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Geleneksel Gıda Ürünlerinden İzole Edilen Laktik Asit Bakterilerinin Probiyotik Özelliklerinin Belirlenmesi
(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2023) Yiğit, Mehmet Burak; Aydın, Aysun Cebeci
Probiotics are microorganisms that live in our bodies and positively affect health when consumed regularly. One of the ways to have a healthy body is to have a healthy microbiota. Because of that, the importance given to the consumption of probiotic foods among the public is increasing. Since probiotics are especially abundant in fermented and traditional foods, consuming these foods is vital to have a healthy microflora. In this thesis, probiotic potentials of bacteria isolated from tarhana, einkorn sourdough, Turkish and Bulgarian-type boza and pickled beetroot foods were investigated, and obtained results were discussed. Based on acid and bile salt tolerance tests, MRS ES-2-3-7-11-12-17, MRS PT-2-14-16, MRS N-1, MRS EB-3, MRS T-1, M17 N-2 -3-4 showed higher viability in acidic environments (pH 2.0 and 3.0) than the control groups, M17 N-3-4 and M17 TB-1-2 strains showed higher viability at 0.3% and 0.5% bile salt conditions than other strains. For 10 strains which are selected for further tests, in the adhesion to Caco-2 cells, MRS ES-3, MRS N-1, MRS T-2, M17 BB-7, M17 N-2 and M17 N-3 showed over 35% adhesion, especially, MRS N-1 and M17 N-2 showed over 85% adhesion to Caco-2 cells. For the antimicrobial activity test, ES-3 strain showed limited effect on S. aureus ATCC 6538 and K. pneumoniae ATCC 4352 pathogens, while other strains showed no inhibitory effect on pathogens. Finally, according to the results of 16S rRNA sequencing, it was determined that MRS ES-3, ES-7, PT-14 strains belonged to L. plantarum, MRS ES-11 strain belonged to L. brevis, M17 BB-7 strain belonged to E. faecium and M17 TB-2 strain belonged to E. durans species.
SARS-CoV-2 Omikron Varyantına Özgü Tek Domainli Antikorların Protein-Protein Kenetlenmesi Yaklaşımlarıyla Tanımlanması
(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2022) İlmek, Özkan; Güner, Şerife Ayaz
Omicron, became the dominant variant in 2022 in terms of spreading rate, has managed to evade from an immune system of patients due to its unique mutations. Single domain antibodies (sdAb) which are functionally important parts of conventional antibodies are commonly used for diagnosis and treatment. Although there are many sdAbs developed to combat coronavirus in recent years, their effectiveness against Omicron variant has not been sufficiently tested and the effect of mutations regarding neutralization level is not clear. In this study, structure modelling of 850 sdAb sequences obtained from previous studies were generated using AlphaFold 2 and effectiveness of these sdAbs against Omicron variant was tested via protein-protein docking approach. In the docking process, within a realistic approach, missing residues were completed into Spike protein PDB structures, and Spike protein homotrimer structure in closed state conformation was used. Finally, top 1000 and top 100 scores are determined as a threshold value for different protein-protein docking scoring functions such as HDOCK, PRODIGY and Bluues. sdAbs that have successful results for Omicron variant were listed. There were 4 sdAbs which exceed the threshold values after 2 different docking experiments against the Omicron variant. The scripting codes and methodological approach developed within this thesis can be used against new SARS-CoV-2 variants that may emerge in the future or other diseases.

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