Search Results (8,149)

The plant NAC (NAM, ATAF1/2, and CUC2) transcription factor family plays an important regulatory role in stress response. In this study, we analyzed the rice transcription factor OsNAC113 and elucidated its tissue-specific characteristics and stress response regulatory mechanisms. qRT-PCR results showed that under laboratory-simulated drought, high salt, temperature stress, and hormone treatments, such as abscisic acid (ABA) and gibberellic acid (GA₃), the expression level of OsNAC113 significantly changed, indicating that OsNAC113 responds to various stress conditions. Targeted creation of the rice (Oryza sativa L. spp. japonica) OsNAC113 (LOC_os08g10080.1) mutant based on the CRISPR-Cas9 genome editing strategy revealed its response to salt stress (200 mM). The growth status and survival rate of the mutant under high-salt stress were significantly higher than those of the wild type. Testing showed that the mutant exhibited increased relative water, chlorophyll, and soluble sugar contents under salt stress than the wild type. The malondialdehyde content in the mutant was lower, and the activities of superoxide dismutase, peroxidase, and catalase were higher than those in the wild type, indicating that the mutant with functional loss caused by knocking out OsNAC113 had a significantly enhanced tolerance to salt treatment. Using RNA-seq to detect genome-wide changes in OsNAC113 mutant materials under stress, KEGG annotation showed that knocking out OsNAC113 resulted in regulatory changes in “plant hormone signaling pathway” and “MAPK signaling pathway,” and GO and KEGG annotations showed significant changes in “amino acid transport and metabolism,” “carbohydrate transport and metabolism,” “lipid transport and metabolism,” and “replication, recombination, and repair.” OsNAC113 may be involved in the response to salt stress by regulating these signaling pathways. Using comparative metabolomic analysis, we further elucidated the function of OsNAC113 in physiological metabolic pathways. The knockout of OsNAC113 resulted in changes in various important metabolic pathways in plants, including flavonoid biosynthesis and ABC transporters. Therefore, it is suggested that OsNAC113 is involved in these metabolic processes and affects their regulation in high-salt environments. These results provide a theoretical foundation and reliable material for the molecular breeding of rice. Full article

Background/Objectives: The cerebral cortex is critical for neurological functions that are strongly affected by the aging process. Astrocytes play a central role in maintaining neurotransmitter balance and regulating antioxidant and anti-inflammatory responses, but these physiological functions may also decline with age. This study aimed to investigate the effects of melatonin, a molecule with known antioxidant, anti-inflammatory and neuroprotective properties, on astrocytes of mature cortical tissue obtained from adult Wistar rats. Methods: Primary cortical astrocyte cultures were obtained from neonatal and 90-day-old Wistar rats and treated with melatonin (300 µM for 24 h). We assessed cell viability and metabolism (MTT and extracellular lactate levels), glutamine synthetase (GS) activity, glutathione (GSH) content, release of cytokines, and the expression of genes and proteins associated with oxidative stress and inflammation by RT-qPCR and Western blotting. Results: Melatonin did not affect cell viability or lactate production. Moreover, there were no changes in GS activity, a key enzyme in glutamate metabolism, or in GSH levels, an antioxidant defense molecule synthesized by astrocytes. However, melatonin significantly reduced the expression of the nuclear factor NFκB, cyclooxygenase 2 (COX-2), and inducible nitric oxide synthase (iNOS), while increasing interleukin 6 and 10 levels. Melatonin also upregulated the gene expression of the transcriptional factors Nrf2 and sirtuin 1 (SIRT1) and downregulated AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α), while PGC-1α protein levels remained unchanged. A complementary analysis of astrocytes obtained from neonatal rats showed that melatonin did not change metabolic or redox parameters under basal conditions. Conclusions: Melatonin exerted anti-inflammatory effects on adult astrocyte cultures, likely through modulation of protective signaling pathways, such as Nrf2/SIRT1. These findings highlight the potential role of melatonin in preserving astrocytic function and mitigating age-related neuroinflammatory processes. Full article

Chronic kidney disease is a significant global health burden and a leading cause of cardiovascular morbidity and mortality. Diabetes mellitus is the primary cause of kidney disease, driving the progression of both micro- and macrovascular complications. Sustained hyperglycemia initiates a cascade of deleterious molecular and cellular events, including mitochondrial dysfunction, inflammation, oxidative stress, and dysregulated apoptosis and autophagy, which collectively contribute to the progression of renal injury. Beyond these well-established mechanisms, a compelling body of evidence highlights the pivotal role of epigenetic alterations (such as DNA methylation, histone post-translational modifications, and non-coding RNAs) in mediated long-term kidney damage. The interplay between transcriptional and epigenetic regulation underlies the phenomenon of the “metabolic memory”, wherein cellular dysfunction persists even after glycemic control is achieved. This review synthesizes the current knowledge on mechanisms sustaining metabolic and epigenetic memory, with a particular focus on the epigenetic machinery that establishes and maintains these signals, a concept increasingly termed “epigenetic memory.” Given their reversible nature, epigenetic determinants are emerging as promising biomarkers and a compelling therapeutic avenue. Targeting these “epifactors” offers a novel strategy to halt progression to end-stage renal disease, thereby paving the way for precision medicine approaches in diabetes-related renal disease. Full article

Transcription factors (TFs) orchestrate plant growth and development, yet the functional landscape of many TF gene families remains incomplete. Here, we systematically characterize OsWRKY7, an unannotated WRKY TF in rice. Phylogenomic analyses revealed that the WRKY7 subfamily originated in basal angiosperms and evolved under strong purifying selection. We demonstrate OsWRKY7 functions as a WRKY transcriptional activator, with its activity uniquely encoded within the N-terminal domain—a distinctive mechanism among WRKY proteins. The promoter is enriched with cis-elements responsive to hormone and stress signaling, and the gene shows predominant expression in seeds. Strikingly, haplotype analysis revealed exceptionally low genetic diversity at the OsWRKY7 locus, suggesting evolutionary constraint or a recent selective sweep. Our findings establish OsWRKY7 as a conserved regulator with unique molecular features, specifically the WRKY domain, providing a strategic target for both fundamental research and crop improvement. Full article

Anthocyanins pigment plant tissues, mitigate biotic and abiotic stresses, and deliver human health benefits; raising their content in mung bean (Vigna radiata) sprouts is a long-standing research target. Transcriptome analysis identified VrNAC25, a NAC transcription factor whose expression closely parallels anthocyanin accumulation; functional validation in mung bean confirmed that VrNAC25 acts as a positive regulator of the pathway. Although VrNAC25 does not bind to the promoters of the key structural genes VrDFR or VrLDOX, it indirectly controls anthocyanin synthesis by interacting with the core R2R3-MYB activator VrMYB90, previously established as the central regulator of anthocyanin production in mung beans. This interaction operates at both transcriptional and protein levels, thereby amplifying the expression of downstream structural genes and boosting pigment accumulation. Our findings refine the molecular network governing anthocyanin biosynthesis in sprouts and provide a clear theoretical basis for breeding or biotechnological strategies aimed at enhancing the nutritional quality and commercial value of mung bean products through light treatment or by selecting an anthocyanin-rich mung bean variety. Full article

Soil salinization poses a significant threat to global agricultural productivity. Among crops, soybean (Glycine max), an important source of oil and protein, is more susceptible to salt stress compared to other major crops such as wheat (Triticum aestivum) and rice (Oryza sativa). To better utilize saline land resources, understanding the mechanisms underlying salt tolerance in soybean is essential for developing new salt-tolerant soybean varieties that contribute to food security. This review synthesizes current knowledge on the molecular mechanisms of salt tolerance in soybean, with a focus on ion homeostasis, osmotic adjustment, oxidative balance restoration, structural adaptations, and transcriptional regulatory networks. Key findings highlight the critical roles of ion transporters—such as GmNHX1, GmSOS1, GmHKT1, and GmCLC1—in maintaining Na⁺/K⁺ and Cl⁻ balance; the accumulation of osmoprotectants like proline and LEA proteins to alleviate osmotic stress; and the activation of antioxidant systems—including SOD, CAT, and APX—to scavenge reactive oxygen species (ROS). Additionally, structural adaptations, such as salt gland-like features observed in wild soybean (Glycine soja), and transcriptional regulation via ABA-dependent and independent pathways (e.g., GmDREB, GmbZIP132, GmNAC) further enhance tolerance. Despite these advances, critical gaps remain regarding Cl⁻ transport mechanisms, rhizosphere microbial interactions, and the genetic basis of natural variation in salt tolerance. Future research should integrate genomic tools, omics-based breeding, genome editing techniques such as CRISPR-Cas9, microbial technologies, and traditional breeding methods to develop salt-tolerant soybean varieties, providing sustainable solutions for the utilization of saline–alkali soils and enhancing global food security. Full article

Background: Hypoxia and ageing both involve impaired oxygen delivery, leading to oxidative damage, and endothelial cell (EC) dysfunction. In the presence of chronic hyperglycemia, these effects are amplified, accelerating EC senescence and vascular impairment. Methods: We assessed key mediators of inflammatory signalling and senescence, as well as transcriptional regulators responsive to oxidative stress in ECs exposed to high glucose (30.5 mmol/L) for 72 h under either normoxia (21% O₂) or prolonged (16 h) hypoxia (2% O₂) followed by 2 h of reoxygenation. Results: ECs exposed to high glucose and hypoxia developed a senescent phenotype, as indicated by increased expression of p21 and p16, and elevated β-galactosidase staining. Interestingly, hypoxia-induced senescence did not coincide with the classical senescence-associated secretory phenotype (SASP). Compared to normoxia, ECs exposed to hypoxia, particularly under high-glucose conditions, showed reduced NF-κB-driven proinflammatory secretome (MCP-1, IL-6, IL-8), downregulation of the NF-κB p50 subunit, and simultaneous upregulation of the angiogenic factor VEGF-A with downregulation of YAP-1, a key regulator of cell survival. Notably, we observed a strong upregulation of A20 and TNIP-3, two well-characterized negative regulators of NF-κB signalling. Conclusions: Hypoxia-induced senescence did not trigger a typical inflammatory SASP. Although ECs enter a senescent state, they activate an anti-inflammatory response, suppressing NF-κB signalling and increasing the expression of its inhibitors, A20 and TNIP-3. This may reflect a non-canonical senescence response whose functional significance remains to be determined. Full article

Soil salinity severely threatens soybean productivity worldwide. While transcriptional responses to salt stress are well-documented, the role of post-transcriptional regulation, particularly alternative splicing (AS), remains underexplored. This study combines physiological phenotyping, transcriptome-wide analysis, and molecular genetics to uncover the mechanisms behind the differences in salt tolerance between the salt-sensitive variety Huachun 6 (HC6) and the resistant variety Fiskeby III. Under salt stress, Fiskeby III exhibited superior survival rates and maintained ion homeostasis, as evidenced by a lower Na⁺/K⁺ ratio, compared with HC6. Transcriptomic and splicing analysis revealed extensive salt-induced alternative splicing reprogramming. Genes undergoing differential AS were enriched in pathways related to stress response, ion transport, and RNA splicing. Based on the overlap with both differentially expressed genes (DEG) and alternative splicing (DAS) genes under salt stress, a key splicing factor, GmSR34b, was identified as a central regulator of AS under salt stress. Under NaCl stress, the expression of GmSR34b in leaves peaked at 1 h and a salt stress-specific splicing variant was rapidly induced. A comparative analysis showed that the Fiskeby III cultivar prioritized maintenance of the full-length transcript during prolonged stress, whereas the HC6 cultivar accumulated higher levels of the splicing variant. This indicates differences in the regulation of alternative splicing between these two cultivars. Functional validation confirmed that overexpression of GmSR34b in soybean hairy roots inhibited salt tolerance. This study provides novel insights into the molecular mechanisms of salt tolerance in soybean, suggesting potential strategies for breeding resilient crops through the manipulation of splicing regulators. Full article

Mechanical pruning has emerged as a viable alternative to traditional hand pruning in apple orchards in labor-constrained and aging population workforces. While mechanical pruning reduces labor demand and enhances operational efficiency, their effects on tree physiology and fruit development remain poorly understood. In this study, we examined the physiological and transcriptional responses of apple trees to mechanical pruning (MP) and hand pruning (HP), with a focus on hormone metabolism, photosynthetic activity, and stress adaptation. Pruning treatments were applied in an orchard using a tractor-mounted mechanical pruner and manual shears, and distinct metabolic responses after pruning were assessed over multiple time points using transcriptomic analysis. At 168 h after MP, trees exhibited downregulation of MdLhcb genes, indicating a reduction in light harvesting capacity. In addition, MdDFR, a key gene in flavonoid biosynthesis, was also downregulated, suggesting a suppression of secondary metabolism and a distinct physiological response to MP. In addition, stress-responsive genes such as MdNHL3 were rather upregulated, indicating the activation of adaptive signaling networks. Conversely, HP trees showed relatively moderate responses in the same pathways, suggesting pruning method-specific regulatory mechanisms. These findings highlight how pruning methods distinctly influence tree recovery and gene expression dynamics, offering insights into optimizing pruning systems for sustainable and high-quality apple production under labor-constrained conditions. Full article

Drought stress significantly impacts potato (Solanum tuberosum) yield and quality, necessitating the identification of molecular regulators involved in stress response. This study presents a systems-level, integrative in silico strategy to characterize StABCG25 transporter homologs, key players in abscisic acid (ABA) export in Arabidopsis, to evaluate their potential role in drought adaptation. We performed a genome-wide scan of the potato genome and identified four StABCG25 isoforms. A comprehensive computational framework was applied, including transcriptomic profiling, Weighted Gene Co-expression Network Analysis (WGCNA), AlphaFold2-based 3D modeling, docking, and long-timescale Molecular Dynamics (MD) simulations. Expression analyses revealed the coordinated upregulation of StABCG25-2 and -4 in the drought-tolerant FB clone, contrasted by suppression or instability in sensitive cultivars. WGCNA placed StABCG25-2 as a hub gene in ABA-enriched stress response modules, while StABCG25-4 was associated with plastid-related pathways, suggesting functional divergence. Structurally, StABCG25-2 and -6 exhibited high conformational stability in MD simulations, supported by consistent RMSD/RMSF profiles and MM/PBSA-based binding energy estimates. In contrast, StABCG25-5B, despite favorable docking scores, demonstrated poor dynamic stability and unreliable binding affinity. Overall, this study highlights the critical role of transcriptional coordination and structural robustness in the functional specialization of StABCG25 isoforms under drought stress. Our findings underscore the value of combining WGCNA and molecular dynamics simulations to identify structurally and functionally relevant ABA transporters for future crop improvement strategies. Full article

Microorganism employs sophisticated strategies to adapt to acidic environments, with transcription factors occupying pivotal nodes within their hierarchical regulatory networks. In this study, we performed functional characterization of the AraR transcription factor LP_RS14895 via integrated multiomics approaches. RNA sequencing revealed 40 acid-responsive targets that were enriched in pathways related to pentose/glucuronate interconversions and amino sugar and nucleotide sugar metabolism. A genome-wide binding analysis via DAP-seq identified 1279 interaction sites and the most significantly enriched motif is “ARCCMATMAHC”. The results revealed that AraR plays a crucial role in regulating acid tolerance and metabolizable sugar (including arabinose, glucose, fructose, ribose, mannose, and trehalose). Overall, these findings offer mechanistic insights into microbial stress responses and provide a valuable method for addressing inhibitory processes of carbohydrate metabolizability under high-acid conditions. Full article

The WUSCHEL-related homeobox (WOX) transcription factors (TF) regulate critical developmental processes in plants, including organ formation and stem cell maintenance. Although characterized in model species, the WOX family remains unexplored in passion fruit (Passiflora edulis). In this study, 10 WOX genes were identified in passion fruit, which are distributed across six chromosomes. We analyzed the phylogenetic relationships, gene structure, conserved motifs, and syntenic relationships of the PeWOX genes. Multiple sequence alignment analysis revealed strong conservation of the homeodomain region among WOX TF family members. Phylogenetic reconstruction further demonstrated that the 10 identified PeWOX genes in passion fruit could be classified into three distinct evolutionary clades: the WUS clade, the Intermediate clade, and the Ancient clade. The conserved motif and gene structure of WOX TF family members in the same evolutionary clade were highly consistent. Expression analysis based on RNA-seq and RT-qPCR showed that most PeWOX genes were expressed during ovule development. The expression level of PeWOX genes varies with different stress conditions. Subcellular localization analysis of tobacco leaf epidermal cells showed that PeWOX3/7/10 proteins were localized in the nucleus and cell membrane. Collectively, this study lays a foundation for future functional studies of passion fruit WOX genes. Full article

Buffalo milk plays a vital role in the dairy industry, with milk yield regulated by both transcriptomic and epigenetic mechanisms. While previous studies have primarily focused on differences among individuals or breeds, the epigenetic basis underlying milk yield variation in genetically identical animals remains poorly understood. In this study, we employed a cloned buffalo model and integrated whole-genome bisulfite sequencing (WGBS) with RNA sequencing (RNA-seq) to investigate how DNA methylation and transcriptional regulation contribute to milk yield variation. Results tentatively revealed that low-yielding buffalo exhibited globally reduced DNA methylation in mammary tissues, with distinct distribution patterns across genomic features and regulatory regions. Differentially methylated genes were enriched in PI3K-Akt, HIF-1, and immune-related pathways, whereas hypomethylated genes were associated with calcium signaling, cAMP pathways, and metabolic processes. Transcriptome analysis showed that high-yielding buffalo upregulated genes involved in lipid metabolism and cell proliferation, while low-yielding buffalo displayed enrichment in immune stress and amino acid metabolism. Integrative analysis identified 126 hypo-upregulated genes and highlighted hub regulators such as KLF6, NR4A1, ESR1, KCNQ1. Collectively, this study outlines a preliminary multi-omics regulatory landscape of milk yield variation in cloned buffalo, suggests the interplay between DNA methylation and transcription, provides preliminary insights into the potential interplay between DNA methylation and transcription, and suggests potential connections that merit further investigation. Full article

In pig production, oxidative stress in the placentas of pregnant sows is one of the most important factors affecting reproductive performance. Superoxide dismutase SOD2 is a critical component of the antioxidant system and determines the antioxidant capacity of cells. The expression of the SOD2 gene is reportedly regulated by DNA methylation. At present, there are abundant reports on the function and structure of SOD2, but how DNA methylation affects the expression of SOD2 in pigs is still unclear. In this study, we identified the core promoters of SOD2 gene and verified the important transcription factor binding sites. Treatment of porcine placental trophoblast cells with a DNA methyltransferase (DNMT) inhibitor reduced promoter methylation and increased SOD2 expression. Treatment of SOD2 promoter fragments with CpG methyltransferase M.SssI reduced promoter activity. In summary, the SOD2 core promoter is located at −275/−66 bp. Hypomethylation of the core promoter promotes the expression of SOD2, while hypermethylation reduces promoter activity. This study provides a theoretical basis for further investigation into the regulation of porcine SOD2 gene by DNA methylation. Full article

Background/Objectives: Sepsis-associated liver injury (SALI) is a critical and often early complication of sepsis, defined by distinct hyper-inflammatory and immunosuppressive phases that shape patient phenotypes. Methods: Characterizing these phases establishes a foundation for immunomodulation strategies tailored to individual immune responses, as discussed subsequently. Results: The initial inflammatory response activates pathways such as NF-κB and the NLRP3 inflammasome, leading to a cytokine storm that damages hepatocytes and is frequently associated with higher SOFA scores and a higher risk of 28-day mortality. Kupffer cells and infiltrating neutrophils exacerbate hepatic injury by releasing proinflammatory cytokines and reactive oxygen species, thereby causing cellular damage and prolonging ICU stays. During the subsequent immunosuppressive phase, impaired infection control and tissue repair can result in recurrent hospital-acquired infections and a poorer prognosis. Concurrently, hepatocytes undergo significant metabolic disturbances, notably impaired fatty acid oxidation due to downregulation of transcription factors such as PPARα and HNF4α. This metabolic alteration corresponds with worsening liver function tests, which may reflect the severity of liver failure in clinical practice. Mitochondrial dysfunction, driven by oxidative stress and defective autophagic quality control, impairs cellular energy production and induces hepatocyte death, which is closely linked to declining liver function and increased mortality. The gut-liver axis plays a central role in SALI pathogenesis, as sepsis-induced gut dysbiosis and increased intestinal permeability allow bacterial products, including lipopolysaccharides, to enter the portal circulation and further inflame the liver. This process is associated with sepsis-related liver failure and greater reliance on vasopressor support. Protective microbial metabolites, such as indole-3-propionic acid (IPA), decrease significantly during sepsis, removing key anti-inflammatory signals and potentially prolonging recovery. Clinically, SALI most commonly presents as septic cholestasis with elevated bilirubin and mild transaminase changes, although conventional liver function tests are insufficiently sensitive for early detection. Novel biomarkers, including protein panels and non-coding RNAs, as well as dynamic liver function tests such as LiMAx (currently in phase II diagnostics) and ICG-PDR, offer promise for improved diagnosis and prognostication. Specifying the developmental stage of these biomarkers, such as identifying LiMAx as phase II, informs investment priorities and translational readiness. Current management is primarily supportive, emphasizing infection control and organ support. Investigational therapies include immunomodulation tailored to immune phenotypes, metabolic and mitochondrial-targeted agents such as pemafibrate and dichloroacetate, and interventions to restore gut microbiota balance, including probiotics and fecal microbiota transplantation. However, translational challenges remain due to limitations of animal models and patient heterogeneity. Conclusion: Future research should focus on developing representative models, validating biomarkers, and conducting clinical trials to enable personalized therapies that modulate inflammation, restore metabolism, and repair the gut-liver axis, with the goal of improving outcomes in SALI. Full article