Search Results (149)

Fruit spine formation in spinach (Spinacia oleracea L.) affects seed processing and mechanized sowing, yet its molecular basis underlying this trait remains unclear. Therefore, we performed comparative transcriptome analysis of two contrasting genotypes, Sp35 (spiny) and Sp34 (spineless), at early morphogenesis and late developmental stages. RNA-seq analysis identified 3002 differentially expressed genes (DEGs) at the early developmental stage and 2737 DEGs at the later stage. Intersection analysis revealed that 1080 DEGs were differentially expressed in both stages, suggesting that these shared genes may play particularly important roles. Functional enrichment analysis of these 1080 shared DEGs revealed involvement in cell wall biogenesis, phenylpropanoid biosynthesis, and carbohydrate metabolism, highlighting roles for secondary cell wall formation and lignification in spine development. To identify the key regulatory gene, weighted gene co-expression network analysis (WGCNA) was conducted and found a significantly correlated gene module. In this co-expression gene module, a MYB transcription factor SOV2g002850 occupies a central position. Additionally, several MADS-box genes and WRKY regulatory genes were also identified in the co-expression network. Overall, this study provides a comprehensive transcriptomic framework for spinach spine development and identifies candidate genes for future functional validation and breeding. Full article

Background/Objectives: Triple-negative breast cancer (TNBC) is frequently characterized by notably elevated Ki-67 expression, a hallmark of uncontrolled rapid cell-cycle progression. However, the underlying mechanisms remain unclear, leading to limited therapeutic options. Methods: In this study, hub gene was identified through integrated bioinformatic analysis of public datasets (TCGA-BRCA and METABRIC). Subsequent functional validation was performed both in vitro and in vivo using siRNA-mediated knockdown and small-molecule inhibitors. Phenotypic effects—including cell viability, cell cycle distribution, DNA synthesis, and clonogenic survival—were comprehensively assessed using MTT assays, flow cytometry, EdU, and colony formation assays. Protein-level changes were confirmed by Western blotting and immunohistochemistry (IHC). To dissect the transcriptional regulation of the key hub gene TTK, we first predicted potential upstream transcription factors using the JASPAR database; binding specificity was then validated through in silico motif analysis, luciferase reporter assays, and chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR). Results: The mitotic kinase TTK is significantly overexpressed in TNBC compared with non-TNBC breast cancers. Notably, TTK overexpression exhibited a strong positive correlation with elevated Ki-67 indices and reduced overall survival in TNBC patients. Functional validation demonstrated that pharmacological or genetic inhibition of TTK effectively induced G2/M cell-cycle arrest and potently suppressed TNBC proliferation in both in vitro cell cultures and in vivo xenograft models. Mechanistically, TTK overexpression stems from enhanced transcriptional initiation driven by the transcription factor NFYA binding to the CCAAT box in the TTK promoter—an interaction newly identified here. Concurrently, TTK blockade disrupted spindle assembly checkpoint (SAC) signaling via BUB1B/MAD1L1 downregulation, triggering mitotic arrest and catastrophe. Conclusions: Collectively, these findings establish TTK as a key cell-cycle regulator driving TNBC proliferation. More importantly, targeting mitotic control through TTK inhibition represents an efficient strategy to impede the aberrantly fast cell cycle progression in TNBC. Full article

Sulfated peptides, such as PSK, PSY, CIF, and RGF, are crucial regulators of plant growth, development, and stress responses, with their activity dependent on post-translational tyrosine sulfation by tyrosylprotein sulfotransferase (TPST). This study explores the evolutionary history and the interaction mechanisms between TPST and sulfated peptides in plants. Systematic analyses of multi-species genomes show that TPST can be traced back to the chlorophyte lineage, whereas PSK, a sulfated peptide, appears to have emerged in gymnosperms. TPST is evolutionarily conserved, typically present in low copy numbers across plant lineages, while its peptide substrates have expanded in angiosperms. In Liriodendron chinense, TPST-sulfated peptide gene promoters are enriched with cis-regulatory elements linked to abscisic acid, gibberellin responsiveness, and anaerobic induction. Synteny analyses revealed collinearity between sulfated peptide genes in L. chinense, Magnolia biondii, Arabidopsis thaliana, and Populus trichocarpa, but not with Oryza sativa. Molecular docking identified key TPST-PSK interaction sites in the sulfotransferase domain, with several critical residues facilitating binding. Transcriptomic and co-expression network analyses revealed that LcTPST was expressed at lower levels than its peptide precursor genes, while LcPSK2 remained highly expressed after the torpedo stage of somatic embryogenesis. Stress conditions significantly increased PSK-associated module connectivity, enriched in transcription factors such as WRKY, bHLH, bZIP, and MADS. This study provides insights into the evolutionary, structural, and regulatory aspects of the TPST-sulfated peptide system in plants. Full article

Safflower (Carthamus tinctorius L.) is a traditional economic crop in China valued for its medicinal petals and high-quality seed oil. Despite the importance of floret number and capitulum architecture for petal yield in safflower, the molecular regulators linking auxin signaling to inflorescence development in this species remain poorly understood. Auxin response factors (ARFs) are key transcriptional regulators mediating auxin-responsive gene expression and developmental processes, yet their functions in safflower inflorescence development have not been systematically investigated. In this study, we identified 25 CtARF genes from the safflower genome and classified them into five phylogenetic subfamilies. Cis-regulatory analysis predicted the presence of hormone- and development-related elements in CtARF-associated promoter regions. Expression profiling revealed that CtARF4, a member of the CtARF III subfamily, exhibits preferential expression during flower development. CtARF4 was localized to the nucleus and shown to interact with the CtMADS24 promoter and the Aux/IAA protein CtIAA9 in heterologous systems. Transient overexpression of CtARF4 increased floret number and length and promoted flowering, whereas virus-induced gene silencing resulted in opposite phenotypes. In addition, CtARF4 perturbation was associated with a reduction in IAA content as measured by a kit-based assay. Collectively, these findings suggest that CtARF4 functions as an auxin-responsive transcriptional regulator contributing to inflorescence development in safflower. Full article

AGL6 genes are critical floral regulators in diverse angiosperms, yet their roles in legumes remain poorly understood. This study aimed to characterize GmAGL6 genes in soybean (Glycine max [L.] Merr. cv. Williams 82). We identified four homologs (GmAGL6a–d) featuring conserved MADS-box and K-box domains that cluster within the AGL6 lineage. Tissue-specific expression profiling revealed significant transcript enrichment during flower bud differentiation and maturation. Using CRISPR/Cas9, we generated quadruple knockout lines to evaluate gene function. Phenotypic analysis showed that, unlike the homeotic transformations typical of AGL6 loss in monocots, Gmagl6 quadruple mutants retained a standard papilionaceous floral structure without keel petal aberrations. However, the mutants did not show significant changes in floral height or width, but exhibited a significantly increased floral height-to-width ratio and smaller mature seeds, while vegetative architecture and podding capacity remained unaffected. These results suggest that GmAGL6 genes in soybean may function primarily in the regulation of floral proportion and seed development rather than floral organ identity. This research provides insights into the evolution of specialized legume flowers and suggests candidate genes for seed size improvement. Full article

Tomato (Solanum lycopersicum L.) is a globally important vegetable crop and a key model species for studying reproductive development in other Solanaceae members with edible fleshy fruits, such as eggplant, sweet and hot peppers, and Physalis spp. The morphogenesis and patterning of tomato floral organs fundamentally determine fruit yield and quality. Recent advances in high-throughput sequencing and gene editing have significantly deepened our understanding of the molecular network regulating tomato reproductive development. This process, from the transition of vegetative shoot apical meristem to the inflorescence meristem, forming floral meristems with primordia of sepals, petals, stamens, carpels, and fruits, is precisely coordinated by a genetic network involving homeobox and other types of transcription factors, along with signaling pathways. This review systematically outlines the core regulatory network, with an emphasis on the MADS-domain transcription factor family and its associated ABCDE model. Integrating insights from hormone signaling and mutant phenotypes, we summarize the maintenance of inflorescence meristem identity, the specification of floral meristems, and the morphogenetic patterns and core gene regulatory mechanisms for each floral whorl in tomato. We further extend this framework to the flower–fruit continuum, examining how carpel development, floral meristem termination, and ovule differentiation influence fruit morphology, locule number, pericarp structure, and metabolic traits. Finally, we discuss the integration of floral organ development with molecular design breeding and formulate a forward-looking research agenda that translates floral regulatory mechanisms to breeding strategies for yield, uniformity, and fruit quality. This synthesis provides a theoretical foundation and genetic resources for the genetic improvement of tomato flower architecture and its underlying regulatory mechanisms. Full article

The coloration of vegetative organs in grapevine (Vitis vinifera L.) is an important phenotypic trait associated with environmental responsiveness and stress adaptation; however, its genetic regulatory mechanisms remain poorly understood. To systematically elucidate the genetic basis of vegetative coloration, a genome-wide association study (GWAS) was performed using 151 grapevine accessions, integrating high-depth whole-genome resequencing data with phenotypic evaluations of eight coloration traits across two consecutive years (2023–2024). Using a mixed linear model (MLM), 13 stable and significant SNP loci were identified on chromosomes 3, 5, 6, 13, 14, 15, 16, and 18, explaining 13.28–19.35% of the phenotypic variation. Within ±15 kb of these loci, 16 candidate genes were identified. qRT-PCR analysis of key candidates revealed that VIT_06s0004g03620 (mitogen-activated protein kinase), VIT_16s0039g01900 (MYB-like domain-containing protein), and VIT_14s0083g01050 (MADS-box protein 2) showed significant positive correlations between expression levels and coloration intensity, with distinct expression patterns among accessions exhibiting different coloration grades. These genes are likely involved in the regulation of anthocyanin accumulation. Collectively, this study elucidates the genomic architecture underlying vegetative organ coloration in grapevine and provides valuable candidate genes and SNP markers for functional validation and molecular-assisted breeding. Full article

Background: Conventional omics analysis often treats outliers as noise, yet they may harbor critical biological insights. Objetive: This study proposes a paradigm shift: actively investigating outliers to discover biologically relevant subtypes within metabolic–inflammatory syndromes. Methods: We applied a comprehensive analytical framework for outlier detection based on a multi-algorithm consensus (IQR, MAD, Isolation Forest) to a clinical cohort of diabetic neuropathy (n = 93) and an in vitro 3T3-L1 adipocyte model (n = 39). The identified outliers were characterized using robust PCA, co-expression networks, unsupervised clustering, and Random Forest predictive modeling. Results: In the clinical cohort, an outlier subgroup (47.3%) exhibited an extreme immune–metabolic phenotype characterized by hyperactivation of Th1/Th17 pathways (elevated T-bet and IL-17; p < 0.001), hypertriglyceridemia, and network reconfiguration (TGFβ and STAT4 hubs). In the cellular model, outlier samples (12.8%) showed autonomous pro-inflammatory behavior characterized by IL-6 overproduction (p = 0.002) and IL-10 suppression. Conclusions: Multivariate analysis confirmed spatial segregation of these profiles. Systematic outlier investigation revealed discrete pathophysiological subtypes invisible to mean-focused analyses, demonstrating that extreme values encapsulate potent biological signals. This framework offers a generalizable approach for uncovering clinical heterogeneity and identifying therapeutic targets in complex diseases. Full article

Colorectal cancer (CRC) is a prevalent and lethal malignancy worldwide. Despite extensive research, core genes for diagnosis and prognosis in CRC remain to be fully elucidated. This study aims to identify novel gene biomarkers for CRC diagnosis and prognosis based on the GEO and TCGA datasets. Integration of TCGA and GEO datasets revealed 197 common differentially expressed genes (DEGs) between CRC tumor and normal samples. Functional enrichment analysis implicated these DEGs in biological processes and signaling pathways critical to CRC progression, including cell cycle regulation and nuclear division. Protein–protein interaction (PPI) network analysis identified 17 hub genes from DEGs, including TROAP, CDKN3, CDCA3, UBE2C, CEP55, KIF11, CDC20, CCNA2, MCM4, CKS2, POLE2, MAD2L1, CCNB1, PTTG1, TPX2, TOP2A, and DLGAP5. All 17 hub genes demonstrated high diagnostic value (AUC > 0.85), including CCNB1 (AUC = 0.944). Based on the Cox proportional hazards regression, an 8-gene prognostic signature (CLCA1, CCNB1, TPM2, MMP3, AOC3, CRYAB, CA4, GUCA2A) effectively stratified patients by survival risk, with a 5-year AUC of 0.71. In vitro, CCNB1 knockdown triggered cell cycle arrest, thereby suppressing the proliferation of colorectal cancer cells. This study validated CCNB1 as a dual-purpose biomarker for CRC diagnosis and favorable prognosis, highlighting its potential utility in clinical management. Full article

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. In Mexico, its higher incidence and lower survival suggest a role for epigenetic factors like DNA methylation (DNAme). We conducted an epigenome-wide association study (EWAS) to define the methylation landscape and identify the profiles associated with ALL and relapse. Bone marrow or peripheral blood samples from pediatric ALL patients at diagnosis and controls without ALL were analyzed using an Infinium MethylationEPIC v2.0 array. Differential methylation was assessed using the ChAMP package. We identified a significant hypermethylated profile in ALL patients compared to controls. Probes in MAD1L1 and RPTOR contained the most differentially methylated CpG sites. Key affected pathways included proliferation, neurotransmission, and neuronal signaling. Survival analysis revealed that hypomethylation of four specific CpGs—cg01052776 (RNH1), cg20747787, cg05001671, and cg01767116 (FBXL22)—was significantly associated with an increased risk of relapse, highlighting their potential as prognostic biomarkers. This study underscores the importance of epigenetic mechanisms in pediatric ALL. Full article

Broccoli (Brassica oleracea L. var. italica) is a biennial or annual herbaceous plant belonging to the species Brassica oleracea in the genus Brassica of the Cruciferae family. The green flower curd serves as the primary edible organ, with its development and preservation critically determining broccoli yield and quality. Given that these processes are regulated by flowering time, understanding the mechanisms underlying floral transition is essential for enhancing broccoli yield and quality. This study aimed to identify the MADS-box family in broccoli and to investigate the function of the BoAGL8 gene in floral induction. We identified a total of 176 MADS-box genes, of which 54 genes were up-regulated and 50 genes were down-regulated under low-temperature treatment. Notably, the expression of BoAGL8 was up-regulated by 6.70-fold under low-temperature induction, prompting us to select and clone this gene for further analysis. Tissue-specific expression profiling further revealed that BoAGL8 is expressed at relatively high level in both mature and young leaves. After 15 days of low-temperature treatment, BoAGL8 expression in shoot tip was significantly upregulated compared to untreated controls. Subcellular localization analysis showed that BoAGL8 protein was located to the nucleus. Ectopic over-expression of BoAGL8 in Arabidopsis exhibited accelerated bolting and flowering, reduced rosette leaf number, and increased seed yield per plant compared to wild-type plants. Furthermore, compared to wild-type controls, transgenic lines exhibited upregulated expression of AtFT, AtAP1 and AtSEP3, alongside downregulation of SVP expression. The above results indicate that BoAGL8 may play a key regulatory role in the process of floral organ development in broccoli, providing an important theoretical basis for future research on flowering time regulation and breeding in broccoli. Full article

The MADS-box gene family is a large family of transcription factors, and its members are widely distributed in the plant kingdom. Members of this family are well known to be crucial regulators of many biological processes and environmental responses. In this study, bioinformatics methods were employed to analyze the MADS-box gene family members in the common oat, focusing on their phylogenetic relationships, gene structures, conserved motifs, evolutionary relationships, promoter analysis and responses to photoperiod and abiotic stress. A total of 175 MADS-box genes were detected in Avena sativa, which were categorized into Type I and Type II. Type II members exhibited more complex gene structures, while each subfamily showed similar gene structures and motifs. Evolutionary analysis identified 138 segmental duplication events and revealed strong syntenic conservation with Triticum aestivum (337 collinear gene pairs). Four categories of cis-elements were detected in the promoter regions of the AsMADS-box genes. qRT-PCR analysis revealed that the expression of six Type II AsMADS-box genes varied in response to ABA, GA, drought and salt. Furthermore, 23 AsMADS-box members were potentially associated with heading date when the common oat plants were exposed to different photoperiod conditions. The overexpression of chr4D_AsMADS95 in Arabidopsis thaliana led to early flowering under long-day and short-day photoperiod conditions, likely associated with a significant increase in the expression levels of flowering-related genes in transgenic plants. These findings will provide useful information for future studies on stress responses and increase our understanding of the network that regulates flowering in the common oat. Full article

Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared with conventional single-petal form. However, the molecular mechanisms underlying this floral trait remain largely undefined. In this study, RNA-based comparative transcriptomic analysis was performed between single- and double-petaled flowers of L. longituba at the fully opened flower stage. Approximately 13,848 differentially expressed genes (DEGs) were identified (6528 upregulated and 7320 downregulated genes). Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed several DEGs potentially involved in double-petal development. Six candidate genes, including the hub genes LlbHLH49, LlNAC1, LlSEP, LlTIFY, and LlAGL11, were identified based on DEG functional annotation and weighted gene co-expression network analysis (WGCNA). Transcription factors responsive to phytohormonal signaling were found to play a pivotal role in modulating double-petal development. Specifically, 123 DEGs were involved in phytohormone biosynthesis and signal transduction pathways, including those associated with auxin, cytokinin, gibberellin, ethylene, brassinosteroid, and jasmonic acid. Moreover, 521 transcription factors (TFs) were identified, including members of the MYB, WRKY, AP2/ERF, and MADS-box families. These results improve the current understanding of the genetic regulation of the double tepal trait in L. longituba and offer a base for future molecular breeding strategies to enhance ornamental characteristics. Full article

Efficient water management is critical for sustainable crop production in arid and semi-arid regions. This study investigated the effects of two irrigation regimes—25% and 50% Management Allowable Depletion (MAD) and two planting patterns (single-row and double-row) on evapotranspiration (ET) partitioning, water use efficiency (WUE), and water footprint (WF) in drip-irrigated faba bean (Vicia faba L.). Field data were combined with a leaf area index (LAI)-based model to estimate the relative contributions of transpiration (T) and evaporation (E) to total ET. The highest grain yield (6171 kg ha⁻¹) and the lowest blue (570 m³ ton⁻¹) and green (68 m³ ton⁻¹) water footprints were recorded under the 25% MAD with double-row planting. This treatment also achieved the highest proportion of transpiration in ET (70%), indicating a shift toward productive water use. In contrast, the lowest-performing treatment (50% MAD, single-row) had the highest total water footprint (792 m³ ton⁻¹) and the lowest transpiration share (44%). Although high-density planting slightly reduced WUE based on transpiration, it improved overall water efficiency when total input (ETc) was considered (1.57 kg m⁻³ for total input WUE, 4.17 kg/m⁻³ for T-based WUE). These findings highlight the importance of integrating irrigation scheduling and planting pattern to improve both physiological and agronomic water productivity. The approach offers a practical strategy for sustainable faba bean production in water-scarce environments and supports climate-resilient irrigation planning aligned with Iraq’s National Water Strategy. Full article

Unconventional food plants (UFPs) are increasingly valued for their nutritional composition and bioactive potential. This study proposes a comprehensive characterization of the chemical and bioactive properties of Pereskia aculeata Miller (Cactaceae) (PA); Xanthosoma sagittifolium (L.) Schott (Araceae) (XS); Stachys byzantina K. Koch (Lamiaceae) (SB); and inflorescences from three cultivars of Musa acuminata (Musaceae) var. Dwarf Cavendish, var. BRS Platina, and var. BRS Conquista (MAD, MAP, and MAC), including the assessment of physical, nutritional, phytochemical, and biological parameters. Notably, detailed phenolic profiles were established for these species, many of which are poorly documented in the literature. XS was characterized by a unique abundance of C-glycosylated flavones, especially apigenin and luteolin derivatives, rarely described for this species. SB exhibited high levels of phenylethanoid glycosides, particularly verbascoside and its isomers (up to 21.32 mg/g extract), while PA was rich in O-glycosylated flavonols such as quercetin, kaempferol, and isorhamnetin derivatives. Nutritionally, XS had the highest protein content (16.3 g/100 g dw), while SB showed remarkable dietary fiber content (59.8 g/100 g). Banana inflorescences presented high fiber (up to 66.5 g/100 g) and lipid levels (up to 7.35 g/100 g). Regarding bioactivity, PA showed the highest DPPH radical scavenging activity (95.21%) and SB the highest reducing power in the FRAP assay (4085.90 µM TE/g). Cellular antioxidant activity exceeded 2000% in most samples, except for SB. Cytotoxic and anti-inflammatory activities were generally low, with only SB showing moderate effects against Caco-2 and AGS cell lines. SB and PA demonstrated the strongest antimicrobial activity, particularly against Yersinia enterocolitica, methicillin-resistant Staphylococcus aureus (MRSA), and Enterococcus faecalis, with minimum inhibitory concentrations ranging from 0.156 to 0.625 mg/mL. Linear discriminant analysis revealed distinctive chemical patterns among the species, with organic acids (e.g., oxalic up to 7.53 g/100 g) and fatty acids (e.g., linolenic acid up to 52.38%) as key discriminant variables. Overall, the study underscores the nutritional and functional relevance of these underutilized plants and contributes rare quantitative data to the scientific literature regarding their phenolic signatures. Full article