should be regarded as preliminary and hypothesis-generating, requiring future independent validation and functional studies to confirm the biological significance and clinical utility of CPED1 and related genes. Full article

To explore the regulatory effects and mechanisms of LED green light (peak at 520 nm) combined with different low temperatures on broccoli postharvest storage, the Brassica oleracea var. italica ‘Meiqing’ was harvested and stored under two temperatures and pretreated with supplemental LED green light. Periodic determinations were conducted on physical and chemical indexes, including appearance, texture, nutritional quality, and antioxidant capacity, along with differential gene expression analysis via transcriptome sequencing. Results showed that 0 °C storage outperformed 4 °C overall, and the 1 h green light pretreatment achieved the optimal effect. This treatment significantly delayed curd yellowing, reduced weight loss, maintained high firmness, preserved nutritional components, enhanced the activities of antioxidant enzymes and key enzymes in the AsA-GSH cycle, and alleviated membrane damage by reducing H₂O₂ and MDA levels. Transcriptome analysis revealed that green light pretreatment regulated gene expression in chlorophyll metabolism and antioxidant-related pathways. Overall, 0 °C combined with 1 h of green light pretreatment effectively prolonged the storage period of broccoli and maintained its commercial and nutritional quality, providing a novel technical strategy for postharvest broccoli preservation. Full article

Oxidative stress and chronic inflammation are major contributors to skin photoaging, highlighting the need for natural antioxidants with multifunctional bioactivities. This study developed an ultrasound-assisted extraction (UAE) strategy to recover an astaxanthin-rich extract from the underutilized freshwater macroalga Chara corallina and evaluated its antioxidant, anti-inflammatory, and anti-photoaging properties. Different solvent systems were evaluated for extraction efficiency, and astaxanthin-equivalent recovery was quantified by high-performance liquid chromatography with photodiode array detection (HPLC–PDA). Antioxidant activity was evaluated using the DPPH radical scavenging assay, whereas biological activities were assessed in human dermal fibroblasts and RAW264.7 macrophages using cell viability assays, quantitative real-time PCR, and extracellular matrix-related enzyme inhibition assays. The selected solvent system (48% ethanol in ethyl acetate) provided the highest astaxanthin-equivalent recovery (0.2598 ± 0.0086% w/w). The selected CCE exhibited DPPH radical-scavenging activity, modulated antioxidant- and inflammation-associated gene expression, increased COL1A2 mRNA expression, and inhibited collagenase, elastase, and hyaluronidase within the evaluated concentration range. HPLC–PDA analysis revealed a chromatographic component with retention-time and UV–visible spectral characteristics corresponding to those of an authentic astaxanthin reference standard; however, comprehensive structural and phytochemical characterization was not performed. Because CCE is a chemically complex extract, the observed biological responses cannot be attributed exclusively to astaxanthin. Overall, these findings provide an initial basis for further investigation of C. corallina as an underexplored freshwater source of carotenoid-containing bioactive extracts rather than establishing it as a commercially competitive source of natural astaxanthin. Full article

Intramuscular fat (IMF) deposition drives premium beef value, but phenotypic selection is costly and slow. Although genome-wide studies have linked the KIRREL3 region to meat quality, whether intronic variants directly affect carcass traits and retain predictive power across physiological stages remains unproven. We genotyped two intronic SNPs (g.29756010C>T and g.29756149C>T) in Woking cattle, a high-quality beef breed developed in Jilin Province, China (n = 473; 226 and 206 heifers at 36 and 48 months, respectively, plus an independent validation cohort of n = 41), assessed for fatty acid composition, meat quality, and multi-tissue gene expression. Both loci were polymorphic and in Hardy–Weinberg equilibrium. At 36 months, TT individuals showed higher dressing percentage, rib thickness, and meat grade than CC at both loci. By 48 months, the 63-bp locus retained broader associations with carcass traits, whereas the 203-bp locus effects weakened. In the validation group, CC animals had higher IMF and muscle KIRREL3 expression than TT, yet received lower meat grades. Five fatty acids differed significantly among genotypes after Benjamini–Hochberg correction (q < 0.05), whereas the dominant fatty acids (C16:0, C18:1n9c, C18:0, C18:2n6c) showed no proportional differences. KIRREL3 was most highly expressed in the kidney among eight tissues examined. These findings identify the 63-bp site as a candidate marker for meat quality in local Chinese cattle, with potential for marker-assisted selection pending confirmation in larger cohorts and functional studies. Full article

Salt stress is frequently encountered by plants and is a major constraint on crop production. Wheat (Triticum aestivum L.) is a staple cereal crop that is important for human health and food security. However, the response mechanisms of roots from different wheat varieties to salt stress remain unclear. In this study, we analyzed the complex response mechanisms of the salt-tolerant variety Longjian 114 (LJ114) and the salt-sensitive variety Chinese Spring (CS) to salt stress using integrated transcriptomic and metabolomic analyses. The results showed that LJ114 maintained better growth and exhibited higher antioxidant enzyme activities and greater osmotic adjustment capacity under salt stress. Differentially expressed genes in LJ114 were predominantly enriched in flavonoid biosynthesis, alpha-linolenic acid metabolism, and zeatin biosynthesis under salt stress. Metabolomic profiling identified 1366 differential metabolites, with LJ114 specifically enriched in tyrosine metabolism, tryptophan metabolism, glycerophospholipid metabolism, and fatty acid metabolism under salt stress. Integrated analyses further highlighted ABC transporters and alanine, aspartate, and glutamate metabolism as hub pathways, with notably higher GAD expression and GABA accumulation under salt stress. These findings suggest new insights into the molecular mechanisms underlying wheat salt tolerance and propose potential candidate targets for enhancing crop salinity tolerance. Full article

Background: Synthetic fructoborate (sFB) is a boron-containing compound with reported biological effects, but its influence on cardiac remodeling remains poorly characterized. Objective: To evaluate the cardiac effects of short-term sFB administration and compare cardiac and extracardiac responses when sFB was administered before or after isoproterenol-induced cardiac hypertrophy. Methods: Male BALB/c mice received sFB (17, 34, or 68 mg/kg) for 3 days to assess cardiac morphology, p38 MAPK phosphorylation, Atrial Natriuretic Peptide (ANP) and Natriuretic Peptide B (BNP) mRNA expression, and oxidative stress-related markers. In a second experiment, cardiac hypertrophy was induced with isoproterenol (50 mg/kg, intraperitoneally, for 7 days), and sFB (34 mg/kg for 3 days) was administered before or after hypertrophy induction. Cardiac and extracardiac histological, molecular, and biochemical responses were evaluated. Results: Short-term sFB administration did not produce a consistent pattern of cardiac injury. The p-p38 MAPK/p38 MAPK ratio decreased, and 17 mg/kg sFB increased plasma glutathione (GSH) levels. When administered after hypertrophy induction, sFB reduced left ventricular wall thickness, cardiomyocyte area, and collagen I and III deposition and increased ventricular lumen area. Administration before isoproterenol exposure produced a different response, with some preserved structural parameters but persistent collagen deposition and increased expression of remodeling-associated genes. Extracardiac responses were heterogeneous and tissue-dependent, with notable hepatic alterations under some conditions. Conclusions: The effects of sFB on isoproterenol-induced cardiac hypertrophy depended on the timing of administration, with more consistent attenuation of structural remodeling when administered after hypertrophy induction. Further studies are required to establish its long-term safety, pharmacokinetics, and potential therapeutic relevance. Full article