Search Results (11,707)

Cabbage (Brassica oleracea var. capitata), a member of the Brassicaceae family, is an important vegetable crop grown worldwide. Self-incompatibility (SI) in cabbage is a key trait that prevents self-fertilization and inbreeding, thereby maintaining genetic diversity within populations. Although several genes related to SI have been reported, its genetic control remains unclear. In this study, we developed an F₂ population from the highly self-compatible (SC) cabbage line 87-534 and the highly self-incompatible (SI) line 01-20, both of which exhibit the S5 haplotype. The segregation analysis of the F₂ population revealed the possible control of SI by a major gene with additional modifying genetic factors. Bulk segregant analysis sequencing (BSA-Seq) and RNA sequencing (RNA-Seq) were performed on SI and SC samples selected from the F₂ population. BSA-Seq revealed a candidate region on chromosome 7 (C07: 7.45 Mb to 8.93 Mb), including 32 differentially expressed genes (DEGs). RNA-Seq identified a total of 2400 DEGs between the two pools, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested that plant hormone biosynthesis and signaling, plant immune response were significantly enriched and may be involved in SI. The combined analysis of BSA-Seq and RNA-Seq identified six candidate genes associated with SI, and their expression was confirmed using quantitative real-time PCR (qRT-PCR). Among them, Bol023956 encodes fructokinase, Bol023986 is involved in plant defense response, Bol024018 is related to pollen development, Bol024012 encodes a transport protein for phytohormones, Bol023943 encodes chorismate mutase 3, and Bol012515 is an important regulatory gene for chloroplast synthesis. These six genes, potentially linked to SI, should be targets for further validation. These findings provide insights into the molecular mechanisms of SI in cabbage and the selection of superior cabbage varieties. Full article

Acaryochloris marina is a distinctive cyanobacterium that uses chlorophyll d as its primary photosynthetic pigment and possesses two major light-harvesting systems: membrane-integral chlorophyll-binding Pcb/CBP complexes and water-soluble phycobiliproteins. How these antenna systems respond at the transcriptome level to contrasting light environments remains incompletely characterized. Here, we re-analyzed a publicly available RNA-seq dataset for A. marina MBIC11017 (NCBI BioProject PRJNA1130970), comparing cells grown under low-irradiance far-red light (LL-FR; 1.5–2 µmol photons m⁻² s⁻¹, 710-nm peak) and high-irradiance white light (HL-WL; 30–35 µmol photons m⁻² s⁻¹). Because light quality and irradiance both differ in this experimental design, the two effects cannot be separated; all transcriptional changes are therefore interpreted as responses to the combined LL-FR versus HL-WL contrast rather than to far-red wavelength alone. Of 8439 expressed genes, 1810 (21.4%) were significantly differentially expressed (adjusted p < 0.05). Using GFF-verified locus tags which corrected mis-annotations propagated in earlier analyses, the PS-I core gene set showed a mean log₂ fold-change of +1.96 (3.9-fold; 11/11 loci significant), whereas the PS-II core gene set showed a mean log₂ fold-change of +1.10 (2.1-fold; 12/20 loci significant). Light-harvesting genes showed the strongest response: 17/18 phycobiliprotein-pathway genes in KEGG amr00196 were upregulated, together with multiple putative Pcb/CBP loci (mean antenna log₂FC = +3.51; 11.4-fold). Weighted gene co-expression network analysis placed the antenna-associate genes examined here within a module positively correlated with the LL-FR condition (r = 0.802, p = 0.017), and STRING analysis supported an enriched network of predicted or known protein associations (1115 nodes, 4763 edges; PPI enrichment p < 1.0 × 10⁻¹⁶). Recent matched-irradiance experiments indicate that, at equal photon flux, far-red wavelengths reduce phycobilisome content relative to white light. The transcriptional pattern reported here is therefore most parsimoniously interpreted as predominantly a low-irradiance response, with possible wavelength-associated CA5 contributions that cannot be isolated in the present design. Overall, the analysis reveals coordinated transcript-level changes across plasmid-encoded reacquired phycobiliprotein genes, chromosomal Pcb/CBP loci, chlorophyll biosynthesis genes, and photosystem core genes, consistent with coordinated regulation of light-harvesting components in A. marina. Full article

Background: Alopecia areata (AA) is a common autoimmune alopecia disease. Evidence suggests that autophagy-related genes (ARGs) may contribute to its pathophysiology. This study aims to explore and identify potential autophagy-related biomarkers and molecular subtypes in AA. Methods: In this study, autophagy-related differential expression genes (ARDEGs) in AA were identified by comparing the differentially expressed genes (DEGs) in the GSE68801 dataset with the ARGs. Then, we applied three different machine learning methods to identify key hub genes and further verified them on independent datasets. We used the receiver operating characteristic (ROC) curve to evaluate the diagnostic potential of these hub genes and constructed a predictive nomogram. In addition, this study also used the consensus clustering method to define two AA subtypes and explored their immune characteristics and functional pathways through ssGSEA, MCPcounter and enrichment analysis. Experimental validation included qRT-PCR for four hub genes and Western blotting for critical autophagy markers. Results: Our analysis detected 10 ARDEGs in AA. Applying three machine learning algorithms, we identified four candidate hub genes, ATG9B, EIF4EBP1, WIPI1 and CCR2, and verified their expression patterns in independent cohorts. The combined four-gene model and nomogram showed potential diagnostic performance. Consensus cluster analysis divided AA cases into two subtypes, each associated with different immune infiltration and functional pathways. Downregulation of ATG9B and EIF4EBP1 and upregulation of CCR2 were verified by qRT-PCR. Western blotting further suggested altered autophagy-related protein expression in AA lesions, characterized by a reduced LC3B-II/I ratio and Beclin-1 expression and increased SQSTM1 expression. Conclusions: This study identified four candidate autophagy-related genes and two exploratory molecular subtypes in AA and may provide clues for understanding autophagy-related immune dysregulation and support further validation of candidate diagnostic markers. Full article

Reparative dentin formation is a defensive response that restores a mineralized barrier to protect the dental pulp following various stimuli, such as bacterial invasion, tooth preparation, or restorative materials. However, reparative dentin is limited, and to avoid pathological calcification or pulp canal obliteration, mineral deposition must be restricted to the injured area and temporally restrained once the barrier is reestablished. This suggests the existence of negative regulators that can halt odontoblastic differentiation; however, such inhibitory regulators remain incompletely defined. Spondin-1 (SPON1) is an extracellular matrix protein known to regulate bone homeostasis and act as a negative regulator of bone mass; however, the effects of SPON1 on odontoblastic differentiation of dental pulp stem cells (DPSCs) remain unclear. This study aimed to analyze the effects of SPON1 on odontoblastic differentiation of human DPSCs (HDPSCs). SPON1 was expressed in the odontoblastic layer and dental pulp tissue, and its expression was significantly decreased at the beginning of reparative dentin formation in rats. Treatment with SPON1 inhibited odontoblastic differentiation of HDPSCs by blocking the expression of non-phosphorylated β-catenin, while neutralizing SPON1 significantly enhanced odontoblastic differentiation of HDPSCs. These findings suggest that SPON1 functions as a negative regulator of odontoblastic differentiation during reparative dentin formation. Full article

The aim of this study was to analyze the effect of concomitant use of cannabigerol (CBG) and 3-O-ethylascorbic acid (EAA) on changes in the proteome of UVA-irradiated skin melanocytes, with particular emphasis on adduct formation between lipid peroxidation products and metabolically important proteins. Proteomic analysis allowed the identification of 1248 proteins with statistically significantly changed expression following melanocytes irradiation and/or incubation with CBG/EAA. The top 25 proteins with the most strongly differentially abundant expression included proteins involved in cell protection/antioxidant response, as well as pro-inflammatory and proapoptotic signalization. Moreover, in melanocytes irradiated with UVA, the levels of lipid peroxidation product, 4-hydroxynonenal (4-HNE) and its protein adducts were increased, as well as significant changes in the profile of proteins modified by 4-HNE were observed. CBG and EAA, especially when used together, largely reverse these effects. This study for the first time demonstrated the combined effect of CBG and EAA on the proteome of melanocytes after their exposure to UVA radiation, which applies to both changes in protein expression and intracellular signaling based on proteins modified by 4-HNE. It can be suggested that CBG and EAA may provide melanocytes with effective protection against the effects of oxidative stress and perhaps even protect the skin from carcinogenesis. Full article

Non-small cell lung cancer (NSCLC) remains a major cause of cancer-related mortality, with poor survival outcomes despite advances in surgery, chemotherapy, targeted therapy, and immunotherapy. The tumor microenvironment (TME) plays a central role in sustaining tumor growth, immune evasion, and systemic metabolic dysfunction. In this study, we performed an integrative analysis of differentially expressed microRNAs (miRNAs) to uncover their contributions to dysregulated signaling networks in NSCLC. hsa-miR-486-5p was identified as a prominent differentially expressed candidate miRNA. Using mathematical modeling and regression-based reduction, we identified Forkhead Box O1 (FOXO1) and Unc-51 like Autophagy Activating Kinase 2 (ULK2) as critical regulatory nodes that integrate oncogenic signaling with cellular homeostasis. Aberrant expression of hsa-miR-486-5p was found to modulate pathways including PI3K/AKT/mTOR, NF-κB, and JAK-STAT3, thereby promoting tumor progression and secretion of inflammatory cytokines. These cytokines, viz., IL-6, TNF-α, and IL-1β, activate muscle-specific protein degradation pathways through E3 ubiquitin ligases TRIM63 and FBXO32, linking NSCLC progression to cancer-associated sarcopenia. Quasipotential landscape analysis further revealed dynamic phenotypic transitions between stable and unstable states, highlighting the adaptability of tumor–host interactions. Collectively, our findings demonstrate that miRNA-mediated regulatory networks not only drive NSCLC progression and inflammation but also contribute to systemic muscle wasting. These insights emphasize the need for novel therapeutic strategies, including RNA-based interventions, to overcome resistance, improve survival, and address the metabolic complications associated with NSCLC. Full article

A common hypoxic scenario in tumors involves unresolved acute hypoxia that eventually leads to sustained (chronic) hypoxia. This shift drives a characteristic “HIF switch”, where the key hypoxia-responsive factors change from HIF-1α to HIF-2α over time, and importantly, this switch is closely linked to stemness regulation. However, the mechanisms underlying this switch and its impact on stemness regulation are not yet fully understood. Here, we developed a mechanistic network model integrating the HIF-1/HIF-2 signaling axis with the stemness regulators OCT4 and SOX2. We found the duration and intensity of hypoxia jointly shape the dynamics of HIF-1α and HIF-2α, ultimately regulating OCT4-mediated stemness. Under physioxia, HIF-2α–mTORC2 positive feedback supports the gradual accumulation of HIF-2α toward a modest steady level and low OCT4 expression, corresponding to a primed state. Under prolonged mild hypoxia, the concurrent induction of HIF-1α, albeit at low levels, and accelerated accumulation of HIF-2α elevate OCT4 to intermediate levels, promoting stem-like traits. Under moderate hypoxia, PHD-2-mediated negative feedback triggers pulsatile HIF-1α dynamics, driving a shift toward HIF-2α dominance. Ultimately, cooperative HIF-1α/HIF-2α signaling induces REDD1 and suppresses mTORC1-dependent protein synthesis, pushing OCT4 into a high-expression state associated with differentiation. This work presents a unified framework for understanding how the HIF signaling hierarchy coordinates metabolic and transcriptional programs to direct cell fate across varying hypoxic landscapes. Full article

Primula nutans Georgi, a medicinal herb used in Mongolian and Tibetan medicine for treating respiratory ailments, is a natural agent with antiobesity potential. We investigated the antiobesity and insulin-sensitizing effects of P. nutans Georgi extract (PGE) using in vitro and in vivo models. In 3T3-L1 preadipocytes, PGE inhibited adipocyte differentiation and lipid accumulation without cytotoxicity, accompanied by the reduced expression of adipogenic transcription factors (PPARG, C/EBPA, and adiponectin) and lipogenic genes (FASN, SCD1, and ACC), particularly during the early stages of adipogenesis. Similar effects were observed in primary stromal vascular cells derived from mouse inguinal white adipose tissue. PGE upregulated C/EBP homologous protein and C/EBPB and was associated with altered cell cycle progression, increased G2/M phase distribution, and the potential disruption of mitotic clonal expansion during early adipogenesis. In HFD-induced obese mice, intraperitoneal administration of PGE (10 or 30 mg/kg) significantly reduced body weight gain, white adipose tissue mass, and hepatic steatosis, independent of food intake. PGE downregulated lipogenic and proinflammatory gene expression in adipose and hepatic tissues and increased AMPK phosphorylation in white adipose tissue. PGE improved glucose tolerance and was associated with enhanced insulin sensitivity, as evidenced by reduced areas under the curve in the glucose tolerance and insulin tolerance tests and increased circulating adiponectin levels. Feature-based molecular networking identified 61 compounds from PGE. Network pharmacology analysis revealed several antiobesity targets, including PPARG and AKT1. Molecular docking analyses suggested favorable binding affinities between major compounds and metabolic regulators. Collectively, these findings suggest that PGE may suppress adipogenesis and improve metabolic parameters in obese mice, supporting its potential as a natural candidate for obesity and related metabolic disorders. Full article

Powdery mildew in wheat, caused by the biotrophic fungus Blumeria graminis f. sp. tritici (Bgt), is a major threat to global wheat production, yet the molecular mechanisms underlying differential cultivar resistance remain largely unresolved. In this study, tandem mass tag (TMT)-based quantitative proteomics was employed to investigate protein dynamics in resistant (Yannong37) and susceptible (Yannong1766) wheat cultivars at 0 and 24 h following Bgt inoculation. A total of 276 proteins exhibited significant changes in abundance after infection, with enrichment in cell wall and plasmodesmata-associated proteins. Comparative analysis further identified 456 differentially expressed proteins between the two cultivars at 24 h post-inoculation. Protein–protein interaction network analysis indicated that proteins involved in secondary metabolism and immune responses form coordinated regulatory networks contributing to disease resistance. RT–qPCR validation supported the reliability of the proteomic data. Notably, TaCAD-A1 displayed higher transcript abundance in the resistant cultivar and was associated with reduced fungal biomass accumulation. Silencing of TaCAD-A1 resulted in decreased expression of multiple defense-related genes. Collectively, these findings suggest that TaCAD-A1 may positively contribute to wheat resistance against Bgt infection and may be associated with defense responses and monolignol biosynthesis-related processes. Full article

Fruit shape is determined by patterns of cell division and expansion during early development, yet the upstream transcription factors coordinating cell wall dynamics and cytoskeletal organization remain largely unknown. Here, we report that SlbHLH113, a bHLH transcription factor, positively regulates tomato fruit elongation. Overexpression (OE) of SlbHLH113 produced elongated fruits with increased length/width ratio, whereas RNAi lines exhibited flattened fruits. Histological analysis revealed that SlbHLH113 alters columella cell polarity—promoting elongated cell morphology without affecting cell area—and reduces columella–placenta width and locule width, without altering pericarp thickness. Transcriptomic profiling identified 87 differentially expressed genes in OE lines, with enrichment in cell wall-related processes. Notably, a pectate lyase gene (PL5) and an expansin gene (EXT90) were down-regulated, while genes involved in oriented cellulose deposition (COBRA4) and ethylene signaling were up-regulated. Importantly, SlbHLH113 physically interacts with the microtubule-associated protein SlIQD21a, as demonstrated by yeast two-hybrid and luciferase complementation assays. Finally, SlbHLH113 did not affect major nutrient contents in red-ripe fruits. Collectively, our findings identify SlbHLH113 as a novel regulator of tomato fruit shape that might act through cell polarity control, cell wall remodeling, and interaction with a microtubule-associated protein, offering a potential target for improving fruit morphology without compromising nutritional quality. Full article

Rice depends on its root system to perceive drought, a major environmental constraint that leads to severe yield losses worldwide. To dissect the underlying molecular basis, we conducted a comparative analysis of drought-sensitive (WAB) and drought-tolerant (IR65) rice genotypes that exhibited divergent drought tolerance at the seedling stage. After exposure to 15% PEG6000 (−0.4 MPa) for two days, the shoot and root architectural traits of IR65 were better than those of WAB seedlings. Measurements of physio-biochemical parameters (SOD, CAT, POD, APX, H₂O₂, and proline) suggest that IR65 seedling roots exhibit greater ROS scavenging and osmotic adjustment capacity than WAB, aligning with tolerance to PEG-induced water deficiency. Transcriptomic assessments of roots identified 802 commonly differentially expressed genes (DEGs) during the drought time course (12, 24, and 48 h) in WAB and IR65. They were clustered into eight groups based on their expression profiles and mainly enriched in phytohormone signaling, protein phosphorylation, and transcription factors. Using weighted gene co-expression network analysis (WGCNA), nine significant modules were identified based on n = 382 of the DEGs. A total of 12 DEGs up-regulated in IR65 were distributed in five modules, and five of them were selected for rapid functional validation through in vivo yeast expression. The results showed that transgenic yeasts were tolerant to simulated drought conditions (135 mM PEG3350), indicating that these genes would be potential targets for rice improvement in drought tolerance in the future. Full article

Global warming-induced extreme heatwaves present a severe threat to global tomato yield and production stability. To elucidate the molecular regulatory mechanisms underlying heat stress tolerance in tomato (Solanum lycopersicum), this study utilized label-free quantitative proteomics to profile alterations in protein abundance in tomato leaves in response to heat stress. A total of 294 differentially expressed proteins (DEPs) were identified, with function enrichment in the systematic activation of core stress-responsive biological processes, including the mitogen-activated protein kinase (MAPK) signaling cascade, the endoplasmic reticulum protein processing, and glutathione metabolism. Among them, heat shock protein (HSP) family members exhibited the most significant changes, particularly two small heat shock proteins (sHSPs), designated as SlsHSP1 and SlHSP17.4. Functional validation showed that silencing either SlsHSP1 or SlHSP17.4 drastically impaired heat tolerance in tomato plants. Specifically, silenced lines displayed excessive reactive oxygen species (ROS) accumulation and reduced antioxidant enzyme activities, with SlsHSP1-silenced plants showing more severe heat-induced phenotypic damage. Subcellular localization assays further demonstrated SlsHSP1 was located in the ER and SlHSP17.4 in the nucleus. Collectively, this study unravels multiple heat defense regulatory networks in tomato, in which organelle-specific sHSPs like SlsHSP1 and SlHSP17.4 synergistically maintain protein homeostasis and cellular redox balance, conferring broad-spectrum stress resistance in plants under high-temperature stress. Full article

Soil salinization is a major abiotic stress limiting maize (Zea mays L.) growth and productivity worldwide. Recently, many genes involved in salt stress have been identified. However, the molecular mechanisms underlying salt tolerance in maize remain largely elusive. In this study, we identified a member of the ZmPIRIN family genes, ZmPRN1, acting as a negative regulator in response to salt stress. The expression levels of ZmPRN1 were down-regulated under salt and H₂O₂ treatment. Subcellular localization analysis showed that ZmPRN1 is localized to the chloroplast. Under salt stress, the Zmprn1-Mu mutant exhibited higher survival rates and lower reactive oxygen species (ROS) accumulation compared to wild-type plants. Whereas, ZmPRN1 overexpression lines were more sensitive to salt stress, and had higher ROS levels and lower chlorophyll content than wild-type plants. Transcriptome analysis showed that the differentially expressed genes (DEGs) were mainly involved in the oxidation-reduction process. Furthermore, yeast-two hybrid and split-luciferase complementation assays revealed that ZmPRN1 can interact with the chloroplast NDH complex subunit NDF4, the RING-type E3 ubiquitin ligase RING371, and the auxin-responsive protein IAA27. Collectively, our findings demonstrated that ZmPRN1 negatively regulates salt tolerance in maize by modulating ROS homeostasis, providing a valuable genetic resource for breeding salt-tolerant maize varieties. Full article

Heterosis utilization is an effective strategy to improve crop yield, stress resistance, and quality, and has been widely used in crop breeding. Soybean is an important oil and protein crop worldwide with heterosis, but the genetic basis of soybean heterosis remains largely unclear. Whole-transcriptome analysis provides a new technical approach to explore the molecular mechanism of heterosis. In this study, HYBSOY2, a registered soybean hybrid variety with the strongest heterosis in China, together with its female parent JLCMS47A, maintainer line JLCMS47B, and male parent JLR2, were used as experimental material. Whole-transcriptome sequencing was performed using RNA extracted from seedling leaves. After mapping high-quality reads to the soybean reference genome, 57 co-expressed differentially expressed genes (DEGs) were identified in HYBSOY2 compared with both JLCMS47B and JLR2. GO and KEGG enrichment analyses shows that these DEGs were mainly enriched in ADP binding, oxidoreductase activity, fatty acid elongation, and pyruvate metabolism. A total of 787 transcription factors were identified between HYBSOY2 and its parents, most of which shows parental expression-level dominance, with the MYB family accounting for the highest proportion. In addition, 10 differentially expressed lncRNAs were detected between HYBSOY2 and its parents. In the comparison between HYBSOY2 and JLCMS47B, 18 differentially expressed miRNAs were identified, among which up-regulated miR396d functions in promoting leaf development and enhancing drought tolerance. In the comparison between HYBSOY2 and JLR2, 20 differentially expressed miRNAs were found, including down-regulated miR172c which is involved in flowering promotion. A total of 12 DEGs were further verified by qRT-PCR, which may be closely related to soybean heterosis. This study provides a comprehensive transcriptomic profile at the seedling stage of the hybrid soybean and offers valuable information for hybrid soybean breeding. These results lay a foundation for further revealing the molecular mechanism underlying soybean heterosis. Full article

High-throughput single-cell RNA sequencing (scRNA-seq) has substantially advanced plant transcriptional landscapes. However, decoding cell-type-specific transcriptional regulation in non-model crops like tomato (Solanum lycopersicum) remains challenging. An integrated computational pipeline was applied using high-dimensional weighted gene co-expression (hdWGCNA) and ensemble machine learning to analyze tomato leaf single-cell transcriptomes. Unsupervised clustering identified 19 cell subpopulations mapped to five major cell-types: mesophyll cells (50.6%), guard cells (31.0%), trichomes (8.3%), vascular cells (7.5%), and lamina epidermis (2.6%). hdWGCNA revealed eight cell-type-specific modules, linking mesophyll cells to photosynthesis and guard cells to redox homeostasis. Machine learning classifiers prioritized candidate transcription factors (TFs), with XGBoost achieving the highest accuracy (0.85) to define cell identity. A consensus of 33 core TFs was identified, from which four candidate TFs (SlWRKY-78, SlWRKY-75, SlERF-57, and SlGLK-49) were selected for in silico knockout (KO) analysis. The simulations predicted that these knockouts might dysregulate core functional pathways, such as serine-type endopeptidase inhibitor activity and protein binding. Furthermore, CellOracle simulations suggested that the virtual deletion of the guard-cell-associated SlWRKY-78 and SlWRKY-75 could induce a directional trajectory shift from the terminally differentiated guard cells back to the less differentiated mesophyll territory. These findings provide a promising computational framework for deciphering cell-type-specific regulatory programs in horticultural crops. Full article