搜索结果：Nature structural & molecular biology

Dipeptidyl peptidase-4 (DPP-4) is an established therapeutic target in the treatment of type 2 diabetes mellitus (T2DM), primarily due to its role in regulating incretin activity and glucose homeostasis. Although clinically approved DPP-4 inhibitors are widely used, their moderate efficacy has driven the search for novel compounds with improved properties. In this context, natural products have attracted considerable attention as a source of structurally diverse and biologically active molecules. At the same time, molecular docking has emerged as a key computational tool for the identification and evaluation of potential DPP-4 inhibitors. This review summarizes and critically analyzes current molecular docking studies of natural compounds targeting DPP-4. Over 150 studies were evaluated with respect to docking methodologies, selection of protein structures, and validation strategies. The results reveal substantial variability in computational protocols. Frequently used protein structures include ligand-bound DPP-4 models such as 1X70 and 6B1E. Among the investigated compounds, flavonoids represent the most extensively studied class, followed by alkaloids, phenolics, terpenoids, and peptides. Despite numerous reports of favorable binding interactions within the DPP-4 active site, many studies rely solely on docking results without further validation. The limited use of molecular dynamics simulations and experimental assays highlights a significant gap in the current literature. Overall, while molecular docking provides valuable preliminary insights, improved standardization and integration with complementary approaches are essential to enhance the reliability and translational relevance of in silico findings.

Structural elucidation of unknown metabolites remains a fundamental bottleneck in plant metabolomics, where the vast chemical diversity of plant secondary metabolites far exceeds the coverage of existing spectral libraries. Here, we present DeepMASS v2, a substantially enhanced platform for LC-MS/MS-based compound annotation designed to address this challenge at scale. DeepMASS v2 leverages a semantic representation model trained on millions of spectra from GNPS, NIST, and in-house resources. By integrating Spec2Vec-based embeddings with Hierarchical Navigable Small World (HNSW) graph retrieval and a unified chemical space defined by molecular fingerprints, DeepMASS v2 identifies structurally related neighbors for unknown spectra and ranks candidate structures based on spatial proximity to these predicted chemical contexts. Benchmarking using CASMI datasets and a curated natural product collection demonstrates that DeepMASS v2 outperforms state-of-the-art in silico annotation tools including SIRIUS, CFM-ID, MetFrag, and MS-Finder. Importantly, DeepMASS v2 maintains strong performance for metabolites absent from spectral libraries, highlighting its capability for genuine unknown discovery. Application of DeepMASS v2 to large-scale plant datasets further reveals its power to expand the accessible metabolome space. Delivered as an intuitive web platform, DeepMASS v2 provides the community with a scalable, interpretable, and high-throughput solution for structural annotation, enabling more comprehensive characterization of plant chemical diversity and accelerating natural product discovery in molecular plant science. The web server of DeepMASS v2 can be accessed through http://deepmass.cn.

Accurate prediction of protein-protein interaction interfaces is critical for understanding molecular recognition and guiding therapeutic design. This study presents a comprehensive machine learning pipeline for predicting interface residues in permanent homodimeric protein complexes. Using a curated dataset of 1311 homodimers, we benchmarked six widely used machine learning algorithms and identified multilayer perceptron and XGBoost as top performers, achieving Matthews correlation coefficients (MCC) exceeding 0.93. To enhance interpretability and efficiency, we employed recursive feature elimination to derive a minimal set of six biologically meaningful features, including solvent accessibility, surface roughness, planarity, and average protrusion index, that retained high predictive power (MCC > 0.90). Structurally stratified models tailored to α-helical, β-strand, and membrane proteins demonstrated comparable or improved accuracy relative to generalized models, particularly when utilizing the reduced feature subset. As a preliminary demonstration of generalizability, we applied our approach to an external heterodimer complex (PDB ID: 9ETL). While limited to a single case study, the structurally specialized models maintained high accuracy, suggesting potential applicability beyond the training domain. Furthermore, our residue-level feature-driven models demonstrated highly competitive performance when compared against the baseline established by the general-purpose ColabFold pipeline. The results highlight the importance of structural context in interface prediction and demonstrate that compact, structure-aware models can achieve high accuracy while reducing computational complexity. This work provides a scalable, interpretable, and biologically informed approach to protein interface prediction, with implications for large-scale structural descriptor, drug target characterization, and protein engineering applications.

The roots of Baphicacanthus cusia (Nees) Bremek, commonly known as Nan-Ban-Lan-Gen, have been used for a long time in traditional Chinese medicine to manage inflammatory and infectious diseases. However, the structural features and bioactive potential of its polysaccharides have not been extensively studied. In the present study, a novel homogeneous polysaccharide (BcP-b2) was isolated from the roots of B. cusia, and its bioactivity was evaluated using an activity-guided purification strategy. Multi-dimensional structural analysis identified BcP-b2 as a highly branched galactoarabinan with a molecular weight of ~38.1 kDa, featuring a well-defined backbone and a variety of side chains. In vitro and in vivo assays demonstrated that BcP-b2 attenuated the accumulation of reactive oxygen species (ROS) and enhanced the activities of endogenous antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px). Additionally, BcP-b2 activated macrophages under basal conditions and alleviated lipopolysaccharide (LPS)-induced cytotoxicity and inflammatory mediator release. Transcriptomic and Western blot analyses revealed that these dual effects were achieved through the simultaneous suppression of the PI3K/Akt inflammatory axis and activation of the Nrf2/HO-1 antioxidant pathway, concomitant with enhanced nuclear translocation of Nrf2. These findings provide a molecular basis for the ethno-pharmacological use of Nan-Ban-Lan-Gen and identify BcP-b2 as a promising candidate for further investigation as a potential therapeutic agent.

Bombyx batryticatus is a traditional Chinese medicinal material derived from Bombyx mori infected by Beauveria bassiana; however, its formation mechanism remains poorly understood. This study compared infection processes in silkworms by two B. bassiana strains with markedly different virulence (highly virulent ZY027 and ARSEF2860). Integrated transcriptomic and proteomic analyses were employed to uncover, for the first time, the molecular basis of B. batryticatus formation at the systems biology level. The results demonstrated significant weight variations in B. batryticatus derived from different fungal strains. ZY027-induced stiff silkworms exhibited higher wet and dry weights than those infected by ARSEF2860. Large-scale gene reprogramming occurred in silkworm hemolymph post-infection, involving marked activation of Toll/Imd immune signaling pathways, ribosome biogenesis, and endoplasmic reticulum stress responses. A notable "uncoupling" between transcriptomic and proteomic profiles was identified, highlighting the critical role of post-translational regulation in host responses. The two strains triggered distinct metabolic reprogramming patterns: ZY027 notably suppressed oxidative phosphorylation and activated detoxification mechanisms, whereas ARSEF2860 presented characteristics of "immune-metabolic optimization." These findings suggest that B. batryticatus formation involves complex fungus-silkworm molecular interactions in hemolymph, and that fungal strain characteristics are associated with significant differences in host molecular responses and product biomass. The study provides a theoretical foundation and innovative guidance for selecting strains with high B. batryticatus production potential and developing novel entomopathogenic fungal resources.

Crop wild relatives are used to improve cultivated plants and precise tracking of genetic introgression requires high-quality genome assemblies. Here we present de novo genome assemblies of two wild tomato species - the broadly stress-resistant Solanum pennellii (LA0716) and the salt-resistant Solanum cheesmaniae (LA1039). The improved S. pennellii genome adds 146 Mbp to the twelve chromosomes compared with the original reference. The alignment of the new assemblies with multiple gold-standard assemblies identified shared and species-specific structural variants. Analysis of repeat content demonstrates independent explosions of Tekay retrotransposons in S. pennellii and S. peruvianum. Genome sequencing of 709 recombinant plants derived from male and female backcrosses of three different hybrids reveals higher crossover rate in female meiosis. Conserved female-enhanced recombination regions were discovered and coldspots were attributed to megabase-scale inversions and insertion-deletion polymorphisms. Our S. pennellii and S. cheesmaniae genome assemblies reveal how repeat content diverged in nature and during breeding, and uncovers how both reproductive gender and structural variants dictate recombination landscapes in tomato hybrids.

Tooth agenesis is a genetically heterogeneous developmental anomaly in which disturbances of morphogen signaling, cytoskeletal organization, and mineralization converge during odontogenesis. Building on a previously published clinical and exome study of two Lebanese families with familial nonsyndromic tooth agenesis that identified rare segregating missense variants in trio Rho guanine nucleotide exchange factor (TRIO) and calcium voltage-gated channel auxiliary subunit alpha2delta 2 (CACNA2D2), this work examines how these genes may participate in a shared mechanistic axis during human tooth development. We performed a secondary, exclusively in silico mechanistic analysis of the originally reported variants, TRIO c.8312C>T (p.Ser2771Leu) and CACNA2D2 c.284G>A (p.Arg95His), without enrolling new participants or generating additional sequencing or clinical data. Protein domain organization was annotated from curated resources, residue-level and local-window conservation were quantified across vertebrate orthologs, and the structural context of each substituted residue was inspected using available experimental templates and full-length AlphaFold models from the AlphaFold Protein Structure Database. Population allele frequencies and clinical annotations were re-evaluated in large reference datasets, and high-confidence protein-protein interaction networks centered on TRIO, ras homolog family member A (RHOA), guanine nucleotide binding protein subunit beta 1 (GNB1), and CACNA2D2 were constructed to assess whether these genes form a common odontogenesis-relevant signaling landscape. Both substitutions localize to structured and functionally annotated regions: CACNA2D2 Arg95 lies in the extracellular N-terminal segment immediately upstream of the von Willebrand factor type A (VWA) domain, and TRIO Ser2771 lies within an immunoglobulin I-set domain adjacent to a C-terminal kinase-like region. In both cases, the affected residue is highly conserved across mammalian orthologs and falls within a locally conserved window. TRIO p.Ser2771Leu remains absent from population reference datasets, whereas CACNA2D2 p.Arg95His (reference SNP identifier, rs149979955) is a very rare allele with a non-dental Clinical Variants (ClinVar) annotation; both variants receive predominantly deleterious predictions. Structural inspection suggests possible effects on local packing, electrostatics, or interaction interfaces. Network analysis places TRIO, RHOA, GNB1, and CACNA2D2 along a high-confidence path enriched for cytoskeletal regulation, vesicle trafficking, calcium signaling, and mineralization, consistent with an ion channel-Rho guanosine triphosphatase (GTPase) coupling model in odontogenesis. This structural and network analysis suggests that the reported TRIO and CACNA2D2 variants may contribute to a testable TRIO-RHOA-GNB1-CACNA2D2 axis in human tooth development. The evidence remains hypothesis-generating and does not establish pathogenicity or causality, but it provides a coherent framework for targeted functional studies in dental and craniofacial models.

Harmful algal blooms pose a persistent threat to the integrity of freshwater ecosystems and public health. However, there are no selective chemical control agents available to suppress cyanobacterial growth without damaging beneficial phytoplankton. In this study, ten structurally diverse monoterpenes were assessed in vitro for their differential activity against the potent toxin-producing cyanobacterium Microcystis aeruginosa and the ecologically valuable microalga Chlorella sorokiniana using disc diffusion (DDM) and minimum inhibitory concentration (MIC) assays. Inhibition zones against M. aeruginosa ranged from 6.9 to 43.6 mm, with thymol recording the largest zone (43.6 mm). MIC values ranged from 0.25 to >1 mg/mL for both organisms, and selectivity indices identified camphor and carvone as the most cyanobacterium-preferential compounds, while carene and α-pinene showed the inverse selectivity pattern. Molecular docking against six AlphaFold2-predicted target proteins, photosynthetic complexes, Adenosine Triphosphate (ATP) synthase subunits, and superoxide dismutase (SOD) from both organisms, revealed binding affinities between -3.9 and -6.2 kcal/mol. Phenolic monoterpenes consistently engaged active-site glutamate and aspartate residues via hydrogen bonds and Pi-Anion interactions, most strikingly in the M. aeruginosa ATP synthase, whereas the M. aeruginosa SOD represented the least amenable target for all compounds. Computational ADMET profiling confirmed favorable pharmacokinetic properties and low predicted toxicity for the full panel.

As liver cancer is a leading cause of death all over the world, there is a need to explore new therapeutic strategies. This study presents an in silico analysis of the genes Caspase3 (CASP3), Caspase9 (CASP9), and BCL-2-associated X protein (BAX) in liver cancer cells to evaluate the apoptosis profile following exposure to green-synthesized plant extract. We assessed the modulatory effects of phytochemicals on the apoptotic pathway by means of bioinformatics tools and a publicly available gene expression dataset. Our findings revealed the possible mechanistic basis of the pro-apoptotic activity observed in vitro, utilizing a structure-based molecular docking method. The biologically synthesized AgNPs at a concentration of 50 µg/mL induced an approximately 4-fold increase in the mRNA expression levels of CASP3, CASP9, and BAX compared with chemically synthesized AgNPs, as determined by qPCR. Rutin was the compound with the highest binding affinities toward all three proteins, with ΔG values of -9.3 kcal/mol (Caspase3), -9.1 kcal/mol (Caspase9), and -9.0 kcal/mol (BAX). These findings offer new insights about the molecular mechanisms that support the cytotoxicity of phytochemicals, and simultaneously highlight the potential of green nanotechnology for the development of therapeutic strategies for liver cancer.

The genus Tamarix L. includes several species widely used in traditional medicine for their therapeutic properties. This study aims to evaluate the bioactive potential of Tamarix gallica extracts from Western Algeria using an integrated in vitro and in silico approach. GC-MS analysis with BSTFA derivatization was performed to characterize the chemical profile of the methanolic fraction. In addition, total phenolic, flavonoid, and tannin contents were determined in methanolic extracts of leaves and stems. The biological activities were assessed using antioxidant (DPPH, ABTS, β-carotene, FRAP, O-phenanthroline, and cupric reducing assays), antimicrobial, antidiabetic, and anti-Alzheimer in vitro assays. Molecular docking was conducted to evaluate the inhibitory potential of selected flavonoids against α-amylase, acetylcholinesterase, and butyrylcholinesterase. Results revealed a rich metabolite profile dominated by long-chain aliphatic alcohols (including hentriacontan-12-ol), phytosterols (β-sitosterol), fatty acids, phenolic derivatives, and sugar alcohols. The extracts exhibited strong antioxidant activity (IC50 = 1.34 ± 0.43 and 12.32 ± 0.36 μg·mL-1), significant antimicrobial effects against the tested pathogens, and notable antidiabetic and anticholinesterase activities (IC50 = 78.65 ± 1.43 and 98.37 ± 1.07 μg·mL-1). Molecular docking analysis supported these findings, showing strong binding affinities of quercetin and rhamnetin toward the target enzymes. Overall, T. gallica exhibits promising multifunctional bioactivities with potential pharmaceutical relevance.

Alcoholic liver disease (ALD) is associated with oxidative stress, impaired alcohol metabolism and progressive liver injury. Mushroom polysaccharides are potential hepatoprotective agents, but the polysaccharides from Pholiota squarrosoides (Peck) Sacc remain poorly characterised. This study optimised the ultrasound-assisted extraction of polysaccharides from P. squarrosoides fruiting bodies, purified the main fraction, characterised its basic structural features and evaluated its protective effect in mice with alcohol-induced liver injury. The optimal extraction conditions were 200 W ultrasonic power, a solid-to-liquid ratio of 1:60 g/mL, 60 °C and 40 min, giving a crude polysaccharide yield of 7.72%. The crude extract was fractionated using DEAE Seplife FF anion-exchange chromatography, and the major neutral fraction was further purified by Sephacryl S-400 HR gel filtration to obtain Pholiota squarrosoides (Peck) Sacc polysaccharide (PSP). The polysaccharide recovery was 78.03%, and the purified fraction showed a total carbohydrate content of 94.49% by the phenol-sulfuric acid method. Ultraviolet analysis indicated no detectable nucleic acid or protein absorption. Structural analysis showed that PSP was mainly composed of galactose, glucose, mannose and glucuronic acid, with a molar ratio of 30.13:39.91:29.18:0.78, and contained pyranose-type residues with α- and β-glycosidic linkages. In mice, medium and high doses of PSP reduced the liver index and serum alanine aminotransferase and aspartate aminotransferase activities. PSP also increased hepatic superoxide dismutase and glutathione peroxidase activities, decreased malondialdehyde content and improved liver histology compared with the alcohol model group. These findings suggest that PSP may attenuate alcohol-induced liver injury, mainly through antioxidant protection and improved alcohol metabolism.

Expansin-like A (EXLA) proteins belong to one of the four main families within the expansin superfamily, a group of plant proteins essential for cell wall loosening. Here, we report, for the first time, the purification of a novel EXLA, named cpEXLA, from canihua seeds. cpEXLA (yield ~0.16 mg per 100 g of seeds) is a 29 kDa glycoprotein with a high melting temperature (Tm of 86.75 ± 1.06 °C). Elucidation of its primary structure reveals that the mature protein consists of 246 amino acids, ten of which are cysteine residues forming five disulphide bridges. Structural studies based on 3D model prediction reveal the presence of N- and C-terminal domains, which are typical of EXLAs and rich in β-sheets, as confirmed by circular dichroism (CD) spectroscopy. Furthermore, comparative analysis of amino acid sequences between cpEXLA and 219 similar EXLAs, retrieved from dicotyledonous genomes and transcriptomes, identified eighteen invariant amino acid residues: eleven in the N-terminal domain and seven in the C-terminal domain. Finally, phylogenetic analysis of EXLAs in dicotyledonous species shows a close relationship with other EXLAs from the Amaranthaceae family, confirming that EXLA proteins are highly conserved among dicotyledonous plants. Overall, cpEXLA represents an intriguing native tool for studying cell wall evolution and the functional role of EXLAs.

Plant pathogenic fungi seriously threaten global crop production, and endophytic fungi are promising reservoirs of bioactive antifungal metabolites. Three undescribed polyester derivatives, talapolyesters I-K (1-3), along with thirteen known compounds including 15G256ω (4), 15G256ι (5), 15G256α (6), talapolyester E (7), 15G256α-1 (8), 15G256α-2 (9), 15G256α-2-me (10), 15G256ν (11), ES-242-3 (12), dongtinganthracene A (13), penicillide (14), 3-methyl-6-hydroxy-8-methoxy-3,4-dihydroisocoumarin (15), and (R)-6-hydroxymellein (16), were isolated from the endophytic fungus Talaromyces striatoconidius WI-F2. Their chemical structures were elucidated comprehensively using NMR and MS spectroscopic analyses, combined with alkaline hydrolysis. Compounds 4-8 exhibited in vitro promising antifungal activity against Fusarium oxysporum f. sp. cubense, with half-maximal inhibitory concentration (IC50) values of 9.72, 21.07, 7.89, 8.91 and 9.65 μg/mL respectively, all markedly lower than that of ketoconazole (46.23 μg/mL). Molecular docking simulations further validated the observed antifungal activity, with binding energies ranging from -9.01 to -12.25 kcal/mol, indicative of stronger binding affinity compared with benzamidine (-6.80 kcal/mol). This study offers new clues for research on antifungal agents.

The genus Tulipa L. is a common group of ornamental plants, characterized by high morphological variability and a complex taxonomy. Despite considerable interest in this group, assessments of its species composition remain inconclusive, as evidenced by discrepancies between contemporary taxonomic sources. The number of recognized taxa varies across major taxonomic databases, including Plants of the World Online, World Flora Online, and Euro+Med PlantBase, reflecting ongoing taxonomic revisions and differences in species concepts. In terms of distribution patterns, 7.6% are widely distributed taxa across transcontinental regions, 28.0% occur across multiple countries within a continent, and 66.9% are range-restricted taxa. The latter group includes 4.2% transnational endemics, 44.1% single-country endemics, 8.5% single-region endemics, and 10.2% single-site endemics. Recent taxonomic and evolutionary studies of Tulipa increasingly rely on molecular approaches, particularly DNA barcoding and chloroplast genome analyses, which have improved phylogenetic resolution and species delimitation in several cases. However, truly comprehensive studies combining morphological, cytogenetic, and molecular datasets remain limited and are typically restricted to individual taxa or species complexes rather than the genus as a whole. Modern molecular genetic studies demonstrate the high informativeness of both nuclear and plastid markers for studying the phylogeny, systematics, and genetic diversity of Tulipa species. Natural populations of Tulipa are under pressure from anthropogenic factors and climate change, resulting in reduced range and habitat degradation. According to the International Union for Conservation of Nature Red List of Threatened Species, among 118 taxa of the genus Tulipa, T. sprengeri Baker is classified as Extinct in the Wild, 5.9% as Critically Endangered, 5.9% as Endangered, 8.5% as Vulnerable, 11.9% as Near Threatened, and 11.0% as Least Concern. The use of exclusively national assessments to determine species extinction risk may be insufficiently objective, whereas global assessments provide a more informative and reliable approach for evaluating conservation status. In this review, we combine investigations of the morphology, taxonomy, and geographic diversity; population genetic structure and molecular diversity; and molecular phylogenetics and plastome-based genomics of the genus Tulipa. Furthermore, the review examines current challenges and future research prospects, emphasizing that studies of the genus Tulipa should integrate morphological, genomic, and ecological approaches to refine taxonomy and conserve genetic resources.

Recent studies have identified microRNAs (miRNAs) in honey, opening a new and promising area of nutrition research. In this view, pasteurized and unpasteurized samples of Eucalyptus, Orange Blossom, Chestnut, and Sulla honeys were analyzed using manual and semi-automated RNA extraction methods. Semi-automated extraction yielded significantly higher RNA amounts than manual methods, while pasteurization selectively affected miRNA presence, depending on the type of honey. The panel of conserved miRNAs monitored was let-7a-5p, miR-1-3p, miR-7-5p, miR-10a-5p, miR-33a-5p, miR-34a-5p, miR-92a-3p, miR-125b-5p and miR-133a-3p, across honey varieties and in their extracellular vesicles with structures approximately 200 nm in diameter that retain four miRNAs in all honey types, miR-1-3p, miR-34a-5p, miR-92a-3p, and miR-133a-3p. Bioinformatic analyses of validated miRNA targets revealed enrichment in pathways related to cytoskeletal organization, transcriptional regulation, protein stability, and immune system processes, with Reactome categories clustering around signal transduction, protein metabolism, and immune interactions. Cell-type-specific enrichment suggested that gastric isthmus progenitor cells, stromal cells, and immune subsets could be potential targets, implying roles in epithelial renewal, immune modulation, and wound healing. Overall, these findings enhance our understanding of honey as a source of conserved miRNAs in extracellular vesicles, highlighting its potential as a natural carrier that protects miRNAs from degradation. This study offers new insights into the health-promoting properties of honey, warranting further preclinical studies.

Natural products are the fundamentals of drug discovery due to their exceptional structural diversity and biological activity's evolutionary optimization. The review provides a critical and integrative analysis of natural products in pharmaceutical chemistry, highlighting their significance for current biomedicine and pharmacotherapy. The review is organized around a system that connects structure, function, and translation, focusing on structural analysis, scaffold design, and mechanistic understanding in major disease-relevant therapeutic areas. Investigations on representative compounds like paclitaxel, artemisinin, and curcumin are presented to explain the way molecular architecture regulates pharmacological activity, drug selectivity, and clinical performance. The review evaluates significant medicinal chemistry strategies, including semisynthetic modification, prodrug design, and scaffold optimization, and their crucial roles in enhancing potency, pharmacokinetics, and safety. We critically examine the latest advancements in drug delivery technologies, particularly those based on nanotechnology and carrier-free methods, regarding their translational potential and regulatory concern. Current challenges pertaining to pharmacokinetics and ADMET properties, as well as the standardization of analysis, are also examined, emphasizing their impact on reproducibility in research. Researchers investigate the role and limitations of emerging fields such as genome mining, synthetic biology, and network pharmacology in enhancing discovery pipelines. Thus, this review integrates chemical, pharmacological, and translational approaches and suggests an effective strategy to overcome challenges in the development of natural products as the next generation of precision medicine therapeutic agents.

The brown frog (Rana dybowskii) is an important cold-temperate amphibian species in northeastern China, with considerable ecological and resource value. Because its survival, metabolism, and reproduction are highly sensitive to environmental temperature, elucidating the molecular mechanism's underlying temperature response is of great significance for understanding environmental adaptation and reproductive regulation in amphibians. In this study, R. dybowskii was used as the experimental model, and a multi-tissue transcriptomic analysis was conducted on the brain, liver, spleen, ovary, oviduct, and testis from both females and males under 2 °C and 12 °C conditions to characterize tissue- and sex-specific responses to temperature variation. The results showed that the global transcriptomic landscape of R. dybowskii was primarily driven by tissue type, whereas temperature effects were mainly manifested within individual tissues. The liver, brain, and spleen exhibited pronounced temperature responsiveness in both sexes, with the liver mainly showing metabolic reprogramming-related functional changes. Intersection analysis further revealed that temperature-responsive genes included not only conserved modules shared across tissues but also a large number of tissue-specific genes. Reproductive tissues displayed more pronounced functional divergence: the ovary showed relatively limited transcriptional changes and remained comparatively stable; the oviduct underwent marked transcriptional remodeling, with upregulated genes mainly involved in glycosylation and macromolecule processing, whereas downregulated genes were primarily associated with ribosomes, translation, and RNA splicing; the testis was likewise highly sensitive to temperature changes, with upregulated genes mainly enriched in amino acid metabolism, mitochondrial function, and DNA repair, while downregulated genes were mainly related to cellular structure and intercellular junctions. Collectively, these findings indicate that the molecular adaptation of R. dybowskii to temperature variation is characterized by strong tissue specificity and sex-biased responses in reproductive tissues. This study provides a transcriptomic basis for elucidating the molecular responses to short-term temperature variation is important for understanding environmental sensitivity and reproductive regulation in amphibians.

Antimicrobial resistance (AMR) continues to outpace the development of new anti-infective agents, particularly against priority bacterial pathogens such as Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Staphylococcus aureus, as well as clinically relevant fungi including Candida auris. In this scenario, biotransformation has emerged as a complementary innovation strategy for antimicrobial discovery because it expands the chemical space around bioactive scaffolds through selective enzymatic or whole-cell modification. Among the available biocatalysts, fungi are especially attractive due to their metabolic plasticity and broad enzymatic repertoire, including cytochrome P450 monooxygenases, unspecific peroxygenases, laccases, peroxidases, and hydrolases. Current evidence shows that fungal systems can mediate regio- and stereoselective transformations of xenobiotics, aromatics, steroids, terpenes, and lipids, generating structurally refined metabolites of pharmacological and biotechnological interest. This narrative review discusses where fungal biotransformation currently stands as a platform for antimicrobial innovation, highlighting representative enzyme-characterized examples, the main fungal groups and catalytic systems involved, and the experimental workflows used to evaluate these processes. Particular emphasis is given to assay design with growing cells, resting cells, and isolated enzymes, as well as to analytical monitoring by time-course sampling, LC-HRMS/MS, dereplication, molecular networking, isolation, and structural elucidation. Overall, fungal biotransformation is presented as a discovery-enabling platform that links biodiversity, enzymatic catalysis, analytical chemistry, and biological prioritization in the search for new anti-infective molecules.

In seed plants, putrescine, spermidine, and spermine are ubiquitously present, whereas a structural isomer of spermine, thermospermine (TSpm), is synthesized mainly in the vascular tissue. Initially identified in the bacterium Thermus thermophilus, TSpm was later shown to be synthesized in Arabidopsis thaliana by ACAULIS5 (ACL5). ACL5 gene homologs may have been acquired early in plant evolution via endosymbiotic gene transfer from a cyanobacterial ancestor. Loss-of-function acl5 mutants exhibit a dwarf phenotype and excessive vascular xylem formation. Subsequent studies, including analysis of suppressor-of-acl5 (sac) mutants, revealed that TSpm exerts a critical role in the repression of vascular xylem proliferation by acting in upstream open-reading-frame (uORF)-dependent translational regulation of specific mRNAs. A recent study revealed functional TSpm binding to the peptidyl transferase center of 25 S rRNA promoted by methylation of residue U2952. Like other polyamines, TSpm has also been shown to participate in stress responses, enhancing tolerance to salt, drought, heat, and pathogen challenges in multiple species. Collectively, TSpm represents a unique polyamine with dual roles in xylem development and stress adaptation, whose evolutionary origin and molecular mechanisms provide insights into the specialization of polyamine biology. Further studies in nonvascular plants and algae are needed to elucidate the ancestral functions of TSpm.