Browsing by Author "Arslan B."

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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.
Effects of Nasal and Paranasal Sinus Variations on Chronic Otitis Media Development in Pediatric Patients
(2021-10-01) Atila N.E.; Topal K.; Bulut Y.E.; Kaya Z.; Arslan B.
Objective: Chronic otitis media is an inflammatory disease of the middle ear. The airflow in the nasal passage affects the development of mastoid air cells through the eustachian tube.Nasal and paranasal pathologies and their anatomical variations cause chronic sinonasal inflammation and affect the middle ear mucosa. This study aims to reveal whether the nasal and paranasal sinus variations in pediatric patients are a factor in developing chronic otitis media. Materials and Methods: Eighty patients, with unilateral chronic otitis media, who were admitted to the otorhinolaryngology clinic between May 2015 and July 2019, were included in this retrospective study. The control group (Group 2) consisted of a total of 51 patients. None of the patients in Group 2 had otorrhea history and no signs of chronic otitis in their otoscopic examination, middle ear pathologies. The patient’s anatomical variations of the nasal cavity and sinuses were evaluated with CT by a radiologist Results: Nasal septum deviation was found to be 53% in children with chronic otitis media. It was found 31.4% in the control group. Since the P value was found to be.04, this rate was considered as significant. Inferior concha hypertrophy was found to be 17.6% in the control group and 38.8% in the group with chronic otitis media, and this rate was considered significant since the P value was.035 Conclusion: We detected that septum deviation and inferior concha hypertrophy increased chronic otitis media formation in children. All these studies show that cases causing nasal obstruction, such as septum deviation, have a negative effect on middle ear pressure and increase the rate of ear diseases.
Phthalocyanines including 2-mercaptobenzimidazole analogs: Synthesis, spectroscopic characteristics, quantum-chemical studies on the relationship between electronic and antioxidant properties
(2020-02-15) Yakan H.; Çavuş M.; Güzel E.; Arslan B.; Bakır T.; Muğlu H.
In this study, peripherally tetra 2-mercaptobenzimidazole group substituted cobalt and indium phthalocyanine complexes (2 and 3) were prepared from 4-(benzo[d]imidazole-2-ylthio)phthalonitrile (1) for the first time. Antioxidant behaviors and theoretical calculations of benzimidazole-substituted metallophthalocyanines are presented. The structures of these compounds were determined by the spectroscopic methods (IR, 1H NMR, UV–Vis and mass spectroscopies) and elemental analysis. Antioxidant activities of the compounds (1–3) were measured using 1,1-diphenyl-2-picrylhydrazyl (DPPH) method. Antioxidant activity was followed by 1 > 3 > 2 > Trolox. In addition, density functional theory (DFT) calculations were carried out to determine the stable electronic structure, charge density distributions, FMO energy eigenvalues, and electronegativity of the ligand (1) and complexes (2 and 3). NBO and QTAIM analysis were performed to investigate the relationship between the electronic properties and antioxidant activity of the compounds.