Resistance gene discovery in forest trees remains challenging because of their large, repeat-rich genomes and the sparse distribution of functional elements, which restrict the direct application of deep learning approaches developed for crop species. While genomic language models have shown promise in crop species, their application to forest trees remains limited. Here, we present MGS-HCT (Multi-scale Gated Sparse Encoder-Hybrid Convolutional Transformer), a deep learning framework tailored for forest tree genomic sequences. The model integrates multi-scale gated units with structure-aware sparse attention for efficient sequence compression, and combines convolutional modules with transformer layers to capture both local motifs and long-range regulatory dependencies. We show that MGS-HCT supports two key applications in forest tree biotechnology: (1) the conditional generation and prioritization of putative NLR candidates for Alnus glutinosa (common alder) and (2) the de novo generation of synthetic DNA sequences containing promoter-like and splice-site-like elements. These results provide a computational foundation for accelerating disease-resistance gene discovery and genomic-assisted breeding in forest tree species, expanding the scope of deep learning from crop plants to forest genomics. By prioritizing candidates supported by multiple computational criteria for subsequent experimental validation, the framework is intended to narrow the experimental search space and help shorten the long breeding cycles of forest trees.

Sex control is crucial for maximizing the economic benefits of sheep husbandry: male lambs increase farm income by 30-40% due to superior growth and feed efficiency, while female lambs are essential for fine-wool production and population expansion. However, the only commercialized method (flow cytometry) has critical sheep-specific limitations, including 25-30% flow channel blockage, sperm DNA oxidative damage, and prohibitive cost for large-scale breeding. TLR7/8 agonist R848 has been validated for sperm separation in mice, cattle and goats, but no sheep-specific optimized system has been established due to unique biological characteristics of ovine sperm. In this study, we systematically optimized key parameters of R848-mediated sheep sperm separation, comprehensively evaluated its effects on sperm biological characteristics, and verified separation efficiency at the embryo level via IVF combined with nested PCR sex identification. The optimal R848 concentration was 1 µM: the upper layer was enriched with 90.30% ± 5.21% TLR8-negative Y sperm (validated by 80.20% ± 3.70% male embryos), and the lower layer was enriched with 80.50% ± 4.96% TLR8-positive X sperm (validated by 87.56% ± 9.51% female embryos). R848 specifically inhibited X-sperm motility by reducing ATP production (24.82% decrease, P = 0.006) and mitochondrial membrane potential (29.75% decrease, P = 0.023), without damaging acrosome or plasma membrane integrity. The optimal supporting conditions were determined as 1000 µL elution twice, Y-sperm storage at 17 °C for up to 120 h with stable in vitro performance, and X-sperm use within 24 h after sorting. This study provides a low-cost, sheep-specific sperm separation system with comprehensive in vitro validation, which has significant potential for application in precision sheep breeding after further in vivo validation.

Knee trauma is an important risk factor for post-traumatic osteoarthritis (PTOA), a progressive joint disease characterized by articular cartilage degeneration and limited disease-modifying treatment options. Matrix metalloproteinase-13 (MMP-13/collagenase-3) contributes to cartilage extracellular matrix degradation through cleavage of type II collagen, making it a relevant molecular target for cartilage-protective drug discovery. This study aimed to identify and prioritize potential small-molecule MMP-13 inhibitors using an integrated in silico workflow. The workflow included MMP-13 sequence retrieval, structural characterization, pharmacophore-based screening, molecular docking, ADMET/toxicity prediction, protein-ligand interaction analysis, protein-protein interaction and co-expression network analysis, and 100 ns molecular dynamics simulation. Among the screened compounds, P4C-BM was prioritized as an early-stage computational lead candidate based on its combined docking score, predicted ADMET profile, interaction pattern, and molecular dynamics stability. However, the findings are preliminary and computational only. The present study does not experimentally demonstrate direct MMP-13 inhibition, selectivity against other MMP family members, cartilage repair, clinical efficacy, or synergy with platelet-rich plasma, physiotherapy, or other treatment modalities. Among the screened compounds, P4C-BM was prioritized as an early-stage computational lead candidate based on its combined docking score, predicted ADMET profile, interaction pattern, and molecular dynamics stability. However, the findings are preliminary and computational only. The present study does not experimentally demonstrate direct MMP-13 inhibition, selectivity against other MMP family members, cartilage protection, cartilage repair, disease modification, or clinical efficacy. Therefore, P4C-BM should be regarded only as a candidate for further experimental validation in enzymatic assays, chondrocyte models, cartilage explant studies, and in vivo osteoarthritis or post-traumatic osteoarthritis models. No practice-related or treatment recommendations can be made from the present data.

The notable characteristic of phenoplasticity in Convolvulus species is flower color polymorphism, with blooms ranging from white to pink. This variation is due to various factors, including genetic drift and natural selection. The primary objective is to conduct a study on the morphoplasticity of eight accessions collected from diverse locations and categorized into three distinct biotypes based on floral pigmentation: Biotype 1 (White; accessions 1, 4, and 7), Biotype 2 (Pale Pink; accessions 2, 5, and 8), and Biotype 3 (Pink; accessions 3 and 6) of Convolvulus arvensis L. Based on the aforementioned characteristics-flower colour, stem outline, leaf shape, pollen features, shape, colpus and pori shapes, epidermal cell shape, and the number of vascular bundles in both stem and petiole-the study employed morphological and anatomical studies, as well as CDDP markers, to evaluate differences among accessions. Leaf tissues are parenchyma above the main vascular bundle, with an angle between the midrib and the wing region. Three distinct biotypes (B1, B2, and B3) have been defined. CDDP marker analysis revealed high polymorphism (74.36%) and Rp (9.50). Samples 7 and 8 (location 3) showed the most informative polymorphism of flower color (white/pale pink/pink). Genetic distances clustered samples primarily by location rather than by color, underscoring the dominant role of location in structuring populations. The interaction between genotype and ecological conditions led to the genetic variation in flower color in C. arvensis.

This study developed a dual-functional 3D-printed poly(ε-caprolactone) (PCL) scaffold loaded with quercetin (Q-PCL) for synergistic inhibition of bone metastatic tumors and promotion of bone regeneration. The scaffold was fabricated via melt extrusion, exhibiting a uniform porous structure conducive to sustained quercetin release. In vitro, Q-PCL significantly suppressed renal carcinoma (RENCA) cell proliferation and induced apoptosis, while enhancing the osteogenic differentiation and mineralization of bone marrow mesenchymal stem cells (BMSCs). In a murine subcutaneous tumor model, Q-PCL implantation effectively inhibited tumor growth via apoptosis induction without systemic toxicity. In a rat femoral defect model, the scaffold markedly accelerated bone repair, showing increased bone volume, improved trabecular morphology, and mature bone formation. The Q-PCL scaffold demonstrates great potential as a localized co-therapy strategy for treating osteolytic bone metastases and facilitating bone regeneration.

Vancomycin-intermediate Staphylococcus aureus (VISA) is a prominent pathogen in burn wound infections, mainly known for biofilm formation. Recently, infections associated with antibiotic-resistant VISA isolates have increasingly posed life-threatening risks. Accordingly, there is an urgent necessity to investigate and develop efficient strategies against the rapid spread of VISA strains in the healthcare system. In this research, a niosomal drug delivery system was developed using the thin-film hydration method and then surface‑modified with polyethylene glycol (PEG). Teicoplanin (TEC) was further incorporated into PEGylated niosome (TEC-PEGylated niosome), and key physicochemical properties, including encapsulation efficiency (EE %), drug release profile, particle size, surface zeta charge, morphology, polydispersity index (PDI), and 30-day stability were measured. The antimicrobial potential of TEC-PEGylated niosome against five VISA strains isolated from burn wounds was investigated by determining the minimum inhibitory/bactericidal concentrations (MIC, MBC) and the time-kill assay. Furthermore, the anti-biofilm properties of the synthesized niosomal formulation were evaluated with a microtiter-plate (MTP) method and compared to those of free drug. FE-SEM results revealed that the niosomal formulation had spherical morphology with an approximate size of 250 nm. Hydrodynamic size, surface zeta charge, and EE% of the formulated niosomes were found be 278.8 ± 5.0 nm, + 9.5 ± 3.4 mV, and 65.9% ± 1.6, respectively. Also, TEC-PEGylated niosome demonstrated a significantly improved antibacterial ability compared to free drug. Additionally, TEC-PEGylated niosome effectively inhibited the biofilm formation capacity in all VISA strains. It was concluded that synthesized niosomal system could be an effective drug delivery system owing to several advantageous characteristics, including sustained-release profiles, acceptable stability, and other desirable features. These properties enable PEGylated niosomes to effectively deliver a diverse array of antimicrobial agents, including TEC. This capability could present a promising novel strategy for addressing burn infections, particularly those caused by VISA strains.

Grifola frondosa is a highly valued medicinal mushroom with diverse bioactive properties; however, its low mycelial biomass remains a major bottleneck affecting the efficiency of liquid fermentation. To address this issue, protoplast-mediated mutagenesis was employed in this study to breed a high-performance G. frondosa mutant with superior fermentation traits. Following optimization using intelligent strategies, the highest yield of protoplasts was achieved (6.573 × 10[6] protoplasts/g fresh weight) under suitable isolation parameters (fungal age of 7.9 days, lywallzyme concentration 2.1%, enzymatic hydrolysis time 5.2 hours, enzymatic temperature of 30 °C, and mannitol concentration of 0.6 mol/L). Subsequently, DES-induced protoplast mutagenesis yielded a stable G. frondosa mutant (D24) showing 62.78% greater mycelial biomass and 111.11% higher protein yield relative to the parental strain. Furthermore, fermentation kinetics profiling and phenotypic observation suggested that the mutant D24 exhibited a shortened lag phase, enhanced hyphal dispersion, and denser mitochondrial distribution compared with the original strain. Additionally, genome resequencing identified 57,216 single nucleotide polymorphisms (SNPs) in D24 relative to the original strain, including 4,068 non-synonymous SNPs. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment indicated that the mutated genes were potentially involved in amino acid synthesis and metabolism, lipid metabolism, and others. These candidate mutations may be associated with the increased mycelial biomass and protein content. Collectively, this study has developed a novel high-yielding mutant of G. frondosa, which may serve as a promising material for future pharmaceutical and biotechnological applications.

Artemisinin, a bioactive compound from Artemisia annua with potent antioxidant, antimicrobial and anticancer properties, faces limited clinical utility due to poor solubility and low bioavailability. Given the rising prevalence of multidrug-resistant (MDR) Pseudomonas aeruginosa alternative therapeutic strategies are essential. This study synthesized and characterized artemisinin-loaded micelle/liposome nanoparticles (Art/PEG400-OA NPs) and evaluated their antibacterial, antibiofilm, and anticancer efficacy. Artemisinin was successfully encapsulated within PEG400-OA NPs and characterized via FT-IR, FE-SEM, TEM, TGA, and zeta potential measurements. The nanoparticles exhibited uniform morphology, particle sizes of 40.8 nm (TEM) and 149.8 nm (FE-SEM), high encapsulation efficiency (92.14%), and strong thermal and colloidal stability. Synergistic and partial synergistic interactions between Art/PEG400-OA NPs and ciprofloxacin were observed in MDR bacterial samples, significantly inhibiting biofilm formation. Quantitative RT-PCR analysis revealed the downregulation of efflux pump genes (mexA, mexB, mexX, mexY, oprM) and biofilm-associated genes (algD, pelA) following combination therapy. In AGS gastric cancer cells, Art/PEG400-OA NPs induced dose- and time-dependent cytotoxicity (IC50: 67.75, 62.25 and 54.98 µg/mL at 24, 48 and 72 h), increased apoptosis (31.76% ± 4.2%), and reduced wound-healing migration (56.65% ± 4.26%). Expression analysis demonstrated upregulation of tumor-suppressive miR-34a, and downregulation of its targets (CTNNB1, TGFB1, MMP2 and MMP9). Conversely, miR-181a was downregulated, leading to the upregulation of apoptotic target genes (TP53, CASP8, CASP9). Molecular docking supported strong artemisinin binding to key bacterial and oncogenic proteins. Overall, Art/PEG400-OA nanoparticles represent a potent dual-action nanotherapeutic platform against antibiotic-resistant infections and gastric cancer.

Polyethylene Terephthalate (PET) is an extensively used plastic whose durability and resistance to degradation contribute to growing environmental pollution and concerns. Enzymatic PET degradation, particularly via PETase from Ideonella sakaiensis, has emerged as a sustainable approach due to its ability to depolymerize PET under mild conditions. While research has largely focused on enhancing the enzyme's thermal stability through distal mutations, less attention has been given to active-site engineering aimed at directly improving catalytic efficiency. Here, we used an automated in silico protein engineering platform called Gene Discovery and Enzyme Engineering (GDEE), designed to exhaustively explore mutations at the active site in a hight-throughput manner. By leveraging the highly active FAST-PETase (FP) as scaffold, we perform a high throughput generation of thousands of variants, evaluated them via docking studies with a PET substrate analogue, and ranked candidates based on binding affinity and catalytic geometry. We identified S238Y as a key mutation that further enhanced PET film degrading performance at 40 °C when inserted in two of the most active PETase variants reported to date: 2.2-fold increase in the FP scaffold and 3.4-fold increase in the ThermoStable-PETase (TSP) background. Compared to wild type PETase, FP S238Y showed a 14.8-fold increase in bulk activity, translating into 9.4-fold more TPA and 20-fold more MHET by UPLC, while TSP S238Y reached a 25.8-fold increase (14.4-fold more TPA and 42.6-fold more MHET). This mutation also enhanced catalytic efficiency and resistance to enzyme concentration inhibition, especially in the TSP scaffold. Molecular dynamics highlight position 238 as a relevant modulator of ligand stabilisation. These findings underscore the potential of targeted active-site engineering, combined with structure-guided prediction, to accelerate the development of efficient mesophilic biocatalysts for plastic waste remediation. Additionally, the GDEE platform provides an automation-ready workflow for active site engineering that is applicable beyond PETase.