Search Results (2,853)

Seed germination is a critical phase in the plant lifecycle of Camellia oleifera (oil tea), directly influencing seedling establishment and crop reproduction. In this study, we examined transcriptomic and physiological changes across five defined germination stages (G0–G4), from radicle dormancy to cotyledon emergence. Using RNA sequencing (RNA-seq), we assembled 169,652 unigenes and identified differentially expressed genes (DEGs) at each stage compared to G0, increasing from 1708 in G1 to 10,250 in G4. Functional enrichment analysis revealed upregulation of genes associated with cell wall organization, glucan metabolism, and Photosystem II assembly. Key genes involved in cell wall remodeling, including cellulose synthase (CESA), phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), caffeoyl-CoA O-methyltransferase (COMT), and peroxidase (POD) showed progressive activation during germination. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed dynamic regulation of phenylpropanoid and flavonoid biosynthesis, photosynthesis, carbohydrate metabolism, and hormone signaling pathways. Transcription factors such as indole-3-acetic acid (IAA), ABA-responsive element binding factor (ABF), and basic helix–loop–helix (bHLH) were upregulated, suggesting hormone-mediated regulation of dormancy release and seedling development. Physiologically, cytokinin (CTK) and IAA levels peaked in G4, antioxidant enzyme activities were highest in G2, and starch content increased toward later stages. These findings provide new insights into the molecular mechanisms underlying seed germination in C. oleifera and identify candidate genes relevant to rootstock breeding and nursery propagation. Full article

Uncaria rhynchophylla, a medicinal plant extensively used in traditional Chinese medicine, is an important plant source of terpenoid indole alkaloids (TIAs), but the mechanism of TIA biosynthesis at molecular level remains unclear. Geraniol synthase (GES) serves as a crucial enzyme in catalyzing the formation of geraniol from geranyl pyrophosphate (GPP) in various plants, but the functional characterization of the GES gene in U. rhynchophylla has not been investigated. In this study, a GES was identified and characterized through genome mining and bioinformatic analysis. Functional validation was performed via a protein catalysis experiment, transient expression in Nicotiana benthamiana, and methyl jasmonate (MeJA) induction experiments. The full-length UrGES gene was 1761 bp, encoding a protein product of 586 amino acids with an estimated 67.5 kDa molecular weight. Multiple sequence alignments and phylogenetic analysis placed UrGES within the terpene synthase g (TPS-g) subfamily, showing high similarity to known GESs from other plants. Enzymatic assays confirmed that recombinant UrGES catalyzed GPP conversion to a single product of geraniol. The transient expression of UrGES resulted in geraniol accumulation in N. benthamiana, further confirming its function in vivo. UrGES expression was observed in leaves, stems, and roots, where leaves had the highest transcript levels. Moreover, MeJA treatment significantly upregulated UrGES expression, which positively correlated with an increase in alkaloid content. This study functionally characterizes UrGES as a geraniol synthase in U. rhynchophylla, contributing to the current knowledge of the TIA biosynthetic pathway. These findings may offer insights for future metabolic engineering aiming to enhance TIA yields for pharmaceutical and industrial applications. Full article

This study elucidates the role of the steroidogenic acute regulatory protein (StAR) in sex steroid hormone dynamics and the gonadal development of the commercially important marine bivalve ark shell Scapharca broughtonii. The sequence of the StAR gene was obtained and verified from the transcriptome of ark shell, then the tissue localization and expression pattern during the gonad development of the StAR gene were detected by in situ hybridization and quantitative real-time PCR, respectively. Additionally, the concentrations of three critical sex steroid hormones (progesterone, testosterone, and estradiol) were measured throughout gonadal development using enzyme-linked immunosorbent assay (ELISA). The results showed that the length of the coding region of StAR was 1446 bp, encoding 481 amino acids. The results of qRT-PCR showed that the expression of the StAR gene varied with gonadal development, increased from the early active stage to the development stage, and decreased from the mature stage to the spent stage. Notably, the expression level in ovaries was higher than that in testes, suggesting the potential involvement of StAR in sex differentiation and gonadal development. Additionally, the results indicated that progesterone, testosterone, and estradiol accounted for 80%, 10%, and 10% of the total hormone content in the gonads, respectively. Correlation analysis revealed a highly significant strong positive correlation between progesterone/estradiol levels and StAR gene expression, demonstrating that StAR serves as a key regulator in sex steroid hormone biosynthesis. These findings provide crucial molecular evidence for StAR-mediated steroidogenesis in bivalve reproduction, offering fundamental insights into invertebrate endocrinology. Full article

Mandelic acid (MA), as an important chiral aromatic hydroxy acid, is widely used in medicine, the chemical industry, and agriculture. With the continuous growth of market demand, traditional chemical synthesis methods are increasingly inadequate to meet the requirements of green and sustainable development due to issues such as complex processes, poor stereoselectivity, numerous byproducts, and serious environmental pollution. MA synthesis strategies based on biocatalytic technology have become a research hotspot due to their high efficiency, environmental friendliness, and excellent stereoselectivity. Significant progress has been made in enzyme engineering modifications, metabolic pathway design, and process optimization. Importantly, biomechanical research provides a transformative perspective for this field. By analyzing the mechanical response characteristics of microbial cells in bioreactors, biomechanics facilitates the regulation of relevant environmental factors during the fermentation process, thereby improving synthesis efficiency. Molecular dynamics simulations are also employed to uncover stability differences in enzyme–substrate complexes, providing a structural mechanics basis for the rational design of highly catalytically active enzyme variants. These biomechanic-driven approaches lay the foundation for the future development of intelligent, responsive biosynthesis systems. The deep integration of biomechanics and synthetic biology is reshaping the process paradigm of green MA manufacturing. This review will provide a comprehensive summary of the applications of MA and recent advances in its biosynthesis, with a particular focus on the pivotal role of biomechanical characteristics. Full article

Naturally occurring prostaglandin E₂ (PGE₂) influences cytokine production regulation in bovine neutrophils exposed to Staphylococcus aureus Rosenbach. Here, we employed bovine neutrophils as the primary experimental system, and administered specific inhibitors targeting various receptors, which were subsequently exposed to S. aureus. Cytokine expression levels in dairy cow neutrophils induced by S. aureus via the endogenous PGE₂-EP2/4 receptor pathway were investigated, and its effects on P38, extracellular signal-regulated kinase (ERK), P65 activation, and phagocytic function in Staphylococcus aureus Rosenbach-induced dairy cow neutrophils, were examined. Blocking cyclooxygenase-2 (COX-2) and microsomal prostaglandin E synthase-1 (mPGES-1) enzymes substantially decreased PGE₂ production and release in S. aureus-exposed bovine neutrophils. Cytokine output showed significant reduction compared to that in SA113-infected controls. Phosphorylation of P38, ERK, and P65 signaling molecules was depressed in the infected group. Pharmacological interference with EP2/EP4 receptors similarly diminished cytokine secretion and phosphorylation patterns of P38, ERK, and P65, with preserved cellular phagocytic function. During S. aureus infection of bovine neutrophils, COX-2 and mPGES-1 participated in controlling PGE₂ biosynthesis, and internally produced PGE₂ molecules triggered NF-κB and MAPK inflammatory pathways via EP2/EP4 receptor activation, later adjusting the equilibrium between cytokine types that promote or suppress inflammation. This signaling mechanism coordinated inflammatory phases through receptor-mediated processes. Full article

The enhancement of flavonoid content and antioxidant capacity in plants remains a significant area of focus in the investigation of plant-derived functional foods. This study systematically investigated the impact of exogenous zinc sulfate (5 mM ZnSO₄) stress on flavonoid content and antioxidant capacity in finger millet (Eleusine coracana L.) sprouts, along with its underlying molecular mechanisms. The results demonstrated that treatment with 5 mM ZnSO₄ significantly increased the flavonoid content in sprouts, reaching a maximum value of 5.59 μg/sprout on the 6th day of germination. ZnSO₄ stress significantly enhanced the activities of PAL, 4CL, and C4H, while also considerably upregulating the expression levels of flavonoid-biosynthesis-related genes. Physiological indicators revealed that ZnSO₄ stress increased the contents of malondialdehyde, hydrogen peroxide, and superoxide anion in the sprouts, while inhibiting sprout growth. As a stress response, ZnSO₄ stress enhances the antioxidant system by increasing antioxidant capacity (ABTS, DPPH, and FRAP), antioxidant enzyme activity (POD and SOD), and related gene expression (POD, CAT, and APX) in sprouts. This study provides experimental evidence for ZnSO₄ stress to improve flavonoid accumulation and antioxidant capacity in finger millet sprouts and provides important theoretical and practical guidance for the development of high-quality functional foods. Full article

Independent studies reported metabolic alterations in connective tissues of hernia patients, especially involving collagen fibers, compared to healthy controls. In the present work, we evaluated plasma concentrations of metalloproteinases (MMPs) and lysyl oxidase (LOX), enzymes involved in collagen metabolism, and peptides produced during collagen biosynthesis (PINP, PIIINP, and PIVNP) as potential biomarkers for the estimation of hernia risk. Zymography and ELISA assays were performed with plasma samples of 51 patients with primary or recurrent inguinal hernia and 42 healthy controls. A reduction in PINP (p = 0.007) and a concomitant increase in PIIINP (p < 0.001) were observed in patients. In controls, PINP levels were inversely related to age, whereas in patients PIIINP levels increased with age. Body mass index (BMI) showed a strong positive correlation with PIIINP plasma levels in controls but not in patients (p < 0.001). Moreover, patients with larger lesions had the lowest PINP/PIIINP ratio (p = 0.003). PIVNP collagen did not differ between controls and hernia patients. Plasma MMP-9 was reduced in patients (p = 0.015), while MMP-2 and LOX were unchanged. However, MMP-2 concentrations appeared lower in patients with familial history of hernia compared to those without. In regression analysis, the PINP/PIIINP ratio was inversely related to hernia risk, and a cut-off value of 0.948 was found by ROC analysis which classified hernia patients with a sensitivity of 82.9% and a specificity of 77.1%. In conclusion, our findings identified the PINP/PIIINP ratio as the most relevant molecular predictor of inguinal hernia risk. Full article

Background/Objectives: This study aimed to evaluate the effects of lung injury induced by insoluble uranium oxide particles on gut microbiota and related metabolites in rats. Methods: The rats were randomly divided into six UO₂ dose groups. A rat lung injury model was established through UO₂ aerosol. The levels of uranium in lung tissues were detected by ICP-MS. The expression levels of the inflammatory factors and fibrosis indexes were measured by enzyme-linked immunosorbent assay. Paraffin embedding-based hematoxylin & eosin staining for the lung tissue was performed to observe the histopathological imaging features. Metagenomic sequencing technology and HM700-targeted metabolomics were conducted in lung tissues. Results: Uranium levels in the lung tissues increased with dose increase. The expression levels of Tumor Necrosis Factor-α (TNF-α), Interleukin-1β (IL-1β), Collagen I, and Hydroxyproline (Hyp) in rat lung homogenate increased with dose increase. Inflammatory cell infiltration and the deposition of extracellular matrix were observed in rat lung tissue post-exposure. Compared to the control group, the ratio of Firmicutes and Bacteroides in the gut microbiota decreased, the relative abundance of Akkermansia_mucinphila decreased, and the relative abundance of Bacteroides increased. The important differential metabolites mainly include αlpha-linolenic acid, gamma-linolenic acid, 2-Hydroxybutyric acid, Beta-Alanine, Maleic acid, Hyocholic acid, L-Lysine, L-Methionine, L-Leucine, which were mainly concentrated in unsaturated fatty acid biosynthesis, propionic acid metabolism, aminoacyl-tRNA biosynthesis, phenylalanine metabolism, and other pathways in the UO₂ group compared to the control group. Conclusions: These findings suggest that uranium-induced lung injury can cause the disturbance of gut microbiota and its metabolites in rats, and these changes are mainly caused by Akkermansia_mucinphila and Bacteroides, focusing on unsaturated fatty acid biosynthesis and the propionic acid metabolism pathway. Full article

Sorghum is a versatile crop that serves as a major source of food, feed, fodder and biofuel globally. Lignin content in sorghum affects multiple important traits, including lodging resistance, forage digestibility and the efficiency of bioenergy production. However, the genetic regulation of lignin content in sorghum remains poorly understood. In this study, we combined transcriptomic and comparative genomic approaches to uncover the genetic network underlying lignin biosynthesis in sorghum. Through comparative genomic analysis, we identified 104 candidate genes involved in lignin biosynthesis. Transcriptome analysis of four sorghum accessions with contrasting lignin contents identified 6132 differentially expressed genes with an enrichment of genes related to phenylpropanoid biosynthesis and cell wall biogenesis. The 104 lignin biosynthesis candidates were significantly enriched (p-value < 0.01) in these differentially expressed genes, with most differentially expressed candidate genes related to monolignol biosynthesis and polymerization being up-regulated in high-lignin accessions. These up-regulated genes are related to all key enzymes involved in lignin biosynthesis, suggesting that the elevated lignin content in these accessions results from a collective increase in enzyme activity. Sequence analysis revealed a significant reduction in genetic diversity across lignin biosynthesis genes in cultivated sorghum compared to wild sorghum. Moreover, selection signals during domestication were identified in 30 lignin biosynthesis genes, 22 of which were differentially expressed, further supporting the functional relevance of these differentially expressed genes in lignin biosynthesis. Overall, our findings uncover the lignin biosynthesis gene network in sorghum and offer potential targets for future functional studies and trait manipulation. Full article

Dopaminergic amacrine cells (DACs) are a subclass of amacrine cells that modulate retinal processing and light adaptation by releasing dopamine. Although the role of dopamine is largely conserved, their retinal distribution across mammals remains incompletely characterized. In mice, rats, thirteen-lined ground squirrels (TLGSs), and macaques, we systematically compared the localization, number, and topography of DACs by their expression of tyrosine hydroxylase (TH), a crucial enzyme in the biosynthesis of dopamine. In all species examined, TH+ cells were primarily located in the inner nuclear layer; however, there was a species-dependent influence on their number and distribution. Mice exhibited the highest density of TH+cells but completely lacked displaced TH+cells (dTH+cells) in the ganglion cell layer. Despite interspecies variation in the total number of TH+cells in the retina, the overall density in rats, TLGSs, and macaques was similar. Most species displayed a higher density of DACs toward central retinal regions. However, rats exhibited a distinctive dorsal concentration, particularly among dTH+cells. Although most species examined exhibited a similar ratio of TH+cells to Brn3a+ retinal ganglion cells, TLGSs showed a marked reduction, indicating a potentially diminished dopaminergic modulatory role. Species-specific DAC topographies aligned with specialized visual regions, such as the visual streak in TLGS and the macula in macaques. These results reveal both conserved and divergent features of retinal dopamine circuitry, reflecting evolutionary adaptations to visual processing demands. Full article

Background/Objectives: Chinese cabbage (Brassica rapa ssp. Pekinensis, AA) growth and development is highly sensitive to cold temperatures. Prolonged low-temperature exposure during early growth stages can induce premature bolting, which reduces market quality and yield. Methods: Here, using comparative leaf RNA-seq transcriptome analysis of plants grown at 6, 9, 12, and 15 °C, we explored key genes and metabolic pathways regulating Chinese cabbage cold response. Results: RNA-seq transcriptome analysis identified a total of 1832 differentially expressed genes (DEGs) in the three comparison groups, with 5452, 1861, and 752 DEGs specifically expressed in the A6_vs_A15, A9_vs_A15, and A12_vs_A15 groups, respectively. KEGG enrichment analysis of DEGs showed that sulfur metabolism, secondary metabolites biosynthesis and photosynthesis pathways were mostly affected by cold stress. K-means clustering revealed distinct expression profiles among the DEGs enriched in cold stress response-associated clusters. Subsequently, DEGs were divided into 18 modules by WGCNA, whereupon co-expression genes that clustered into similar modules exhibited diverse expression and were annotated to various GO terms at different temperatures. Module-trait association analysis revealed M1, M2, M3, and M6 modules as key clusters potentially linked to vernalization-related processes. These modules harbored candidate hub genes encoding transcription factors (including MYB, bZIP, and WRKY), protein kinases, and cold-stress-responsive genes. Additionally, phenotypic analysis showed that 12 °C to 15 °C supported optimal growth, whereas <9 °C temperature inhibited growth. Physiological measurements showed increased antioxidant enzyme activity and proline accumulation at 6 °C. Conclusions: Overall, our study provides a set of candidate cold-stress-responsive genes and co-expression modules that may support cold stress tolerance breeding in Chinese cabbage. Full article

Caleosin/peroxygenases (CLO/PXGs) play critical functional roles during plant development, oxylipin metabolism, and the response to abiotic/biotic stressors and environmental toxins. In Oryza sativa, peroxygenase-9 (OsPXG9) catabolizes intermediates in oxylipin biosynthesis produced by lipoxygenase-9 (9-LOX) and scavenges HOOH and CuOOH by transferring oxygen to hydroxy fatty acids (HFAs) but not to the free fatty acids. The resulting epoxide derivatives of HFAs are then enzymatically or non-enzymatically hydrolyzed into the corresponding trihydroxy derivatives. Results presented here demonstrate OsPXG9′s specificity for catabolizing products of the 9-LOX (and not for the 13-LOX) pathway of oxylipin biosynthesis. Overexpression of OsPXG9 reduces ROS (reactive oxygen species) abundance and reduces drought- and salt-stress-induced apoptotic cell death. The high expression level of OsPXG9 also stimulates drought- and salt-induced but not basal expression of antioxidant enzymes/pathways in plants, thereby increasing cellular resistance to drought. These results suggest that OsPXG9 decreases ROS abundance and is essential to increase resilience in rice plants exposed to exogenous or endogenous abiotic stress. Full article

The filamentous fungal genus Aspergillus represents an industrially significant group of eukaryotic microorganisms. For nearly a century, it has been widely utilized in the production of diverse high-value products, including organic acids, industrial enzymes, recombinant proteins, and various bioactive natural compounds. With the rapid advancement of synthetic biology, Aspergillus has been extensively exploited as a heterologous chassis for the production of heterologous proteins (e.g., sweet proteins and antibodies) and the synthesis of natural products (e.g., terpenoids and polyketides) due to its distinct advantages, such as superior protein secretion capacity, robust precursor supply, and efficient eukaryotic post-translational modifications. In this review, we provide a comprehensive summary of the advancements in the successful expression of heterologous proteins and the biosynthesis of natural products using Aspergillus platforms (including Aspergillus niger, Aspergillus nidulans, and Aspergillus oryzae) in recent years. Emphasis is placed on the applications of A. oryzae in the heterologous biosynthesis of terpenoids. More importantly, we thoroughly examine the current state of the art in utilizing CRISPR-Cas9 for genetic modifications in A. oryzae and A. niger. In addition, future perspectives on developing Aspergillus expression systems are discussed in this article, along with an exploration of their potential applications in natural product biosynthesis. Full article

To identify differentially abundant polyketide synthases (PKSs) and to characterize the biochemical consequences of brevetoxin biosynthesis, bottom-up, TMT-based quantitative proteomics and redox proteomics were conducted to compare two strains of the Florida red tide dinoflagellate Karenia brevis, which differ significantly in their brevetoxin content. Forty-eight PKS enzymes potentially linked to brevetoxin production were identified, with thirty-eight showing up to 16-fold higher abundance in the high-toxin strain. A pronounced shift toward a more oxidized redox state was observed in this strain’s proteome. Notably, 25 antioxidant-related proteins were significantly elevated, including alternative oxidase (AOX), which increased by 17-fold. These results elucidate the cellular consequences of toxin biosynthesis in K. brevis, offer new leads for the study of brevetoxin biosynthesis, and suggest a novel red tide mitigation approach targeting high toxin-producing strains. Full article

Phytoene synthase (PSY) is a multimeric enzyme that serves as the first enzyme in carotenoid synthesis within plant tissues and plays a crucial role in the production of carotenoids in plants. To understand the function of the PSY gene in Panax japonicus C. A. Meyer. fruit, the gene’s transcript was obtained by analyzing the transcriptome sequencing data of Panax japonicus fruit. The CDS sequence of the gene was cloned from Panax japonicus fruit using the RT-PCR cloning technique and named PjPSY1, which was then subjected to biosynthetic analysis and functional verification. The results showed that the open reading frame of the gene was 1269 bp, encoding 423 amino acids, with a protein molecular mass of 47,654.67 KDa and an isoelectric point (pI) of 8.63; the protein encoded by these amino acids was hydrophilic and localized in chloroplasts, and its three-dimensional structure was predicted by combining the pymol software to annotate the N site of action and active centre of the protein. Phylogenetic analysis demonstrated that PjPSY1 had the closest affinity to DcPSY from Daucus carota. Overexpression of PjPSY1 led to a significant increase in the content of carotenoid-related monomers in Arabidopsis thaliana, with Violaxanthin being synthesized in transgenic Arabidopsis thaliana but not in wild-type Arabidopsis thaliana. The PjPSY1 clone obtained in this study was able to promote carotenoid synthesis in the fruits of Panax japonicus, revealing that the mode of action of PjPSY1 in the carotenoid biosynthesis pathway of Panax japonicus fruits has a positive regulatory effect. Full article