Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Author: search.filters.author.Arslanoğlu, AlperDepartment: search.filters.department.Thesis (Master)--İzmir Institute of Technology, Bioengineering

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Now showing 1 - 5 of 5
  • Master Thesis
    Investigation of Gas Phase Fragmentation Mechanism of Doubly Charged a Ions by Mass Spectrometry
    (Izmir Institute of Technology, 2019) Kızılkoca, Doğacan; Yalçın, Talat; Arslanoğlu, Alper
    This dissertation presents studies of gas-phase fragmentation mechanism of doubly-charged a7 ions from basic amino acid containing model peptides under low-energy collision-induced dissociation (CID). The study includes three sets of C-terminal amidated model peptides which are alanine series containing basic amino acids (His – Arg – Lys). Position of His, Arg and Lys residue is varied from N-to-C terminal. Both positional effect and peptide sequence effect were examined for the fragmentation reactions of doubly-protonated a7 ions for these heptapeptides. The CID-MS4 mass spectra of doubly-protonated a7 ions have internal amino acid losses which provide an evidence for macrocyclization reaction. The proposed reaction mechanism involves production of doubly-charge a ions and charge-separation reaction of doubly-protonated a ions in the gas-phase which generates a protonated direct and non-direct a ion. All model peptides were also studied to understand behavior of doubly-protonated a ions better. Direct and non-direct sequence fragmentations which are singly or doubly protonated were observed for all studies. The reactions mechanisms were adjusted according to the results. In conclusions, the results presented in this dissertation can be used to elucidate the correct and reliable peptide sequences, and this improve protein identification strategies which is required for high-throughput proteomic studies.
  • Master Thesis
    Real-Time Pcr as a Molecular Tool for the Enumeration of Probiotics in Commercial Products
    (Izmir Institute of Technology, 2016) Öz, Ödül; Baysal, Ayşe Handan; Arslanoğlu, Alper
    Quantitative Real-Time PCR (qPCR) assays targeting the 16S rDNA was developed as a genus and species specific detection tool for Bifidobacterium and Lactobacillus, and Bifidobacterium animalis subsp. lactis BB-12 and Lactobacillus acidophilus LA-5, respectively. Standard curves were established to quantify these probiotic bacteria. The linear regression of standard curves indicated high correlations between the log numbers of pure probiotic culture cells and the Ct values. The assay had a high efficiency and the limit of detection was estimated to be 1.54 ng DNA (corresponding to 104 cells). Results show that qPCR method may be very useful as a rapid, sensitive and specific tool for detecting and quantifying B. animalis subsp. lactis BB-12 and L. acidophilus LA-5 in probiotic supplements. FTIR spectroscopy was used for the first time to determine the ratios of different microorganisms in commercial probiotic supplements. FTIR analysis was also performed for the pure probiotic cultures of B. animalis subsp. lactis BB-12 and L. acidophilus LA-5. Results obtained in this study showed that FTIR spectroscopy is potentially a rapid method for determining probiotic cell components and their ratios in the supplements and verification their detection and identification.
  • Master Thesis
    Development of Antibacterial Polymer Based Nanocomposite Materials
    (Izmir Institute of Technology, 2015) Abatay, Ezgi; Arslanoğlu, Alper; Tanoğlu, Metin
    Human beings are often infected by microorganisms such as bacterium, mold, yeast, virus, etc. in the living environment. It became a requirement and a necessity to create sterile fields in areas. Composite stones are one of the main materials that can be used for the contact surfaces in indoor and outdoor places due to their being of highly resistant to abrasives, chemicals and impacts. Research has been intensive in antibacterial material containing various inorganic substances. The aim of this thesis is investigating the antibacterial effect of inorganic substances such as silver, zinc oxide, calcium oxide, titanium oxide and magnesium oxide on stone products. This study also deals with the silver doped zinc oxide powder and their antibacterial efficacies. Stone product is formed of mainly two type compound which are quartz aggregates as reinforced and filler and thermoset polyester resin as matrix. The manufacturing process begins with selection of raw quartz materials. They are crushed and blended in the ratio of 90 % quartz aggregates to 10% polyester matrix and other additives such as antibacterial agent, pigment. These united constituents are used for production of composite stones by applying those combined vacuum, vibration and pressing processes which are named as vibropress, simultaneously. Following it, they are subjected to surface preparation and polishing processes. In this study, mechanical, thermal, and morphological properties of the particles, polyester matrix and stone product were investigated. Antibacterial efficacies of these were investigated based on colony-count method against gram negative (E.coli) and gram positive (Bacillus subtilis) bacteria. Silver-containing stone samples showed best antibacterial property about ninety-nine percent reduction.
  • Master Thesis
    Cloning and Expression of the Pseudomonas Ke38 Extra-Cellular Lipase Gene in E. Coli
    (Izmir Institute of Technology, 2013) Karakaş, Fulya; Arslanoğlu, Alper
    Lipases are serine hydrolases that catalyze both the hydrolysis and synthesis of insoluble or poorly soluble long-chain triacylglycerols with an acyl chain length ≥ 10 carbon atoms based on the presence or absence of water. Lipases are produced and secreted by all kingdoms of life that are eukaryotes including plants, animals, fungi and prokaryotes including bacteria and archaea. However, microbial lipases, especially from bacteria, more useful than their plant and animal derivatives because of several important properties. Because of their acitivities in both aqueous and nonaqueous environments, lipases have specific applications in industry and medicine. The primary goals of this thesis were to clone and express the extra-cellular lipase gene from Pseudomonas sp. KE38, isolated from soil samples of Erciyes mountain in Kayseri, in E. coli and partial purification of the gene product. To achieve this aim, genome walking technique was used to obtain lipase gene from Pseudomonas sp. KE38, that gene was then cloned into pET28a expression vector and expressed in E. coli. The lipase expression of E. coli BL21 and its activity was screened with olive oil-Rhodamin B plate assay. After expression recombinant lipase was partially purified via inclusion body isolation. Moreover the optimum lipase production time of E. coli BL21 cells were determined and analyzed with SDS-PAGE. According to SDS-PAGE analysis the recombinant lipase was approximately 64 kDa and lipase production reached to the highest level after two hours of IPTG induction. As conclusion, recombinant lipase from Pseudomonas sp. KE38 was cloned into E. coli, expressed and partially purified.
  • Master Thesis
    Generation of Improved E.coli Strains To Be Used in the Construction of Ligand Libraries
    (Izmir Institute of Technology, 2005) Elmacı, Zehra Seda; Arslanoğlu, Alper
    The first step in the construction of ligand libraries is the total cloning of gene fragments coding millions of ligand variants into selected plasmid vectors. Since ligand proteins are expressed in fusion with the phage pIII protein, they can be incorporated into the newly synthesized phage particles in bacteria. The other proteins that make up the phage particle are supplied by the super infection of bacteria containing the ligand DNA clones with the helper phage. The diversity of the ligand libraries is directly proportional to the number of different gene fragments. In the current phage display technology, there are some drawbacks which can dramatically influence the diversity of a given ligand library. One of the drawbacks arises from the fact that, theoretically half of the phage particles, which are produced after super-infection, can carry only the helper phage genome instead of the ligand gene, even though they display a specific ligand protein. These phages can compete with those which carry both the ligand gene and its protein during the selection process and consequently they loose the ligand protein during the second round of selection. In any given library, this problem can cause the loss of rare but functionally very important ligands during the sequential selection procedure. Another drawback is the reinfection of a super-infected bacteria during or after the super-infection. This can increase the frequency of those phage particles which only carry the helper-phage genome, in the total phage population.These two disadvantages in the phage display technology are due to super-infection.This study aimed at the elimination of the super-infection step from the phage display technology by the insertion of M13 phage genome excluding intergenic region which contains the DNA sequences necessary for replication instead of uses of helper phage.To accomplish this purpose, Homologous Recombination method was used. It is an in vivo method for the replacement, deletion or insertion of sequences in bacteria.After Homologous Recombination, three colonies were observed and observed colonies were exposed some confirmation tests. First step of these tests was related to the presence of unique recombination cassette sequences in chromosomal DNA.Results we obtained showed that the presence of such fragments in chromosomal DNA. However, the functional test of the M13 genes in E.coli chromosome suggested the toxicity of an unidentified M13 gene products on E.coli chromosome.