Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
Browse
158 results
Search Results
Master Thesis Image-Based Bioassays in Microfluidic Devices(Izmir Institute of Technology, 2023) Doyran, Öykü; Teki̇n, Hüseyi̇n CumhurSon zamanlarda, mikroakışkan uygulamalar, tıbbi bozuklukların teşhisini ve izlenmesini amaçlayan minyatür cihazlarla, standart laboratuvar prosedürlerinin yerini almıştır. İyi tanınan geleneksel mikroskobik teknikler, hala alışılagelmiş olarak mikroakışkan teknolojilerinde görüntüleme için kullanılmaktadır. Ancak bu mikroskopların hantal ve pahalı yapıları, yeni nesil hasta başı test cihazları ile uyumlu değildir. Minyatür cihazlarda optik elemanların uygulanması, ölçüm doğruluğu ve kesinliğinin yanı sıra taşınabilir enstrümantasyon sunar. Spesifik olarak, lenssiz görüntüleme teknolojilerinin mikro teknolojilerle entegrasyonu, yeni cihazlar geliştirmenin yolunu açmıştır. Bu tezde entegre lenssiz holografik mikroskopların iki farklı uygulaması sunulmuştur. İlk uygulama, boyutlarına ve morfolojilerine göre kanda sirküle eden tümör mikroembolilerini lökositlerden ayırmak, saflaştırmak ve izole etmek için yeni bir lenssiz holografik mikroskop entegreli mikroakışkan tabanlı filtreleme yönteminin geliştirilmesini içermektedir. Geliştirilen yöntem, mikrofiltrasyon ve lenssiz holografik mikroskop teknolojilerinin avantajlarını kullanarak, ticari hücre ayırma cihazlarıyla karşılaştırılabilir şekilde kanda sirküle eden tümör mikroemboli ayırma verimliliği ve saflığı sağlamıştır. Ayrıca, lenssiz holografik mikroskop entegre manyetik levitasyon tabanlı sıvı viskozitesi ve özkütle ölçümü olarak başka bir yeni yöntem tanıtılmıştır. Bu yöntemde, sıvıların özkütle ve viskozitelerini belirlemek için mikrosensör olarak mikropartiküller ölçüm yapılacak sıvı içinde kullanılmıştır. Bu parçacıkların levitasyon yüksekliği ve hızı sıvının özkütlesi ve viskozitesi ile ilişkilendirilmiştir. Bu tez kapsamında sunulan, mikroakışkan tabanlı teknolojilere entegre lenssiz holografik mikroskop sistemleri, uygun maliyetli ve taşınabilir görüntü tabanlı yeni cihazların geliştirilmesinin önünü açabilecektir.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 Cloning of Novel Sericin Like Proteins and Optimization of Their Expression(Izmir Institute of Technology, 2022) Gürerk, Gamze; Şanlı Mohamed, Gülşah; Şanlı Mohamed, GülşahSericin is a protein that helps fibroin fibers link together to create the cocoon, and it forms silk with fibroin. Fibroin is used in textile production as well as in biomaterial applications. Sericin has essential biocompatibility, biodegradability, cryoprotection, antioxidant properties, and a multi-component structure. Thanks to these properties, its use in biomaterial and biomedical fields is expanding and also used in cosmetic research and wound healing, and drug delivery thanks to its high fiber structure. Sericin can be obtained from silkworm cocoons by degumming method but changes the structure of the obtained protein since the protein is exposed to high temperatures. Sericin produced in different batches is obtained in different quantities and these create inconsistencies in the quality of the biomaterials obtained from the sericin, limiting the use of the sericin as a biomaterial. Besides, obtaining protein by recombinant production provides the advantage that the repetitive chain length can adjust as desired and the protein can be standardized. In this thesis, recombinantly generated and optimized a novel sericin-like protein (Ser-12mer) with the native sericin sequence encoding twelve repeats of recombinantly conserved 38 amino acid motifs in Escherichia coli and characterized its structural properties. In addition, the effects of induction cell density and cell culture media on the expression of the previously produced sericin-like protein (Ser-4mer) was investigated and its expression and concentration were increased by optimization. Recombinant production of a sericin-like protein will provide an understanding of the sequence-structure relationships and significantly expand their applications as biomaterials.Master Thesis Optimizing the Dispersion of Ceramic Nanoparticles and Assessing the Role of Aggregation in Mediating Biological Activity(Izmir Institute of Technology, 2022) Önder, Anıl Can; Öksel Karakuş, Ceyda; Öksel Karakuş, CeydaThe aim of this study is to optimize the sample preparation protocol for dispersing powder-form ceramic nanoparticles (CeNPs) in liquid media by leveraging the power of the design of experiment approach to narrow down potential causes of aggregation and to investigate the subsequent effect of CeNP aggregation on the biological activity of SaOS-2 human osteosarcoma cells. Dispersion of the nanopowders is one of the problems in the nanotechnology field because of the tendency of the nanoparticles for aggregation. Although there are existing dispersion protocols, they offer a one-size-fits-all approach overseeing the unique physicochemical properties of the different nanomaterials. In this study, optimization of the sample preparation protocol for two CeNPs was assessed via the investigation of the most contributing parameters and their synergetic effect through measurements of Z-average and zeta potential. Evaluation of these parameters allowed the development of two different models for each nanomaterial, predicting Z-average and zeta potential for given parameter sets. Through these models, two different sample sets were selected to evaluate the effect of aggregation on the SaOS-2 cell line. Outcomes show that the concentration of nanomaterial, pH, and the presence of additive molecule are three main parameters that affect dispersion stability. It was seen that these parameters can be included in a design to develop an efficient model to predict Z-average and zeta potential for investigated nanomaterials. Moreover, cell viability tests show that there is no significant difference between untreated and nanomaterial-treated cells. The findings promise that tailor-made and reliable dispersion protocols for different nanopowders can be developed via design of experiment.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 Developing a Lamp Pcr Based Diagnostic Test for Crimean Congo Hemorrhagic Fever Virus(Izmir Institute of Technology, 2022) Üstün, Selcen; Taşkent Sezgin, HümeyraCrimean-Congo hemorrhagic fever infection is one of the most common tickborne viral infections, non-infectious in animals and fatal to humans with a mortality rate around 40%. The high mortality rate and lack of vaccines or drug treatment point to the potential danger of infection. The aim of this thesis was to detect 21 complete S-segment Crimean-Congo hemorrhagic fever virus strains originating in Turkey using Fluorimetric Loop Mediated Isothermal Amplification (LAMP) method, which is one of the PCRbased isothermal amplification methods for detecting viral infections. Conserved regions of the 21 strains of the CCHFV observed in Turkey were determined by sequence alignment and LAMP primers for these conserved regions were designed. DNA of CCHFV Ank-2 (GeneBank accession number: MK309333) strain was used and optimum LAMP reaction conditions were determined by changing the temperature, primer amount and MgSO4 concentration. LAMP results were compared with qPCR, which is considered the gold standard. The detection limit for LAMP and qPCR was 2x106 copies/µl. In the study, the CCHFV LAMP primer set-1 gave similar results to the qPCR primer set. The CCHFV LAMP primer set-4 performed better by turning positive 9 minutes earlier than the qPCR primer set. This results indicate LAMP is an alternative method for detecting CCHFV but reveals the necessity of improving the sensitivity of the test.Master Thesis Investigation of the Interaction and Olgiomerization of Hiv Capsid and Single Domain Antibody as a Biotechnological Drug Against Hiv(Izmir Institute of Technology, 2022) Güney, Seniha; Taşkent Sezgin, HümeyraHuman immunodeficiency virus (HIV) causes AIDS which is still a global public health threat. Current drugs against HIV infection cannot eradicate the virus therefore, research on new drug targets continues. HIV capsid protein, which has a highly conserved sequence and is sensitive to mutations, has critical roles in the virus lifecycle, making it a high-potential drug target. A nanobody is the antigen-binding domain of heavy-chain only antibodies of camelids. Small size, thermal stability and ease of production makes nanobodies ideal antibody fragments for therapeutic and diagnostic purposes. In the literature, a nanobody binding to the HIV-1 capsid-N terminal domain (NTD) has been reported. The aim of this thesis is to examine the potential of this nanobody as a biotechnological drug candidate against the HIV-1 and HIV-2 capsid proteins. In the study, HIV-1 capsid was expressed, purified and biophysically characterized. Thermal and chemical denaturation of the protein were done, the melting temperature and unfolding free-energy values of the protein were determined. In-vitro oligomerization of the HIV-1 capsid was performed and observed that the protein self-oligomerized over time. Pure HIV-2 capsid protein could not be produced recombinantly. Thereupon, HIV1 capsid-NTD and HIV-2 capsid-NTD proteins were expressed and purified. Secondary structure of HIV-1 capsid, HIV-1 capsid-NTD and nanobody were analyzed with circular dichroism (CD) spectroscopy and the results matched with the literature. Isothermal titration calorimetry (ITC) experiments were done to examine the HIV-1 capsidnanobody interaction, but good binding was not observed between the two proteins. Future work requires repeating ITC experiments.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 Effects of Centella Asiatica Saponins on Telomerase Activation and Wound Healing(Izmir Institute of Technology, 2021) Demirbaş, Devran; Bedir, Erdal; Büyükkileci, Ali OğuzCentella asiatica L. is a well-known plant species endemic to Southeast Asia that has noteworthy biological effects. Triterpenoid saponins, comprising more than 80% of the content, are suggested to be the chief compounds responsible for the biological effects. A recent study has described that the extract of Centella asiatica exhibits telomerase activation. In line with these developments, as part of our studies on natural products demonstrating anti-aging properties, we decided to engage Centella asiatica and its components. Within the scope of this thesis, four major compounds, viz. madecassoside, asiaticoside, madecassic acid, and asiatic acid were isolated from the standardized extract of Centella asiatica, and their structures were elucidated by spectroscopic methods. Using in vitro methods, the effects of the extract and purified compounds on cell proliferation under standard culture and oxidative stress (H2O2) conditions, wound healing, and human Telomerase Reverse Transcriptase (hTERT) protein level were investigated. Our experiments were conducted on MRC-5 and HEKn cell lines. It was observed that the standardized extract of Centella asiatica increased the proliferation of the MRC-5 cells meaningfully between 5 to 100 µg/ml. Moreover, the extract showed protective effects on MRC-5 cells at 500 and 1000 ng/ml under oxidative stress conditions. Madecassoside, madecassic acid, asiaticoside, and asiatic acid exhibited the highest proliferative effects on MRC-5 cells at concentrations of 1000 nM (28%), 2 nM (66%), 300 nM (61%), and 300 nM (56%), respectively. Asiatic acid and the extract accelerated cell migration in wound areas that were made on MRC-5 cells up to 32% and 36% in the range of 10 to 300 nM or ng/ml, respectively. The immunoblotting assay studies showed that madecassoside and asiaticoside were increased the expression of hTERT protein level on HEKn cell line by 3.16-fold and 5.62-fold, respectively, at 30 nM concentration. Furthermore, the extract was observed to increase the protein level by 2.62-fold at 300 ng/ml.Master Thesis Development of Conductive Oxide Based Thin Film Modified Electrodes and Biosensors Applications(Izmir Institute of Technology, 2021) Yurttaş, Betül; Özyüzer, Lütfi; Erdem Gürsan, Kadriye ArzumFrom the first biosensor produced in 1956 to the present day, biosensors have been highly developed and diversified. In biosensor manufacturing, thin films have become a rapidly emerging field. Depending on the thin film material used, thin films have many advantageous properties for biosensors, such as high surface-to-volume ratio, conductivity, stability, specificity, biocompatibility, and good electrocatalytic activity. Dopamine is a neurotransmitter that has a significant impact on the emergence and treatment of certain diseases such as Alzheimer's and Parkinson's diseases. Dopamine monitoring is important for the prevention of these diseases, and it is a favorable option to use biosensors, which are useful and practical tools, instead of time-consuming and expensive conventional methods. For this purpose, in this thesis, a non-enzymatic electrochemical biosensor based on thin film electrodes was developed for monitoring dopamine levels. The electrodes were developed by deposition of Zn2SnO4 (ZTO) thin film on ITO thin film substrate by DC magnetron sputtering technique. The properties of the electrodes were determined by thickness, optical transmittance, XRD and SEM analysis. Electrochemical analysis, namely CV, EIS and DPV measurements, were performed before and after the electrodes were sonicated and modified with APTES before their application to the voltammetric detection of dopamine. In addition, electrochemical measurements were performed before/after sonication, APTES modification. Dopamine was detected by a voltammetric method using DPV technique. Furthermore, experiments in the presence of interferents such as ascorbic acid (AA), uric acid (UA) etc. showed that the thin film electrodes can be successfully applied for voltammetric determination of dopamine. As a result, the biosensor technology developed in this study has the potential to be wearable in the future, enabling non-invasive monitoring of dopamine levels in body fluids such as saliva, tears and sweat.