Search Results (14,831)

Background: Starch accumulation contributes substantially to maize grain yield and quality. Starch synthase III (SSIII) is a key component of the starch biosynthetic enzyme complex. However, its regulatory role in starch accumulation in maize endosperm remains incompletely understood. Methods: The du1-2018 mutant arose spontaneously during a conventional maize breeding program. Phenotypic characterization, storage compound contents, and starch structure were compared between the mutant and wild-type lines. BSA-seq, genetic linkage analysis, and transcriptomic analysis were employed to identify the candidate gene responsible for the mutant phenotype. Transcriptome sequencing was performed on developing kernels to evaluate the genome-wide effects of the du1-2018 mutation. Results: The du1-2018 mutant exhibited dull, glassy, and mildly shrunken kernels, with decreased starch levels and elevated soluble sugar and protein contents. The du1-2018 mutation disrupted starch accumulation, resulting in smaller, irregularly shaped starch granules and significant changes in starch composition and fine structure. This mutation was identified as a severe loss-of-function allele of the dull1 (du1) gene, evidenced by almost undetectable Du1 transcripts in developing kernels. Notably, transcriptomic analysis revealed that a substantial proportion of differentially expressed genes (DEGs) were involved in amino acid and protein metabolism. Conclusions: The novel du1 allelic variant, du1-2018, disrupts starch biosynthesis in maize endosperm, leading to reduced starch accumulation, altered starch structure, and transcriptional changes in nitrogen-related metabolic pathways. Our results provide new insights into the regulatory mechanisms underlying SSIII function in starch synthesis and endosperm development, and suggest potential links to carbon/nitrogen balance, with implications for future genetic improvement of maize grain quality. Full article

Background/Objectives: Cryptorchidism is a common cause of male infertility and often results in azoospermia. However, the metabolic perturbations underlying cryptorchidism complicated with azoospermia and their association with surgical sperm retrieval outcomes remain poorly defined. Methods: A total of 35 patients with cryptorchidism and azoospermia, as well as 40 controls with normal semen parameters, were enrolled in the study. Seminal plasma samples from all participants were subjected to metabolomic analysis. Additionally, some patients underwent micro-TESE; the association between metabolomic features and the success or failure of surgical sperm retrieval was further analyzed. Results: A total of 931 differential metabolites were identified between patients and controls, primarily enriched in lipid metabolism and amino acid metabolism pathways. Lipid metabolites were broadly downregulated in patients, while several inflammation-related metabolites, including Prostaglandin E2, were upregulated. Routine clinical parameters showed no significant differences between patients with successful and failed micro-TESE. However, metabolomic profiles effectively distinguished these two subgroups. These differential metabolites between the two subgroups were mainly involved in three key pathways: phenylalanine–tyrosine–tryptophan biosynthesis, aminoacyl-tRNA biosynthesis, and folate biosynthesis. Most metabolites in the first two pathways were downregulated in the successful retrieval group, while those in the folate biosynthesis pathway showed the opposite regulatory trend. Four metabolites, including Leucine, 7,8-Dihydroneopterin, L-Tyrosine and Pterin, exhibited robust predictive value for micro-TESE outcomes. Conclusions: This study reveals distinct metabolic signatures in patients of cryptorchidism with azoospermia. The identified metabolic biomarkers provide valuable references for clinical decision-making regarding micro-TESE, facilitating a personalized assessment of sperm retrieval feasibility. Full article

Metabolic reprogramming is a defining feature of breast cancer, enabling tumor cells to sustain rapid proliferation, survive under stress, and resist therapy. Key pathways including glycolysis, glutaminolysis, lipid metabolism, and one-carbon metabolism, play central roles in meeting the energetic and biosynthetic demands of malignant cells. Enhanced glycolytic flux supports ATP generation and lactate production, while glutamine metabolism fuels the tricarboxylic acid cycle and provides nitrogen for nucleotide synthesis. Lipid metabolic pathways, particularly fatty acid synthesis, contribute to membrane biogenesis and signaling, and one-carbon metabolism driven by serine and glycine supplies methyl groups for epigenetic regulation and nucleotide production. These metabolic adaptations not only promote tumor growth but also create vulnerabilities that can be exploited therapeutically. Inhibiting these pathways has shown promise in preclinical models; however, challenges such as metabolic plasticity, tumor heterogeneity, and potential toxicity in normal tissues underscore the need for biomarker-driven strategies and rational combination therapies. Herein, we describe current knowledge of the role of these pathways in breast cancer progression, highlighting the role of key enzymes in promoting breast cancer tumor cell growth and in breast cancer prognoses. Full article

Cibotium barometz (L.) J. Sm., a medicinally significant fern in traditional Chinese medicine, is little explored at the genomic level regarding its bioactive compounds. Using an integrated approach combining Illumina and PacBio sequencing technologies, we profiled its root, rachis, and pinna transcriptomes, identifying 12,718, 21,341, and 11,441 unigenes, respectively. Our analysis systematically characterized the transcriptional features of transcription factors (TFs), simple sequence repeats (SSRs), long non-coding RNAs (lncRNAs), and differentially expressed genes (DEGs). Enrichment analyses highlighted the roles of highly expressed unigenes in secondary metabolism. Seventeen key enzymes involved in polysaccharide biosynthesis showed tissue-specific expression patterns. Notably, total polysaccharide content correlated positively with UDP-arabinose 4-epimerase (UXE) expression but negatively with phosphoglucomutase (PGM) and 3,5-epimerase/4-reductase (UER1). Flavonoid accumulation inversely correlated with chalcone synthase (CHS) expression. Two lignin pathways (H-lignin and G-lignin) were characterized, with phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), and cinnamyl alcohol dehydrogenase (CAD) as key genes. The absence of ferulate-5-hydroxylase (F5H) explains the undetected S-lignin pathway. Regulatory network analysis revealed positive correlations between PAL expression and NAC72/NAC78/WRKY35 and C4H expression and WRKY65/WRKY69/WRKY71, while a negative correlation was revealed between flavonoid 3′,5′-hydroxylase (F3′5′H) and MYB3R4. This study provides comprehensive transcriptomic insights into C. barometz bioactive compound biosynthesis, serving as a foundation for mechanistic research. Full article

YUCCA belongs to the flavin-containing monooxygenas and catalyzes the rate-limiting step in endogenous auxin biosynthesis, thereby regulating local auxin homeostasis and participating in diverse aspects of plant growth, development, and physiological processes. However, the relationship between the YUCCA genes and male fertility regulation in wheat remains unclear. In this study, we identified 64 TaYUCCA genes through whole-genome analysis and classified them into three clades, each of which is conserved in motif composition and gene structure. A synteny analysis indicated that family expansion was primarily driven by segmental duplication and tandem duplication, and Ka/Ks analysis suggested that all members are under purifying selection. An analysis of the expression patterns showed that the TaYUCCA genes displayed differential expression across various tissues and reproductive developmental stages. In the temperature-sensitive male-sterile wheat line YS3038, TaYUCCA19, TaYUCCA22, and TaYUCCA25 were specifically highly expressed at the uninucleate pollen stage under fertile conditions. The silencing of TaYUCCA19 resulted in abnormal pollen morphology and a significant reduction in the seed set rate, indicating that it is a key gene required for normal pollen development in wheat. Overall, this study systematically characterizes the wheat YUCCA gene family and provides the first functional evidence of TaYUCCA genes in male reproductive development, offering an important foundation for studies on wheat male sterility mechanisms and the exploitation of heterosis. Full article

Fusarium verticillioides is a significant agricultural pathogen and an emerging causative agent of invasive fusariosis in clinical settings. Fusarium species frequently exhibit resistance to available antifungal agents, yet the molecular mechanisms underlying azole resistance remain poorly characterized. In this study, we identified the Zn(II)₂Cys₆ transcription factor FvADS-1 as a positive regulator of the azole stress response in F. verticillioides. The transcription of FvADS-1 was significantly induced by ketoconazole (KTC), and its deletion increased susceptibility to multiple azole compounds. Mechanistically, FvADS-1 positively regulates the KTC-induced expression of genes encoding ABC transporters and ergosterol biosynthesis enzymes, thereby modulating intracellular KTC accumulation and sterol homeostasis under azole stress. Furthermore, FvADS-1 positively regulates the transcriptional response of peroxisomal genes and contributes to fungal tolerance to oxidative stress. Notably, deletion of FvADS-1 attenuates the virulence of F. verticillioides on maize. The function of ADS-1 is evolutionarily conserved: heterologous expression of N. crassa ads-1 restored azole resistance in FvADS-1 deletion mutant, and the deletion of the F. oxysporum homolog FoADS-1 similarly increased azole susceptibility. Collectively, our study demonstrates that the conserved transcription factor ADS-1 plays a central role in regulating azole resistance and virulence in the pathogen F. verticillioides, offering new insights into antifungal resistance mechanisms in pathogenic filamentous fungi. Full article

Fruit ripening and color change form a complex physiological and biochemical process involving the accumulation and breakdown of a series of metabolites. Brassinolide plays an important role in the regulation of fruit ripening. In this study, the effects of exogenous EBR (2,4-epibrassinolide) and BRZ (Brassinazole, an inhibitor of BR biosynthesis) on fruit color change were investigated using ‘Micro-Tom’ tomatoes (Solanum lycopersicum L.) as an experimental material. The experiment was set up with five treatments: CK (distilled water + 0.01% Tween-80) and T1–T4 (0.05, 0.1, 0.15, 0.2 mg/L EBR). In addition, a BRZ-treated group (4 μmol/L BRZ + 0.01% Tween-80) was set up in a follow-up experiment. The results showed that different concentrations of EBR treatments significantly increased the carotenoid and lycopene contents and decreased the chlorophyll contents in fruits compared with CK, with the T3 treatment (0.15 mg/L EBR) showing the most significant effect. Simultaneously, EBR induced the expression of the carotenoid metabolism genes SlGGPPS, SlPSY, SlPDS and SlZDS and promoted carotenoid accumulation. On the 20th day, compared with the CK and BRZ treatments, chlorophyll a and chlorophyll b contents were significantly reduced by 20.06% and 46.03% respectively; the expression of the chlorophyll degradation-related genes SlNYC, SlSGR1, SlPPH, and SlPAO was upregulated under a 0.15 mg/L EBR treatment, accelerating chlorophyll degradation. Furthermore, the EBR treatment reduced fruit brightness (L*) and increased fruit red saturation (a*), while yellow saturation (b*) showed an increasing and then decreasing trend; on the 20th day, compared with CK and BRZ, the red saturation of the EBR treatment group increased by 125.57% and 67.37% respectively, while the brightness decreased significantly by 24.28% and 23.83% respectively. In conclusion, exogenous application of 0.15 mg/L EBR significantly accelerated fruit ripening and color transformation by promoting the accumulation of carotenoids and the degradation of chlorophyll. Full article

Background/Objectives: Candidozyma auris is the most frequent multidrug-resistant fungal infection in the Arabian Peninsula, with high mortality rates; therefore, new medications are in high demand. Microbes in marine habitats have genetically evolved to survive under a variety of adverse conditions, including severe temperatures, salinity, pH, and other stress factors, by generating various bioactive metabolites. These bioactive secondary metabolites have strong potential for use as antifungal agents. Due to the shortage of antifungal medications and the emergence of treatment resistance in C. auris, identifying new therapeutics from synthetic bacterial components or natural materials has become a necessity. Natural molecules have numerous advantages over synthetic substances, including structural variation and low toxicity. Few next-generation sequence-based investigations have been carried out on anti-Candidozyma auris bacterial species to identify potential therapeutic candidates. Therefore, the aim of this study is to identify biosynthetic gene clusters from marine bacteria using next-generation sequencing to discover novel drug compounds against multidrug-resistant C. auris. Methods: More than 68 isolates were collected from various marine environments using standard techniques. All isolates were tested against the multidrug-resistant C. auris. Scanning electron microscopy was utilized to investigate the cell membrane rupture caused by defused metabolites of the IRMCESH58L bacterium in C. auris. The Vibrio sp. IRMCESH58L genome was sequenced using long-read nanopore sequencing technology. Results: The bacterial strain IRMCESH58L, isolated from a fish liver sample, showed the highest and most constant activity against C. auris. An in vitro toxicity test found that IRMCESH58L had no cell cytotoxicity against HFF-1 cells. The assembled plasmid-free genome is 6,556,025 bp (48.93% G+C), with an N50 of 909243. Comparative analysis confirmed its relation to Vibrio alginolyticus. Conclusions: Whole-genome analysis of the native bacterial strain IRMCESH58L revealed various biosynthetic gene clusters, including those involved in surfactin’s biosynthesis of putative natural anti-C. auris chemicals, but no pathogenic protein-coding genes, emphasizing the importance of marine bacteria in the fight against C. auris. Following this in vivo study, therapeutic targets will later be selected for further pre-clinical studies. Full article

Mitochondrial biogenesis requires coordinated expression from both nuclear and mitochondrial genomes. To understand the consequences of mitochondrial genome loss, we generated a mitochondrial DNA-depleted line (crm⁻) in Chlamydomonas reinhardtii via long-term ethidium bromide treatment. We then examined how mtDNA disruption affects mitochondrial ultrastructure, chloroplast function, and the mitochondrial transcription termination factor (mTERF) gene family. Our results reveal that mitochondrial dysfunction is associated with severe organelle remodeling, including mitochondrial elongation, matrix condensation, and cristae collapse. Consequently, mitochondria reduce the electron sink capacity which appears to over-reduce the chloroplast electron transport chain, correlating with causing damage to photosystem II (PSII), as indicated by higher plastoquinone PQ redox state and PSII excitation pressure and lower non-photochemical quantum yield [Y(NPQ)]. Furthermore, we identified and characterized eight nuclear-encoded mTERF genes in C. reinhardtii (CrmTERFs). Phylogenetic analysis grouped them into three clades with potential functional conservation. Collinearity analysis suggested potential evolutionary relationships between mTERF genes in Chlamydomonas and Marchantia polymorpha. Gene ontology annotation linked CrmTERFs to transcription termination and RNA biosynthesis regulation. Additionally, in silico prediction identified twelve putative miRNAs targeting seven of the eight CrmTERFs, with CrmTERF3 as the only exception, providing candidates for future experimental validation. This study provides the first comprehensive analysis of the nuclear encoded mTERF gene family in Chlamydomonas and demonstrates that mtDNA loss is correlated with mTERF genes expression, as well as mitochondrial structure and chloroplast photoprotective impairments. These findings suggest a potential role for CrmTERFs in mitochondrial retrograde signaling and organellar crosstalk, though functional validation is required to establish causality. Full article

Silphium perfoliatum is a promising economic plant rich in bioactive secondary metabolites, yet the molecular regulation of phenylpropanoid biosynthesis across development remains unclear. To elucidate the regulatory networks underlying these metabolic processes, we integrated metabolomic and transcriptomic analyses across six developmental stages, from cotyledon to flowering. LC–MS/MS identified 1964 metabolites, with phenylpropanoids representing the largest class (601 compounds). Differential accumulation analysis showed pronounced temporal dynamics in phenylpropanoid levels, especially chlorogenic acid and its derivatives, with many compounds peaking at the flowering stage. In parallel, RNA-seq revealed 31,624 differentially expressed genes (DEGs). Functional enrichment highlighted phenylpropanoid and flavonoid biosynthetic pathways as major metabolic hubs. Correlation analysis indicated that PAL, 4CL, HCT, F3H, FLS, and F3′H expression was tightly coordinated with the accumulation of phenolic acids and flavonoids, suggesting these gene encoded enzymes may represent rate-limiting steps. Furthermore, weighted gene co-expression network analysis (WGCNA) identified a “blue” module strongly associated with phenylpropanoid accumulation and significantly enriched in pathway-related genes. Together, these results provide a comprehensive regulatory framework for phenylpropanoid biosynthesis in S. perfoliatum and offer valuable genetic targets for metabolic engineering and molecular breeding to enhance bioactive compound production. Full article

(1) Background: The objective of this study was to investigate the modulatory effects of thiamine on BHBA metabolism, milk yield, and the rumen microbial ecosystem. (2) Methods: A total of 24 SCK dairy cows with similar body conditions were selected and randomly allocated to SCK (SCK) or SCK with thiamine supplement (SCKT) treatment. Twelve healthy dairy cows served as the control (CON) treatment. Milk yield, milk quality, ruminal fermentability parameters, rumen and fecal microbial communities were further measured. (3) Results: Thiamine significantly decreased BHBA content, milk CFUs, and somatic cells, while significantly increasing milk yield, milk fat, acetate, and the A/P ratio (p < 0.05). Thiamine-treated cows exhibited significantly increased ruminal and fecal Proteobacteria but significantly decreased ruminal Firmicutes (p < 0.05) as well as fecal Spirochaetes and Cyanobacteria (p < 0.05), compared with SCK cows. Functional analysis showed that differential rumen bacteria exhibited high energy metabolism, nucleotide metabolism, and glycan biosynthesis and metabolism, while the metabolism of terpenoids and polyketides were the primary functional pathways of differential fecal microbiota. (4) Conclusions: Thiamine supplementation in SCK cows effectively alleviated subclinical ketosis by reducing BHBA content, enhancing ruminal fermentability, and proliferating rumen microbial communities, leading to improved milk yield in the early-lactation period. Full article

Silver nanoparticles were biosynthesized using the culture supernatant of Staphylococcus sp. YRA, a strain isolated from Colombian mining sediments. Synthesis was optimized at 1 mM AgNO₃, pH 7, 40 °C and 7 μg/mL extract, producing spherical, protein-capped AgNPs with primary sizes in the tens-of-nanometers range (~35–90 nm by SEM), while DLS indicated larger hydrodynamic diameters (~250–320 nm) consistent with aggregation in suspension (ζ-potential −16.6 mV). These nanoparticles remained stable over 6 months. Characterization by UV–Vis, SEM, AFM, EDS and FTIR confirmed extracellular protein-mediated reduction and capping. The AgNPs showed antibacterial activity against multidrug-resistant clinical isolates (Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Salmonella bongori, Enterococcus spp.), with inhibition zones of 8–16 mm at 400–1000 μg/mL. Biofilm formation was reduced by >50% at 700 μg/mL in both Gram-positive and Gram-negative strains. In Phaseolus vulgaris (P. vulgaris), low concentrations (5–100 μg/mL) increased growth and chlorophyll content, while 500 μg/mL caused moderate inhibition. FTIR analysis identified amide and thiol groups from bacterial enzymes as capping agents. These results suggest Staphylococcus sp. YRA as a bacterial platform for AgNPs production with antibiofilm activity against MDR pathogens and acceptable phytotoxicity profile for potential applications. Full article

The tumor microenvironment (TME) plays a key role in driving tumor progression, metastasis, and resistance to therapy. The TME is a highly variable ecosystem composed of both cancer and surrounding normal cells, immune survey cells and the extracellular matrix, also composed of signaling molecules that mediate interactions between them. Blood cancer cells pose a unique challenge because of their circulation and widespread distribution along with their capacity to invade various niches, interacting with a wide range of host cells such as fibroblasts, immune cells, endothelial cells, and adipocytes. Metabolism reprogramming in this tumor context, notably referring to elevated cholesterol and fatty acid metabolism, emerges as a crucial event in shaping an immune-suppressive microenvironment that promotes tumor progression. Cholesterol and fatty acids are supplied by both de novo biosynthesis and exogenous uptake from lipoproteins. Lipoproteins are pseudo-micellar structures, designed to transport essential water-insoluble metabolites, including triacylglycerols and cholesterol, in the plasma, lymph, and interstitial fluids. A number of studies have reported abnormal circulating lipoprotein levels in leukemic patients and have suggested that lipoproteins are key for cancer cells to thrive. However, the role of lipoprotein metabolism in cancer cells in the context of the TME is still incompletely discussed so far. The aim of this review is to consider the importance of lipoprotein metabolism in shaping the tumor microenvironment in the context of hematological malignancies. Full article

Understanding the ecological drivers of plant-associated microbiota is essential for predicting grassland ecosystem resilience. This study aimed to characterize the community structure, functional potential, and soil environmental drivers of rhizosphere and root endophytic microbiota associated with Polygonum divaricatum across three Hulunbuir Grassland sites. A nested sampling design was applied with three replicated plots per site, from which paired rhizosphere soil and root samples were collected. Each sample represented a composite of 15 plants, yielding six samples per site (total n = 18) and allowing the separation of compartmental and environmental effects on community assembly. P. divaricatum plays a key role in nutrient cycling and soil stability; however, its rhizosphere and root microbiomes remain poorly characterized. Fungal diversity was consistently higher in the root endosphere, whereas bacterial diversity was greater in rhizosphere soils. Fungal assemblages were dominated by Ascomycota and Mortierellomycota, primarily represented by Mortierella and Trichoderma, while bacterial communities were dominated by Actinomycetota and Pseudomonadota, enriched in Bradyrhizobium and Pseudonocardia. Community differentiation reflected strong compartmental filtering and responses to soil pH, organic carbon, nitrogen, and enzyme activities. Functional prediction indicated clear compartmental partitioning: in the rhizosphere, bacterial communities were enriched in pathways related to carbon and nitrogen metabolism and secondary metabolite biosynthesis, whereas in the root endosphere, functional profiles were more associated with transport, uptake, and fermentation; fungal communities were dominated by saprotrophic and symbiotrophic guilds. These findings demonstrate that soil biochemical gradients and host-driven filtering jointly structure the P. divaricatum microbiome, providing ecological insights into plant–microbe–soil interactions and the maintenance of grassland ecosystem stability. Full article

Aril paleness (AP) is a new physiological disorder of pomegranate (Punica granatum L.) characterized by pale, dry and tasteless arils, while the peel remains healthy-looking. Its molecular basis is unknown. We used an integrated metabolomic and targeted gene expression approach on arils from four Iranian cultivars displaying no to severe AP symptoms. LC-MS profiling detected 617 reliable metabolites, with 266 metabolites consistently reduced in all symptomatic samples. Enrichment analysis revealed that arginine biosynthesis, glutathione metabolism and primary amino acid metabolism were the processes most strongly affected by AP. Protein interaction network analysis indicated that the arginine degradation pathway is the primary down-regulated module that interacts with the anthocyanin biosynthetic machinery, primarily through phenylalanine ammonia-lyase (PAL) hubs. Based on this network, seven genes representing both pathways were selected for targeted expression analysis. The qPCR analysis showed strong repression of arginase (PgADS, XM-031537872), aldehyde dehydrogenase (PgAL12A1, XM-031551051) and anthocyanin synthase (PgOXKF, KF841619.1) in the cultivar ‘Torud’ exhibiting severe AP symptoms compared with the symptom-free cultivar ‘Damavand’. In contrast, phenylalanine ammonia-lyase (PgPAL1, KY094504.2) was unexpectedly induced 33-fold in the cultivar ‘Torud’, while the downstream anthocyanin-related UDP-glucosyltransferase (PgUGT, MK058491.1) remained unchanged. These findings suggest that the collapse of arginine metabolism, combined with the downstream blockage of anthocyanin biosynthesis, underlies AP. These findings provide the first molecular insights into the mechanisms underlying AP, offering a basis for breeding and post-harvest strategies aimed at enhancing pomegranate’s AP tolerance. Full article