Phd Degree / Doktora

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Department: search.filters.department.Thesis (Doctoral)--İzmir Institute of Technology, Molecular Biology and GeneticsPublisher: search.filters.publisher.Izmir Institute of Technology

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Now showing 1 - 10 of 25
  • Doctoral Thesis
    Molecular Genetic Analysis in Cotton (gossypium Hirsutum L.)
    (Izmir Institute of Technology, 2021) Akköse Baytar, Asena; Akköse Baytar, Asena; Doğanlar, Sami; Doğanlar, Sami; 04.03. Department of Molecular Biology and Genetics; 01. Izmir Institute of Technology; 04. Faculty of Science
    Cotton is a valuable fiber crop for different industries especially the textile, food and oil industries. Drought causes serious yield losses in cotton throughout the world. Association mapping reveals genomic loci controlling fiber quality and drought-related traits which will be helpful in cotton breeding because these loci can provide the genetic adaptability needed to produce good fibers and yield under water limitation. In the present study, 177 simple sequence repeat (SSR) markers were used to characterize an Upland cotton germplasm panel consisting of 99 G. hirsutum cultivars for their genetic diversity and to detect the ancestral structure of the population. Moreover, association analysis was conducted to reveal significant quantitative trait loci (QTLs) linked to a total of 22 traits for fiber quality, plant structure, yield and drought-related parameters in the panel using GLM and MLM analysis. The morphological characters were tested under both well-watered and water-limited irrigation in two locations. At both locations, GLM and MLM identified different sets of QTLs at significance level of p ≤ 0.005 and p ≤ 0.001. Of the identified QTLs, some loci were considered as stable and reliable QTLs detected in both locations. The QTLs identified herein could be useful in the development of cotton cultivars with high yield that have adaptability to drought conditions worldwide
  • Doctoral Thesis
    Investigating the Role of Connexin 32 in Breast Cancer
    (Izmir Institute of Technology, 2020) Meşe Özçivici, Gülistan; Uğur, Deniz; Meşe Özçivici, Gülistan; 04.03. Department of Molecular Biology and Genetics; 01. Izmir Institute of Technology; 04. Faculty of Science
    Connexins (Cx) are primary components of gap junctions, selectively allowing molecules to be exchanged between adjacent cells. Along with their channel forming functions, connexins play variety of roles in different stages in tumorigenesis, both dependent and independent of gap junctions in connexin and cancer dependent manner. Cytoplasmic accumulation of Cx32 was shown in some breast cancers; and compared to the primary tumors Cx32 is further upregulated in metastasis. However, the complete picture for the role of Cx32 in breast cancer remains to be elusive. Through overexpressing Cx32, its functions in breast cancer cells were investigated in Hs578T and MCF7 breast cancer cells. Cx32 overexpression increased cellular proliferation with significant increase in S phase in Hs578T cells with no significant change on MCF7 cells. Cx32 overexpression did not induce hemichannel activity in neither cell; it reduced gap junctional functions in Hs578T cells. Cx32 in both cells localized in cytoplasm did not form intercellular plaques, and decreased Cx43 expression. Cx32 overexpression reduced the migration and invasion capacity in both cells and in Hs578T cells showed reduction of mesenchymal and increase of epithelial marker expressions. In conclusion, Cx32 increases proliferation and decreases communication in Hs578T cells while not affecting MCF7 cells. It decreases aggressiveness and metastatic potential for both cell lines. Due to changes in gap junctional functions, Cx32 might be acting in relation to GJIC in Hs578T cells and outside of it in MCF7 cells. All in all, presence of Cx32 made Hs578T cells act similar to endogenously Cx32 expressing MCF7 cells.
  • Doctoral Thesis
    Molecular Characterization of Long Non Coding Rnas That Mediate Apoptosis in Human
    (Izmir Institute of Technology, 2019) Sweef, Osama Abdel Hady Biaomy; Akgül, Bünyamin; Akgül, Bünyamin; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Apoptosis is an evolutionarily form of programmed cell death for development and tissue homeostasis. Apoptosis is regulated by protein-coding genes and plays an important role in a wide range of biological processes. We aimed to identify and characterize differentially expressed lncRNAs in apoptosis. HeLa cells were used as a model system to identify the lncRNAs. The total RNAs was subjected to deep sequencing by next-generation sequencing. OmicsBOX Bioinformatics tools were used for differential expression analysis of lncRNAs that are apoptosis-induced. Gene set enrichment analysis (GSEA) was used to profile the miRNAs targeting lncRNAs. Cytoscape software was used to reconstruct lncRNA-miRNA targeting networks. RT-qPCR was used to validate miRNAs and their targets of lncRNAs and it was found that the overexpression of miR-519d-3p causes downregulation of lncRNAs RAB22A-202, PARD3-211, and AC027237.1-210. Also, the overexpression of miR-124-3p down-regulates the expression level of APEX2-202 and CD59-209. GTF2A1-AS, TNFRSF10B-AS, and CAMTA1-DT were detected in the nucleus and have no poly (A) tail and they belong to TATA-less promoter genes. TNFRSF10B-AS has a coding probability of 0.99 and alignment to High-scoring Segment Pair (HSP) clarifies one hit to Q9UBN6 protein. ChIRP clarifies that TNFRSF10B-AS binds to a protein (25 kDa). miR-519d-3p and miR-124-3p interact with lncRNA targets by miRNA-mediated lncRNA degradation pattern under apoptosis conditions. TNFRSF10B-AS has a putative regulatory function in the nucleus during apoptosis via binding specifically to the ribonucleoprotein partner.
  • Doctoral Thesis
    Sensitization of Philadelphia Positive Acute Lymphoblastic Leukemia Cells Resistant To Imatinib by Targeting Sphingolipid Metabolism
    (Izmir Institute of Technology, 2019) Kiraz, Yağmur; Baran, Yusuf; Kiraz, Yağmur; Baran, Yusuf; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Philadelphia positive acute lymphoblastic leukemia (Ph+ALL) is a common subtype of ALL and characterized by having BCR/ABL translocation. Tyrosine kinase inhibitors (TKI) such as imatinib are used for the treatment in Ph+ALL, however, 60-75% of the patients can develop resistance against the TKIs. Bioactive sphingolipids are a group of lipids that play roles in various cellular mechanisms. Previous studies showed that sphingolipids and genes in the pathway were involved in response to TKI treatment in Ph+ALL. Here, we investigated the roles of SPL on the growth inhibitory effects of imatinib and exploit sphingolipid metabolism by majorly inhibiting glucosylceramide synthase (GCS) to accumulate ceramide or sphingosine to further sensitize cells to imatinib and/or overcome resistance to imatinib in Ph+ALL. Firstly, we detected that, sphingosine kinase-1 (SK-1) a well-studied SPL enzyme inhibition did not contribute to cytotoxic effects of imatinib in SD-1 Ph+ALL cells. Moreover, we determined that imatinib is inducing de novo synthesis pathway of SPL and increasing the levels of ceramide, sphingosine, hexosylceramides and sphingomyelin in SD-1 cells. Interestingly, newly generated imatinib-resistant cell line SD-1R was detected to have an aberration in this pathway resulting in development of resistance. Combination treatment with eliglustat (GCS inhibitor) resulted in a significant increase in ceramide and sphingosine levels and reflected on cell growth and sensitized cells to imatinib. Taken together, it was shown for the first time in the literature that the cytotoxic effects of imatinib was due to induction of de novo synthesis pathway of sphingolipids and inhibition of GCS together with imatinib has synergistic cytotoxic effects on imatinib resistant Ph+ALL cells. As a conclusion, increasing the intracellular levels of ceramide (and/or sphingosine) can be a novel approach to sensitize drug resistant Ph+ALL cells.
  • Doctoral Thesis
    Understanding the Biological Role of Sialidase Neu3 in Tay-Sachs Disease Mouse Model
    (Izmir Institute of Technology, 2019) Akyıldız Demir, Seçil; Seyrantepe, Volkan; Seyrantepe, Volkan; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Tay-Sachs disease is a severe lysosomal storage disorder characterized by mutations in the lysosomal ß-Hexosaminidase A (HEXA) enzyme which converts GM2 to GM3 ganglioside. The GM2 ganglioside accumulation is observed predominantly in the neurons. The infants appear normal in their inborn time, but the progressive accumulation of undegraded GM2 results with death. Hexa-/- mice were created. However, they have a normal lifespan with no obvious neurological impairment until one year. It was thought that stored GM2 catabolized to GA2 using sialidase(s), which is further processed by HEXB. To determine the contribution of sialidase NEU3 to degradation of GM2, a mouse with combined deficiencies of Hexa and Neu3 genes was generated. The Hexa-/-Neu3-/- mice were healthy at birth, but they died between 1.5 and 5 months of age. Thin-layer chromatography and mass spectrometric analysis of the brains of Hexa-/-Neu3-/- mice revealed the abnormal accumulation of GM2. The progressive GM2 accumulation was also verified on testes, liver, and kidney of Hexa-/- Neu3-/- mice. GM2 accumulation in the brain leads to increased lysosomes with membranous cytoplasmic bodies, Purkinje cell depletion, cytoplasmic vacuolization, astrogliosis, and age-dependent lessening in neurons and oligodendrocytes. These mice have prominent disorders such as growth impairment, skeletal bones abnormalities, slow movement, tremors, anxiety and age-dependent loss in both memory and muscle strength. Consequently, the Hexa-/-Neu3-/- mice mimic the pathological, biochemical and clinical abnormalities of the Tay-Sachs patients, and useful model for the future understanding of cellular pathologies that drive the progression of the disease. They are a suitable model for the future pre-clinical testing of possible treatments.
  • Doctoral Thesis
    Development of Tomato Plants Over-Expressing Cytokinin Synthesis Gene and Characterization by Proteomic Approach
    (Izmir Institute of Technology, 2020) Şelale, Hatice; Şelale, Hatice; Frary, Anne; Frary, Anne; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Cytokinins (CKs) are plant hormones controlling growth and development including cell division and differentiation, apical dominance and delay of senescence. CKs take part in regulation of the abiotic stress response in plants. In this study, transgenic tomato plants overexpressing the IPT (CK biosynthetic gene) were developed. Homozygous transgenic plants exhibited a phenotype with reduced plant stature and lost apical dominance. Increased shoot biomass and leaf water content with a reduction in fruit yield were observed in all transgenic lines. Proteomics analysis was conducted to understand high CK response in molecular level. Proteins supporting a strong sink phenotype and vasculature development were upregulated in transgenic lines and reflected the phenotypic changes observed in homozygous plants. Proteins related to stress response such as detoxification enzymes and PR proteins were upregulated in a gradual manner in transgenic lines with the strongest up-regulation in T6 homozygous line indicating the metabolic stress induced by high CK levels. The transgenic plants were tested for drought stress and observed to have improved water use efficiency, antioxidant response and delayed senescence compared to nontransgenic plants. Proteomic analyses from leaf total and nuclear enriched extracts were conducted to understand the molecular basis of improved drought tolerance. Proteins related to photosynthesis and oxidative stress response were the most prominent groups of differentially abundant proteins in the transgenic line under drought, which could contribute to tolerance. Eighteen transcription factors were differentially abundant in the nuclear proteome of drought stressed plants. These transcription factors could control the gene expression contributing to tolerance.
  • Doctoral Thesis
    Molecular Genetic Analyis in Faba Bean (vicia Faba L.)
    (Izmir Institute of Technology, 2019) Abuzayed, Mazen Ali; Doğanlar, Sami; Doğanlar, Sami; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Faba bean (Vicia faba L.) is an important food legume crop with a huge genome. In this study, we used Next Generation Sequencing (NGS) technology for development of genomic simple sequence repeat (SSR) markers. A total of 14,027,500 sequence reads were obtained comprising 4,208 Mb. From these reads, 56,063 contigs were assembled (16,367 Mb) and 2138 SSRs were identified. Mono and dinucleotides were the most abundant, accounting for 57.5% and 20.9% of all SSR repeats, respectively. A total of 430 primer pairs were designed from contigs larger than 350 nucleotides and 50 primers pairs were tested for validation of SSR locus amplification. Nearly all (96%) of the markers were found to produce clear amplicons and to be reproducible. Thirty-nine SSR markers were then applied to 46 faba bean accessions from worldwide origins, resulting in 161 alleles with 87.5% polymorphism, and an average of 4.1 alleles per marker. Gene diversity (GD) of the markers ranged from 0.00 to 0.48 with an average of 0.27. Testing of the markers showed that they were useful in determining genetic relationships and population structure in faba bean accessions. In addition, 26 morphological and seven biochemical (phenolics content, flavonoids, protein, L-DOPA, tannins, vicine and convicine) characters of 61 landraces and 53 faba bean cultivars were analyzed. There was high diversity for the studied characters among the accessions. Association mapping for these morphological and biochemical characters with 59 SSR markers (442 fragments) was conducted using a general linear model based on the Q matrix. As a result, 48 significant loci were detected for 22 morphological characters, and 26 loci were detected for six biochemical traits. The range of LD (r2) was from 0.09 to 0.18, and from 0.06 to 0.13 for morphological and biochemical associations, respectively. This study can help breeding programs in selection and improvement of faba bean production.
  • Doctoral Thesis
    Molecular Investigation of Pathogenic Bacteria in the Presence of Phenolic Acids
    (Izmir Institute of Technology, 2019) Özdemir, Özgün Öykü; Soyer, Ferda; Soyer, Ferda; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    Pathogenic bacteria, including P. aeruginosa, are serious threats for human health with their antibiotic resistance and virulence factors. Since phenolic acids, secondary metabolites of plants, can be good candidates as antimicrobial agents, their mode of action should be investigated. Proteomics is one of the main approaches for elucidating the mode of action of such compounds. In addition, in order to enhance the antimicrobial effects and stabilities of phenolics, they can be encapsulated into nanoparticles. The nanoparticles can be produced from chitosan and alginate which are biocompatible polymers. In this study, the antimicrobial effects of 3-HPAA and 4-HBA were presented with MIC values of 2.1 and 1.9 mg/ml, respectively. The bacteriocidal effects of them were also shown as 2.3 mg/ml for 3-HPAA and 2.1 mg/ml for 4-HBA. The morphological changes of bacteria were determined after phenolic acid exposure via SEM. The LC-ESI-MS/MS technique was used to show changes in the protein profile of bacteria arose from antimicrobial effects. Both phenolic exposures resulted in various protein changes especially in membrane-related proteins as well as ribosome and protein synthesis related-proteins. In addition, they caused serious oxidative stress depending on the protein profile changes related to redox proteins. Alginate-chitosan nanoparticles resulted increased antimicrobial effects of the phenolics which were produced, characterized and tested on various pathogenic bacteria via agar diffussion and spectrophotometric measurements. Hence, free or encapsulated forms of phenolic acids were demonstrated as effective antimicrobial agents and based on proteomic results, the effect of phenolic acids may be multi targetted.
  • Doctoral Thesis
    Investigation of Molecular Effect of Phenolic Acids on Methicillin-Resistant and Methicillin-Susceptible Staphylococcus Aureus in Comparison To Their Phenolic Acid Resistant Mutants
    (Izmir Institute of Technology, 2018) Keman, Deniz; Keman, Deniz; Soyer, Ferda; Soyer, Ferda; 01. Izmir Institute of Technology; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science
    Staphylococcus aureus is a Gram-positive bacterium whose acquisition through an open wound results in various infections. Methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) strains are responsible for diseases ranging from soft tissue infections to fatal pneumonia which cannot be treated due to multiple drug-resistances of these strains. This situation increases the importance of searching for alternative antimicrobials worldwide. Having all these in mind, the capacity of phenolic acids cannot be denied to be used against pathogenic bacteria. Phenolic acids produced as plant secondary metabolites show antibacterial effects besides many beneficial properties for human health. The aim of this study was to investigate the antibacterial action mechanisms of vanillic acid and 2-hydroxycinnamic acid on MRSA and MSSA. To achieve this, firstly the antibacterial effects of phenolic acids on both bacteria were investigated by determination of minimum inhibitory concentrations. Then, the resistance development ability of bacteria against phenolic acids was tested by continuous exposure to subinhibitory concentrations. Finally, the action mechanisms of phenolic acids on bacteria were elucidated using two different proteomic approaches. According to the results, bacteria were not able to develop resistance against phenolic acids. Proteomic studies displayed alterations in the protein profiles of phenolic acid treated bacteria and provided potential targets in the battle with pathogenic bacteria. By showing the inability of MRSA and MSSA to develop resistance to phenolic acids and the important proteomic alterations that are induced by phenolic acid treatment, this study highlights the significance of phenolic acids to be used against antibiotic-resistant bacteria.
  • Doctoral Thesis
    Identification of Molecular Resistance Mechanisms Against Systemically Used Antifungal Drugs, Amphotericin B and Caspofungin
    (Izmir Institute of Technology, 2018) Balkan, Çiğdem; Arslanoğlu, Alper; Arslanoğlu, Alper; 04.03. Department of Molecular Biology and Genetics; 04. Faculty of Science; 01. Izmir Institute of Technology
    The invasive fungal infections have been evolving for the last few decades and become a crucial factor that negatively affects the survival ability of the patients. Moreover, developing new resistance mechanisms of infectious organisms to the antifungal drugs make this problem more critical. In this study, we identified four different genes PDR16 and PMP3, RMD9 and SWH1which are resistant to amphotericin B and caspofungin, respectively, in Saccharomyces cerevisiae. We also screened whole yeast genome at transcriptional level via microarray analysis and identified metabolic pathways affected by these antifungal drugs. In addition, we applied several characterization methods including physiological and morphological analyses to understand the resistance mechanisms. We found that rmd9 mutants were extremely hyperpolarized and pdr16 and pmp3 mutants were depolarized when compared to control group. In contrast, overexpression of SWH1 increased the membrane potential of wild type cells. Further analyses showed that the absence of RMD9 disrupts the cellular morphology. To show that these genes are clinically important, Candida albicans orthologs of PDR16 and PMP3 were cloned and their roles in amphotericin B drug resistance were confirmed. RMD9 and SWH1 have no known C. albicans orthologs, so the confirmation with pathogenic yeast genome could not be performed against caspofungin.