Search Results (9,790)

2,4-Dichlorophenoxyacetic acid (2,4-D) is a vital exogenous auxin for the induction and proliferation of litchi embryogenic callus. At present, its molecular regulation mechanism remains unclear. In this study, transcriptome sequencing samples were selected based on different cell growth phenotypes observed in ‘Feizixiao’ litchi embryogenic callus cultured in liquid medium with or without 2,4-D. By integrating transcriptome profiling with weighted gene co-expression network analysis (WGCNA), we identified key genes and signaling pathways dynamically responsive to 2,4-D concentration changes. We identified 558 commonly differentially expressed genes (DEGs), of which 117 were up-regulated and 387 were down-regulated; functional enrichment analysis revealed significant enrichment in the “plant hormone signal transduction” and “phenylpropanoid biosynthesis” pathways. In the former pathway, genes such as AUX28, GH3.17, GH3.6, and ARR5 were up-regulated; in the latter, by comparison, β-glucosidase 47 and Peroxidase 61 exhibited increased expression levels induced by 2,4-D. Furthermore, among these DEGs, 57 transcription factors belonged to 24 families. Notably, VRN1, FEZ, and DOF5.4 were significantly and rapidly induced by 2,4-D. WGCNA results demonstrated a significant positive correlation between the yellow module and 2,4-D treatment. Small heat shock protein (sHSP) genes constituted the core hub genes in the yellow module. Through Venn analysis of DEGs and key modules, 38 cross-genes were identified, of which non-specific lipid-transfer protein-like genes (nsLTP) were found to be specifically up-regulated without 2,4-D. The transcription factors and genes identified work in synergy to ensure the formation and sustained proliferation of embryogenic callus by precisely regulating the dynamic balance of auxin and cytokinin within cells and maintaining the stability of cell structure. Our findings provide a crucial theoretical foundation for understanding the molecular mechanism of 2,4-D in regulating litchi embryogenic callus proliferation. Full article

Fetal skeletal muscle development involves coordinated interactions among myogenic, stromal, vascular, and immune compartments, yet the cellular and molecular programs guiding tissue maturation remain incompletely understood. To address this, we generated a high-resolution single-cell atlas of fetal female goat skeletal muscle and performed trajectory analysis, transcription factor activity profiling, and intercellular communication mapping. Unsupervised clustering identified RUNX2 mesenchymal progenitors, fibro-adipogenic progenitors (FAPs), myofibroblasts, endothelial cells, macrophages, differentiating myocytes, and mature skeletal muscle fibers, revealing a heterogeneous ecosystem in which stromal populations support myogenic progression and vascular and immune cells contribute to tissue organization. Pseudotime analysis traced a maturation continuum from differentiation-competent myocytes to contractile fibers, marked by sequential activation of extracellular matrix remodeling, cytoskeletal stabilization, and sarcomere assembly. KEGG and GO enrichment highlighted stage-specific engagement of ErbB, Hedgehog, and Hippo signaling, as well as cell cycle and ubiquitin-mediated proteolysis pathways, linking proliferation, differentiation, and structural maturation. Transcription factor profiling revealed early-stage proliferative and morphogenetically permissive states driven by E2F4/5, HMGA2, and HAND2, transitioning to late-stage differentiation, ECM remodeling, and tissue stabilization orchestrated by CEBPB, CREB3L1, ELK1, and E2F2. Cell–cell communication analysis showed a developmental redistribution of signaling authority, from ECM-driven, progenitor-centered networks to modular, structurally stabilized interactions. These findings define the cellular, transcriptional, and signaling framework orchestrating fetal skeletal muscle maturation. Full article

Stress has been prevalent and has become an epidemic health burden, loaded with chronic disorders. The stress response is an adaptive mechanism that prepares an individual to respond to threats or other stressors in a fight-or-flight situation. The stress response involves the induction of neurological and hormonal networks and is usually resolved when stress subsides; however, persistent stress leads to permanent and detrimental impacts on health. With the rise of advanced single-cell analysis technologies, a wave of basic and translational research aimed at elucidating stress has shed light on the underlying mechanisms. Among 80 studies in this review, stressors are classified into acute/chronic physical, physiological, and psychological groups, whereas some studies have more than one stress source. Single-cell RNA-seq was the dominant technology utilized in these studies. This advanced technique systematically reveals cellular heterogeneity in gene expression patterns and the differential transcriptomic landscape of stress response in a wide array of tissues and organ systems, e.g., the nervous system, the endocrine system, the immune system, and others. Bioinformatics identified a single-cell atlas of stress-specific cell subtypes, cell-to-cell interactions, and enriched pathways, showing promise for stress syndrome biomarkers, attenuation, and targeted therapy. The limits of these stress studies were mainly focused on transcriptomics, so future studies using multi-omics approaches across multiple organ systems will yield insights into stress disorders and novel therapeutic strategies. Full article

The papaya aril is a specialized seed appendage that has been reported to contain germination-inhibiting substances and usually requires removal before seed germination, thereby limiting breeding efficiency. However, the cellular origin and candidate molecular regulators of papaya aril development remain poorly understood. To investigate the early developmental process and candidate regulatory genes of the papaya aril, we combined histological analysis, bulk RNA-seq, and single-cell RNA-seq. Histological observations suggested that aril differentiation begins around 10 days after pollination (DAP) in the funiculus region. Based on this initiation stage, bulk RNA-seq profiling of seeds at 5, 10, and 15 DAP identified genes with initiation-stage-specific expression and prioritized candidate genes potentially related to seed appendage development, including CpRING-like, CpMBR2, and CpNDR8. Single-cell RNA-seq of seeds at 10 and 15 DAP annotated a putative aril cell population and reconstructed its developmental trajectory, revealing five trajectory-associated genes: CpATJ3, CpDYL1, CpGRP-like, CpHIRD11, and CpERD15. Integrative analysis of bulk and single-cell transcriptomic datasets further identified three candidate genes potentially involved in aril development: CpFER3, CpUVI4, and CpCEP1. These findings support the funiculus region as the likely anatomical origin of the papaya aril and provide candidate genes for future functional validation. Full article

Rheumatoid arthritis (RA) is an autoimmune disorder characterized by synovial inflammation and progressive joint destruction. There is no cure, and patient responses to current therapies vary, reflecting underlying pathogenic heterogeneity. Leveraging single-cell RNA sequencing (scRNA-seq) of RA synovium, we identified a PLAUR/uPAR-high myeloid subset that co-expresses pathogenic mediators, including IL1B and CXCL8. To target these cells, we developed anti-uPAR antibody–drug conjugates (ADCs) and evaluated various payloads in vitro and in vivo. ADCs bearing BCL-2 family inhibitors selectively induced apoptosis in proinflammatory human monocytes and macrophages with elevated uPAR, while sparing unstimulated monocytes with low basal uPAR in vitro. The treatment also reduced CXCL8 secretion. Given that murine myeloid cells exhibited lower uPAR expression and reduced sensitivity to BCL-2 family inhibitors, we used a monomethyl auristatin F (MMAF) payload to demonstrate in vivo proof-of-concept. In an air-pouch model, the anti-uPAR–MMAF conjugate reduced uPAR^highCD11b⁺F4/80⁺ macrophages by 39% compared with the isotype control. Together, our study underscores the potential of ADCs to eliminate disease-relevant cell types with inducible cell surface markers. This work opens new avenues for exploring cytotoxic ADCs as targeted therapies for autoimmune and inflammatory diseases. Full article

Potato early blight (EB), caused by Alternaria, is an economically devastating fungal disease affecting global potato production. Using a hybrid population derived from distantly related varieties, we combined resistance evaluation, histological analysis, Bulked Segregant Analysis sequencing, RNA sequencing and molecular dynamics simulation, which successfully identified key candidate resistance genes. Genetic mapping localized three major resistance-associated regions on chromosome 8 spanning positions 25.07–29.20 Mb, 38.05–38.80 Mb, and 39.40–40.78 Mb. Through candidate gene analysis, we identified CND41, encoding an aspartic protease, as the prime candidate. This gene exhibited significantly higher basal expression levels and stronger pathogen-induced upregulation in resistant genotypes. Molecular dynamics simulations further identified six crucial non-synonymous mutations in the TAXI-N domain that likely contribute to enhanced resistance by destabilizing the susceptibility-associated protein conformation. Transient overexpression of CND41 provided functional evidence supporting its likely involvement in early blight resistance (EBR). These findings contribute valuable genetic resources and a strong candidate gene for molecular breeding toward EBR potato varieties. Full article

Aflatoxin B1 (AFB1) is a prevalent and highly toxic mycotoxin in the food and feed chain and can directly injure the intestinal epithelium. Yet, its upstream determinants linking epithelial stress to cytotoxicity remain insufficiently defined. Here, we used porcine intestinal epithelial IPEC-J2 cells to characterize AFB1-induced cytotoxic and transcriptomic responses and to determine the role of the tight-junction scaffold, Cingulin-like 1 (CGNL1), a candidate gene identified through genome-scale CRISPR knockout library screening. The results showed that AFB1 exposure reduced cell viability in a dose-dependent manner and induced oxidative stress. RNA-seq profiling analysis revealed broad transcriptional remodeling, with activation of inflammatory pathways (including NF-κB and JAK–STAT signaling). Based on our constructed CGNL1-knockout IPEC-J2 cell line (CGNL1-KO IPEC-J2) using CRISPR/Cas9, it was found that CGNL1 deficiency markedly alleviated AFB1-induced cytotoxicity and oxidative stress. Comparative transcriptomics analysis showed that CGNL1 knockout attenuated AFB1-triggered aberrant expression of some CGNL1-dependent AFB1-responsive genes related to immune response under AFB1 challenge. Together, these findings identify CGNL1 as a potential modulator of epithelial susceptibility to AFB1 and support its involvement in the regulation of toxin-induced oxidative response. Full article

Background/Objectives: Src homology 2 domain-containing protein tyrosine phosphatase 1 (SHP-1), also known as protein tyrosine phosphatase non-receptor type 6, functions as a tumor suppressor in breast, hepatocellular, and prostate cancers and an oncogene in glioblastoma and cervical cancer. A previous analysis of The Cancer Genome Atlas (TCGA) dataset revealed that lower SHP-1 transcript levels in bladder tumors were associated with poorer overall survival. Methods: This study aimed to evaluate the role of SHP-1 in bladder cancer and to assess the functional impact of its forced expression and knockdown in bladder carcinoma cell lines. SHP-1 expression was assessed in 19 bladder cancer cell lines and 26 bladder tissues. Lentiviral transduction was used to knock down or overexpress SHP-1 in four cell lines, followed by Western blot analysis of SHP-1 and pAkt/Akt protein expression. Results: SHP-1 protein levels were significantly lower in highly invasive cell lines (p < 0.001) and muscle-invasive tumors (p < 0.05). Functional studies demonstrated that SHP-1 modulation influenced the epithelial–mesenchymal transition (EMT) phenotype. SHP-1 expression was positively correlated with E-cadherin expression (p < 0.001) and negatively correlated with N-cadherin (p < 0.01) and Vimentin (p < 0.05) expression. Alteration of SHP-1 expression in bladder cancer cell lines affected proliferation, invasion, and migration (p < 0.05). RNA-seq analysis of the transduced cell lines revealed enrichment of gene sets related to EMT and signaling pathways involving MYC, PI3K, Akt, and mTOR. Furthermore, SHP-1 alteration impacted pAkt/Akt ratios (p < 0.05). Conclusions: Collectively, lower SHP-1 protein expression correlated with more aggressive phenotypes in bladder cancer cell lines and bladder tumors. In our limited dataset, reduced SHP-1 expression correlated with muscle-invasive disease, suggesting a potential link to more advanced tumor biology, consistent with TCGA associating reduced SHP-1 transcript expression to poorer survival rates. Our data provide preliminary functional evidence that SHP-1 may modulate Akt signaling in bladder cancer. Together, these results support further investigation of SHP-1 as a possible tumor suppressor, candidate prognostic biomarker, and potential therapeutic target in bladder cancer. Full article

Agricultural pests can rapidly adapt to chemical pressures, and expression-based surveys of chemosensory genes may not fully capture the associated genomic variation. We hypothesized that the molecular profiles of chemosensory and detoxification genes in the mulberry thrips Pseudodendrothrips mori Niwa (Thysanoptera: Thripidae) are associated with local genomic variability and methylation context alongside transcript abundance. To explore this, we integrated PacBio HiFi-derived single-nucleotide polymorphisms (SNPs), structural variants (SVs), DNA methylation, and RNA-seq data on a chromosome-level reference genome. We analyzed 179 focal genes from six families, applying a consensus prioritization framework—based on weighted percentiles of feature values, principal component distances, and anomaly-detection scores—to rank the candidates. The integrated priority score correlated positively with SNP (r = 0.603) and SV burden (r = 0.632) and negatively with local methylation (r = −0.524), whereas its correlation with expression was weaker (r = 0.427). Three OBPs—PSMOgene01223, PSMOgene012530, and PSMOgene012982—emerged among the highest-priority candidates, exhibiting favorable in silico docking scores (−5.038 to −6.792 kcal/mol) with (Z)-octadec-11-enyl acetate and a long-chain oxygenated acetate. These findings indicate potential linkages between multi-omics plasticity and chemosensory gene variation. Furthermore, these computationally prioritized OBPs suggest potential targets for exploring semiochemical-based management tools. Full article

Background/Objectives: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. Emerging evidence highlights the role of the gut microbiota in the development and progression of CRC. Microbial dysbiosis is hypothesized to contribute to chronic inflammation through a variety of mechanisms, such as the production of free radicals, which induce mutagenesis and immune dysregulation in the host, ultimately leading to diseases such as cancer. Methods: Tumor tissue samples or healthy mucosa tissue were collected for bacterial DNA extraction. The V3–V4 region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Bioinformatics analysis was performed with QIIME2, including quality control, DADA2 denoising, alpha and beta diversity calculation, and taxonomic classification using the SILVA database. Results: Differences in microbial composition were observed between groups. The healthy controls exhibited high relative abundances of beneficial genera such as Faecalibacterium, Bacteroides, and Asteroleplasma, whereas the patients with CRC showed enrichment of atypical genera including Novosphingobium, Bradyrhizobium, and Undibacterium. Alpha diversity was lower in the CRC group, and clear clustering by group was observed in the beta diversity analysis. LEfSe analysis identified potential bacterial biomarkers associated with CRC at both the species and genus levels. Conclusions: The findings of this study support the hypothesis that colorectal cancer is associated with distinct alterations in gut microbiota composition, such as an increase in the Novosphingobium genus and a decrease in the Bacteroides genus. An exploratory description of these microbial profiles may aid in the development of microbiome-based diagnostic and therapeutic strategies and contribute to current knowledge of the role of the gut microbiota in CRC in southern Peru. Full article

Background/Objectives: Cervical cancer, primarily driven by persistent high-risk HPV infection, remains a major global health issue. Xiao-ai-fei honey ointment, a traditional Uyghur multi-ingredient preparation, has shown clinical promise in cancer treatment, but its mechanisms against cervical cancer are not fully understood. This study aimed to investigate the potential molecular mechanisms of ethanolic extract of Xiao-ai-fei honey ointment (XAFHO) in cervical cancer using network pharmacology, single-cell RNA sequencing, and experimental validation. Methods: Differentially expressed genes (DEGs) in cervical cancer were identified from TCGA database. Active components and corresponding targets of XAFHO were retrieved from the TCMSP database, and disease targets were obtained from GeneCard, OMIM, and the TTD. Intersection targets were subjected to multivariate Cox and LASSO regression to construct a prognostic model. Immune infiltration, TMB, and MSI were compared between risk groups. Single-cell RNA-seq data were analyzed to determine cellular origins and inter-cellular communication. In vitro assays were performed on HeLa and SiHa cells to assess the anti-cancer activity of XAFHO. Molecular docking evaluated binding affinities between active compounds and core targets. The expression and functional roles of FASN and SPP1 were further validated by RT-qPCR, Western blotting, and siRNA transfection. Results: Sixty-three potential XAFHO targets were identified, and an 11-gene prognostic model was established, effectively stratifying patients into high- and low-risk groups with significantly different overall survival (AUC > 0.7). The high-risk group exhibited an immunosuppressive microenvironment and higher TMB. Single-cell analysis revealed that FASN and ACACA were predominantly expressed in tumor cells, while SPP1 was enriched in macrophages/monocytes. Tumor cells communicated with immune cells via the TGFB1–TGFβR1/R2 axis, promoting immune evasion. In vitro, XAFHO significantly inhibited proliferation, colony formation, migration, and invasion of cervical cancer cells. Molecular docking confirmed the strong binding of quercetin, kaempferol, and isorhamnetin to FASN and SPP1 (binding energy < –6.0 kcal/mol). Functional validation indicated that upregulated FASN and SPP1 contribute to malignant behaviors in cervical cancer cells. Conclusions: This study integrates network pharmacology with single-cell and experimental approaches to demonstrate that XAFHO exerts multi-target and multi-cell anti-cervical cancer effects, potentially by modulating lipid metabolism and immune-related pathways via FASN and SPP1. These findings provide a scientific basis for the therapeutic application of XAFHO in cervical cancer. Full article

Starch synthesis is critical for crop yield and quality and is regulated and coordinated by a series of key enzymes encoded by starch synthesis-related genes (SSRGs). Although this process is well characterized in many crops, the genomic location and expression patterns of SSRGs in wheat remain unclear. Here, we performed a genome-wide analysis and identified 78 SSRGs in wheat, classified into the AGPase, SSS, GBSS, SBE, and DBE subfamilies. SSRGs within each subfamily showed conserved motifs and domain organization. RNA-seq analysis indicated that most SSRGs are expressed during early grain development. We further examined genetic variation in SSRGs across wheat and its progenitors using re-sequencing data. Diploid wheat showed greater genetic differentiation and diversity than tetraploid and hexaploid wheat. Five SSRGs exhibited significant haplotype differences between emmer wheat and common wheat; emmer wheat displayed diverse haplotypes, whereas common wheat showed a single dominant haplotype. Finally, starch characteristics differed between emmer wheat and common wheat in amylose content and thermodynamic properties, while viscosity, crystal structure, and morphology were largely similar. Overall, this study systematically characterizes SSRGs in wheat and provides insights for improving starch quality. Full article

This study employed a 2 × 2 factorial design to investigate the transcriptomic responses of common carp intestine under the single and combined stress of high temperature and zinc. Results from Illumina RNA-seq, WGCNA, and qPCR showed high-quality sequencing data with good reproducibility. High temperature was the core driver of global transcriptomic reprogramming, inducing numerous DEGs via activating metabolic and stress signaling pathways. Zinc alleviated heat stress by reducing DEGs by 43.2% and activating DNA repair and cell cycle pathways. WGCNA identified core modules for heat response and zinc mitigation, revealing “emergency defense” and “repair adaptation” strategies. This study enriches the teleost stress adaptation theory and provides a scientific basis for healthy carp aquaculture. Full article

The objective of this study was to investigate the effects of supplemental starter feeding on the development of the ruminal epithelium in suckling yak calves using transcriptomic analysis. Twenty healthy one-month-old male yak calves with similar body weights were selected and randomly assigned to two groups. The pre-feeding adaptation period lasted 14 days, followed by a 120-day experimental feeding period. At the end of the trial, five calves from each group were slaughtered, and samples of abomasum tissue and ruminal contents were collected for subsequent analyses. The results demonstrated that early concentrate supplementation markedly increased the final body weight and ruminal NH₃-N concentration of calves in the RAS group compared with the control (RA) group (p < 0.05). Similarly, dry matter intake and ruminal microbial protein (MCP) content were significantly higher in the RAS group (p < 0.05). In contrast, the concentration of acetic acid in ruminal fluid was significantly higher in the RA group, whereas valeric acid concentration was higher in the RAS group. Furthermore, ruminal TNF-α, TNF-γ, and IL-2 concentrations were significantly elevated in the RAS group (p < 0.05), suggesting enhanced ruminal immune function. Transcriptomic analysis revealed that both up- and down-regulated gene expression contributed to the morphological development and overall health of the ruminal epithelium. Up-regulated genes were enriched in pathways related to chemical carcinogenesis, cytochrome P450 metabolism, steroid hormone biosynthesis, retinol metabolism, ascorbate and aldarate metabolism, drug metabolism-cytochrome P450, pentose and glucuronate interconversions, ovarian steroidogenesis, and porphyrin and chlorophyll metabolism. Conversely, down-regulated genes were mainly associated with cytokine–cytokine receptor interactions, mineral absorption, arachidonic acid metabolism, and viral protein interactions with cytokine receptors. Overall, early supplementation with concentrate feed enhanced the expression of genes associated with ruminal epithelial development, improved immune responses, and promoted better growth performance in suckling yak calves. Full article

In this study, we report the draft genome sequence of Pseudomonas aeruginosa strain ASK-80, a multidrug-resistant bacterium isolated from municipal wastewater in Baddi, district Solan, Himachal Pradesh, India. The whole genome was sequenced through Illumina MiSeq sequencing (150 bp paired-end). The size of the assembled genome was 6,261,345 bp, and the genome annotation revealed 5834 genes, including 5778 CDSs, 5748 protein-coding genes, 56 RNA genes and 30 pseudo genes. Genomic characterization revealed the occurrence of multiple antibiotic resistance genes (bla_OXA-396, bla_OXA-486, bla_OXA-494, bla_PAO, bla_PDC-8, aph(3′)-IIb, catB7, fosA and others), virulence genes (algB, chpA, clpV1, exsA, flgA, pilB, pvcA, toxA, tse1, and waaA), insertion sequences, transposable elements and phage sequences. This genome data may serve as a valuable resource for comparative genomics of P. aeruginosa and research on the antibiotic resistance surveillance of wastewater. Full article