Search Results (7,184)

Phyllostachys edulis is a vital bamboo resource in China, known for its economic benefits and ecological functions. However, under natural conditions, its seed germination rate is very low. Exogenous gibberellin (GA) directly supplements endogenous GA levels, while paclobutrazol (PAC) is an inhibitor of GA biosynthesis that can prevent seed germination. Preliminary experiment indicated that a treatment of 50 mg/L GA₃ markedly enhanced the germination rate of P. edulis seeds, whereas 50 μmol/L PAC had an opposite function. To study the exogenous GA₃ effects on the seed germination of P. edulis, seeds were soaked in ddH₂O (CK), Gibberellic acid 3 (GA₃), and PAC solutions for 24 h, respectively. Then, we analyzed and compared the physiology, biochemistry, and transcriptome at different germination stages. The results demonstrated that exogenous GA₃ treatment significantly reduced the contents of starch and soluble protein while increasing the levels of soluble sugar by inducing the activities of β-amylase and protease, respectively. In addition, the activities of superoxide dismutase (SOD), polyphenol (PPO), and ascorbate peroxidase (APX) were enhanced to eliminate ROS during seed germination under exogenous GA₃ treatment compared to CK and PAC treatments. Moreover, the endogenous levels of GA₃ and JA were found to be higher in exogenous GA₃-treated seeds than those in CK and PAC-treated seeds. Furthermore, RNA-seq results revealed that the expressions of 10 related genes are consistent with the observed physiological changes. In summary, exogenous GA₃ effectively accelerated the seed germination of P. edulis by influencing storage reserves, antioxidant enzymes activity, and endogenous hormone through the coordinated transcriptional regulation of related genes. These findings provide novel insights into the regulation mechanisms of exogenous GA₃ on the seed germination of P. edulis. Full article

Background: Freeze tolerance is an uncommon but highly effective strategy that allows certain vertebrates to survive prolonged exposure to subzero temperatures in a frozen, ischemic state. While past studies have characterized the metabolic and biochemical adaptations involved, including cryoprotectant accumulation and metabolic rate suppression, the contribution of post-transcriptional gene regulation by microRNAs (miRNAs) remains largely unexplored. This study investigated freeze-responsive miRNAs in cardiac tissue of the gray tree frog, Dryophytes versicolor, to better understand the molecular mechanisms that support ischemic survival and tissue preservation. Methods: Adult frogs were subjected to controlled freezing at −2.5 °C, and cardiac tissue was collected from frozen and control animals. Total RNA was extracted and analyzed via small RNA sequencing to identify differentially expressed miRNAs, followed by target gene prediction and KEGG pathway enrichment analysis. Results: A total of 3 miRNAs were differentially expressed during freezing, with significant upregulation of miR-93-5p and let-7b-5p and downregulation of miR-4485-3p. Predicted targets of upregulated miRNAs included genes involved in immune signaling pathways (e.g., cytokine–cytokine receptor interaction), steroid hormone biosynthesis, and neuroactive ligand–receptor interaction, suggesting suppression of energetically costly signaling processes. Downregulation of miRNAs targeting cell cycle, insulin signaling, and WNT pathways indicates possible selective preservation of cytoprotective and repair functions. Conclusion: Overall, these results suggest that D. versicolor employs miRNA-mediated regulatory networks to support metabolic suppression, maintain essential signaling, and prevent damage during prolonged cardiac arrest. This work expands our understanding of freeze tolerance at the molecular level and may offer insights into biomedical strategies for cryopreservation and ischemia–reperfusion injury. Full article

(1) Background: As a high-biomass cereal crop, maize provides substantial raw materials for food, animal feed, and processing industries. Plant root systems, vital for nutritional support, are directly vulnerable to diverse stressors that result in developmental abnormalities. Anthocyanins function as essential antioxidants, serving not only as natural pigments, but also playing crucial roles in plant stress resistance. As an essential plant hormone, jasmonic acid (JA) mediates plant stress adaptation and developmental processes, and is frequently employed to stimulate anthocyanin production. (2) Methods: Due to scarce reports on JA functions in maize, we specifically examined JA-triggered developmental regulation and anthocyanin biosynthesis using transcriptomic and metabolomic analysis. (3) Results: Phenotypic analyses revealed that exogenous JA application promoted culm development and intensified pigmentation, while enlarging the areas of stems and primary roots. Combined with phenotypic variations, our integrated transcriptomic and metabolomic analyses of root tissues also indicated that significantly altered metabolites specifically clustered within the flavonoid biosynthesis pathway. Moreover, GO and KEGG enrichment analyses of the associated differentially expressed genes confirmed their participation in this synthetic pathway with high confidence. These findings strongly suggest that methyl jasmonate (MeJA) exposure primarily modulates flavonoid biosynthesis, particularly through regulation of F3H and DFR gene expression, thereby enhancing flavonoid/anthocyanin accumulation in roots. Additionally, our correlation analysis of transcription factors revealed that Zm00001d018097 (MYB), Zm00001d029963 (MYB), and Zm00001d000236 (bHLH) likely participate in regulating the expression of structural genes, thereby promoting the upregulation of functional gene expression. (4) Conclusions: These results provide a robust framework for deciphering the MeJA-mediated regulation of anthocyanin biosynthesis in maize radicles, specifically demonstrating that Zm00001d018097 (MYB), Zm00001d029963 (MYB), and Zm00001d000236 (bHLH) coordinately enhance the expression of F3H and DFR. Full article

This study investigated the beneficial effect of sea cucumber polysaccharides (SCP) on gut microbiota composition, metabolic profiles, and liver gene expression in mice. Using an integrative approach combining microbiome, metabolome, and transcriptome analyses, we demonstrated that SCP supplementation led to a marked rise in norank_f_Muribaculaceae levels and reduced the Firmicutes-to-Bacteroidota ratio. Metabolomic analysis revealed key alterations in amino acid and lipid metabolism, with L-arginine and 7-dehydrocholesterol identified as potential mediators of SCP’s beneficial effects. Transcriptomics revealed genes expression across nine metabolic pathways, with genes involved in steroid biosynthesis being upregulated, while those related to protein digestion and absorption were downregulated. Spearman’s correlation analysis highlighted strong associations between gut microbiota, lipid metabolism-related genes, and corresponding metabolites. Integration omics data further suggested that SCP primarily supports arginine biosynthesis through gut–liver axis crosstalk. These results provide an important basis for developing SCP-based functional food with prebiotic properties to support metabolic and liver health. Full article

Verticillium wilt (VW), caused by Verticillium dahliae, poses a significant threat to global cotton production. Through analysis of public transcriptome databases, this study identified GhSTZ, a C2H2 zinc finger protein transcription factor gene, which was significantly induced by V. dahliae. Suppressing GhSTZ expression via virus-induced gene silencing significantly enhanced cotton resistance to VW. This resistance manifested as a 1.2-fold increase in lignin deposition, optimized ROS (reactive oxygen species) homeostasis, and a 1.3-fold elevation in glucose levels. Transcriptome analysis revealed 338 differentially expressed genes in GhSTZ-silenced plants, with 97 upregulated and 241 downregulated. Key downregulated genes included PME (pectin methylesterase) and PG1-pec (polygalacturonase) in the pentose phosphate pathway, while the key upregulated genes comprised C4H (cinnamate 4-hydroxylase) and C3H (p-coumarate 3-hydroxylase) in the phenylpropanoid biosynthesis pathway. Notably, in the plant–pathogen interaction signaling pathway, approximately half of the genes exhibited upregulated expression while the other half showed downregulation. Protein–protein interaction network analysis further revealed cooperative interaction between PME and the secoisolariciresinol dehydrogenase SIRD. This study is the first to elucidate GhSTZ as a negative regulator that compromises cotton disease resistance through a tripartite mechanism. These findings offer a novel approach to enhancing crop disease resistance by targeting the negative regulatory genes. Full article

Chlorophyll biosynthesis is essential for photosynthesis and plant development. Disruptions in this pathway often manifest as pigment-deficient phenotypes. This study characterizes the morphological, anatomical, and physiological consequences of a chlorophyll-deficient rice mutant (yellow seedling, YS) caused by a loss-of-function mutation in the OsCHLI gene, which encodes the ATPase subunit of magnesium chelatase. Comparative analyses between YSs and wild-type green seedlings (GSs) revealed that YSs exhibited severe growth retardation, altered mesophyll structure, reduced xylem and bulliform cell areas, and higher stomatal and papillae density. These phenotypes were strongly light-dependent, indicating that OsCHLI plays a crucial role in light-mediated chloroplast development and growth. Transcriptome analysis further revealed global down-regulation of photosynthesis-, TCA cycle-, and cell wall-related genes, alongside selective up-regulation of redox-related pathways. These results suggest that chlorophyll deficiency induces systemic metabolic reprogramming, prioritizing stress responses over growth. This study highlights the multifaceted role of OsCHLI in plastid maturation, retrograde signaling, and developmental regulation, providing new insights for improving photosynthetic efficiency and stress resilience in rice. Full article

Drought stress limits seedling growth, hindering morphological development and population establishment. Artocarpus nanchuanensis, a critically endangered species endemic to the karst regions of southwest China, exhibits poor population structure and limited natural regeneration in the wild, with water deficit during the seedling stage identified as a major factor contributing to its endangered status. Elucidating the physiological and molecular mechanisms underlying drought tolerance in A. nanchuanensis seedlings is essential for improving their drought adaptability and facilitating population recovery. In this study, 72 two-year-old seedlings were divided into two groups: drought (PEG) and ethephon (PEG + Ethephon), and subjected to drought-rehydration experiments. The results showed that exogenous application of 100 mg·L⁻¹ ethephon significantly improved stomatal conductance and photosynthetic pigment content in A. nanchuanensis seedlings. Under drought stress, the PEG + Ethephon group exhibited rapid stomatal closure, maintaining water balance and higher photosynthetic pigment levels. After rehydration, the PEG + Ethephon group significantly outperformed the PEG group in terms of photosynthetic rate. Ethephon treatment reduced H₂O₂ and MDA levels, enhanced antioxidant enzyme activity (SOD, CAT, POD, GR), and increased osmotic regulator activity (soluble sugars, soluble proteins, and proline), improving ROS-scavenging capacity and reducing oxidative damage. Ethephon application significantly enhanced ethylene accumulation in seedlings, while drought stress stimulated the concentrations of key ethylene biosynthetic enzymes (SAMS, ACS, and ACO), thereby further contributing to improved drought resistance. Transcriptomic data revealed that drought stress significantly upregulated key ethylene biosynthesis genes, with expression levels increasing with stress duration and rapidly decreasing after rehydration. WGCNA analysis identified eight key drought-resistance genes, providing valuable targets for future research. This study provides the first mechanistic insight into the physiological and molecular responses of A. nanchuanensis seedlings to drought and rehydration, underscoring the central role of endogenous ethylene in drought tolerance. Ethephon treatment effectively enhanced ethylene accumulation and biosynthetic enzyme activity, thereby improving drought adaptability. These findings lay a theoretical foundation for subsequent molecular functional studies and the conservation biology of this endangered species. Full article

Polyamines (PAs), including putrescine, spermidine, spermine, and thermospermine, play essential roles in plant growth, development, and responses to stress. However, the structure and function of PA biosynthetic genes in pepper remain poorly characterized. This study aimed to identify PA biosynthesis genes in the pepper genome using bioinformatics approaches and to assess their expression under various stress conditions. A total of 16 PA biosynthesis-related genes were identified, representing members of the arginine decarboxylase (ADC), ornithine decarboxylase (ODC), agmatine iminohydrolase (AIH), N-carbamoylputrescine amidohydrolase (CPA), S-adenosylmethionine decarboxylase (SAMDC), spermidine synthase (SPDS), spermine synthase (SPMS), and ACAULIS5 (ACL5) gene families. These genes encode proteins with an average molecular weight of approximately 40 kDa, primarily localized in the mitochondria and cytoplasm. Promoter analysis revealed multiple cis-acting elements associated with stress and phytohormone responsiveness. Gene expression was induced by various abiotic stresses, including saline-alkaline, drought, heat, cold, and hydrogen peroxide, as well as by phytohormones such as abscisic acid, ethylene, salicylic acid, auxin, and gibberellin. Overall, this study provides a comprehensive analysis of PA biosynthesis genes in pepper and highlights their potential roles in stress adaptation and hormone signalling, offering a foundation for further exploration of PA-mediated stress tolerance mechanisms. Full article

Starch serves as a crucial storage substance in both cereal crops and root/tuber crops, with its composition and properties determining the quality of storage organs. The Waxy (Wx) gene, encoding a key enzyme in starch biosynthesis, plays a pivotal role in this metabolic pathway. However, existing reviews seldom systematically elaborate on Wx gene regulatory mechanisms from the perspective of intrinsic molecular networks. Focusing on the model crop rice, this article synthesizes research advances in Wx-mediated starch biosynthesis regulation over the past decade. We analyze the structural features of the Wx gene and factors influencing its regulatory function during starch synthesis. In conclusion, future research directions are proposed to provide references for Wx gene studies in other crops, as well as theoretical foundations for rice varietal improvement and molecular design breeding. Full article

Capsicum is one of the most economically significant vegetable crops worldwide, owing to its high content of bioactive compounds with nutritional, pharmacological, and industrial relevance. However, research has focused on C. annuum, often disregarding local diversity and secondary gene pools, which may contain hidden variation for quality traits. Therefore, this study evaluated the genetic and phenotypic diversity of 283 accessions from the Colombian germplasm collection in the agrobiodiversity hotspot of northwest South America, representing all five domesticated species of the genus. A total of 18 morphological, physicochemical, and biochemical fruit traits were assessed, including texture, color, capsaicinoid, and carotenoid content. The phenotypic data were integrated with genomic information obtained through genotyping-by-sequencing (GBS) using the C. annuum reference genome and a multispecies pangenome. Fixed-and-Random-Model-Circulating-Probability-Unification (FarmCPU) and Bayesian-information-and-Linkage-disequilibrium-Iteratively-Nested-Keyway (BLINK) genome-wide association studies (GWAS) were performed on both alignments, respectively, leading to the identification of complex polygenic architectures with 144 and 150 single nucleotide polymorphisms (SNPs) significantly associated with key fruit quality traits. Candidate genes involved in capsaicinoid biosynthesis were identified within associated genomic regions, terpenoid and sterol pathways, and cell wall modifiers. These findings highlight the potential of integrating pangenomic resources with multi-omics approaches to accelerate Capsicum improvement programs and facilitate the development of cultivars with enhanced quality traits and increased agro-industrial value. Full article

Saline–alkaline water resources are globally widespread, and their rational development offers significant potential to alleviate freshwater scarcity. Saline–alkaline water aquaculture farming not only affects fish growth and survival but also impairs reproductive and developmental functions. Largemouth bass (Micropterus salmoides), an economically important fish, has demonstrated excellent high tolerance to such environments, in order to investigate the effects of alkaline water aquaculture environments on its growth performance, sex hormone levels, gonadal development, and molecular adaptation mechanisms. In this study, largemouth bass were chronically exposed to freshwater (0.55 mmol/L), low alkalinity (10 mmol/L), or high alkalinity (25 mmol/L) and cultured for 80 days. Alkalinity exposure more severely impacted the growth rate of females. High alkalinity significantly increased the hepatosomatic index and decreased the gonadosomatic index in both sexes; moreover, it induced oxidative stress in both sexes, evidenced by reduced superoxide dismutase (SOD), catalase (CAT), and total antioxidant capacity (TAOC) levels and elevated malondialdehyde (MDA) content. Furthermore, the levels of sex hormones Serum estradiol (E2), 11-ketotestosterone (11-KT), and testosterone were significantly reduced, accompanied by either an elevated ratio of primary oocytes and follicular atresia, or by reduced spermatogenesis. Apoptotic signals appeared in gonadal interstitial cells, with upregulated expression of genes P53, Bax, Casp3, and Casp8. Ultrastructural damage included fewer mitochondria and cristae blurring, further indicating tissue damage causing dysfunction. Transcriptome results showed that oxidative stress damage and energy metabolism imbalance caused by carbonate alkalinity were key to the delayed gonadal development, which was mainly manifested in enrichment of the ECM–receptor interaction and PI3K-Akt signaling pathways in females exposed to low alkalinity, and the GnRH secretion and chemokine signaling pathways in males. Glycosphingolipid biosynthesis and Ferroptosis pathway were enriched in females exposed to high alkalinity, and the Cortisol synthesis and secretion pathway were enriched in males. Overall, high-alkalinity exposure significantly delayed gonadal development in both sexes of largemouth bass, leading to reproductive impairment. Full article

The progression of metabolic dysfunction-associated steatotic liver disease (MASLD) to severe forms, including metabolic dysfunction-associated steatohepatitis (MASH) and liver fibrosis, involves metabolic dysfunction, genetics, and gut dysbiosis. People with HIV (PWH) represent a high-risk group for MASLD, but the role of gut microbiota alterations in disease severity within this population remains poorly understood. We prospectively recruited PWH with MASLD, defined as the controlled attenuation parameter (CAP) ≥ 238 dB/m, and excluded those with viral hepatitis coinfection or alcohol abuse. Severe MASLD was defined as the presence of MASH (cytokeratin-18 ≥ 130.5 U/L) and/or significant liver fibrosis (liver stiffness ≥ 7.1 kPa). Stool samples were collected for 16S rRNA gene sequencing to characterize gut microbiota composition. Functional predictions were generated using PICRUSt. The differential abundance of bacterial taxa and predicted functions were analyzed using a generalized linear model with a negative binomial distribution. Among 34 PWH with MASLD, 18 (53%) met the criteria for severe MASLD. Microbiota profiling revealed significant differences in bacterial genera between the PWH with and without severe MASLD. Enrichment was observed in the Ruminococcus gnavus group, Negativibacillus, Holdemanella, Subdoligranulum, the Eubacterium hallii group, and Butyricicoccus, while depletion was seen in Prevotella, Alloprevotella, Dialister, Catenibacterium, the Christensenellaceae R 7 group, Clostridium sensu stricto, Olsenella, Oscillospiraceae UCG-005, Libanicoccus, and the Eubacterium siraeum group. Predicted functional pathways related to fatty acid degradation, folate biosynthesis, and amino acids metabolism did not differ between groups. MASLD severity in PWH is associated with a distinct gut microbiota signature, though not with functional pathway alterations. Microbial profiling may complement existing non-invasive biomarkers for risk stratification in this high-risk population. Full article

Peach (Prunus persica) leaves, usually discarded in traditional Chinese medicine, were explored as a source of laxative agents. Using zebrafish larvae for bioactivity-guided fractionation, we isolated a single active flavanone that was identified by NMR and HR-MS as Sakuranetin. In vivo assays demonstrated that Sakuranetin (10–25 µM) accelerated intestinal transit in a dose-dependent fashion; at 25 µM, 64.8% of the fluorescent intestinal content was expelled. Untargeted LC-MS metabolomic analysis revealed significant perturbations in serine biosynthesis and N-glycan precursor biosynthesis, suggesting energetic rewiring of enterocytes. RNA-Seq analysis highlighted gnat1 as the most responsive gene, and molecular docking predicted a stable Sakuranetin–Gnat1 complex with a binding free energy of −8.7 kcal/mol. Concurrent down-regulation of rho transcripts indicated suppression of inflammatory signaling that often accompanies constipation. Our findings identified Sakuranetin as a potent promoter of gut motility and position the otherwise wasted peach leaves as an untapped botanical resource for developing anti-constipation therapeutics. Full article

The NAC gene family, as a group of plant-specific transcription factors, plays crucial roles in plant growth, development, abiotic stress regulation, and biosynthesis of medicinal components. However, research on this family in the medicinal true mangrove Acanthus ebracteatus remains unreported. In this study, 56 NAC genes (AeNAC01-AeNAC56) were identified from A. ebracteatus transcriptome data, all encoding proteins with the NAM domain. Phylogenetic analysis classified them into two groups, with 51 in Group I and 5 in Group II. Comparative transcriptome analysis of roots, leaves, and flowers, validated by qRT-PCR, revealed lower AeNAC genes expression in leaves, with AeNAC10, AeNAC31, and AeNAC48 showing the lowest levels. Under salt, cold, and waterlogging, AeNAC03/44, /48/56 exhibited differential expression, suggesting their key roles in stress responses. Metabolome analysis further demonstrated that AeNAC14 and AeNAC48 significantly correlated with the biosynthesis of verproside and verbascoside, major bioactive phenythanoid glycodides in A. ebracteatus leaves with anti-inflammatory and antioxidant properties. This study provides insights into the A. ebracteatus NAC gene family, identifying candidate targets for understanding the synergistic regulation of abiotic stress responses and medicinal component biosynthesis, which is significant for optimizing the plant’s growth and medicinal value via genetic engineering. Full article

The rust disease caused by Melampsora apocyni seriously affects the growth of Poacynum hendersonii. However, the defense mechanisms against rust infection remain unclear. This study explored the regulatory mechanisms of P. hendersonii in response to rust disease through combined physiological, biochemical, and transcriptomic analyses. The results showed that with the increase in disease severity, the chlorophyll content of leaves decreased significantly, while the antioxidant and phenylalanine ammonia lyase activities progressively increased. Mild infection triggered an 11.9-fold surge in salicylic acid levels and a sharp decline in abscisic acid compared to controls, as well as increased synthesis of total phenolics, total flavonoids, chlorogenic acid, cryptochlorogenic acid, isoquercetin, hyperoside, rutin, and astragalin. Transcriptome analysis showed that the “plant–pathogen interaction, plant hormone signal transduction and phenylpropanoid biosynthesis” pathways were significantly up-regulated in the mild infection stage, while “glycerophospholipid metabolism, fatty acid degradation and ABC transporters” were activated in the severe infection stage. In summary, P. hendersonii regulates energy metabolism and phenylpropanoid metabolism through salicylic acid signaling and promotes the accumulation of secondary metabolites and the lignification process of leaves, thereby enhancing rust resistance. Key enzyme genes (COMT, POD, CAD, F5H) and metabolites (chlorogenic acid, isoquercitrin, rutin) can be used as important targets for disease resistance breeding. Our research provides important reference for the prevention and control of M. apocyni in P. hendersonii. Full article