Search Results (7,241)

Background: We recently generated T cell receptor (TCR) transgenic (Tg) mice specific to cardiac myosin heavy chain-α (Myhc-α 334–352) on both myocarditis-resistant (C57BL/6) and susceptible (A/J) genetic backgrounds. We noted that the antigen-specific TCRs were expressed in CD4⁺ and CD8⁺ T cells in both strains, but their responses differed. While the T cells from naïve Tg C57BL/6 mice do not respond to Myhc-α 334–352, whereas those from A/J mice spontaneously respond to the antigen, suggesting their underlying molecular mechanisms might differ. Methods: To investigate the mechanisms of differences in the antigen-responsiveness between the Tg C57BL/6 and A/J mice, we performed bulk RNA sequencing on CD4⁺ and CD8⁺ T cells sorted by flow cytometry. Differentially expressed genes, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, gene set enrichment analysis (GSEA) of GO and KEGG, and transcription factor (TF) network analyses were performed to identify pathways and regulators of immune responses. Results: First, the principal component analysis of the transcriptomic profiles distinguished CD4⁺ from CD8⁺ T cells, which also differed between the two strains. Second, the differentially expressed cytokine and cytotoxicity genes revealed similar patterns between CD4⁺ and CD8⁺ T cells. Importantly, KEGG enrichment analysis revealed downregulated pathways in both CD4⁺ and CD8⁺ T cells that are associated with viral myocarditis, and various autoimmune conditions in C57BL/6 as compared to A/J mice. Similarly, the GSEA of GO revealed negative regulation of heart contraction and positive regulation of cardiac muscle hypertrophy processes were negatively enriched in CD4⁺ T cells of C57BL/6 mice. Finally, by generating the transcription factor (TF) networks, 22 TFs were found common to both CD4⁺ and CD8⁺ T cells, whereas eight TFs were unique to CD4⁺ or CD8⁺ T cells that have a role in T cell activation, tolerance, and T regulatory cells. Conclusions: Our data provide new insights into the transcriptomic profiles that may contribute to the genetic resistance mechanisms for developing cardiac autoimmunity. Full article

Myotonic dystrophy type 1 (DM1) is a progressive multisystemic disease caused by a CTG repeat expansion in the DMPK gene. The toxic mutant mRNA sequesters MBNL proteins, disrupting global RNA metabolism. Although alternative splicing in DM1 skeletal muscle pathology has been extensively studied, early-stage transcriptomic changes remained uncharacterized. To gain deeper and contextual insight into DM1 transcriptome, we performed the first Weighted Gene Co-expression Network Analysis (WGCNA) on skeletal muscle RNA sequencing data from the widely used DM1 mouse model HSA^LR (~250 CTG repeats). We identified 532 core genes using data from 16-week-old mice, an age before the onset of muscle weakness. Additional differential expression analysis across multiple HSA^LR datasets revealed 42 common up-regulated coding and non-coding genes. Within identified core genes, the pathway gene-pair signature analysis enabled contextual selection of functionally related genes involved in maintaining proteostasis, including endoplasmic reticulum (ER) protein processing, the ubiquitin-proteasome system (UPS), macroautophagy and mitophagy, and muscle contraction. The enrichment of ER protein processing with prevailing core genes related to ER-associated degradation suggests adaptive chaperone and UPS activation, while core genes such as Ambra1, Mfn2, and Usp30 indicate adaptations in mitochondrial quality control. Coordinated early alterations in processes maintaining protein homeostasis, critical for muscle mass and function, possibly reflect a response to cellular stress due to repeat expansion and appears before muscle weakness development. Although the study relies exclusively on transcriptomic analyses, it offers a comprehensive, hypothesis-generating perspective that pinpoints candidate pathways, preceding muscle weakness, for future mechanistic validation. Full article

Antimony (Sb), a toxic metalloid, inhibits plant growth and threatens human health. Yellow Stripe-Like (YSL) proteins play crucial roles in metal ion transport and cellular homeostasis. While the OPT gene family has been characterized in some species, its genome-wide organization and functional involvement in Sb stress response remain unexplored in Brassica juncea. Here, we identified 47 high-confidence BjOPT genes and combined transcriptomic approaches to elucidate their regulatory roles under Sb stress. Phylogenetic tree, conserved motifs, and gene structure analyses consistently distinguished the BjOPT and BjYSL subfamilies. Comparative and collinearity analyses indicated that OPT genes in Brassica species (including B. rapa, B. nigra, and B. juncea) expanded independently of whole-genome triplication events. Transcriptomic profiling revealed significant enrichment of differentially expressed genes (DEGs) related to key biological processes (oxidative and toxic stress response, metal ion transport, and auxin efflux) and pathways (glutathione metabolism, MAPK signaling, and phytohormone transduction), highlighting their roles in Sb detoxification and tolerance. Notably, three BjYSL3 (BjA10.YSL3, BjB02.YSL3, and BjB05.YSL3) genes exhibited strong up-regulation under Sb stress. Heterologous expression in yeast demonstrated that both BjA10.YSL3 and BjB02.YSL3 enhance Sb tolerance, suggesting their potential role in transporting Sb–nicotianamine (NA) or phytosiderophore (PS) complexes. These findings advance our understanding of Sb tolerance mechanisms and provide a basis for developing metal-resistant crops and phytoremediation strategies. Full article

Triterpenoid saponins are important secondary metabolites in plants. Abscisic acid (ABA), as one of the indispensable regulatory hormones in plants, promotes the accumulation of bioactive components in various plants, including triterpenoid saponins; however, its induced mechanism in Hedera helix remains unclear. In this study, the treatment of H. helix leaves with 100 μM ABA led to the identification of 7108 differentially expressed genes (DEGs) within 6 h post-treatment through transcriptomic and bioinformatic analysis. Enrichment analyses of GO terms and KEGG pathways indicated significant enrichment of DEGs in terpenoid backbone biosynthesis pathways. Analysis of DEGs revealed the NAC transcription factor, which is crucial for plant growth regulation, stress response, and secondary metabolite biosynthesis. A total of 182 HhNACs were identified at the genome-wide level, named HhNAC1 to HhNAC182 according to their chromosomal positions. Numerous ABA-responsive cis-regulatory elements (CREs) were presented at upstream promoters of HhNAC1 to HhNAC182. They demonstrated diversified tissue-specific expression profiling among stems, roots, and leaves of H. helix. Notably, HhNAC93 was predominantly expressed in H. helix leaves. Correlation analysis unveiled a markedly positive relationship among ABA-induced HhNAC93 expression, triterpenoid saponin accumulation, and the expression of essential saponin biosynthetic genes. HhNAC93 likely functions as a candidate regulator in triterpenoid saponin biosynthesis. These findings provide crucial evidence for further exploring the biological role of HhNAC transcription factor in H. helix. Full article

Phthonandria atrilineata, also known as the mulberry looper, is a major defoliator of mulberry trees. This feeding behavior directly affects the growth of the trees and reduces the quality and yield of mulberry leaves for its use in sericulture. Despite its importance the molecular basis of its resistance to insecticides remains poorly understood. Therefore, this study aimed to comprehensively characterize the cytochrome P450 monooxygenases (P450s) gene family in P. atrilineata and identify key effectors responsible for responses to diverse chemical stressors. We integrated genome-wide re-annotation, phylogenetic analysis, and comparative transcriptomics following exposure to five chemically distinct insecticides. We identified a high-confidence set of 70 P450 genes, dominated by the CYP6 and CYP4 families, whose expansion was driven by tandem gene duplication. Transcriptomic analysis revealed a powerful yet highly selective “elite-driven” response, wherein a small subset of P450s was strongly induced by multiple insecticides. Random Forest and Support Vector Machine (SVM) models converged with differential expression data to pinpoint a core trio of P450s as primary drivers of detoxification: two generalists, CYP6(09521) and CYP6(04876), responsive to all compounds, and one potent specialist, CYP4(04803), exhibiting massive induction to a specific subset of insecticides. Our findings uncover a complex, energy-efficient metabolic strategy in P. atrilineata and identify pivotal P450 genes for broad-spectrum detoxification. These genes represent high-priority targets for developing molecular diagnostic tools for resistance monitoring and informing scientifically guided insecticide rotation strategies. Full article

Lamiophlomis rotata (Benth.) Kudo is a typical alpine medicinal plant. However, the mechanism underlying its adaptation to high altitudes remains incompletely understood. In this study, we integrated transcriptome and metabolome analyses. Specifically, we used third-generation sequencing for building a reference transcriptome and second-generation sequencing for differential gene expression analysis. Our findings revealed that the activation of the hydrogen sulfide signaling pathway and the reprogramming of amino acid metabolism are probable adaptation mechanisms. Different from previous reports, the hydrogen sulfide signaling may regulate the activity of cellulose synthase in addition to enhancement of antioxidant capacity and accumulation of osmolytes. By altering the agronomic traits of plants in a cell wall remodeling-dependent manner, it enables L. rotata to adapt to alpine stress. The accumulated amino acids not only store energy-efficient organic nitrogen as precursors for the synthesis of secondary metabolites but also act as signaling molecules to activate defense responses. Additionally, we propose a potential link between the hydrogen sulfide signaling pathway and amino acid metabolism. Overall, this study systematically explores the adaptation mechanism of L. rotata to high-altitude environments, offering a novel perspective for understanding the growth, development, stress responses, and secondary metabolic processes of alpine plants. Full article

Soil salinity poses a critical threat to global agricultural productivity, exacerbating food security challenges in arid and semi-arid regions. This review synthesizes current knowledge on the physiological and biochemical impacts of salinity stress in plants, with a focus on the role of gibberellic acid (GA₃) in mitigating these effects. Salinity disrupts ion homeostasis, induces osmotic stress, and generates reactive oxygen species (ROS), leading to reduced chlorophyll content, impaired photosynthesis, and stunted growth across all developmental stages, i.e., from seed germination to flowering. Excess sodium (Na⁺) and chloride (Cl⁻) accumulation disrupts nutrient uptake, destabilizes membranes, and inhibits enzymes critical for carbon fixation, such as Rubisco. GA₃ emerges as a key regulator of salinity resilience, enhancing stress tolerance through various mechanisms like scavenging ROS, stabilizing photosynthetic machinery, modulating stomatal conductance, and promoting osmotic adjustment via osmolyte accumulation (e.g., proline). Plant hormone’s interaction with DELLA proteins and cross-talk with abscisic acid, ethylene, and calcium signaling pathways further fine-tune stress responses. However, gaps persist in understanding GA₃-mediated floral induction under salinity and its precise role in restoring photosynthetic efficiency. While exogenous GA₃ application improves growth parameters, its efficacy depends on the concentration- and species-dependent, with lower doses often proving beneficial and optimum doses potentially inhibitory. Field validation of lab-based findings is critical, given variations in soil chemistry and irrigation practices. Future research must integrate biotechnological tools (CRISPR, transcriptomics) to unravel GA₃ signaling networks, optimize delivery methods, and develop climate-resilient crops. This review underscores the urgency of interdisciplinary approaches to harness GA₃’s potential in sustainable salinity management, ensuring food security and safety in the rapidly salinizing world. Full article

Improving plant water use efficiency (WUE) and drought tolerance by modulating stomatal activity constitutes a promising strategy for mitigating the impacts of water scarcity. SnRK2, a key component of the abscisic acid (ABA) signaling pathway, plays a critical role in modulating stomatal behavior under abiotic stress. However, the functional role of SnRK2 in regulating stomatal movement to enhance WUE and drought tolerance in Populus euphratica remains to be characterized. In this study, 11 PeSnRK2 genes were identified in the P. euphratica genome, each comprising 9–14 exons and exhibiting an uneven distribution across seven chromosomes. Subcellular localization predictions indicated that these proteins are predominantly localized in the Cytoplasm and Cytoskeleton. Phylogenetic analysis grouped the PeSnRK2 genes into three distinct subfamilies, and conserved gene structures were observed within each clade. Analysis of cis-acting regulatory elements suggested that PeSnRK2 genes were involved in hormonal signaling and stress response pathways. Further transcriptomic data also indicated substantial alterations in PeSnRK2 expression due to polyethylene glycol (PEG) and abscisic acid (ABA) treatment. Finally, qRT-PCR and subcellular localization showed that PeSnRK2.6 is highly induced by ABA and functions in both nucleus and cytoplasm. This first characterization in a desert woody species bridged gaps in SnRK2 evolution and function. Full article

Key pigments and genes associated with peel color variation between Shiranui Mandarin and its Citrine Mutant were investigated. Combining liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis detected carotenoids in the peel of Shiranui mandarin and its mutant, Citrine Shiranui. Transcriptomic analysis revealed genes enriched in the carotenoid biosynthesis and chlorophyll degradation pathways. Weighted Gene Coexpression Network Analysis (WGCNA) predicted potential regulatory transcription factors. Dual-Luciferase Reporter Assays (LUC) demonstrated the regulatory relationships between the predicted transcription factors and key functional genes involved in carotenoid biosynthesis and chlorophyll degradation. During fruit ripening, the accumulation of β-cryptoxanthin was significantly lower in Citrine Shiranui. In fully ripened fruit, β-cryptoxanthin accounted for 43.62% of the peel pigments in Shiranui, compared to only 8.21% in Citrine Shiranui. Additionally, while chlorophyll degradation occurred during ripening in both varieties, Citrine Shiranui retained higher chlorophyll level. Notably, the expression patterns of CitBCH1 and CitNCY1 were associated with reduced β-cryptoxanthin synthesis and delayed chlorophyll degradation in Citrine Shiranui. LUC further demonstrated that CitBCH1 and CitNCY1 were positively regulated by an ethylene-responsive transcription factor (CitERF5) and an ABA-responsive element-binding factor (CitABF2), respectively. In summary, the citrine/yellow peel color of the Citrine Shiranui mutant primarily resulted from reduced β-cryptoxanthin accumulation due to down-regulation of CitBCH1, while the retention of chlorophyll, linked to lower CitNCY1 expression, might also contribute modestly to the phenotype. Full article

Tomato fruit malformation causes substantial yield and economic losses, but its molecular mechanisms are not well understood. This study compared floral traits of WT ‘QT57’ and malformed-fruit mutant ‘QT2’, integrated transcriptomic data, and qRT-PCR analysis to screen key candidate genes, and analyzed the pectinase gene family. The results found the ‘QT2’ mutant differed from WT ‘QT57’ in flower and fruit development. Expression analysis of CLAVATA-WUSCHEL pathway genes preliminarily validated the compensatory mechanism of SlCRCa and SlCRCb in ‘QT2’ malformed fruit. Six pectinase genes were identified as key candidates via RNA-seq and qRT-PCR analysis. Transcriptomic and qRT-PCR analyses of the pectinase gene family revealed their potential role in regulating tomato fruit malformation. Family analysis showed 34 pectinase genes distributed unevenly across 12 chromosomes. Subcellular localization confirmed SlPL7 in the nucleus and SlPME9 in the cell membrane/endoplasmic reticulum. The PL and PME genes were evolutionarily close, suggesting a potential functional overlap. Gibberellin-responsive elements were found in most pectinase genes. Pectinase genes may regulate tomato fruit malformation through the gibberellin-WUS pathway, carbohydrate metabolism, or cell wall metabolic disorder. This pathway provides new targets gene for the precise regulation of fruit malformation and offers significant reference value for practical production. Full article

Microplastics are widely distributed, but their potential impact on crops cannot be ig-nored. Most current studies focus on common crops such as rice and buckwheat and are mostly at the macro level. In this study, we explored for the first time the changes in agro-nomic traits of Pleurotus pulmonarius by PE-MPs with different concentrations and particle sizes and applied confocal scanning microscopy (CLSM) to observe the uptake of PE-MPs by P. pulmonarius hyphae and combined it with transcriptomics to reveal the stress mech-anism of PE-MPs at the molecular level. Results indicate that among the small-particle groups, only the A5 and A20 groups exhibited significantly lower fresh weight than the CK group. The A5 group was 33.83% lower than the control, while the A20 group was 63.21% lower than CK (p < 0.05). Both the A5 and A20 groups showed significantly lower dry weight than the CK group (p < 0.05). Cap thickness was only greater in the B5 and B10 groups, exceeding the control by 1.46 mm and 1.58 mm, respectively. Cap length was longer only in the A10 group, increasing by 7.85% compared to the control (p < 0.05). Cap width in the A5 and A20 groups was 25.44% and 6.65% lower than the control, respec-tively (p < 0.05). Transcriptomics showed that as the concentration of PE-MPs increased, P. pulmonarius responded to PE-MPs stress by up-regulating the expression of cell membrane composition and metal–ion binding-related genes, while as the particle size increased, P. pulmonarius resisted the toxic effects by up-regulating the coming carbon metabolism and amino acid metabolism. Compared with the CK group, 1706, 1378, and 792 DEGs were identified in the A5, B5, and B10 groups, respectively. A total of 1610 DEGs were identified between the A5 and B5 groups. Additionally, 295 DEGs were identified between the A5 and B10 groups, while 1424 DEGs were identified between the B5 and B10 groups. This study reveals the effects of PE-MPs on the agronomic traits of P. pulmonarius and their re-sponse mechanisms, further indicating their potential risk to edible fungi. Full article

Sweetpotato (Ipomoea batatas L. Lam) production is threatened by complex viral diseases, notably sweet potato virus disease (SPVD) worldwide, which results from co-infection by sweet potato feathery mottle virus (SPFMV) and sweet potato chlorotic stunt virus (SPCSV). This study provides virus-specific transcriptomic insights into the immune responses of three sweetpotato cultivars, ‘Beauregard’, ‘Tanzania’, and ‘New Kawogo’, to SPFMV, SPCSV, and SPVD. Using RNA-seq profiling across three timepoints post-infection at 3, 6, and 12 weeks, we identified distinct virus- and genotype-specific gene expression responses. ‘New Kawogo’ activated early and sustained immune pathways involving redox regulation, transcriptional control, and hormonal signaling in response to both SPCSV and SPFMV, while showing minimal transcriptional disruption under SPVD, reflecting robust tolerance. ‘Beauregard’ exhibited early suppression of immune and metabolic genes, with delayed and disorganized recovery efforts, particularly under SPVD. Defense-related pathways including NBS-LRR signaling, RNA silencing, and hormonal regulation were consistently upregulated in ‘New Kawogo’ and to a lesser extent in ‘Tanzania’, but remained inactive in ‘Beauregard’. This study highlights candidate resistance and susceptibility genes for each virus, providing a molecular basis for developing virus-resilient sweetpotato cultivars through functional genomics and marker-assisted breeding. These findings elucidate the molecular basis of virus resistance in sweetpotato and identify candidate genes for marker-assisted breeding, despite limitations arising from the use of a diploid reference genome and discrete sampling intervals. Full article

Background: Reproductive efficiency is a significant hurdle to the sustainability of the beef cattle industry. Method: This study employed transcriptomic profiling to investigate endometrial gene expression differences in heifers with divergent fertility outcomes. Caruncular endometrial samples from fertile (n = 7) and subfertile (n = 5) heifers were subjected to RNA-Seq analysis, yielding 894 differentially expressed genes (DEGs) (p ≤ 0.05 and |log2FC| ≥ 0.5). Results: The MAPK (Mitogen-activated protein kinase) and Rap1 (Ras-associated protein 1) signaling pathways and immune response regulation were identified among the over-represented pathways underlying the DEGs. Transcriptional regulators, such as DUSP2, DUSP10, and MAPK13, were downregulated in subfertile heifers, suggesting disrupted signal transduction and immune function. Gene co-expression network analysis showed network rewiring and increased connectivity of genes related to cilium organization, motility, and microtubule-based processes in the subfertile group. Over-represented hub genes were enriched in the subfertile endometrium, including DNAH2, DNAI2, DNAAF4, CCDC65, and the transcription factor FOXJ1. Our results suggest that impaired ciliary function and disrupted MAPK and immune signaling could potentially contribute to subfertility. Conclusions: This study highlights novel molecular signatures in the uterine endometrium that may serve as predictive markers of fertility potential in beef heifers, providing a foundation for targeted strategies to improve reproductive performance in cattle. Full article

Human immunodeficiency virus (HIV) remains a global public health challenge. Antiretroviral therapy (ART) improves outcomes by suppressing viral replication and enabling immune recovery, yet the early molecular mechanisms of immune-related transcriptional change after ART remain insufficiently characterized. We enrolled eight ART-naïve male patients with HIV aged 18–35. Peripheral blood mononuclear cells (PBMCs) were collected before and after 24 weeks of combination ART (TDF, 3TC, DTG) and underwent bulk RNA-seq (Illumina HiSeq 1500, Illumina, Inc., San Diego, CA, USA). Differential expression was assessed with DESeq2 (paired design); gene set enrichment analysis (GSEA), principal component analysis (PCA), hierarchical clustering, and protein–protein interaction (PPI) networks (STRING/NetworkX) explored functional patterns and transcriptomic shifts. We identified 87 differentially expressed genes, including 67 downregulated interferon-stimulated genes (e.g., IFI44L, ISG15, STAT1) and 20 upregulated transcripts, mostly pseudogenes related to ribosomal proteins. Functional enrichment revealed suppression of type I interferon and other antiviral signaling pathways. PCA and hierarchical clustering indicated a post-ART transcriptional shift. These findings suggest that early immune recovery following ART involves downregulation of chronic interferon-driven activation. This observation may correspond to partial restoration of T-cell functional capacity, reduced immune exhaustion, and a rebalanced antiviral immune environment. Full article

Background: Bletilla striata is a medicinal orchid, whose bioactive constituent militarine has therapeutic interest but limited natural availability. Suspension culture coupled with transcriptomics offers a scalable production route and a means to uncover biosynthetic regulators. Methods: Four B. striata landraces were evaluated. Single-factor experiments and response surface methodology optimized sucrose, NH₄NO₃, and agitation to maximize biomass and militarine yield. Militarine and four related metabolites were quantified by HPLC-UV. For transcriptomics, RNA from high- and low-producing landraces was sequenced on Illumina HiSeq, assembled de novo, and analyzed with RSEM (FPKM) and DESeq2 to identify DEGs. Results: The landrace SMPF-NL achieved the highest militarine yield (33.06 mg/g) under optimized conditions (sucrose, 35 g/L; NH₄NO₃, 625 mg/L; agitation, 135 rpm; and half-strength MS medium with 1.0 mg/L of 6-BA, 3.0 mg/L of 2,4-D, and 0.5 mg/L of NAA). Transcriptomic profiling highlighted candidate biosynthetic and regulatory genes, including SuSy2, SUS, ALDO, AOC3, Comt, GOT2, MAOB, BGLU20, and BGLU22. Conclusions: We present an optimized suspension culture system and transcriptomic leads that lay the groundwork for the functional validation and scale-up of controlled militarine production. Full article