Master Degree / Yüksek Lisans Tezleri

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

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Department: search.filters.department.Thesis (Master)--İzmir Institute of Technology, Molecular Biology and GeneticsSubject: search.filters.subject.Mass spectrometry

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Now showing 1 - 4 of 4
  • Master Thesis
    Identification of Cytosolic Sialidase Neu2 Associated Proteins Bt Mass Spectrometric Analysis
    (Izmir Institute of Technology, 2013) Akyıldız Demir, Seçil; Seyrantepe, Volkan; Seyrantepe, Volkan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Sialidases (Neuraminidases) are the enzymes which remove sialic acids from glycoproteins, oligosacharides and glycolipids. Four mammalian sialidases have been identified which are lysosomal sialidase (Neu1), cytosolic sialidase (Neu2), plasma membrane sialidase (Neu3), and mitochondrial/lysosomal sialidase (Neu4). These enzymes differ in their subcellular localizations, expression levels in different cells and tissues, substrate specificities and optimum pH levels. Cytosolic Neu2 enzyme has an active role on a wide range of subtances including oligosaccharides, glycopeptides and gangliosides. Studies on the Neu2 enzyme also showed that this enzyme is involved in different cellular events including cancer metabolism, neuronal differentiation and myoblast differentiation, proliferation and hypertrophy. However, it has not been shown whether Neu2 interacts with other proteins within the cell. Therefore, in this study we aimed to identify Neu2 associated proteins by using InterPlay Mammalian TAP System and ESI-LC-MS/MS analysis. Proteins in the Neu2 protein complex were identified by three different database search software such as PGLS, Mascot and X!Tandem. As a result of experiment Actin proteins (Alpha Actin, Gamma Actin and Beta Actin), and Calsyntenin-2 protein were found as a candidate protein for Neu2 association. The interaction between Neu2 and β-Actin proteins was confirmed by western blot analysis.
  • Master Thesis
    Analysis of Lysosomal Neu4 Sialidase Associated Proteins by Using Mass Spectrometry (ms/Ms)
    (Izmir Institute of Technology, 2012) Öztürk, Süleyman Can; Seyrantepe, Volkan; Seyrantepe, Volkan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Sialidases are glycohydrolytic enzymes which remove sialic acid residues from glycoproteins, oligosaccharides and glycolipids. There are 4 different sialidases known in mammalians. These are Neu1 (lysosomal), Neu2 (cytoplasmic), Neu3 (cell membrane) and Neu4 (lysosomal/mitochondrial) sialidase. Sialidases are involved in many metabolic and cellular processes interactioning with another proteins or work together in multiprotein complexes. For example, Neu1 is only active with betagalactosidase and cathepsin A enzyme in lysosome. Interactions of sialidases Neu2, Neu3 and Neu4 enzyme with other proteins remain unknown In our study, we aimed to identify proteins which have interaction with sialidase Neu4 as well as Neu1 by using mass spectrometry analysis to find new possible roles of sialidases. Our bait protein's cDNA was tagged with calmodulin binding protein as well as streptavidin binding protein. After transfection and expression of vectors to mammalian cells, proteins were purified using tandem affinity purification (TAP). We identified some associated proteins with sialidase Neu1 and Neu4 by using MS/MS analysis and bioinformatics.
  • Master Thesis
    Identification of Salt Stress Responsive Protyeins in Wild Sugar Beet (beta Maritima) Using 2d-Page With Maldi-tof/Tof System
    (Izmir Institute of Technology, 2012) Çakıroğlu, Çiğdem; Karakaya, Hüseyin Çağlar; Karakaya, Hüseyin Çağlar; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    High salinity is one of the abiotic stresses, which affects the homeostasis, growth and productivity of plants. In plants, uptake of the non-essential salt ions negatively affects the anatomy, physiology and metabolism, changes the osmotic balance in cells and causes abundant dehydration. In this case, higher plants develop salt tolerance mechanisms such as induction of related signaling pathways, effluxion of salt ions, accumulation of these toxic ions in their vacuoles, activation of their detoxification mechanisms and production of osmoprotectans. In this study, identification of salt responsive proteins in moderately halophyte wild type sugar beet Beta vulgaris ssp. maritima was aimed. In order to investigate the protein-based natural stress tolerating mechanisms, plants were exposed to 150 mM NaCl and total proteins were extracted. Differentially expressed proteins were identified by proteomic approaches including MALDI-TOF/TOF mass spectrometry combined two dimensional polyacrylamide gel electrophoresis. The results revealed that enzymatic antioxidants and secondary members of antioxidative pathways are responsive in salt stress. In conclusion, these detected proteins demonstrate that antioxidative system may be the major defense mechanism in halophytic plants.
  • Master Thesis
    Exploiting Fragment-Ion Complementarity for Peptide De Novo Sequencing From Collision Induced Dissociation Tandem Mass Spectra
    (Izmir Institute of Technology, 2011) Aytun, Belgin; Allmer, Jens; Allmer, Jens; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Peptide identification from mass spectrometric data is a key step in proteomics because this field provides sequence, quantitative, and modification data of actually expressed proteins. Two approaches are generally deployed to interpret experimental MS/MS data, database searching and de novo sequencing. Database search method has been used successfully in proteomics projects for organisms with well-studied genomes. However, it is not applicable in situations where a target sequence is not in the protein database. This can happen for a number of reasons, including novel proteins, protein mutations and post-translational modifications. Because of the disadvantages of database searching method, a lot of research has focused on de novo sequencing method which assigns amino acid sequences to MS/MS spectra without the need for a database. The aim of this study is to enhance the accuracy of de novo sequencing tools. One step commonly employed in all de novo sequencing tools is naming of fragment ions. It is essential to know which peak represents which ion type in order to traverse a spectrum graph to find an amino acid sequence that best explains the MS/MS spectrum. Different approaches have been tried to name ions and some success has been achieved in naming b-type ions and y-type ions. We have presented a new approach which enables the naming of not only b- and y-type ions but other arbitrary ion types as well. This enabled the detection of b-ion ladder. In the latter case, missing fragments were determined by using other named ion types. Furthermore, unexplained data in tandem mass spectra were reduced as much as possible. Therefore, a complete sequence will be derived by the new approach.