Master Degree / Yüksek Lisans Tezleri

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Author: search.filters.author.Şanlı Mohamed, Gülşah

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  • Master Thesis
    Cloning of Novel Sericin Like Proteins and Optimization of Their Expression
    (Izmir Institute of Technology, 2022) Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    Sericin is a protein that helps fibroin fibers link together to create the cocoon, and it forms silk with fibroin. Fibroin is used in textile production as well as in biomaterial applications. Sericin has essential biocompatibility, biodegradability, cryoprotection, antioxidant properties, and a multi-component structure. Thanks to these properties, its use in biomaterial and biomedical fields is expanding and also used in cosmetic research and wound healing, and drug delivery thanks to its high fiber structure. Sericin can be obtained from silkworm cocoons by degumming method but changes the structure of the obtained protein since the protein is exposed to high temperatures. Sericin produced in different batches is obtained in different quantities and these create inconsistencies in the quality of the biomaterials obtained from the sericin, limiting the use of the sericin as a biomaterial. Besides, obtaining protein by recombinant production provides the advantage that the repetitive chain length can adjust as desired and the protein can be standardized. In this thesis, recombinantly generated and optimized a novel sericin-like protein (Ser-12mer) with the native sericin sequence encoding twelve repeats of recombinantly conserved 38 amino acid motifs in Escherichia coli and characterized its structural properties. In addition, the effects of induction cell density and cell culture media on the expression of the previously produced sericin-like protein (Ser-4mer) was investigated and its expression and concentration were increased by optimization. Recombinant production of a sericin-like protein will provide an understanding of the sequence-structure relationships and significantly expand their applications as biomaterials.
  • Master Thesis
    The Effect of Enzyme Use on the Formation of Carbonyls and Structural Properties of Cakes
    (01. Izmir Institute of Technology, 2021) Ceylan, Çağatay; Er, Ayşe Ege; Şanlı Mohamed, Gülşah; Ceylan, Çağatay; Şanlı Mohamed, Gülşah; 01. Izmir Institute of Technology; 03.08. Department of Food Engineering; 04.01. Department of Chemistry; 03. Faculty of Engineering; 04. Faculty of Science
    Enzymes are used as additives to improve the quality parameters of cakes. However, high temperature conditions produce carbonyl-containing compounds as precursors of toxic maillard reaction products. In this study three food grade enzymes were used as agents to decrease the formation of carbonyl-containig compounds while preserving the cake quality factors. For this purpose transglutaminase, lipase and amylase enzymes were used. All of the three enzymes lowered the amounts of carbonyls with the largest decrease by lipase of 31.83% (p<0.05) with respect to the control cake. Transglutaminase and lipase addition changed the carbonyl profile of cakes. Both transglutaminase and lipase caused important changes in protein secondary structures with large increases in alpha helix, turns and anti-parallel beta structures, however, amylase did not cause such large changes. The three enzymes used caused the lipid/protein ratio to decrease. The level of lipid unsaturation did not change for transglutaminase and lipase, however, the level unsaturation decreased in the case of amylase indicating the formation of dicarbonyls was via Maillard reaction not due to lipid peroxidation. However, the GC-MS analysis results indicated that there was no change in the formation of neither the Maillard reaction products nor the lipid oxidation products in the head space analysis. The amorphous structure of the starch in cake samples increased depending on the enzyme concentration used.
  • Master Thesis
    Investigation of Cytotoxic Properties of New Isoindol Derivatives in Lung and Cervical Cancers
    (Izmir Institute of Technology, 2019) Almusawi, Yasir; Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    Cancer is one of the most common diseases in the world. Recently, there are many methods developed by researchers to treat this disease. One of these treatments is targeted for chemotherapy. It is preferred by researchers because it is less toxic and has fewer side effects than other cancer treatments. This study emphasizes the anticancer properties of the newly synthesized Isoindole derivatives. Thus, it was hoped to be a significant improvement based on new generation anticancer compounds with high efficacy and fewer side effects. The main objective of this study was to investigate the biological activity of seven newly synthesized Isoindole derivatives. The anticancer activity of these compounds was evaluated against HeLa (cervical carcinoma) and A549 (lung adenocarcinoma) cancer cell lines. This study is divided into three parts. Firstly, the cytotoxic activity of these compounds was determined by measuring the cell viability of each compound on HeLa and A549 cell lines. The main objective of this analysis is to measure the IC50 value of each compound and determine which compound is best to kill at least half of the cells. Secondly, the effects of programmed cell death and cell cycle were investigated for compounds with the best IC50 for each cell line by using Annexin V-FITC in flow cytometry. Finally, a scratch assay was performed to investigate the effect of these new Isoindole derivatives on cell migration.
  • Master Thesis
    Dual Therapy Opportunities for Tuberculosis and Prostate Cancer Based on Crystal Engineering Principles
    (Izmir Institute of Technology, 2019) Arpacıoğlu, Merve; Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    Within this work, it is aimed to facilitate dual therapy opportunities for the treatment of tuberculosis and prostate cancer separately based on crystal engineering principles. In this regard, a quinolone family member antibiotic namely Sparfloxacin (SPX) is combined with another antibiotic called 4-aminosalicylic acid (4-ASA). Due to the drug-drug combination, it is expected to have superior biological activity since both drugs are stated and offered to be used in the treatment of tuberculosis. In addition to that, Apalutamide (APA) a recent drug in the treatment of castration-sensitive metastatic prostate cancer (CSMPC), is metallo-encapsulated by using zeolitic imidazolate framework-8 (ZIF-8). Owing to pH-sensitive decomposition, the new formulation is expected to combine the benefit of free zinc release and APA release to the targeted cancerous section. Both new compounds are synthesized characterized by various methods such as single crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), Fourier-transform infrared radiation (FTIR), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), scanning electron microscopy (SEM) and high-performance liquid chromatography (HPLC).
  • Master Thesis
    Optimization of Expression and Isolation of a Thermophilic P450 Enzyme
    (Izmir Institute of Technology, 2018) Aslantaş, Yaprak; Sürmeli, Nur Başak; Şanlı Mohamed, Gülşah; Sürmeli, Nur Başak; Şanlı Mohamed, Gülşah; 03.01. Department of Bioengineering; 04.01. Department of Chemistry; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of Technology
    Cytochrome P450 enzymes (CYP or P450) are monooxygenases that catalyze the oxidation of hydrocarbons with high efficiency and selectivity, and many other reactions like hydroxylation, epoxidation, reduction, demethylation. CYP119, is a thermophilic P450 from Sulfolobus acidocaldarius. Thanks to thermophilic properties, CYP119 has potential to be widely used as a biocatalyst in production of fine chemicals and pharmaceuticals. However, production and purification of CYP119s is quite difficult and time consuming. Here, through recombinant protein production techniques, the optimum production and purification of heat-tolerant CYP119 has been successfully carried out. N-terminal and C-terminal histidine tags were cloned to CYP119. Protein expression was induced in Escherichia coli BL21 (DE3) cells with isopropyl β-D-1-thiogalactopyranoside (IPTG). δ-aminolevulinic acid (ALA) was also used to increase the heme biosynthesis. Different IPTG and ALA concentrations, expression temperature and duration were used to optimize production. CYP119 was isolated and purified with Ni-NTA affinity column. The thermostability of purified N (N-His-CYP119) and C (C-His-CYP119) terminal His-tagged were compared with wild type CYP119 (Wt-CYP119). Oxidation reaction of CYP119 and variants carried out and compared at 25 °C and 65 °C. Also, epoxidation of styrene was performed with N-His-CYP119 in different temperatures. The effects of histidine tags on stability and activity of the CYP119s were observed. Here, conditions for the production of CYP119 were optimized and the histidine tags were found to cause changes in stability and function of proteins. This project will lead to increase in the production of the important enzyme CYP119, which will increase its utilization in the industry.
  • Master Thesis
    Investigation of Anticancer Properties of the Novel Synthesixed Pyrrole Derivatives as Potential Tyrosine Kinase Inhibitors
    (Izmir Institute of Technology, 2017) Kaya, Meltem; Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    In cancer treatment, chemotherapy has some serious side effects, because it targets active cells which might not be cancer cells. Mouth, hair, nail, bone marrow cells are some examples of active cells. For the reason that chemotherapy has side effects, targeted therapy become more important. Tyrosine kinases are most interested target, because they are necessary for cell growth and metastasis. Active form of tyrosine kinases can cause tumour growth and proliferation, angiogenesis, metastasis and antiapoptotic effects. Based on these vital role of tyrosine kinases, they became more important target in cancer treatment. Pyrrole derivatives have been used chemotherapy drugs for years. Semaxanib and Sunitinib, indole derivatives, are tyrosine kinase inhibitors. The main purpose of this research is to investigate the biologic activities of novel synthesized seven pyrrole derivatives, their activities on migration, apoptosis, cell cycle, and mTOR downstream as a potential tyrosine kinase inhibitor. The results of this research proved that these seven compounds have toxicity on HeLa cells with the IC50 values of 140.60 μM, 382.82 μM, 366.44 μM, 542.00 μM, 255.86 μM, 148.59 μM, 171.40 μM, respectively, but toxicity effects of drugs do not depend on apoptosis mechanism. Beside this, D1 and D3 were able to effect cell cycle by arresting at S phase for D1 and G1 phase for D3. It was demonstrated that D1 and D3 inhibited cell migration. And this inhibition was reported as in a relation with overexpression of p- 4EBP1, inhibition of p-p70S6K (Thr) and p-p70S6K (Shr) proteins. Considering all results, D1 and D3 might be potent inhibitory of metastasis of HeLa cells with respect to its effect on cell cycle, migration, p-4EBP1, p-p70S6K (Ser), and p-p70S6K (Thr) protein levels.
  • Master Thesis
    Antiproliferative and Anticancerogenic Effects of 5-Asa and Its Novel Synthesized Oligomer
    (Izmir Institute of Technology, 2017) Atahanova, Hurshida; Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    In the world, colorectal cancer (CRC) is third common malignant diseases and fourth leading cause of cancer-related death. More recently, epidemiological studies have suggested that regular intake of 5-aminosalicylic acid (5-ASA), the drug used in treatment of inflammatory bowel disease (IBD), reduces the risk of CRC developing in patients with ulcerative colitis. Several action mechanisms of 5-ASA are proposed which are independent from its weak cyclooxygenase (COX) inhibitory property, found overexpressed in many cancer types. Lately, polymeric prodrugs developed which contain bioactive unit and have prolonged activity by sustained release, consequently reduced toxicity. However, large molecular weight and long chain can be challenging in penetrating into the cell membrane. Thus, oligomers with shorter chain of monomer units and lower molecular weight can be preferred choice. In the present study we evaluated antiprolifertaive and anticancerogenic effect of novel synthesized 5-ASA based oligomer compared to its active monomer, 5-ASA in Caco-2, DLD-1, HeLa and CCD-18Co cells. According to MTT, apoptotic rate, cell cycle phase distribution and scratch assay analysis the oligomer showed higher activity compared to its monomer, 5- ASA at lower doses. The oligomer induced cell death and cell cycle arrest in colorectal cancer cells and in HeLa cells. However, no significant induced cell death and cell cycle arrest observed in normal human colon cells, CCD-18Co when exposed to 5-ASA and the oligomer. Overall results indicate that the oligomer can be promising candidate for prodrugs in treatment and prevention of colorectal cancer.
  • Master Thesis
    Cloning and Purification of Biosynthetic Enzymes
    (Izmir Institute of Technology, 2016) Gürelme, Ebru; Şanlı Mohamed, Gülşah; Sürmeli, Nur Başak; Sürmeli, Nur Başak; Şanlı Mohamed, Gülşah; 03.01. Department of Bioengineering; 04.01. Department of Chemistry; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of Technology
    Bioproducts have become prominent with their sustainable, eco-friendly and renewable features. In recent years, research and development studies focused on production of biodiesel and pharmaceuticals. Biodiesel can be synthesized in the form of fatty acid ethyl ester (FAEE) by in vivo activity. This synthesis is catalyzed by wax ester synthases (WS). This study aims cloning and purification of wax ester synthases from Psychrobacter arcticus 273-4 (PaWES) and Mus musculus C57BL/6 (MmWES). PaWES was cloned and expressed by Escherichia coli BL21(DE3) strain, at the proper conditions with using pET expression system. It was purified with approximately 1 mg yield. Cloning of the second wax ester synthase (MmWES) was achieved to Saccha-romyces cerevisiae and it was purified with lower than 1 mg yield. The other aim of this study is related to taxadien-5α-ol-O-acetyltransferase from Taxus cuspidata (TcT5AT). This enzyme belongs to the biosynthesis pathway of Taxol, which is the most commonly used chemotherapy drug. Cloning and purification studies of this enzyme were successfully performed. It was expressed by Escherichia coli BL21(DE3) Star strain and purified with the yield of 23 mg. Immobilized Metal Affinity Chromatog-raphy (IMAC) is used for all three enzymes as a purification strategy. This project can pave the way for structural studies of all biosynthetic enzymes mentioned above. In summary, the findings of this study will circuitously help for solving the relationship between function and structure of these enzymes. It may lead to increased generation of Taxol and FAEE based biodiesel.
  • Master Thesis
    Immobilization of Thermophilic Esterase on Magnetic Cornstarch Nanoparticles for Biological Applications
    (Izmir Institute of Technology, 2016) Öz, Yasin; Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; 04.01. Department of Chemistry; 04. Faculty of Science; 01. Izmir Institute of Technology
    In last three decades, even the role of enzymes for biological and industrial applications has become more worthy, enzymes also have some defects. The enzyme immobilization allows to overcome these defects by improving abilities of reusing of catalysts by multiple times, easier reactor operation and product separation. Due to its potential use in biological and industrial applications, isolated thermophilic esterase from Geobacillus sp. was immobilized on magnetic cornstarch nanoparticles. In order to determine activity performance of immobilized enzyme, the effects of temperature, pH and some chemicals on enzyme activity were investigated. The results have shown that after immobilization, the relative activity of immobilized esterase has increased to 80% at 80 0C in comparison to free esterase. Therewithal, the reusability of immobilized esterase has increased fourfold in comparison to free esterase. The magnetic character of the support media has brought ease to separate biocatalysts from reaction media.
  • Master Thesis
    Chitosan-Plasmid Dna Nanoparticles: Cytotoxic and Cytostatic Effects on Human Cell Lines
    (Izmir Institute of Technology, 2015) Bor, Gizem; Demir, Mustafa Muammer; Şanlı Mohamed, Gülşah; Şanlı Mohamed, Gülşah; Demir, Mustafa Muammer; 03.09. Department of Materials Science and Engineering; 04.01. Department of Chemistry; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of Technology
    Although chitosan nanoparticles (CNs) became a promising tool for several biological and medical applications owing to their inherent biocompatibility and biodegrability, studies regarding their effects on cytotoxicity and cytostatic properties still remain insufficient. Therefore, in the present study, we decided to perform comprehensive analysis of the interactions between CNs – pKindling-Red-Mito (pDNA) and different cell line models derived from blood system and human solid tissues cancers. The resulting CNs-pDNA was investigated with regard to their physical-chemical properties, cellular uptake and transfection efficiency, cytotoxic and cytostatic properties. The nanoparticles showed high encapsulation efficiency and physical stability even after 2 days for various formulations. Moreover, high gene expression levels were observed already 96 h after transfection. CNs-pDNA treatment, despite the absence of oxidative stress induction, caused cell cycle arrest in G0/G1 phase and as consequence led to premature senescence, which turned out to be both, p21-dependent and p21-independent. Also, observed DNMT2 upregulation may suggest the activation of different pathways protecting from the resulting CNs-mediated stress. In conclusion, treatment of different cell lines with CNs-pDNA showed that their biocompatibility was limited and effects were cell type-dependent.