Browsing by Author "Bayarslan A.U."

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Comparative bioinformatics analysis and abiotic stress responses of expansin proteins in Cucurbitaceae members: watermelon and melon
(2023-03-01) İncili Ç.Y.; Arslan B.; Çelik E.N.Y.; Ulu F.; Horuz E.; Baloglu M.C.; Çağlıyan E.; Burcu G.; Bayarslan A.U.; Altunoglu Y.C.
Watermelon and melon are members of the Cucurbitaceae family including economically significant crops in the world. The expansin protein family, which is one of the members of the cell wall, breaks down the non-covalent bonds between cell wall polysaccharides, causing pressure-dependent cell expansion. Comparative bioinformatics and molecular characterization analysis of the expansin protein family were carried out in the watermelon (Citrullus lanatus) and melon (Cucumis melo) plants in the study. Gene expression levels of expansin family members were analyzed in leaf and root tissues of watermelon and melon under ABA, drought, heat, cold, and salt stress conditions by quantitative real-time PCR analysis. After comprehensive searches, 40 expansin proteins (22 ClaEXPA, 14 ClaEXPLA, and 4 ClaEXPB) in watermelon and 43 expansin proteins (19 CmEXPA, 15 CmEXPLA, 3 CmEXPB, and 6 CmEXPLB) in melon were identified. The greatest orthologous genes were identified with soybean expansin genes for watermelon and melon. However, the latest divergence time between orthologous genes was determined with poplar expansin genes for watermelon and melon expansin genes. ClaEXPA-04, ClaEXPA-09, ClaEXPB-01, ClaEXPB-03, and ClaEXPLA-13 genes in watermelon and CmEXPA-12, CmEXPA-10, and CmEXPLA-01 genes in melon can be involved in tissue development and abiotic stress response of the plant. The current study combining bioinformatics and experimental analysis can provide a detailed characterization of the expansin superfamily which has roles in growth and reaction to the stress of the plant. The study ensures detailed data for future studies examining gene functions including the roles in plant growth and stress conditions.
Comparative genomic analysis of expansin superfamily gene members in zucchini and cucumber and their expression profiles under different abiotic stresses
(2021-12-01) Arslan B.; İncili Ç.Y.; Ulu F.; Horuz E.; Bayarslan A.U.; Öçal M.; Kalyoncuoğlu E.; Baloglu M.C.; Altunoglu Y.C.
Zucchini and cucumber belong to the Cucurbitaceae family, a group of economical and nutritious food plants that is consumed worldwide. Expansin superfamily proteins are generally localized in the cell wall of plants and are known to possess an effect on cell wall modification by causing the expansion of this region. Although the whole genome sequences of cucumber and zucchini plants have been resolved, the determination and characterization of expansin superfamily members in these plants using whole genomic data have not been implemented yet. In the current study, a genome-wide analysis of zucchini (Cucurbita pepo) and cucumber (Cucumis sativus) genomes was performed to determine the expansin superfamily genes. In total, 49 and 41 expansin genes were identified in zucchini and cucumber genomes, respectively. All expansin superfamily members were subjected to further bioinformatics analysis including gene and protein structure, ontology of the proteins, phylogenetic relations and conserved motifs, orthologous relations with other plants, targeting miRNAs of those genes and in silico gene expression profiles. In addition, various abiotic stress responses of zucchini and cucumber expansin genes were examined to determine their roles in stress tolerance. CsEXPB-04 and CsEXPA-11 from cucumber and CpEXPA-20 and CpEXPLA-14 from zucchini can be candidate genes for abiotic stress response and tolerance in addition to their roles in the normal developmental processes, which are supported by the gene expression analysis. This work can provide new perspectives for the roles of expansin superfamily genes and offers comprehensive knowledge for future studies investigating the modes of action of expansin proteins.
New perspectives into the chemical characterization of Sida acuta Burm. f. extracts with respect to its anti-cancer, antioxidant and enzyme inhibitory effects
(2021-06-01) Uysal S.; Gevrenova R.; Sinan K.I.; Bayarslan A.U.; Altunoglu Y.C.; Zheleva-Dimitrova D.; Ak G.; Baloglu M.C.; Etienne O.K.; Lobine D.; Mahomoodally M.F.; Zengin G.
The chemical components, in vitro antioxidant capacities and enzyme inhibitory effects of dichloromethane (DCM), ethyl acetate (EA), methanol (MeOH) and water extracts of the medicinal plant, Sida acuta Burm. f. were evaluated. The individual phenolic components were assessed via ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS). In terms of chemical composition, phenolics (hydroxybenzoic and hydroxycinnamic acids) and flavonoids were identified as main groups. The antioxidant capacities were evaluated using a panoply of cell-free bioassays and the enzymatic inhibitory potentials against key enzymes involved in human diseases were also determined. The water extract exhibited the strongest scavenging abilities on DPPH (IC50: 1.05 mg/mL) and ABTS (IC50: 1.02 mg /mL). The best cholinesterase inhibitory abilities were observed with the methanol extract (IC50: 0.51 and 0.52 mg/mL for AChE and BChE, respectively), while DCM exhibited the strongest α-amylase (IC50: 1.21 mg/mL) and α-glucosidase (IC50: 0.62 mg/mL) inhibitory effects. The anti-cancer effects of methanol and water extracts were tested on human breast cancer cells, MDA-MB-231, and the methanol extract showed the best anti-cancer effect with an IC50 value of 102.4 μg/mL. In conclusion, the experimental data have demonstrated promising pharmacological activities of S. acuta extracts obtained using different solvents, thereby providing a scientific basis for the validation of the traditional medicinal uses of this plant.
Surface chemistry dependent toxicity of inorganic nanostructure glycoconjugates on bacterial cells and cancer cell lines
(2023-01-01) Sancak S.; Yazgan İ.; Bayarslan A.U.; Ayna A.; Evecen S.; Taşdelen Z.; Gümüş A.; Sönmez H.A.; Demir M.A.; Demir S.; Bakar F.; Dilek-Tepe H.; Kasemets K.; Otsus M.; Çeter T.
Surface functionalized nanostructures have outstanding potential in biological applications owing to their target-specific design. In this study, we utilized laboratory synthesized carbohydrate-derivatives (i.e., galactose, mannose, lactose, and cellobiose derivatives) for aqueous one-pot synthesis of gold (Au) and silver (Ag) nanostructure glycoconjugates (NSs), and iron metal-organic framework glycoconjugates (FeMOFs). This work aims to test whether differences in the surface chemistry of the inorganic nanostructures play roles in revealing their toxicities towards bacterial cells and cancerous cell lines. As of the first step, biological activity of AuNSs, AgNSs, and FeMOFs were tested against a variety of gram (−) and gram (+) bacterial strains, where AgNSs possessed moderate to high antibacterial activities against all the tested bacterial strains, while AuNSs and FeMOFs showed their bacterial toxicity mostly depending on the strain. Minimum inhibitory concentration (MIC) and Minimum bactericidal concentration (MBC) determination studies were performed for the nanostructure glycoconjugates, for which μg/mL MBC values were obtained such as (Cellobiose p-aminobenzoic acid_AgNS) CBpAB_AgNS gave 50 μg/mL MBC value for P.aeruginosa and S.kentucy. The activity of selected sugar ligands and corresponding glycoconjugates were further tested on MDA-MB-231 breast cancer and A549 lung cancer cell lines, where selective anticancer activity was observed depending on the surface chemistry as well. Besides, D-penicillamine was introduced to galectin specific sugar ligand coated AuNS glycoconjugates, which showed very strong anticancer activities even at low doses. Overall, the importance of this work is that the surface chemistry of the inorganic nanostructures can be critical to reveal their toxicity towards bacterial cells and cancerous cell lines.