Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
Browse
9 results
Search Results
Master Thesis Screening Spirulina Stranins for Protein Productivity Based on Cultivation Under Photobioreactor Conditionsy(01. Izmir Institute of Technology, 2022) Binkanat, Tahir Burak; Özkan, Altan; Büyükkileci, Ali OğuzSpirulina is an industrially produced algae for consumption as a nutritional supplement owing to its exceptionally high protein content. The delivery of the desired metabolite profiles highly depends on selecting the correct strains for growth. In this regard, the information in the literature is limited as the strains cultivated industrially are unknown, and the strains of academic research were mostly locally isolated or procured from local sources. The current study is the first step of research activities planned to assess the large-scale production potential of Spirulina in Izmir. Thus in this work, Spirulina platensis 2340, Spirulina maxima 84.79, Spirulina platensis 85.79, Spirulina platensis 86.79, and Spirulina platensis 29 were screened for biomass and protein productivity during cultivation under standardized process conditions of a bubble column photobioreactor. The final biomass concentrations were strain specific and ranged from 1.2 to 1.9 g/L. An inverse relationship existed between the logistic model-based final biomass concentrations and the production rate constants. Thus, the peak productivities were more evenly distributed and ranged between 0.15 to 0.20 g/L-day. SP 29 had the ideal protein content vs. cultivation time profile as it was consistently high and varied in the narrow range of 60 to 64%. Higher protein contents could be reached with the other strains, but they also had higher variations during the growth period. The final protein concentrations varied from 0.4 g/L to 1.4 g/L. The highest peak productivity obtained was about 0.11 g/L-day, which could be obtained by three of the strains. The results clearly show the importance of strain selection for sustaining protein-rich biomass production with Spirulina.Master Thesis Investigation of the Proteins of Leishmania Tropica Causing Viscerotropism in Humans Using Mass Spectrometry(Izmir Institute of Technology, 2022) Beyaz, Merve; Yalçın, TalatLeishmaniasis is a neglected tropical disease in 98 countries and five continents worldwide. The most prevalent forms of this parasitic disease are Cutaneous, Mucocutaneous, and Visceral Leishmaniasis. While Cutaneous Leishmaniasis causes disfiguring skin conditions and lesions, Mucocutaneous Leishmaniasis damages the mucosal tissues of the mouth, nose, and throat. The visceral form of Leishmaniasis causes weight loss, fever, diarrhea, lymph nodes, and spleen or liver enlargement. Today, Leishmania tropica, one of the strains of the Leishmania parasite, no longer causes only Cutaneous Leishmaniasis (CL) but also Visceral Leishmaniasis (VL). The reason for this visceralism in L. tropica is not fully understood. Mass spectrometry has a vital place in proteomic analyses; it provides information about expression levels and the identification of proteins. In this study, the proteins of L. tropica causing CL and CL are analyzed using the mass spectrometric shotgun method. Off-line HPLC separation followed by LC-MS/MS analyses are performed, and differential proteins between CL and VL isolates of L. tropica are determined. Results indicate that among the differentially abundant proteins between two sample groups, paraflagellar rod proteins, elongation factor 1-alpha protein, and surface antigen proteins might play a role in avoiding immune recognition. Also, proteins with peroxidoxin function, cytochrome b5, and endoribonuclease might help parasite survival in macrophages. And finally, thiol-specific antioxidant protein may have a role in viscerotropism in L. tropica.Master Thesis Investigation of Bcl-2 Proteins in Th17 Cell Functions(01. Izmir Institute of Technology, 2021) Çimen, Tuğçe; Nalbant Aldanmaz, AytenInterleukin 17 producing T helper 17 cells are the distinct subset of CD4⁺ T cells. Th17 cells are an important part of the immune response of host defense. Dysregulation of Th17 cells plays a role in various pathologies including autoimmune diseases and cancer types. Bcl-2 family proteins are mostly known regulators of apoptotic cell death. The apoptotic and survival mechanisms of Th17 cells are not well known yet. Therefore, this study aims to investigate Bcl-2 protein family functions in Th17 cell survival and to understand the regulation network of apoptotic mechanisms of Th17 cells. To do that, Peripheral Blood Mononuclear Cells were isolated from a healthy buffy coat by Ficoll separation. Naive T cells were sorted from PBMC and cultured under Th17 polarizing conditions. Th17 cells were phenotypically characterized by flow cytometry. Afterward, cell lysates were obtained from Th0 and Th17 cells at different time points. The expressions of human transcription factor RORC2, proapoptotic Bik, Bid, Puma and Bim and, antiapoptotic Mcl-1 and Bcl-xL at cell groups were detected by Western blotting. The increased expressions of Bcl-xL and Mcl-1 were detected where the diminished expressions of Bim and Puma were detected in proportional with Th17 differentiation by increased RORC2 and elevated RORC/IL17A levels. Bik was undetectable in both cell groups while non-truncated isoform of Bid was barely decreased among cell groups. Outputs of this study allow us to understand the dynamics of Bcl-2 family proteins in human Th17 cell survival. The understanding roles of Bcl-2 proteins in Th17 cells may help to develop different therapeutics for Th17 associated diseases in the future.Master Thesis Role of Sema6d in Proliferation, Epithelial-Mesenchymal Transition and Migration of Breast Cancer Cell Lines(Izmir Institute of Technology, 2017) Şahi, Ece; Yalçın Özuysal, ÖzdenBreast cancer is one of the most common cancer types around world and the second leading cause of cancer related deaths among women. Not the primary tumor but distant metastases are mainly the reason of deaths. For metastasis, the cells may go through epithelial-mesenchymal transition (EMT), and acquire migration and invasion abilities. SEMA6D is a transmembrane protein that belongs to a large semaphorin family. SEMA6D is involved in the migration of embryonic cardiac cells. Recently it was validated as an oncogene in osteosarcoma. Also, its oncogenic roles were investigated in gastric cancer and mesothelioma. According to in silico analysis of the Cancer Genome Atlas (TCGA), high SEMA6D expression level is associated with better survival of triple negative breast cancer patients. However, there is not any published study which investigates roles of SEMA6D in breast cancer yet, other than bioinformatic analysis. Therefore, we aimed to understand role of SEMA6D in proliferation, EMT and migration of breast cancer cells. We observed that overexpression of SEMA6D reduces proliferation but enhances migration in non-invasive breast cancer cell line MCF7. Thereby, SEMA6D may increase metastatic ability of MCF7 cells. Its metastatic ability was also supported by changes in EMT markers. On the other hand, proliferation of metastatic breast cancer cell line MDAMB231 was not significantly changed by overexpression of SEMA6D and migration ability was slightly reduced but mesenchymal markers tended to increase in SEMA6D overexpressing MDAMB231 cells. As a conclusion, SEMA6D tends to enhance proliferation, migration through EMT in MCF7 cell line whereas overexpression of SEMA6D did not demonstrate significant effect on metastatic MDA-MB-231 cell line. Therefore, we should separately evaluate role of SEMA6D in different breast cancer cell lines and further studies are required to understand role of SEMA6D in breast cancer.Master Thesis A Computational Study on the Structures and Proton Affinities of B3+ Ions; Peptide Mass Fragment Product(Izmir Institute of Technology, 2015) Boz, Seçkin; Elmacı Irmak, NuranMass spectrometry is the tool of choice during most of the proteomics studies to get amino acid sequence. However, unambiguously identifying amino acid sequence from mass spectra is not easy and straight forward task. Deeper understanding is needed to support both existing knowledge and develop newer models on dissociation patterns of protonated peptides and it will help to improve efficiency of current algorithms used in peptide identification. In this study, the structures of b3+ ions and their neutral forms were investigated by using computational methods. First, potential energy surface of b ions are scanned using molecular dynamics simulations and conformer samples are collected. Then, in order to reduce number of conformers, principal coordinate analysis was applied to find and select different structures within the sample. Selected conformers were optimized using density functional theory calculations. Proton affinities of b ions are determined by the energy difference between most stable conformers of the positively charged and neutral peptide fragments. Different amino acids were used to understand the role of side chain of amino acids on both structures and proton affinities of b3+ ions; XA2+ where X=N, H, C, Y, D, L and F. The results showed that, b3+ ions prefer to have linear oxazolone structure. However, in their neutral states, cyclic structures are relatively far more stable than linear isomers. Histidine display different behavior than other amino acids. Side chain of histidine holds protons and forms stable structures. The energies of cyclic and linear isomers of Histidine containing b ions are close to each other. Histidine containing peptide fragments have larger proton affinity comparing to others. Difference of proton affinities between linear and cyclic conformers varies based on amino acid used. This difference is lower than 10kcal/mol in histidine, asparagine and aspartic acid containing peptide fragments. There is no dramatic position preference of the X-amino acid for the N- or C- terminals or middle position with the exception of Asn and Asp (unlike the center) and Histidine which likes to be at C-terminal.Master Thesis Investigation of Heat Stress-Induced Proteins of Cold-Adapted Pseudomonas Marginals Using Proteomic Approach(Izmir Institute of Technology, 2008) Taşoğlu, Çağdaş; Yalçın, TalatTemperature alteration is known as a common environmental stress condition which all living organisms encounter and response by producing evolutionary wellconserved specific proteins called heat stress or heat shock proteins in the cell in order to adapt and survive. In the current study, the induction of heat stress proteins in a coldadapted bacterial strain of Pseudomonas marginalis cells grown under heat stress was investigated by proteomic approach. Five different temperatures, 5, 10, 15, 24, and 30C, were examined for the purpose of determining the optimum growth temperature for the bacterium. Consequently, 15°C was observed as optimum temperature for growth while 30C was established as heat stress temperature. Total proteins from Pseudomonas marginalis cells in the late exponential phase of growth at these two temperatures were extracted and separated by two-dimensional polyacrylamide gel electrophoresis. Totally 1391 protein spots were visualized for 15C and 1384 protein spots for 30C. After comparing with 15C, 13 protein spots that were differentially expressed in the cells exposed to heat stress (30C) were cut from the gel and fragmented into their peptides by in-gel digestion method. Finally, these proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and database searching. Among them, ribosome recycling factor, universal stress protein family and chaperonin GroEL were established as direct sensors of heat stress. As a result, the genes encoding these two heat stress proteins can be isolated and cloned into any other useful microorganism such as bacteria used for detoxification of industrial waste or used in bioremediation but not capable of surviving at high temperatures so that they can be efficient at those temperatures, too.Master Thesis Characterization of Antioxdant Activity and Protein Functionality in Some Legume Cultivars Grown in Turkey(Izmir Institute of Technology, 2008) Aydemir, Levent Yurdaer; Yemenicioğlu, AhmetTurkish chickpeas (4 cultivars) and lentils (6 cultivars) show similar total phenolic contents and free radical scavenging capacities in aqueous extracts ranging between 2869 and 4312 mg gallic acid equivalents/kg legume and 24.42 and 38.20 mmol Trolox equivalents/kg legume, respectively. However, the free radical scavenging capacity of lentil and chickpea protein extracts, range between 110 and 185 mmol Trolox/kg protein and 58 and 144 mmol Trolox/kg protein, respectively, clearly showed the higher free radical scavenging capacity of lentil proteins than chickpea proteins.Protein extracts of chickpeas and lentils showed considerable emulsifying and foaming capacities in almost at the same range, but emulsions and foams formed by chickpea proteins are more stable than those of lentil proteins. The lentil protein extracts are highly soluble and showed poor water absorption and gelling characteristics. In contrast, chickpea protein extracts showed moderate water absorption and gelling capacity.Chickpea protein extracts are also good oil absorbers with almost 1.5 to 2 fold better oil adsorption capacity than lentil protein extracts. Thus, chickpea proteins are suggested as soy and whey protein alternatives for functional proteins used in the food, drug and cosmetics industries. Considering functional properties of proteins for different cultivars, the outstanding Turkish chickpea cultivars are Gökçe and Cevdetbey, while the outstanding Turkish lentil cultivar is Alidayı. Variations in the functional properties of protein suggest the diversity of genes in chickpeas and lentils responsible for these properties. Thus, this study showed the possibility of improving functional properties of chickpeas and lentils by breeding programs.Master Thesis Characterization and Modification of Antioxidant Proteins From Plat Materials(Izmir Institute of Technology, 2005) Arcan, İskender; Yemenicioğlu, AhmetIn this study, the radical scavenging and iron chelating capacity of proteins from heat treated (20 min at 90 oC) or thermally processed (20 min at 121 oC) chick-peas andkidney-beans were compared. Lyophilized crude protein extracts from chick-peas contained more protein (1.5-3 fold) and showed higher free radical scavenging (up to 2.3 fold) and iron binding capacity (up to 3 fold) than lyophilized crude protein extracts form kidney-beans. The thermal processing of chick-peas did not cause a significant change in the radical scavenging capacity of their lyophilized crude protein extracts, but improved the iron chelating capacity of these proteins almost 80 %. However, the thermal processing reduced both the radical scavenging and iron binding capacity of crude lyophilized proteins form kidney beans by 20-40 % and 60 %, respectively.Partial purification by ammonium sulfate precipitation or DEAE-cellulose chromatography increased the antioxidant capacity of thermally processed chick-pea proteins. The DEAE cellulose chromatography also showed the presence of 5 and 3 antioxidant protein fractions in heat treated and thermally processed chick-peas, respectively. Hot acidic hydrolysis at 80 oC for 30 min in presence of 1.5 M HCl increases the specific antioxidant activity of protein extracts, but causes the formation of undesired Maillard reaction products. Hot extraction at 85 oC for 30 min at pH 2.5 extracts the antioxidant proteins selectively, whereas 85 oC for 30 min at pH 9.5 extracts both antioxidant proteins and other proteins.Master Thesis Identification and Detection of Phosphorylated Proteins by Laser Induced Breakdown Spectroscopy(Izmir Institute of Technology, 2011) Aras, Nadir; Yalçın, ŞerifeLaser-Induced Breakdown Spectroscopy (LIBS) is an optical atomic emission spectroscopic technique that uses an energetic laser source to generate a luminous plasma. Spectrochemical analysis of the light emitted from the plasma reveals information about the elemental composition of the sample. Phosphorylation is an important regulatory mechanism that activates or deactivates many proteins and enzymes in a wide range of cellular process. Identification and detection of phosphoproteins have a crucial importance in phosphopeptide mapping. This study is based on the assessment of the capabilities and limitations of LIBS as a quick and simple method for in-gel identification and determination of phosphorylated proteins, specifically casein and ovalbumin before mass spectrometric analysis for the elucidation of phosporylation sites. For this purpose, an optical LIBS set-up was constructed from its commercially available parts and the system was optimized for LIBS analysis of polyacrylamide gels. Nd:YAG laser operating at 532 nm wavelength and at 10 Hz frequency was used to create plasma on dry gel surfaces. Emitted light from a luminous plasma was analyzed and detected by an Echelle type spectrograph containing Intensified CCD, detector. With this study, LIBS detection of phosphorous proteins after electrophoretic separation of phosphorylated proteins has been shown, for the first time. After SDS-PAGE gel separation process, phosphoproteins were recognized from prominent P(I) lines (at 253.5 nm and 255.3 nm) in a plasma formed by the focused laser pulses on the gel, just in the center or in the vicinity of the electrophoretic spot. Spectral emission intensity of P(I) lines from LIBS data has been optimized with respect to laser energy and detector timing parameters by using standard Na2HPO4. It has been shown that phosphorylated proteins (casein and ovalbumin in mixture) can be identified by LIBS after both coomassie brilliant blue and silver staining procedures. Technique shows a great promise in microlocal spotting of phosphorylated proteins in gel before MS analysis for the determination of the phosphorylation sites.