Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Molecular Investigation of P. Aeruginosa in the Presence of 4-Hba(01. Izmir Institute of Technology, 2023) Soyer, Ferda; Soyer Dönmez, Ferda; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyThe escalating threat to human health posed by bacterial pathogens is increasingly attributed to the growing prevalence and distribution of antibiotic-resistant bacteria. In response to antibiotics, microorganisms have developed resistance mechanisms to elude and survive the impacts of these drugs. Phenolic acids have emerged as potent candidates in the battle against bacterial infections due to their unique property of not inducing resistance. This study focuses explicitly on 4-hydroxybenzoic acid (4-HBA), a type of phenolic acid, as an effective antimicrobial agent. Proteomics research has become an indispensable tool in the fight against antimicrobial resistance. Pseudomonas aeruginosa, a bacterium capable of existing in both planktonic and biofilm states and known to cause numerous human diseases, is of particular significance in this context. Furthermore, the study explores the molecular aspects of P. aeruginosa when exposed to 4-HBA through proteomic analysis, revealing a significant impact on protein biosynthesis as a predominantly affected function. Additionally, P. aeruginosa, the study investigates the effects of phenolic acid and antibiotic-loaded bone cements on Methicillin-sensitive Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecium, and P. aeruginosa. Remarkably, 20 percent inhibition rate is achieved after 48 hours of treatment. Moreover, the study examines biofilm produced by P. aeruginosa in the presence of 4-HBA, utilizing both the Crystal Violet assay and Scanning Electron Microscopy. Significantly, the biofilm formation is observed to be disrupted by these methodologies. Overall, this study underscores the effectiveness of 4-HBA as antimicrobial compound against diverse range of pathogens, as demonstrated through both phenotypic and proteomic approaches.Master Thesis Proteomic Analysis of Boron Stress Response in Yeast Saccharomyces Cerevisiale(Izmir Institute of Technology, 2011) Avşar, Kadir; Koç, Ahmet; Koç, Ahmet; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of TechnologyBoron is a versatile element distributed in every part of the environment but most of its deposit reserves are localized in a few countries, Turkey being one of the most prominent. Boron is known to be an essential micronutrient for plants and some animals. Like any other essential element it has toxicity in high concentrations. Herein the mechanism of toxicity and the elements of the boron stress response were investigated in Saccharomyces cerevisiae with a proteomics approach. Boron is believed to have played a role in the evolution of life on earth. It has strongly electrophile organic compounds, the most important physiological form being boric acid. Boric acid has a capacity to bind cis-located hydroxl groups and some amino groups. Some of these groups are located at the active sites of some enzymes and at the carbohydrates with five-membered furanose rings. The riboses of some metabolically important molecules like S-adenosyl methionine, diadenosine phosphate family members and 3'end of RNAs are prone to be affected. The yeast cells subjected to boron in this study expressed higher amounts of carbohydrate metabolic enzymes, proteins involved in protein synthesis, protein folding and catabolism, redox homeostasis and nucleotide synthesis. All of these proteins are common to metal stress responses in yeasts. Some of them involve in other stress responses like peroxide, salt or herbicide stresses showing complex interplay between responses.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 TechnologyPeptide 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.