https://hdl.handle.net/20.500.12809/69 2026-07-10T08:51:08Z https://hdl.handle.net/20.500.12809/11236 Bacillus velezensis EU07 suppresses Fusarium graminearum via transcriptomic reprogramming Baysal, Ömür; Jimenez‑Quiro, Catherine; Cevher‑Keskin, Birsen; Tör, Mahmut Fusarium graminearum poses a major threat to global cereal production, necessitating sustainable control measures. This study elucidates the antagonistic mechanism of the biocontrol agent Bacillus velezensis EU07 against F. graminearum through combined transcriptomic and morphological analyses. Exposure to EU07 compromised fungal cellular integrity, causing severe hyphal distortion. RNA-seq profiling revealed that EU07 triggers a profound transcriptomic collapse rather than a standard stress response. Over 35% of the altered fungal transcriptome caused critical suppression, targeting essential metabolic hubs, secretome effectors, and master transcription factors to inhibit growth and loss of pathogenicity. In a compensatory defensive shift, the pathogen massively reallocated its transcriptional resources. This defence was characterised by a similar to 30-fold enrichment of transmembrane amino acid transporters for putative toxin efflux and an 80-fold enrichment of glutathione S-transferases to mitigate severe oxidative stress. Furthermore, EU07 suppressed core vulnerability nodes, including proline dehydrogenase (PRODH) and apolipophorin, disrupting the pathogen's osmotic resilience and membrane integrity. Molecular docking analysis indicated that the Bacillus lipopeptide iturin A directly targets apolipophorin with high affinity (- 7.2 kcal/mol). Our findings indicated that B. velezensis EU07 overwhelms F. graminearum through simultaneous metabolic starvation and loss of virulence, revealing highly vulnerable fungal targets for next-generation RNAi-based biocontrol. 2026-01-01T00:00:00Z https://hdl.handle.net/20.500.12809/11232 Natural Product r esearch Alkaloid contents and biological activities of Genista lydia Boiss. Sabudak, Temine; Argon, Merve; Çakır, Cansel; c This study aimed to investigate the biological activities and alkaloid composition of Genista lydia Boiss. (syn. Genista januensis subsp. lydia) growing in the Trakya Region. The plant material was sequentially extracted using chloroform, ethyl acetate, and methanol. The alkaloid composition of the methanolic extract was analyzed by GC-MS. In addition, the extracts were evaluated for their anticholinesterase, antibacterial, tyrosinase-inhibitory, urease-inhibitory, alpha-glucosidase-inhibitory, and alpha-amylase-inhibitory activities. GC-MS analysis of the methanolic extract revealed the presence of 14 alkaloid compounds. The major constituents were identified as N-methylcytisine (60.45%), cytisine (22.24%) and anagyrine (13.55%). 2026-01-01T00:00:00Z https://hdl.handle.net/20.500.12809/11230 Pocket-Surface Discrete Differential Geometry as a Leakage-Robust Feature Class for Protein–Ligand Binding Affinity Prediction Balcı, Mehmet Ali; Çetin, Erbil; Çalıbaşı-Kocal, Gizem; Akgüller, Ömer Protein-ligand binding affinity prediction underpins structure-based drug discovery, yet random partitions of public benchmarks overestimate generalisation due to protein-family and ligand leakage, and the marginal value of explicit pocket-geometry descriptors over atom-level graph neural networks remains unclear. We computed a 59-dimensional discrete differential geometry descriptor on the ligand-aware solvent-excluded surface of 3285 PDBBind v2020 complexes, combining curvature distributions, the leading sixteen Laplace-Beltrami eigenvalues and a ten-point heat-kernel signature, and evaluated it in gradient-boosted tree pipelines across progressively stricter split regimes and two leak-proof external benchmarks, together with four mechanistically distinct injection strategies in a SchNet-style graph neural network. The descriptor lifted Pearson correlations by 0.111 on cluster-disjoint testing, 0.258 on LP-PDBBind DataSAIL S2 and 0.365 on CASF-2016, while in isolation reaching 0.456 to 0.594 on external benchmarks, on a par with X-Score and AutoDock Vina (version 1.2). TreeSHAP attribution localised the dominant signal to the heat-kernel signature. The four graph neural network injection strategies produced no statistically significant lift, indicating that distance-based message passing on atomic coordinates already captures much of the geometric content. Pocket-surface discrete differential geometry, therefore, offers an interpretable, leakage-robust and lightweight feature class for early-stage virtual screening, and motivates hybrid mesh-to-atom architectures. 2026-01-01T00:00:00Z https://hdl.handle.net/20.500.12809/11224 Sustainable Bioactive Hydrogels Engineered with Liquidambar orientalis Extracts: pH-Dependent Release Behavior and Wound Healing Potential Taş Küçükaydın, Meltem; Duru, Mehmet Emin; Demiray, Aydın; Küçükadın, Selçuk; Ceylan, Özgür Bioactive hydrogel films were developed by incorporating Liquidambar orientalis leaf extract (LOLE) and resin extract (LORE) into PVA/starch, PVA/chitosan, chitosan/gelatin, and chitosan matrices. HPLC-DAD identified myricetin as a major LOLE marker and trans-cinnamic acid as the predominant LORE compound, while SEM and FT-IR analyses supported extract incorporation and possible interactions within the hydrogel networks. The films exhibited polymer- and extract-dependent physicochemical behavior. LOLE-loaded chitosan films showed the highest swelling capacity (350%) and the highest in vitro mass loss after 14 days. Release studies demonstrated matrix-dependent and pH-dependent behavior within the tested pH range, with faster release generally observed at pH 5.5 than at pH 7.4; LOLE-loaded chitosan/gelatin films released 85.3% of the extract within 12 h at pH 5.5. LOLE-loaded hydrogels showed stronger antioxidant activity, whereas LORE-loaded films exhibited stronger antimicrobial performance against wound-associated microorganisms, reflecting their distinct phytochemical profiles. The extracts also showed antibiofilm, anti-quorum sensing, enzyme-inhibitory, and preliminary scratch wound closure activities, with no apparent cytotoxicity toward HEK-293T cells. LORE showed notable tyrosinase inhibition (IC50: 20.18 & micro;g/mL), suggesting pigmentation-related relevance. Overall, these findings support further investigation of L. orientalis-derived hydrogel films as sustainable bioactive wound dressing platforms, although mechanical, stability, and in vivo validations remain necessary. 2026-01-01T00:00:00Z