Search Results (739)

Improving forage biomass utilization is an important strategy for increasing the efficiency of ruminant production systems. Lignin limits the accessibility of structural polysaccharides to hydrolytic enzymes, reducing biomass deconstruction and nutrient utilization. Modulation of lignin biosynthesis during plant development has emerged as a promising approach to decrease cell wall recalcitrance and improve biomass digestibility. In this study, we evaluated the effects of two lignin biosynthesis modulators, piperonylic acid (PIP) and methylenedioxy cinnamic acid (MDCA), on maize biomass saccharification and plant development under field conditions. Maize plants received one or two foliar applications of each modulator, and saccharification was assessed in different plant organs. Neither treatment affected plant morphology, growth, or biomass productivity. Both modulators significantly increased biomass saccharification across multiple plant organs, with gains ranging from 31% to 72%. For whole-plant biomass, PIP increased saccharification by 62% and 74% after single and double applications, respectively, whereas MDCA increased saccharification by 42% and 76%. Although both compounds were effective, PIP showed a consistent performance following a single low-dose application. These results demonstrate the potential of lignin biosynthesis modulators to improve maize biomass digestibility without compromising agronomic performance, supporting their use as a potential strategy to enhance forage quality and livestock production efficiency. Full article

Anthocyanin is the primary determinant of visual quality in red-fleshed apples. Iron (Fe) contributes to alleviating chlorosis and improving fruit quality, including anthocyanin accumulation. However, the mechanism linking Fe nutrition to anthocyanin content remains unclear, particularly in red-fleshed cultivars. Here, we evaluated how foliar Fe application influenced anthocyanin and soluble sugar contents in apple flesh and investigated the associated transcriptional responses using RNA-seq. Fe increased leaf chlorophyll content and promoted the accumulation of soluble sugars and anthocyanins in fruits grown in calcareous soil. RNA-seq analysis identified 323 differentially expressed genes (DEGs) in response to Fe treatment. Specifically, multiple DEGs were associated with sugar biosynthesis and transport, anthocyanin biosynthesis, and phytohormone biosynthesis. Based on RNA-seq and physiological analyses, we proposed that Fe may promote anthocyanin accumulation through three putative mechanisms: (i) elevating sugar levels via increased leaf chlorophyll content, thereby providing substrates and signals; (ii) activating key anthocyanin structural genes and related transcription factors; and (iii) stimulating ethylene and brassinosteroid biosynthesis and signaling pathways involved in anthocyanin accumulation. This work provides new insight into the Fe-mediated regulatory network underlying anthocyanin accumulation, offering a practical basis to refine fertilization strategies for fruit quality improvement in red-fleshed apples. Full article

Magnesium (Mg) deficiency is common in acidic orchard soils and can limit fruit crop growth and quality. This study evaluated whether foliar-applied magnesium oxide nanoparticles (MgO NPs) could improve Mg nutrition and fruit quality in ‘Ninghaibai’ loquat grown under Mg-deficient acidic soil conditions. Pot and field experiments were conducted using water as the control and MgSO₄-50eq as an equimolar Mg comparator. MgO NPs showed a concentration-dependent effect, and 200 mg/L produced the best overall performance among the tested concentrations. At this concentration, total biomass increased by 47.27%, compared with CK, accompanied by enhanced chlorophyll accumulation, antioxidant enzyme activities, and Mg uptake. In fruit, 200 mg/L MgO NPs increased soluble solids content by 45.67% and reduced titratable acidity by 53.26%, while also improving fruit size and sugar–acid balance. Leaf transcriptome analysis suggested that MgO NPs altered the expression of genes involved in metabolism, stress response, and secondary metabolite biosynthesis. At the 50 mg/L level, MgO NPs produced stronger responses than the equimolar MgSO₄ treatment in Mg uptake, nutrient acquisition, and several fruit-quality traits. However, excessive application at 500 mg/L weakened growth and quality improvement. Overall, foliar application of 200 mg/L MgO NPs may represent a promising strategy for improving loquat growth and fruit quality under the tested Mg-deficient conditions. Full article

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by limited treatment options and poor prognosis. Gemcitabine is a commonly used chemotherapy; however, gemcitabine resistance in PDAC poses a critical barrier to effective treatment, as the underlying mechanisms are not yet fully understood. Methods: This study employs an exploratory untargeted metabolomics approach to investigate metabolic differences in PDAC cells in the presence and absence of gemcitabine treatment. HPAF-II, MIA PaCa-2, and BxPC-3 cell lines were used as models for gemcitabine-resistant, moderately responsive, and permissive PDAC cells, respectively. Results: MTT assay results revealed that BxPC-3 cells are highly sensitive to gemcitabine treatment, HPAF-II cells are the most resistant, and MIA PaCa-2 cells exhibit moderate sensitivity. Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) of the metabolomics data demonstrated clear differentiation of gemcitabine-treated and untreated (control) cells. When comparing the treated vs. control conditions, 170 metabolites matched to an in-house library of standards were significant (p < 0.05 or fold change ≥ 2 or VIP ≥ 1) differentiators in HPAF-II cells, whereas MIA PaCa-2 and BxPC-3 cells had 178 and 218 differentiating metabolites, respectively. HPAF-II cells treated with gemcitabine had significantly higher levels of N-acetylneuraminic acid and 7-dehydrocholesterol compared with the control group. In contrast, these metabolites were significantly lower or non-significant in BxPC-3 treated cells. Pathway analysis revealed that the steroid biosynthesis pathway was significantly perturbed in HPAF-II cells, whereas amino sugar and nucleotide sugar metabolism was predominantly altered in BxPC-3 cells. Conclusions: Overall, this exploratory study reveals metabolic differences between treated and untreated cells to derive targeted therapeutic strategies that could be used in the future to improve treatment outcomes for PDAC patients. Full article

Beyond nutrition, taste quality is a key quality trait driving the global popularity of Agaricus bisporus. This study systematically investigated non-volatile taste-related metabolite dynamics in caps and stipes during fruiting body development using non-targeted metabolomics. Among 1358 identified metabolites (974 in caps, 997 in stipes), 328 taste-related metabolites were screened. Applying screening criteria of VIP > 1, p < 0.01, and fold change ≥ 2 or ≤ 0.5, 492 and 446 differentially accumulated metabolites (DAMs) were identified in cap and stipe during fruiting body development, respectively. Cross-tissue comparison revealed 975 tissue-specific DAMs between cap and stipe across all developmental stages. Notably, 127 and 116 taste-related DAMs in cap and stipe, respectively, exhibited seven distinct accumulation profiles. Key umami-related compounds, aroma precursors, and antioxidants peaked in cap tissue at stage 3 (closed cup stage), suggesting a preliminary optimal harvest timing for market-quality mushrooms based on metabolic profiling of non-volatile taste-active compounds. Organic acids and nucleotides were more abundant in immature stages, while phosphorylated six-carbon sugars showed stipe-dominant accumulation at middle–late stages. Notably, all taste-related conclusions are inferred from non-volatile metabolite characterization rather than direct sensory measurements. KEGG pathway enrichment highlighted that taste-related metabolites primarily shaped taste via amino acid biosynthesis, cofactor metabolism, lysine biosynthesis, and nucleotide pathways. These insights provide a metabolic foundation for optimizing cultivation strategies and enhancing product quality in Agaricus bisporus. Full article

Glycosphingolipids (GSLs) are glycoconjugates in which a short and heterogeneous saccharide chain is attached to a lipid moiety called ceramide. Based on their sugar backbone, mammalian GSLs are primarily grouped into the ganglio-, lacto-/neolacto-, and globo-series. Sialic acid—containing GSLs are known as gangliosides. Complex ganglio-series gangliosides are particularly abundant in the brain, whereas simple ganglio-series gangliosides, as well as those belonging to other series or neutral GSLs, are less abundant and typical of non-neural tissues. Congenital disorders in the biosynthesis of the lipid moiety of sphingolipids (SLs) result from defects in enzymes and proteins involved in ceramide biosynthesis and transport. Congenital disorders in the biosynthesis of the sugar chain of GSLs specifically affect ganglio-series ganglioside biosynthesis and are caused by pathogenic variants in GM3 synthase (ST3GAL5) or GM2/GD2/asialo-GM2 synthase (B4GALNT1). Defective variants of the sialyltransferase ST3GAL3 and the galactosyltransferase B4GALT5 have been reported and proposed to impair GSL biosynthesis. The occurrence of these syndromes has provided new insights into the physiological and pathological roles of GSLs. Most of these disorders are associated with completely inactive enzyme variants, leading to severe neurological syndromes. Only a few cases highlighted variants that retained partial activity, resulting in milder phenotypes, which included non-syndromic intellectual disability. It is therefore conceivable that many undiagnosed patients, with mild neurological symptoms, may carry variants retaining residual enzyme activity, insufficient to ensure normal levels of brain GSLs. The purpose of this article is to encourage clinicians to look for additional GLS hereditary disorders associated with a milder phenotype. We also hope to boost future investigations by highlighting the most critical issues emerging from recent literature on SL and GSL biosynthesis and their related defects. Full article

Southern corn leaf blight (SCLB), caused by Bipolaris maydis, poses a serious threat to maize production worldwide. In our previous study, Bacillus velezensis BV3 was isolated and demonstrated strong antagonistic activity against maize leaf spot pathogens and effective disease control in greenhouse experiments. In this study, we evaluated the plant growth-promoting effects of BV3 on two maize cultivars through root application in pot experiments, and investigated the underlying molecular mechanisms using transcriptomic and metabolomic analyses. Inoculation with BV3 significantly promoted maize growth. Moreover, BV3 treatment induced extensive transcriptional and metabolic reprogramming in maize. Transcriptomic analysis identified numerous differentially expressed genes (DEGs) mainly enriched in plant–pathogen interaction, plant hormone signal transduction, MAPK signaling pathway, and phenylpropanoid biosynthesis pathways. Metabolomic analysis revealed substantial changes in metabolite accumulation, particularly in lipids, amino acids, sugars, organic acids, and polyphenols, with enriched pathways including secondary metabolite biosynthesis, phenylpropanoid biosynthesis, and flavonoid biosynthesis. LC/MS and GC/MS analyses further revealed that BV3 produced diverse bioactive compounds. 2,4-DTBP and surfactin exhibited strong antifungal activities, particularly against B. maydis and Exserohilum turcicum. Overall, Bacillus sp. BV3 exhibits strong biocontrol efficacy against maize leaf spot pathogens and significant plant growth-promoting activity, highlighting its potential as an eco-friendly biocontrol agent for the management of southern corn leaf blight. Full article

Packing density regulates the microenvironment of tobacco (Nicotiana tabacum L.) fermentation and may thereby influence microbial activity and product quality. However, its effects on microbial community assembly and quality formation remain poorly understood. This study aimed to clarify how packing density affects flue-cured tobacco quality by shaping microbial communities, functional potential, and ecological interactions. Here, we investigated the effects of three packing densities (60%, 70%, and 80%) on chemical components, aroma compounds, microbial community structure, functional potential, co-occurrence networks, and assembly mechanisms of flue-cured tobacco (cv. Piaohe No. 2) after 10 days of fermentation. Moderate density (70%) achieved the most balanced chemical profile, with appropriate nicotine retention, potassium/chlorine ratio, and sugar/nicotine balance. T70 also exhibited the highest levels of total esters, total ketones, and β-ionone, key contributors to fruity, floral, and woody aromas. Microbial analysis revealed that T70 supported the highest diversity and was characterized by the enrichment of aroma-related bacterial taxa, including Bacillus and lactic acid bacteria, as well as the fungal genus Pichia. In contrast, T60 favored aerobic nicotine degraders, whereas T80 selected for obligate anaerobes associated with off-odor production. Functional predictions and network analysis showed that T70 upregulated fatty acid and carotenoid biosynthesis pathways and exhibited the highest modularity, indicating a compartmentalized, functionally complementary community. Neutral model fitting revealed increasing stochasticity with density, with T70 displaying a mixed assembly regime. Collectively, our findings show that packing density influences tobacco quality by regulating microbial community composition, functional potential, network interactions, and assembly processes. These results provide a scientific basis for optimizing packing density in tobacco processing. Full article

Soil salinity severely limits plant growth by disrupting cellular homeostasis and inducing oxidative damage. Although ethylene-responsive transcription factors (ERFs) are central regulators of stress responses, the function of ERF013 in salt stress responses remains poorly understood. In this study, we investigated the role of ERF013 in Arabidopsis thaliana using ERF013 overexpression lines (OE-ERF013) and genome-edited (ge-erf013) under 250 mM NaCl stress, in comparison with wild-type control (CK) and salt-treated wild-type (WT) plants. Under salinity stress, OE-ERF013 plants maintained vigorous shoot and root growth, exhibiting a 17% increase in shoot fresh weight and a 100% in root fresh weight relative to WT-T plants, whereas ge-erf013 mutants displayed severe growth inhibition. Salt stress markedly elevated superoxide (O₂⁻) and hydrogen peroxide (H₂O₂) levels in WT-T (62% and 134%) and ge-erf013 plants (122% and 193%) compared with CK, while OE-ERF013 plants showed a significant reduction in O₂⁻·and H₂O₂ levels, which decreased by 34% and 64%, respectively, relative to WT-T. Improved redox homeostasis in OE-ERF013 plants was associated with enhanced catalase (CAT) and superoxide dismutase (SOD) activities (55% and 44%), increased DPPH radical-scavenging activity (62%), maintained total antioxidant capacity (ABTS), and reduced lipid peroxidation, whereas ge-erf013 plants exhibited a 47% increase in malondialdehyde (MDA) content relative to WT-T. Furthermore, OE-ERF013 plants displayed reduced electrolyte leakage and sustained higher relative water content (RWC), with only a 15% decline under salt stress. Transcript analysis revealed strong upregulation of key ion homeostasis genes (SOS1, SOS2, NHX1, and HKT1) in OE-ERF013 plants, while their expression was suppressed in ge-erf013 mutants relative to WT-T. Additionally, OE-ERF013 plants accumulated higher abscisic acid (ABA) levels and showed increased expression of ABA biosynthesis-related genes (ATAO3 and ATABA3), accompanied by enhanced osmotic adjustment through elevated proline, soluble sugars, and sucrose accumulation, as well as improved chlorophyll stability. Collectively, these results demonstrate that ERF013 acts as a positive regulator of responses to salinity by coordinating ABA signaling, antioxidant defense, ion homeostasis, and osmotic regulation in Arabidopsis thaliana. Full article

The intestine, particularly the gut microbiota, and the liver play key roles in digestion, nutrient transformation, and immune regulation in fish. However, limited information is available regarding how different ornamental fish species regulate these systems under identical aquaculture conditions. Therefore, this study systematically compared gut microbiota diversity, structural variation, and predicted ecological functions among eight ornamental fish species reared in the same environment, using 16S rRNA high-throughput sequencing combined with digestive enzyme indices and histological analysis of intestinal and liver tissues. The results showed that goldfish (Carassius auratus) and crucian carp exhibited efficient digestive and absorptive capacities, supported by a thickened muscularis and prominent mucosal layers (p < 0.001). High goblet cell density was observed in red swordtail (Xiphophorus hellerii) and Mickey Mouse platy (Xiphophorus hellerii × X. maculatus) (p < 0.001). Larger hepatocyte perimeter and area were observed in red swordtail (p = 0.022, p = 0.015), whereas platinum mini parrot cichlid and sapphire mini parrot cichlid showed significant hepatocyte vacuolization. Microbial analysis showed that the eight fish species had similar α diversity indices, while the gut microbial profiles of Mickey Mouse platy and golden crucian carp differed the most. At the genus level, beneficial taxa such as Lactococcus, Paracoccus, and Cetobacterium were significantly enriched in red swordtail, sailfin molly, and goldfish, respectively, whereas opportunistic pathogens, including Edwardsiella, Aeromonas, and Acinetobacter, were enriched in Mickey Mouse platy, sapphire mini parrot cichlid, and golden crucian carp, respectively (p < 0.05). Functional prediction based on KEGG pathways indicated that sailfin molly and Mickey Mouse platy exhibited the broadest functional enrichment, primarily involving amino acid metabolism, fatty acid metabolism, and antibiotic biosynthesis. Crucian carp and golden crucian carp showed higher activity in amino acid biosynthesis and glycolysis/gluconeogenesis pathways. The two parrot cichlid species were characterized by enrichment in biofilm formation pathways of pathogenic bacteria and amino sugar and nucleotide sugar metabolism pathways. Goldfish and red swordtail were mainly associated with quorum sensing and ABC transporter pathways. These results provide a theoretical foundation for optimizing aquaculture conditions for ornamental fish and improving fish health and production efficiency. Full article

Salicylic acid (SA) is an important signaling molecule that regulates plant primary and secondary metabolites accumulation. Although SA has been shown to promote folate accumulation, the underlying mechanism remains unclear. In this study, the effect of SA on folate biosynthesis in spinach (Spinacia oleracea L.) and its regulatory mechanisms were investigated. Physiological and metabolomic analyses showed that foliar SA application increased the contents of folate, soluble protein, and soluble sugar and the abundance of 5-methyltetrahydrofolate, p-aminobenzoate (pABA), and Trp, while the abundance of Ser decreased. The expression of aminodeoxychorismate synthase (ADCS) and alkaline phosphatase (ALP) genes in the folate biosynthesis pathway was upregulated, while the expression of five genes in the folate interconversion pathway and two genes in the Phe/Tyr synthesis pathway was downregulated. Fifty-one transcription factors (TFs) showed expression patterns correlated with those of ADCS and ALP and were predicted to bind to their promoter regions. SA upregulated many hormone genes, and 12 of these correlated strongly with both ADCS and ALP. Moreover, transgenic Arabidopsis lines overexpressing SoADCS constitutively displayed higher folate content in leaves. Taken together, our results suggested that SA may promote folate accumulation by enhancing folate precursor supply, and several candidate TFs and hormone-related genes that may be involved in the regulation of this pathway warrant further study. Full article

The rhizosphere microbiome and phytohormone signaling are critical determinants of plant growth and stress resilience. This study evaluated the combined effects of Streptomyces sp. HU2014 and coronatine (COR) on maize (Zea mays L.) seedlings. Four treatments were established: control (CK), COR seed soaking (Cor), HU2014 soil inoculation (S), and combined S + Cor (SCor). Growth parameters, chlorophyll content, and antioxidant/oxidative stress markers were measured, and root and leaf transcriptomes, together with root metabolomes, were compared between SCor and CK, followed by qRT-PCR validation. Compared with CK, SCor treatment significantly increased stem diameter (~60%), plant height (~20%), and relative chlorophyll content (SPAD, ~50%). Soluble sugar levels were elevated by over 40% in both leaves and roots, accompanied by tissue-specific modulation of antioxidant enzymes. Transcriptomic analysis of SCor vs. CK revealed 2459 differentially expressed genes (DEGs) in leaves and 3444 DEGs in roots; leaves exhibited upregulation of photosynthetic pigment metabolism (porphyrin and carotenoid pathways) and volatile defense compounds (alkaloids and monoterpenoids), whereas roots showed enrichment in phenylpropanoid/flavonoid biosynthesis, benzoxazinoid synthesis, and starch/sucrose metabolism. Metabolomics of SCor vs. CK identified 526 differentially accumulated metabolites (DAMs) in roots, with significant enrichment in aminoacyl-tRNA biosynthesis, phenylalanine metabolism, and linoleic acid metabolism. Integrative multi-omics analysis further revealed that the JA precursor 13-epi-12-oxo-phytodienoic acid co-clustered with stress-responsive transcription factors (e.g., DREB1C), while tricarboxylic acid (TCA) intermediates and phenylpropanoid metabolites were linked to energy and lignin biosynthesis genes. qRT-PCR confirmed the expression trends of 14 out of 15 tested genes. Collectively, combined HU2014 and COR application triggers tissue-specific transcriptional and metabolic reprogramming in maize, coupling JA-mediated stress signaling with enhanced carbon metabolism and secondary defense compound synthesis to promote rhizosphere adaptation and seedling vigor. Full article

The production of biodegradable plastics is considered one of the best alternatives to combat plastic waste and global pollution. Polyhydroxybutyrate (PHB) stands out as the most studied bioplastic, but its introduction into global industries and markets still presents challenges due to the high final cost. Understanding the entire synthesis process of this biopolymer becomes a more effective way to address this problem. This review describes the four main natural metabolic pathways related to PHB biosynthesis, associated with stages involving sugars, fatty acid metabolism, de novo fatty acid synthesis, and the butyric acid pathway, while also addressing the role of acetyl-CoA as the central precursor molecule. Approaches regarding physicochemical conditions and the selection of ideal substrates were also conducted, aiming at the production of PHB that is both economically viable and environmentally sustainable. Thus, this review distinguishes itself by bringing an updated and comprehensive overview of PHB biosynthesis, whereas other reviews tend to address specific aspects of PHA production. Furthermore, some knowledge gaps were identified, and different genetic engineering strategies were discussed, such as gene overexpression, deletion of competitive pathways, application of the CRISPRi technique, and two-stage fermentation, which have shown promise in optimizing PHB synthesis and reducing production costs. Full article

Anthocyanin-rich dark pigmentation is increasingly recognized as more than a simple consequence of flavonoid accumulation. Here, we define the anthocyanin-driven dark phenotype (ADP) as a coordinated stress-responsive state characterized by intense anthocyanin accumulation coupled with cellular and regulatory reprogramming. Recent studies show that reactive oxygen species, sugar signaling, temperature stress, and hormonal crosstalk converge on MYB–bHLH–WD40-centered regulatory networks that integrate pigment biosynthesis with vacuolar organization, transport activity, and stress adaptation. Epigenetic remodeling, chromatin dynamics, and post-transcriptional regulation further influence pigment intensity and persistence. Importantly, ADPs do not represent an alternative biosynthetic pathway or merely pigment abundance, but instead reflect a systems-level regulatory state governed by coordinated transcriptional, hormonal, and epigenetic control of the canonical anthocyanin machinery. However, several important questions remain unresolved, including how plants retain phenotypic stability under various environmental and developmental settings, whether ADPs contribute to long-term stress memory, and how anthocyanin accumulation is balanced with growth and energy expenditures. To translate ADP-associated features into crop development techniques, these gaps must be filled. We also emphasize spatial omics and CRISPR-based engineering as new methods for analyzing and modifying stress-resilient phenotypes. Full article

Koji production is a critical process that determines the flavor and quality of the final soy sauce product. However, the complex mechanisms underlying microbial metabolism and the evolution of the physicochemical environment still require further analysis. This study focuses on three parallel koji rooms in an industrialized koji fermentation process. This work tracked the dynamics of physicochemical indices, volatile flavor compounds, and microbial communities over a full 40 h cycle. Data integration and correlation analysis elucidated the close linkage between the microbial community, the fermentation environment, and flavor formation. Koji moisture declined gradually, with faster losses at later fermentation stages. This physiological dehydration arose from microbial metabolic heat, forced aeration and structural loosening of koji, not simple physical evaporation. System pH displayed a typical U-shaped trend across fermentation. Values dropped early, most likely driven by accumulating organic acids, before rising from mid to late fermentation. This pH rebound was tentatively attributed to ammonia release from proteolytic breakdown, which may neutralize acidic compounds. These observations cast doubt on the conventional assumption that organic acid levels may be reliably estimated solely from pH measurements. Physicochemical analysis showed continuous accumulation of amino acid nitrogen (0.6–0.9 g/100 g) and total acidity throughout fermentation. By contrast, reducing sugar concentrations differed across individual koji rooms, presumably owing to divergent microbial adaptation in early fermentation. A total of 77 common compounds were identified, among which 13 key odor-active compounds with OAV ≥ 1, such as 4-vinylguaiacol and 3-methylbutyraldehyde, constitute the characteristic flavor profile of soy sauce starter culture. High-throughput sequencing uncovered a distinct ecological pattern: eukaryotic communities, dominated by Aspergillus oryzae, converged under controlled regulation. While prokaryotic communities differentiated dynamically, driven by spatial heterogeneity in the semi-open fermentation environment. Spearman correlation analysis further indicated potential functional partitioning: high-abundance taxa (e.g., Aspergillus oryzae, Weissella) were predominantly associated with macromolecular substrate degradation, whereas rare low-abundance taxa (e.g., Alternaria) displayed significant correlations with the biosynthesis of key characteristic flavor compounds. This study clarifies the synergistic regulatory mechanisms linking physicochemical conditions, microbial metabolism, and flavor precursor formation during industrial koji production. The findings establish a scientific foundation for optimizing process parameters and achieving standardized quality control in soy sauce manufacturing. Full article