Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
Browse
6 results
Search Results
Now showing 1 - 6 of 6
Master Thesis Dynamics and Bioinformatis of Microbial Spoilage Ecology of Kefir(Izmir Institute of Technology, 2022) Memon, Ayşe; Baysal, Ayşe Handan; Sezgin, EfeIn this study, it was aimed to characterize the microbiological properties, bacterial composition, and microbial stability of 5 different commercial milk kefir beverage products during refrigerated storage. In order to determine the microbiological load and compositions, total mesophilic aerobic bacteria, yeast and molds, lactic acid bacteria, Lactobacilli, Lactococci, total coliforms, and E.coli were investigated by cultural conventional analysis for milk kefir beverages. According to the obtained data, microbiological and hygienic characteristics of the samples were found acceptable. The bacterial load of the kefir beverage samples ranged between 7.086 and 8.794 log10 cfu.ml-1 for viable total aerobic mesophilic bacteria (TAMB), 6.792 and 8.382 og10 cfu.ml-1 for lactic bacteria (LAB), <10 and 6.322 log10 cfu.ml-1for Lactobacillus, 5.857 and 8.146 log10 cfu.ml-1 Lactococcus, 5.176 and 7.218 log10 cfu.ml-1 for yeasts, negative for molds, coliform bacteria and negative for E. coli. Principal component analysis (PCA) of the compounds separated the kefir beverages according to the storage time and kefir brands. Strong relationship were found between storage time and PC1 and between kefir brands and PC2. To date, information on microbial properties, bacterial composition, and constancy of commercial kefir is scant, and to the best of our knowledge, this is the first research to contribute information on kefir beverages in microbial properties, bacterial composition, and their stability during refrigerated storage by evaluating Fourier Transform Infrared Spectroscopy (FTIR) spectra analysis and Bioinformatics besides cultural conventional analysis.Master Thesis Microbial Mapping in Air and Surface Samples Collected From Schools(Izmir Institute of Technology, 2022) Alkan, Kutlu Şafak; Ökten, Hatice Eser; Sezgin, EfeIndoor environmental quality has gained attention in the past decades due to the increased periods of time spent enclosed in buildings. Parameters such as ventilation, water damage, type of paints used, use of carpets, etc. affect the indoor air quality significantly. With the rising concern regarding outbreaks and pandemic, it is important to investigate the microbial load and consortium structure in schools. This thesis aims at determining the microbial loads in three selected schools in the Balçova District of İzmir, Türkiye. Two sampling campaigns were conducted, one in the winter break (February 2022) and one in the spring semester (May 2022). Surface swab samples and settle-plate air samples were collected from pre-defined spots at schools. Surface swab samples and settle-plate air samples were examined via both classical microbial culture methods and modern DNA analysis methods. Via classical microbial culture methods, culture comparison from the database, fungi cultures were dedicated up to genus level. Via modern DNA analysis method, Sanger sequencing, bacterial cultures were dedicated up to genus level too. All the results indicated that three schools were hosting possibly dangerous genera of both fungi and bacteria. But, this also showed that genus-level discrimination is still not enough to utter exact indoor air quality from the perspective of indoor microbiota to the identification of possible health risks for occupants. For further studies, microbial mapping should discriminate up to species level to demonstrate exact indoor air quality and indoor microbiota vie high throughput sequencing methods.Master Thesis Molecular Evolution and Population Genetics of Acid Resistant Pathway Glutamate Decarboxylase in Lactic Acid Bacteria(Izmir Institute of Technology, 2022) Tekin, Burcu; Sezgin, EfeThe Glutamate Decarboxylase(GAD) Pathway (GDP) is a major acid resistance mechanism that allows Lactic acid bacteria (LABs) to survive in low pH food environments. In the thesis, we aimed to study the molecular evolution and population genetics of GDP genes in LABs to understand evolutionary processes shaping adaptation to high acid environments by contrasting species where the GDP genes are organized as an operon structure (Levilactobacillus brevis) versus lack of an operon structure (Lactiplantibacillus plantarum). Intraspecies molecular population genetic analyses with GDP genes of L. brevis and L. plantarum from various environments revealed that synonymous and non-synonymous nucleotide diversity is driven mainly by low-frequency changes. Neutrality tests revealed mostly negative values indicating negative selection against replacement changes. Similarly, molecular structure and amino acid characteristic analyses showed that none of the replacement changes on the GDP genes alter the important residues of the proteins supporting negative selection against non-conservative amino acid changes. Interspecies analyses were used to identify the closely related LABs. Moreover, phylogenetic analyses showed that the GDP gene tree topologies differed from the LAB species tree, indicating divergent evolutionary histories. The functionally preserved two gad copies of the L. brevis grouped separate phylogenetic clades, showing that the origin of the second gad gene might be via horizontal gene transfer from a phylogenetically distant LAB species rather than gene duplication. In conclusion, GDP in LABs exhibits a dynamic molecular evolutionary history that enables organisms to thrive in high acid environments.Master Thesis Development of Functional Chocolate Using Gamma-Amino Butyric Acid Producer Probiotic: Prominent To Alleviate Anxiety Disorder(Izmir Institute of Technology, 2019) Özer, Merve; Harsa, Hayriye Şebnem; Sezgin, EfeThe purpose of this study was screening of four probiotics to investigate for their gamma-aminobutyric acid producing capabilities. Lactobacillus rhamnosus NRRL B- 442 strain has been selected for its maximum gamma-aminobutyric acid concentration. In this study, a new chocolate product has been developed by incorporation of probiotic cells; stability of the probiotics was improved by microencapsulation by water-in-oil emulsion technique using whey-pullulan complex. Survival rates of microencapsulated and free-cells of probiotic bacteria in chocolate have been compared. Probiotic counts were found as 6.75 log CFU/g and 7.20 log CFU/g in chocolate, for encapsulated and free-cells, respectively, at the end of 60 days. High cell counts and increased cell resistances were remained at 4oC when compared at 25oC, in chocolate samples. Furthermore, probiotics did not affect the physical, chemical and sensory properties of chocolate, whereas the texture analysis showed an increase in the hardness of free-cell in chocolate bacteria on the 0th and 60th day. Survival rate of microencapsulated bacteria in chocolate samples was observed at higher percentage 87% than free-cell bacteria e.g. 75% during simulated in-vitro analysis. Consequently, Lb. rhamnosus with the highest GABA producing capability may provide insight for patients having an anxiety disorder, since this strain has been thought as having a therapeutic effect. A new functional food model was developed for “Gut- Brain Axis” phenomena since the chocolate could be accepted as a good carrier for probiotics.Master Thesis Effect of Interleukin-10 Pathway Genes and Diet on Behcet's Disease(Izmir Institute of Technology, 2019) Arpaz, Goncagül; Sezgin, EfeBehcet's disease (BD) is an inflammatory disease characterized by recurrent oral and genital aphthae with unknown etiology. The disease is most prevalent along the Silk Road populations. BD is complex disease influenced by genetic and environmental factors. Identification of contribution of these factors to BD is an active research question. The first aim of the thesis is to determine the biological pathways in the etiopathology of BD by a comprehensive literature review of published genetic research. The second aim of the thesis is to investigate the genetic changes and gene expression in IL-10, an anti-inflammatory pathway cytokine, and its primary receptor. IL-10R1 in BD. The third aim of the thesis is to discover potential novel functional foods that can benefit patients with BD. 241 variants from 119 genes were identified to be associated with BD. Frequency distribution of the 241 variants among world populations was rather different. IL-10 was idendified to be most significantly associated with BD and differentiated high BD risk populations from the rest based on principal component analyses. Sequence analyses of IL-10 and IL-10R1 identified rs3024498 and rs9610 variants, respectively, in Turkish BD patients. Rs3024498 wa not associated with BD risk; however, IL-10R1 rs 9610 variant showed a marginally significant relationship with BD. IL-10 gene expression was 9.6 fold higher in BD compared to normal controls. As an anti-inflammatory IL-10 pathway is identified to influence BD, novel food supplements with high anti-inflammatory ingredients need to be developed to benefit patients with BD.Master Thesis Developing a Guide of Bioinformatic Database for Probiotic Products(Izmir Institute of Technology, 2019) Yılmaz, Melike; Harsa, Hayriye Şebnem; Sezgin, EfeRecently, probiotic use has rapidly expanded, as they have potential health effects for microbiota to protect homeostasis in the human body. Bioinformatics is generally defined as collecting and analysing biological data. Establishing a bioinformatic system for probiotics, would have a potential to emphasize the beneficial impacts for human health, while enabling cross examination on diseases and products. In this study, new information has been collected about probiotics based on in vitro, in vivo, clinical trials and meta-analysis to develop a comprehensive guide. Metaanalyses of sixteen and seventeen randomized, controlled trials of S. boulardii (Sb) against diarrhea reported pooled relative risks of 0.51 (95% CI [0.40-0.64]) in adults and 0.55 (95% CI [0.42-0.72]) in children, respectively. These results demonstrated that Sb was effective for preventing and treating different types of diarrhea in adult and children patients. An in silico gene expression study conducted in Tecnico Lisboa* comparing Sb probiotic and non-probiotic Saccharomyces cerevisiae (Sc) strains showed transcription regulation differences in 26 genes. An in silico pipeline that was used as the basis for a new query in the ProBioYeastract database was developed. A cross-strain promoter analysis, comparing Sb CNCM I-745 and Unique28 strains with Sc S288C strain showed that the expression of 26 probiotic-related genes was predicted to be controlled by different transcription factors in probiotic vs non-probiotic strains. Among the evaluated six selected genes, a gene involved in biofilm formation, aggregation, and adhesion, EFG1, was found to be up-regulated in Sb CNCM I-745 compared to Sc BY4741.