Search Results (583)

Early blight, caused by the pathogen Alternaria solani, is a major fungal disease impacting potato production globally, with reported yield losses of up to 40% in susceptible varieties. As one of the most common diseases affecting potatoes, its incidence has been steadily increasing year after year. This study aimed to elucidate the molecular mechanisms underlying resistance to early blight by comparing gene expression profiles in resistant (B1) and susceptible (D30) potato seedlings. Transcriptome sequencing was conducted at three time points post-infection (3, 7, and 10 dpi) to identify differentially expressed genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) and pathway enrichment analyses were performed to explore resistance-associated pathways and hub genes. Over 11,537 DEGs were identified, with the highest number observed at 10 dpi. Genes such as LOC102603761 and LOC102573998 were significantly differentially expressed across multiple comparisons. In the resistant B1 variety, upregulated genes were enriched in plant–pathogen interaction, MAPK signaling, hormonal signaling, and secondary metabolite biosynthesis pathways, particularly flavonoid biosynthesis, which likely contributes to biochemical defense against A. solani. WGCNA identified 24 distinct modules, with hub transcription factors (e.g., WRKY33, MYB, and NAC) as key regulators of resistance. These findings highlight critical molecular pathways and candidate genes involved in early blight resistance, providing a foundation for further functional studies and breeding strategies to enhance potato resilience. Full article

Soil salinization is a major constraint to global crop productivity, highlighting the need to identify salt tolerance genes and their molecular mechanisms. Here, we integrated mRNA and miRNA profile analyses to investigate the molecular basis of salt tolerance of an elite Brassica napus cultivar S268. Time-course RNA-seq analysis revealed dynamic transcriptional reprogramming under 215 mM NaCl stress, with 212 core genes significantly enriched in organic acid degradation and glyoxylate/dicarboxylate metabolism pathways. Combined with weighted gene co-expression network analysis (WGCNA) and RT-qPCR validation, five candidate genes (WRKY6, WRKY70, NHX1, AVP1, and NAC072) were identified as the regulators of salt tolerance in rapeseed. Haplotype analysis based on association mapping showed that NAC072, ABI5, and NHX1 exhibited two major haplotypes that were significantly associated with salt tolerance variation under salt stress in rapeseed. Integrated miRNA-mRNA analysis and RT-qPCR identified three regulatory miRNA-mRNA pairs (bna-miR160a/BnaA03.BAG1, novel-miR-126/BnaA08.TPS9, and novel-miR-70/BnaA07.AHA1) that might be involved in S268 salt tolerance. These results provide novel insights into the post-transcriptional regulation of salt tolerance in B. napus, offering potential targets for genetic improvement. Full article

Background: Oxidative stress is a critical factor contributing to male infertility, impairing spermatogonial stem cells (SSCs) and disrupting normal spermatogenesis. This study aimed to isolate and characterize human SSCs and to investigate oxidative stress-related gene expression, protein interaction networks, and developmental trajectories involved in SSC function. Methods: SSCs were enriched from human orchiectomy samples using CD49f-based magnetic-activated cell sorting (MACS) and laminin-binding matrix selection. Enriched cultures were assessed through morphological criteria and immunocytochemistry using VASA and SSEA4. Transcriptomic profiling was performed using microarray and single-cell RNA sequencing (scRNA-seq) to identify oxidative stress-related genes. Bioinformatic analyses included STRING-based protein–protein interaction (PPI) networks, FunRich enrichment, weighted gene co-expression network analysis (WGCNA), and predictive modeling using machine learning algorithms. Results: The enriched SSC populations displayed characteristic morphology, positive germline marker expression, and minimal fibroblast contamination. Microarray analysis revealed six significantly upregulated oxidative stress-related genes in SSCs—including CYB5R3 and NDUFA10—and three downregulated genes, such as TXN and SQLE, compared to fibroblasts. PPI and functional enrichment analyses highlighted tightly clustered gene networks involved in mitochondrial function, redox balance, and spermatogenesis. scRNA-seq data further confirmed stage-specific expression of antioxidant genes during spermatogenic differentiation, particularly in late germ cell stages. Among the machine learning models tested, logistic regression demonstrated the highest predictive accuracy for antioxidant gene expression, with an area under the curve (AUC) of 0.741. Protein oxidation was implicated as a major mechanism of oxidative damage, affecting sperm motility, metabolism, and acrosome integrity. Conclusion: This study identifies key oxidative stress-related genes and pathways in human SSCs that may regulate spermatogenesis and impact sperm function. These findings offer potential targets for future functional validation and therapeutic interventions, including antioxidant-based strategies to improve male fertility outcomes. Full article

Flowering is a key agronomic trait that directly influences the yield of the tea-oil tree (Camellia oleifera). Floral initiation, which precedes flower bud differentiation, represents a critical developmental stage affecting the flowering outcomes. However, the molecular mechanisms underlying floral initiation in C. oleifera remain poorly understood. In this study, buds from five key developmental stages of a 12-year-old C. oleifera cultivar ‘changlin53’ were collected as experimental samples. Scanning electron microscopy was employed to identify the stage of floral initiation. UPLC-MS/MS was used to analyze endogenous gibberellin (GA) concentrations, while transcriptomic analysis was performed to reveal the underlying transcriptional regulatory network. Six GA types were detected during floral initiation and petal development. GA₄ was exclusively detected at the sprouting stage (BII), while GA₃ was present in all samples but was significantly lower in BII and the flower bud primordium formation stage (BIII) than in the other samples. A total of 64 differentially expressed genes were concurrently enriched in flower development, reproductive shoot system development, and shoot system development. Weighted gene co-expression network analysis (WGCNA) identified eight specific modules significantly associated with different developmental stages. The magenta module, containing Unigene0084708 (CoFT) and Unigene0037067 (CoLEAFY), emerged as a key regulatory module driving floral initiation. Additionally, GA20OX1 and GA2OX8 were identified as candidate genes involved in GA-mediated regulation of floral initiation. Based on morphological and transcriptomic analyses, we conclude that floral initiation of C. oleifera is a continuous regulatory process governed by multiple genes, with the FT-LFY module playing a central role in the transition from apical meristem to floral meristem. Full article

Background: In recent years, changes in climate conditions and long-term continuous cropping have led to the increased occurrence of Verticillium wilt in various cotton-growing regions, causing significant economic losses in cotton production. Research has shown that volatile substances are closely linked to plant disease resistance; however, studies on their roles in the response of cotton to Verticillium wilt, including their relationship with gene regulation, are limited. Methods: In this study, the transcriptomes and metabolomes of Xinluzao 57 (a highly susceptible Verticillium wilt variety) and 192,868 (a highly resistant Verticillium wilt variety) were sequenced at different time points after inoculation with Verticillium wilt. Results: A total of 21,911 commonly differentially expressed genes (DEGs) were identified within and between the materials, and they were clustered into eight groups. Significant annotations were made in pathways related to amino acids and anthocyanins. Metabolomics identified and annotated 26,200 volatile metabolites across nine categories. A total of 158 differentially accumulated metabolites (DAMs) were found within and between the materials; three clusters were identified, and the 10 metabolites with the most significant fold changes were highlighted. Weighted gene coexpression network analysis (WGCNA) revealed that 13 genes were significantly correlated with guanosine, 6 genes were correlated with 2-deoxyerythritol, and 32 genes were correlated with raffinose. Conclusions: Our results provide a foundation for understanding the role of volatile substances in the response of cotton to Verticillium wilt and offer new gene resources for future research on Verticillium wilt resistance. Full article

Auxin (IAA), a key natural signaling molecule, plays a pivotal role in regulating plant growth, development, and stress responses. Understanding its signal transduction mechanisms is crucial for improving crop yields. In this study, we conducted a comparative transcriptome analysis of wheat leaf and root tissues treated with different concentrations of IAA (0, 1, and 50 μM). Functional enrichment analysis revealed that differentially expressed genes (DEGs) exhibited tissue-specific regulatory patterns in response to auxin. Weighted Gene Co-expression Network Analysis (WGCNA) identified receptor-like kinase genes within the MEgreen module as highly correlated with auxin response, suggesting their involvement in both root and leaf regulation. Among them, TaPBL7-2B, a receptor-like kinase gene significantly upregulated under 50 μM IAA treatment, was selected for functional validation. Ectopic overexpression of TaPBL7-2B in Arabidopsis thaliana (Col-0) enhanced auxin sensitivity and inhibited plant growth by suppressing root development and leaf expansion. In contrast, knockout of the Arabidopsis homolog AtPBL7 reduced auxin sensitivity and promoted both root and leaf growth. Transcriptome analysis of Col-0, the TaPBL7-2B overexpression line, and the pbl7 mutant indicated that TaPBL7-2B primarily functions through the MAPK signaling pathway and plant hormone signal transduction pathway. Furthermore, qRT-PCR analysis of wheat varieties with differing auxin sensitivities confirmed a positive correlation between TaPBL7-2B expression and auxin response. In conclusion, TaPBL7-2B acts as a negative regulator of plant growth, affecting root development and leaf expansion in both Arabidopsis and wheat. These findings enhance our understanding of auxin signaling and provide new insights for optimizing crop architecture and productivity. Full article

Background: Personalized anti-tumor therapy that activates the immune response has demonstrated clinical benefits in various cancers. However, its efficacy against testicular cancer (TC) remains uncertain. This study aims to identify suitable patients for anti-tumor immunotherapy and to uncover potential therapeutic targets in TC for the development of tailored anti-tumor immunotherapy. Methods: Consensus clustering analysis was conducted to delineate immune subtypes, while weighted gene co-expression network analysis (WGCNA), least absolute shrinkage and selection operator (LASSO) regression, and support vector machine (SVM) algorithms were employed to evaluate the potential efficacy of anti-tumor immunotherapy. Candidate immunotherapy targets were systematically identified through multi-gene panel analyses and subsequently validated using molecular biology assays. A prioritized target emerging from cellular screening was further evaluated for its capacity to potentiate anti-tumor immunity. The therapeutic efficacy of this candidate was rigorously confirmed through a comprehensive suite of immunological experiments. Results: Following systematic screening of five candidate genes (WNT11, FAM181B, GRK5, FSCN1, and ECHS1), GRK5 emerged as a promising therapeutic target for immunotherapy based on its distinct functional and molecular associations with immune evasion mechanisms. Cellular functional assays revealed that GRK5 knockdown significantly attenuated the malignant phenotype of testicular cancer cells, as evidenced by reduced proliferative capacity and invasive potential. Complementary immunological validation established that specific targeting of GRK5 with the selective antagonist GRK5-IN-2 disrupts immune evasion pathways in testicular cancer, as quantified by T-cell-mediated cytotoxicity. Conclusions: These findings position GRK5 as a critical modulator of tumor-immune escape, warranting further preclinical exploration of GRK5-IN-2 as a candidate immunotherapeutic agent. Full article

Background/Objectives: Alveolar echinococcosis (AE), caused by Echinococcus multilocularis larvae, poses a significant global health concern. Primarily affecting regions in the northern hemisphere, such as northwest China, which are vital for animal husbandry, it often results in severe hepatic impairment in the host. However, there remains a dearth of knowledge concerning changes in gene expression profiles during the progression of AE. In this study, we employed transcriptome sequencing (RNA sequencing, RNA-Seq) to detect alterations in gene expression profiles in the liver tissues of mice with AE. Our aims were to understand the transcriptome differences in the liver during E. multilocularis infection and to explore the molecular mechanisms underlying the early progression of this disease. Methods: We established a mouse model of AE by intraperitoneally injecting protoscoleces of E. multilocularis. All the inoculated mice were randomly divided into four groups. Liver tissues were collected at 6, 12, 19, and 25 weeks after inoculation. Paired non-infected mouse-derived liver tissues were used as controls, and transcriptome sequencing was carried out. Results: A total of 629 differentially expressed genes (DEGs) were identified. Among them, 370 genes were upregulated and 259 genes were downregulated. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were significantly associated with immune system modulation, the cell cycle, and the fibrosis process during the pathological changes. Additionally, weighted gene co-expression network analysis (WGCNA) identified several genes, including CCNA2, BIRC5, KIF2C, OTC, TLR2, and NCKAP1L. These hub genes involved in immunoinflammatory processes may be related to E. multilocularis larvae infection. Conclusions: The findings of this research provide a theoretical foundation for a more in-depth understanding of the molecular mechanisms of AE. They offer valuable insights into the molecular mechanisms and potential key factors involved in the pathogenesis of this disease. Full article

Hippeastrum, a perennial herbaceous plant belonging to the Amaryllidaceae family, is widely cultivated for its large, vibrant flowers with diverse petal colors, which have significant ornamental and economic value. However, the mechanisms underlying anthocyanin accumulation in Hippeastrum petals remain poorly understood. To fully explore the involved regulation mechanism was significant for the breeding of Hippeastrum and other Amaryllidaceae family plants. In this study, we selected six Hippeastrum cultivars with distinctly different petal colors. We used metabolomic profiling and high-throughput transcriptomic sequencing to assess varied anthocyanin profiles and associated expression of genes in their biosynthetic pathways. Four key anthocyanins were identified: cyanidin, cyanidin-3-O-rutinoside, delphinidin-3-glucoside, and delphinidin-3-rutinoside. Weighted gene co-expression network analysis (WGCNA) correlated the abundance of these four anthocyanins with transcriptomic data, to suggest three regulatory modules. Nine transcription factors families in these modules were identified and some of them were validated using qRT-PCR. Y2H assay isolated some transcription factors interacted with TTG1 (WD40 protein), including MYB3/39/44/306 and bHLH13/34/110, illustrating the possibility of forming MBW complexes. Our study provides a comprehensive characterization of anthocyanin composition. These findings laid a theoretical foundation for future research on the regulatory mechanisms of pigment accumulation and the breeding of Hippeastrum cultivars with novel petal colors. Full article

Cold shock represents a prevalent but harmful environmental stress factor that poses significant threats to fish survival and reproductive success. In fish, the brain acts as a central regulator of thermoregulatory processes. Nevertheless, how different brain regions respond molecularly to cold exposure remains largely unknown. To address this, this study systematically investigated the effects of acute cold stress on five specific brain regions of Leiocassis longirostris using RNA-seq. The findings demonstrated that all five brain regions were significantly impacted by cold treatment, with the mesencephalon (MB) showing the most substantial changes. GO and KEGG enrichment analyses indicated that cold stress disrupted processes including gene expression regulation, circadian rhythms, and immune function within brain tissues. Through Weighted Gene Co-Expression Network Analysis (WGCNA), the MB was identified as the core responsive region, and the brain’s reaction to cold stress was strongly correlated with circadian rhythm, spliceosome, and ubiquitination. In summary, our investigation demonstrates that the MB represents a principal region for cold stress response in L. longirostris, involving alterations in circadian clocks, immune function, and inflammatory responses, alongside suppression of gene expression processes and ubiquitination-mediated proteolysis. Full article

The phosphofructokinase (PFK) gene family plays a pivotal role in glycolysis and energy metabolism in plants. This study aimed to systematically characterize the PFK gene family in Arabidopsis thaliana at the genome-wide level and to investigate the function of AtPFK2 (ATP-dependent phosphofructokinase 2) in response to salt and drought stress. Through bioinformatics analysis, 11 AtPFK genes were identified. Phylogenetic analysis revealed that these PFK genes can be classified into two subfamilies: PFK and PFP. Notably, AtPFK2 possesses a unique structure, containing only a single intron, and its promoter is enriched with stress- and hormone-responsive elements, such as ABRE and MBS. T-DNA insertion mutants (pfk2) exhibited slightly shorter roots but slightly higher fresh weight under stress conditions, whereas Arabidopsis lines AtPFK2-overexpressing (OE-PFK2) showed increased stress sensitivity, with inhibited root and leaf growth, leaf wilting, reduced malondialdehyde and chlorophyll content, and enhanced accumulation of proline and soluble sugars. Weighted gene co-expression network analysis (WGCNA) identified 14 stress-related modules, from which six core genes—LBD41, TRP3, PP2-A3, SAUR10, IAA6, and JAZ1—were selected. These genes are involved in glycine metabolism and plant hormone signaling. The results of this study indicate that AtPFK2 mediates stress responses by regulating osmoregulatory substances and hormone signaling pathways, offering new insights into the mechanisms of stress resistance in crops. Full article

Meat quality is a critical determinant of consumer preference and economic value in the livestock industry. However, the relationship between carcass performance and meat quality remains poorly understood. In our study, we conducted an integrative analysis of transcriptomics and metabolomics to investigate the molecular mechanisms underlying meat quality differences in Hu sheep with high (HHS, n = 10) and low (LHS, n = 10) carcass performance. Phenotypic analysis revealed that the HHS group exhibited superior meat quality traits, including higher intramuscular fat (IMF) content (reflected in elevated marbling scores), along with lower shear force, drip loss, and cooking loss, compared to the LHS group. Transcriptomic analysis identified 376 differentially expressed genes (DEGs) enriched in pathways linked to lipid metabolism, such as the PPAR signaling pathway and long-chain fatty acid metabolic process. Weighted gene co-expression network analysis (WGCNA) revealed important modules and key genes (e.g., ELOVL6, PLIN1, and ARHGEF2) associated with meat quality traits. Metabolomic profiling identified 132 differentially accumulated metabolites (DAMs), with significant enrichment in amino acid metabolism pathways, including D-amino acid metabolism, arginine biosynthesis, and glycine, serine, and threonine metabolism. Integrative analysis of transcriptomic and metabolomic data highlighted six co-enriched pathways, such as the mTOR signaling pathway and amino acid metabolism, underscoring their role in regulating meat quality. These findings provide valuable insights into the genetic and metabolic networks driving meat quality variation and offer potential biomarkers for genetic selection and nutritional strategies to enhance both carcass yield and eating quality in Hu sheep. This research enhances knowledge of the molecular basis of meat quality and supports precision breeding in livestock production. Full article

Background: Bambusaoldhamii is an important economic bamboo species. However, flowering occurred after its introduction and cultivation, resulting in damage to the economy of bamboo forests. Currently, the molecular mechanism of flowering induced by introduction stress is still unclear. This study systematically explored the key genes and regulatory pathways of flowering in Bambusaoldhamii under introduction stress through field experiments combined with transcriptome sequencing and weighted gene co-expression network analysis (WGCNA), with the aim of providing a basis for flower-resistant cultivation and molecular breeding of bamboo. Results: The study conducted transcriptome sequencing on flowering and non-flowering Bambusaoldhamii bamboo introduced from Youxi, Fujian Province for 2 years, constructed a reference transcriptome containing 213,747 Unigenes, and screened out 36,800–42,980 significantly differentially expressed genes (FDR < 0.05). The results indicated that the photosensitive gene CRY and the temperature response gene COR413-PM were significantly upregulated in the flowering group; the expression level of the heavy metal detoxification gene MT3 increased by 27.77 times, combined with the upregulation of the symbiotic signaling gene NIN. WGCNA analysis showed that the expression level of the flower meristem determination gene AP1/CAL/FUL in the flowering group was 90.38 times that of the control group. Moreover, its expression is regulated by the cascade synergy of CRY-HRE/RAP2-12-COR413-PM signals. Conclusions: This study clarifies for the first time that the stress of introducing Bambusaoldhamii species activates the triad pathways of photo-temperature signal perception (CRY/COR413-PM), heavy metal detoxification (MT3), and symbiotic regulation (NIN), collaboratively driving the AP1/CAL/FUL gene expression network and ultimately triggering the flowering process. Full article

Cardiac cachexia (CC) is an advanced stage of heart failure (HF) characterized by structural and functional abnormalities in skeletal muscle, leading to muscle loss. Aerobic training provides benefits; however, the underlying molecular mechanisms remain poorly understood. This study aimed to investigate the therapeutic effects of aerobic training on transcriptomic alterations associated with disease progression in cachectic skeletal muscle. HF was induced in male Wistar rats by a single monocrotaline injection (60 mg/Kg). Aerobic training consisted of 30 min treadmill running at ~55% of maximal capacity, 5×/week for 4 weeks. Assessments included body mass, right ventricle mass, skeletal muscle fiber size and exercise tolerance. RNA-seq analysis was performed on the medial gastrocnemius muscle. Sedentary cachectic rats exhibited 114 differentially expressed genes (DEGs) while exercised cachectic rats had only 18 DEGs. Enrichment pathways analyses and weighted gene co-expression network analysis (WGCNA) identified potential key genes involved in disrupted lipid metabolism in sedentary cachectic rats, which were not observed in the exercised cachectic rats. Validation of DEGs related to lipid metabolism confirmed that Dgat2 gene expression was modulated by aerobic training in CC rats. These findings suggest that aerobic training mitigates transcriptional alterations related to lipid metabolism in rats with CC, highlighting its therapeutic potential. Full article

Compelling evidence has demonstrated a bidirectional relationship between Sjögren’s syndrome (SS) and periodontitis (PD). Nevertheless, the underlying mechanisms driving their co-occurrence remain unclear, highlighting the need for finding the hub gene. This study sought to examine the common genes and any connections between SS and PD. Differently expressed genes (DEGs) were analyzed by means of gene set enrichment analysis (GSEA), weighted gene co-expression network analysis (WGCNA), and least absolute shrinkage and selection operator (LASSO) methods. The test and validation sets were used to depict the receiver operating characteristic (ROC) curves. The immune cell infiltration was performed via the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) methodology. The relationships between immune infiltrating cells and the common gene were examined. Ninety-five common genes with similar expression trends were obtained after DEGs analysis, which were enriched in cytokine—cytokine receptor interaction, chemokine signaling pathway, proteasome, intestinal immune network for IgA production, and cytosolic DNA sensing pathway. Thirty-nine common genes were obtained after WGCNA. Sixteen shared genes of DEGs analysis and WGCNA were incorporated into the LASSO model to obtain the unique shared gene, C-C motif chemokine receptor 1 (CCR1), which overexpressed and owned predictable ROC curves in test and validation sets. The examination of immune cell infiltration underscored its crucial roles in the disturbance of immune homeostasis and the emergence of pathogenic circumstances with the simultaneous occurrence of SS and PD. CCR1 overexpresses and serves as a critical pathogenic hub linking SS and PD, which may play a role through immune cell infiltration. Full article