Sürdürülebilir Yeşil Kampüs Koleksiyonu / Sustainable Green Campus Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7755

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Access type: Open accessDepartment: search.filters.department.Thesis (Doctoral)--İzmir Institute of Technology, Chemistry

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Now showing 1 - 4 of 4
  • Doctoral Thesis
    Proteomic Analyses of Biological Samples by Using Different Mass Spectrometric Strategies
    (Izmir Institute of Technology, 2018) Dinç, Melilke; Yalçın, Talat; Yalçın, Talat; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    The advent of soft ionization techniques MALDI and ESI have opened the doors of mass spectrometry to biological samples. Particularly protein research exploited this opportunity to the utmost that qualitative, quantitative, structural and distributional analyses of proteins have become achievable. Comparison of all expressed proteins belonging to two or more states is defined as differential proteomics and commonly performed either separating the proteins on a gel or separating the peptides in the mixture within a column. In this study, both of these methods were applied to a parasite that causes to the infectious disease, Leishmaniasis. Consequences of the disease become severe when parasite is multiplied in viscera rather than skin. Occurrence of different clinical manifestations is attributed to the variety in species however some species can cause to both such as L.infantum and L.tropica. The purpose of this study was to investigate this duality in L.infantum. Despite originating from two different species, cutaneous leishmaniasis isolates obtained from ten different patients exhibited considerably similar protein profiling on the gels however isolates belonging to five visceral leishmaniasis patients were discriminated from them with regards to protein abundances. Additionally, several differential proteins between cutaneous leishmaniasis and visceral leishmaniasis samples were determined by gel-free approach. Apart from that, another mass spectrometric strategy for the abovementioned distributional analysis namely mass spectrometry imaging was included in the last section. Herein, a method incorporating the application of enzyme with matrix was developed for easy sample preparation to on-tissue digestion and promising results were obtained for a start.
  • Doctoral Thesis
    Design and Synthesis of Rhodamine Based Fluorescent and Colorimetric Sensors for the Detection of Gold Ions
    (Izmir Institute of Technology, 2017) Karakuş, Erman; Emrullahoğlu, Mustafa; Emrullahoğlu, Mustafa; 04.04. Department of Photonics; 04. Faculty of Science; 01. Izmir Institute of Technology
    The usage of chemosensors for the detection of heavy and transition metal ions is prevalent. Because these metal ions play crucial roles in living systems and have extremely toxic effects on the environment. Among these metal ions, gold species have interesting biological properties and uses. They play important roles in biological systems and often have significant impacts on human health. For instance, gold based drugs have long been used in the treatment of rheumatoid arthritis and other autoimmune diseases. In addition, gold nanoparticles function as carriers for drugs and gene delivery systems. Gold ions, on the other hand, are potentially toxic to humans. Because of their reactive nature, ionic gold species can interact with proteins, DNA and other biomolecules and disturb a series of cellular processes, leading to serious health problems. Detection of gold ions can be performed by spectroscopic methods such as atomic absorption and atomic emission spectroscopy and inductively-coupled plasma spectrometry that required complicated sample preparation steps, and sophisticated instrumentation. In contrast to these highly expensive and time consuming methods, fluorogenic or chromogenic methods can be good alternatives for the detection of these species that provides high analyte sensitivity and selectivity, visual simplicity, instantaneous response, as well as real time monitoring. The rhodamine scaffold is an ideal template for the construction of metal ion chemosensors because they have large molar extinction coefficient, long excitation and emission wavelengths, high fluorescence quantum yields, good water solubility, and the potential for colorimetric and turn-on fluorescent detection. In this thesis work, we focus on design and synthesis of novel rhodamine based molecules for the detection of gold ions. Moreover, we investigate the photophysical properties of synthesized molecules in the absence and presence of gold ions in both synthetic samples and living cells.
  • Doctoral Thesis
    Proteomic Studies and Its Application To Biological Samples Using Mass Spectrometry
    (Izmir Institute of Technology, 2017) Güray, Melda Zeynep; Karakaya, Hüseyin Çağlar; Yalçın, Talat; Yalçın, Talat; Karakaya, Hüseyin Çağlar; 04.03. Department of Molecular Biology and Genetics; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    Mass spectrometry (MS) is a powerful analytical tool with its application in the field of biological sciences for identification of proteins, defining post-translational modifications, studying protein expression and protein interactions. This thesis presents MS analyses of proteins for defining modifications observed during sample preparation and identification of proteins isolated from clinical samples and microorganisms. The first part of the thesis includes proteomic analysis of antimony resistant L. tropica. The results clearly indicated that the generation of antimony resistance by parasites, either in host organism or in vitro, causes alteration of protein expression levels, and the mechanism of antimony resistance in host organism and in vitro conditions follow different strategies. In the second part of the study, proteomic analysis of Bence Jones proteins isolated from urine of multiple myeloma patients was performed. Gel electrophoresis and MS analysis revealed that the proteins from different patients with different nephrotoxicity have different tendencies to form multimeric structures and contained different type of light chain. In the third part, it was shown that precipitation of proteins in acetone causes +98 u mass artifacts on proteins when analyzed by MS. The parameters affecting the formation of modification was studied and it was revealed that this modification is dependent on solution pH, incubation time and temperature. In the last part, aspartic acid and glutamic acid containing synthetic peptides were shown to be methylated upon incubation in acidified methanol solution. MS analysis revealed that the reaction is dependent on temperature and time and is affected by the type of acid included in methanol solution. All in all, this thesis provides a comprehensive study of proteins by mass spectrometry for identification of proteins from different sources, as well as defining protein modifications observed as artifacts during sample handling in proteomic workflows.
  • Doctoral Thesis
    Design, Construction and Optimization Studies of a Hydride Generation Laser-Induced Breakdown Spectrometric System, (hg-Libes), for the Determination of Toxic Elements in Aqueous Samples
    (Izmir Institute of Technology, 2013) Ünal Yeşiller, Semira; Yalçın, Şerife; Yalçın, Şerife Hanım; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    In this thesis study, design, construction and optimization of a continuous flow hydride generation laser-induced breakdown spectroscopic system, HG-LIBS, for the determination toxic and environmentally important elements: arsenic, selenium, lead, antimony, tin, bismuth, germanium and tellurium, has been performed. The HG-LIBS system, which has been constructed from its commercially available components, consisted of four main parts: a laser source, a hydride generation unit, a sample/plasma cell and a detection unit. In order to maximize LIBS emission signal, some instrumental parameters such as laser energy and detector gating parameters were investigated. Some chemical parameters such as acid/reductant concentration and flow rate, carrier gas type and flow rate, presence of pre-reducing/oxidizing agent that effect hydride generation efficiency and transportation of hydrides were also studied. Under optimized conditions detection limits of 0.2 mg L-1, 1.1 mg L-1, 1.0 mg L-1, 1.3 mg L-1 and 0.2 mg L-1 were obtained for Sn, As, Sb, Pb and Ge, respectively. No analytical signal could be detected from Se and Te elements with the system developed. The applicability of the HG-LIBS system for the determination of As, Sb, Pb and Ge in aqueous environments has been tested on several real water samples including tap water, drinking water and reference river water standard. Temporal variation of electron temperature and electron density values for tin and germanium hydride plasma was determined under argon and nitrogen environment. Electron temperatures were calculated by making use of neutral atomic lines in Boltzmann equation. Plasma electron density was evaluated from the Stark-broadened line shapes of Hα line at 656.3 nm. In order to investigate the main cause of increase in germanium signal under argon environment, physical plasma parameters were evaluated in argon and nitrogen gas mixtures. With this thesis study, the applicability of the HG-LIBS system for on-line monitoring of environmental pollutants has been shown.