Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
Browse
14 results
Search Results
Master Thesis Design of Localized Surface Plasmon Resonance (lspr) Based Biosensor for Detecting a Potential Cancer Biomarker(Izmir Institute of Technology, 2020) Bulmuş Zareie, Volga; Bulmuş Zareie, Esma Volga; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyConventional methods for detection of cancer are invasive, expensive and not suitable for early diagnosis. Therefore, demand for simple, sensitive and rapid biosensors for detection of cancer have been enormous. Gold nanorods (GNRs) have been ideal materials for utilization in biosensors because of their exceptional optical properties. Localized surface plasmon resonance (LSPR) which is created on GNR surface can be used for the development of label-free and sensitive biosensor systems. LSPR responds to changes in the refractive index of the surroundings and this change can be observed as the shift in the maximum absorption wavelengths. In this thesis, an LSPR based GNR biosensor was developed for sensitive detection of a sialic acid as a potential cancer biomarker. For this purpose, GNRs were synthesized at around 40-50 nm in length. Afterwards, glass surfaces were coated with GNRs and functionalized with self-assembling molecules. Specific monoclonal antibodies(Ab) were conjugated to the surface. The surface modifications were characterized via contact angle, scanning electron microscope, Fourier transform infrared spectroscopy and zeta potential. Ab-functionalized glass surfaces were used to quantitatively detect specific molecular bindings via LSPR. The sensitivity of the biosensor was determined as 281 RIU/nm. The detection limit in PBS was 1 nM, while in serum it was found to be as 10 nM because of the high protein content of serum. Control experiments showed that the developed biosensor chip was selective. The proposed system is promising for early diagnosis of cancer since it can detect a potential cancer biomarker at concentrations as low as nanomolar level.Master Thesis Synthesis of Cationic Star Polymers Via Raft Polymerization(Izmir Institute of Technology, 2018) Dursun, Gürbüz; Bulmuş Zareie, Volga; Bulmuş Zareie, Esma Volga; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe aim of this master thesis is to synthesize cleavable, core-crosslinked, cationic, new star polymers as potential siRNA carrier systems. The core-crosslinked star polymers of aminoethyl aminoethyl methacrylate (AEAEMA) monomer were synthesized for the first time in the literature. A crosslinker, potentially cleavable in cell cytosol, bis(2-methacryloyl) oxyethyl disulfide, and AEAEMA monomer with Boc-protection groups (BocAEAEMA) were polymerized using P(OEGMA) macroRAFT agents (5 kDa or 10 kDa). The polymerization kinetics revealed a linear increase in ([M]0/[M]) with increasing polymerization time, indicating the RAFT-controlled polymerization mechanism. The incorporation of arms into star structure completed between 2 and 8 hours of polymerization, leading to star formation yields of approx. 55%. Star polymers with narrow PDI values (between 1.52 and 1.80) and controllable molecular weights (between 116 kDa and 620 kDa) were synthesized using a P(OEGMA) macroRAFT agent of 10 kDa. Increasing crosslinker to macroRAFT agent ratio led to increase in crosslinker conversion and decrease in BocAEAEMA conversion. Increasing BocAEAEMA to macroRAFT agent ratio had the exact opposite effect. The use of a macroRAFT agent of 5 kDa led to a dramatic increase in molecular weight (up to 3370 kDa). The hydrodynamic sizes (Dh) of water soluble, cationic star polymers, obtained after deprotection of amino groups, dropped from 2-36 nm to 1-18 nm after treatment with a reducing agent in water, indicating the cleavable nature of the star structures. Among the star polymers tested, the polymer having 7 arms of POEGMA (10 kDa) and a degree of polymerization of AEAEMA (DPAEAEMA) of 70 efficiently complexed with siRNA at a nitrogen/phosphate ratio of 1. While this polymer showed higher cytotoxicity, when compared with other star polymers tested, all polymers were significantly less toxic, compared to branched PEI, a golden standard cationic polymer for siRNA delivery.Master Thesis Sericin-Polymer Conjugates: Preparation and Physicochemical Characterization(Izmir Institute of Technology, 2017) Gül, Abdulkadir; Bulmuş Zareie, Volga; Bulmuş Zareie, Esma Volga; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologySericin is a protein derived from silkworm, Bombyx mori, and has several useful properties as a natural biomaterial such as antioxidant character, moisturizing ability, hydrogel forming property and most importantly immunogenic inertness. The aim of this thesis is to prepare and physicochemically characterize sericin-polymer conjugates as potential natural-synthetic hybrid biomaterials with enhanced properties for drug delivery and tissue engineering applications. For this purpose, three polymers having the same degree of polymerization (n~42) and varying chemical nature, i.e. poly(oligoethylene glycol methacrylate), P(OEGMA) hydrophilic and neutral, poly(hydroxyethylmethacrylate) P(HEMA) less hydrophilic and neutral, and poly(dimethylaminoethyl methacrylate) P(DMAEMA) hydrophilic and cationic after quaternization, were first synthesized via reversible addition fragmentation chain transfer (RAFT) polymerization. Each polymer was characterized via nuclear magnetic resonance (1H-NMR) and gel permeation chromatography (GPC). Separately, molecular weight and isoelectric point of sericin were characterized using various techniques including Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) and High-Resolution Two-Dimensional Polyacrylamide Gel Electrophoresis (2D-PAGE). Polymers were then covalently conjugated to sericin using NHS/EDC chemistry. The conjugates were characterized using SDS-PAGE, GPC and DLS (Dynamic Light Scattering). The SDS-PAGE and GPC results showed the successful preparation of the conjugates. DLS revealed that the hydrodynamic size of P(OEGMA) and P(DMAEMA) polymers and their conjugates were between 1 and 10 nm as they are soluble in PBS and do not form aggregates. Unlike the other two polymers, although the size of P(HEMA) polymer was observed to be 3.24 ± 0.62 nm, the DLS measurements of P(HEMA) conjugates indicated the presence of self-organization and aggregation of Sericin-P(HEMA) conjugates in aqeuous solution. Consequently, the size of sericin-P(HEMA) conjugates were found to be 530 ± 60.83 and 223.3 ± 25.2, respectively.Master Thesis Design and Construction of Portable Localized Surface Plasmon Resonance Device for Detection of Biological Molecules(Izmir Institute of Technology, 2017) Gül, Aytaç; Bulmuş Zareie, Volga; Bulmuş Zareie, Esma Volga; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyPoint-of-care devices giving rapid results in non-laboratory settings have become important for biosensor applicattions in a wide range of fields including medical, food, agriculture and pharmaceutical. This work aims to portable device based on localized surface plasmon resonance spectroscopy (LSPR-S) as a potential biosensor platform that can be used in non-laboratory settings for rapid detection of biological molecules at hifh sensivity. The thesis can be divided into two parts: In the first part, the design and consctruction of the device including both the mechanical and electronic parts are presented. The mechanical section includes the integration of the parts to build the device and microchannels designed with the aid of a three-dimensional drawing program Solid Works 2015. The second step of the construction process was the installation of electronic components onto the device. The electronicpart consists of a light source, fiber optic cables, a spectrometer and a temperature sensor. In conclusion, a portable LSPR-S device with an integrated microchannel system has been produced, which potentially allows analysing low volumes of sample without the need to label the molecules. The second part of the thesis covers the studies towards the preparation and application of sensing platforms for the LSPR-S device constructed to enable the rapid detection of biplogical molecules at high sensitivity. These included the preparation of gold nanorods and nanoparticles-based LSPR-S detection of model antibody-antigen and bacteria-bacteriophage interactions, respectively. Studies conducted in this section have led to the conclusion that LSPR-S-based biosensor platforms developed in thisis are promising solutions to overcome current challenges in biosensor applications.Master Thesis Interactions of Cancer Cells and Macrophages on the Egf-Egfr Axis: Chemotaxis, Haptotaxis or Direct Contact?(Izmir Institute of Technology, 2017) Önal, Sevgi; Pesen Okvur, Devrim; Bulmuş Zareie, Volga; Pesen Okvur, Devrim; Bulmuş Zareie, Esma Volga; 04.03. Department of Molecular Biology and Genetics; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of TechnologyBreast cancer cells (BCC) and macrophages are known to interact via epidermal growth factor (EGF) produced by macrophages and colony stimulating factor-1 (CSF-1) produced by BCC. Despite contradictory findings, this interaction is perceived as a paracrine loop. Yet, the underlying mechanism of interaction remains unclear. Here, we investigated interactions of BCC with macrophages in 2D and 3D. BCC did not show chemotaxis to macrophages in custom designed 3D cell-on-a-chip devices, which was in agreement with ELISA results showing that macrophage-derived-EGF was not secreted into macrophage-conditioned-medium. Live cell imaging of BCC in the presence and absence of iressa showed that macrophages but not macrophage-derivedmatrix modulated adhesion and motility of BCC in 2D. 3D co-culture experiments in matrigel and collagen showed that BCC changed their multicellular organization in the presence of macrophages. In custom designed 3D co-culture cell-on-a-chip devices, macrophages reduced and promoted migration of BCC in matrigel and collagen, respectively. Furthermore, adherent but not suspended BCC endocytosed EGFR when in contact with macrophages. Collectively, our data revealed that macrophages showed chemotaxis towards BCC-derived-CSF-1 whereas BCC required direct contact to interact with macrophage-derived-EGF. We propose that the interaction between cancer cells and macrophages is a paracrine-juxtacrine loop of CSF-1 and EGF, respectively.Master Thesis In Vitro Evaluation of Poly (2-((2 Amino) Ethyl Methacrylate) as a Potential Sirna Delivery Agent(Izmir Institute of Technology, 2015) Seyrantepe, Volkan; Seyrantepe, Volkan; Bulmuş Zareie, Volga; Bulmuş Zareie, Esma Volga; Seyrantepe, Volkan; 03.01. Department of Bioengineering; 04.03. Department of Molecular Biology and Genetics; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of TechnologyThe aim of this thesis is to investigate poly(2-((2-aminoethyl)amino)ethyl methacrylate) (P(AEAEMA)) as a potential siRNA carrier. For this purpose, an amine containing monomer 2-((tert-butoxycarbonyl) (2-((tert-butoxy carbonyl) amino) ethyl) amino) ethyl methacrylate (BocAEAEMA) was synthesized. Reversible addition-fragmentation chain transfer (RAFT) polymerization was performed to prepare homo- and block co-polymers of BocAEAEMA. The synthesized polymers -P(AEAEMA)19, P(AEAEMA)41 and P(PEGMA)12-b-P(AEAEMA)32- were characterized via NMR and GPC. The cytotoxicity of the polymers was investigated in vitro using ovarian cancer cell line (Skov-3-luc) via MTT assay. The polymers did not show any toxic effect on cells in 24 h. The ability of the BocAEAEMA polymers to form polyplexes with siRNA was investigated via gel electrophoresis. P(AEAEMA)19, P(AEAEMA)41 and P(PEGMA)12-b-P(AEAEMA)32 could efficiently form complexes with siRNA at an N/P ratio of 5, 2, and 2 respectively. Gel electrophoresis analysis revealed that P(AEAEMA)41 and P(PEGMA)12-b-P(AEAEMA)32 could protect siRNA against serum components at least for 6 h. Block copolymer, when complexed with siRNA at an N/P ratio of 10, could protect siRNA longer (24 h) when compared with the homopolymer. The size and surface charge of the polyplexes were investigated by DLS. The diameter of the P(AEAEMA)41-siRNA complexes was found to be lower than 110 nm at all N/P ratios tested. In contrast, P(PEGMA)12-b-P(AEAEMA)32-siRNA complexes (except the complex prepared at the N/P ratio of 2), displayed aggregation tendency. All polyplexes displayed positive zeta potential. The zeta potential of the homopolymer was found to be higher than the copolymer at the N/P ratio of 2. Finally, in order to determine siRNA transfection ability of the polymers, luciferase assay was optimized using a commercial transfection reagent lipofectamine RNAimax. The optimized assay conditions will be used in future studies to determine the transfection efficiency of the polymers.Master Thesis Development of Arginine-Containing Well-Defined Polymers(Izmir Institute of Technology, 2014) Taykoz, Damla; Bulmuş Zareie, Volga; Bulmuş Zareie, Esma Volga; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe aim of this work is to synthesize arginine-containing well-defined polymers via reversible addition-fragmentation chain transfer (RAFT) polymerization and perform preliminary investigation on the use of these polymers in nucleic acid complexation for potential gene therapy applications. Pentafluorophenyl methacrylate (PFMA) was chosen as an active ester monomer to produce polymers having functional groups available for further modification. RAFT polymerization of PFMA was performed varying polymerization conditions such as feed composition and polymerization temperature. Polymers (PPFMA) were characterized using nuclear magnetic resonance (NMR) spectroscopy and gel permeation chromatography. Linear increase in ln[M]0/[M] with polymerization time, and number average molecular weight (Mn) with monomer conversion indicated RAFT controlled polymerization of PFMA under the conditions tested. Furthermore, block copolymers of PFMA with poly(ethylene glycol) methacrylate (PEGMA) as a biocompatible component were prepared. Copolymerization was studied using both P(PFMA) and P(PEGMA) as macro RAFT agent. Copolymerization kinetic studies indicated that chain extension block copolymerizations were successfully performed using both macroRAFT agents. P(PFMA) was reacted with arginine methylester (AME) in the presence of triethylamine (TEA). 100% of P(PFMA) active ester groups could be modified with AME at a polymer/AME/TEA mole ratio of 1/1/3, as determined by 1H-NMR spectroscopy. The AME modified polymers were complexed with a 681-bp DNA fragment through electrostatic interactions at varying nitrogen/phosphate (N/P) ratios. Gel electrophoresis experiments revealed that AME-modified P(PFMA) was able to complex with DNA at a N/P ratio of 200. Furthermore, the hydrodynamic diameter (Dh) of polymer/DNA complexes in phosphate buffer saline was found to be 58 nm, while the free DNA displayed a Dh of 109 nm, indicating the complexation of DNA by AME-modified P(PFMA).Master Thesis Synthesis and Raft Polymerization of Arginine Containing Monomer To Investigate the Cell Membrane Translocation(Izmir Institute of Technology, 2014) Uğur, Deniz; Bulmuş Zareie, Volga; Uğur, Deniz; Bulmuş Zareie, Esma Volga; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of EngineeringIn this study, a higly cationic biosynthetic polymer, poly(Arginine Methyl Ester Methacrylamide) (p(AMME)) has been designed as a potential component of intracellular delivery systems for biological macromolecular therapeutics such as nucleic acids. Accordingly, an arginine derivative monomer; Arginine Methyl Ester Methacrylamide (AMME) was synthesized by the reaction of an active ester monomer, pentafluorophenylmethacrylate (PFMA) and the L-arginine methyl ester hydrochloride (AME) in the presence of excess triethyl amine. AMME was then polymerized via both conventional free radical polymerization and reversible addition-fragmentation chain transfer (RAFT) polymerization. The polymers p(AMME) were characterized via nuclear magnetic resonance and gel permeation chromatography techniques. The conventional free radical polymerization experiments yielded polymers with uncontrolled molecular weights and wide molecular weight distribution, whereas RAFT polymerizations performed both in aqueous solution and organic solvent yielded polymers with controlled molecular weights and narrow molecular weight distributions. The RAFT polymerization kinetic experiments showed the RAFT-controlled character of AMME polymerization in the presence of 4-cyano-4-(ethylthiocarbonylthioylthio) sulfanylpentanoic acid (ECT) as a RAFT agent. The cytotoxicity of P(AMME) before and after aminolysis was determined via MTT assay using A549 human lung cancer cell line. P(AMME) before aminolysis of the RAFT end-group displayed dose-dependent toxicity after 24 hours incubation with cells. It was highly toxic to cells at 25 μM concentration, killing almost more than 60% of cells after 24 hours incubation. On the other hand, the aminolyzed polymer has no significant toxicity in the concentration range studied (upto 500 μM), which was comparable with octaarginine, a widely used transfection agent. In conclusion, well-defined arginine-polymers synthesized in this study show potential for further investigations as potential components of intracellular delivery systems for therapeutics.Master Thesis Synthesis of Ph-Sensitive Cholesterol Polymers and in Vitro Investigation of Interactions With Cell Membrane(Izmir Institute of Technology, 2014) Güven, Vildan; Bulmuş Zareie, Volga; Bulmuş Zareie, Esma Volga; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe aim of this thesis is to synthesize pH-sensitive, cholesterol containing polymers via reversible addition fragmentation chain transfer (RAFT) polymerization, as potential membrane-destabilizing agents for intracellular drug delivery applications and investigate interaction of these polymers with cell membrane. For this purpose, cholesteryl methacrylate (CMA) and 2-((tert-butoxycarbony)(2-((tert-butoxycarbonyl) amino) ethyl) amino)ethyl methacrylate (Boc-AEAEMA) were first synthesized. CMA was copolymerized with t-butyl methacrylate (t-BMA) or Boc-AEAEMA via RAFT polymerization to produce cholesterol containing copolymers having varying molecular weights and compositions. Copolymers were characterized using 1H-NMR spectroscopy and gel permeation chromatography (GPC). Linear increase in ln [M]0/[M] with polymerization time, and Mn with monomer conversion indicated the RAFT-controlled copolymerizations under the conditions tested. P(t-BMA-co-CMA) and P(Boc-AEAEMA-co-CMA) copolymers were hydrolyzed to methacrylic acid-co-CMA (p(MAA-co-CMA) and p(AEAEMA-co-CMA) copolymers, respectively, to obtain water soluble, pH-sensitive copolymers. The pH-responsive behavior of copolymers was demonstrated via UV−visible spectroscopy and dynamic light scattering measurements. These measurements revealed that (p(MAA-co-CMA) copolymers having 2 and 4 mol% CMA form nanoparticles at pH 5.5 while they exist as unimers at pH 7.4. Copolymers having 8% CMA form aggregates at both pH values. Hemolysis assays revealed that p(MAA-co-CMA) having a molecular weight above 20,000 g/mol did not show pH-dependent hemolytic activity regardless of CMA content. The cell viability results (obtained by MTT assay) indicated that p(MAA-co-CMA) at 250 μg/ml concentration is not cytotoxic to NIH3T3 cell line.Master Thesis Synthesis of Well-Defined Fatty Acid Polymers as Potential Membrane Destabilizing Agents(Izmir Institute of Technology, 2014) Aydınlıoğlu, Esra; Bulmuş Zareie, Volga; Bulmuş Zareie, Esma Volga; 03.01. Department of Bioengineering; 03. Faculty of Engineering; 01. Izmir Institute of TechnologyThe aim of this thesis is to synthesize well-defined, fatty acid polymers via reversible addition fragmentation chain transfer (RAFT) polymerization, as potential membrane destabilizing agents which can be used for intracellular drug delivery applications. A new methacrylate monomer, derived from an unsaturated fatty acid, 11-[2-(2-methyl-acryloyloxy)-ethylsulfanyl] undecanoic acid (UDAMA), was synthesized using 10-undecenoic acid as a starting compound. Monomer synthesis was composed of two steps: In the first step, thiol-ene thermal addition of 2-mercaptoethanol to 10-undecenoic acid was performed. The yield of the reaction was 85 %. In the second step, the addition product was reacted with methacryoyl chloride to yield a new monomer, UDAMA. The yield of the second synthetic step was 92%, calculated from 1H NMR spectroscopy. UDAMA was polymerized via both conventional free radical and RAFT polymerization techniques. Polymers were characterized using 1H-NMR spectroscopy and gel permeation chromatography (GPC). Linear increase in ln [M]0/[M] with polymerization time, and Mn with monomer conversion indicated the RAFT-controlled polymerization of UDAMA monomer under the conditions tested. The new monomer, UDAMA was also copolymerized with methacrylic acid (MAA) via RAFT polymerization to obtain water-soluble, pH-responsive polymers. Random copolymers of MAA and UDAMA were synthesized using two different polymerization feed composition having 20 mol% or 50 mol% UDAMA content. Copolymerizations were also found to be controlled by RAFT mechanism, as evidenced by measurements via 1H-NMR spectroscopy and GPC. The pH-responsive behavior of copolymers was demonstrated via UV−visible spectroscopy and dynamic light scattering measurements. Hemolysis assays revealed that the copolymers with 20 mol% UDAMA content demonstrated pH-dependent hemolytic activity.