Sürdürülebilir Yeşil Kampüs Koleksiyonu / Sustainable Green Campus Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7755
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Master Thesis Plant-On Devices for Sed Screening(Izmir Institute of Technology, 2019) Yetgin, Ali; Pesen Okvur, Devrim; Canlı, KeremThanks to their roots, plants take the required molecules from the soil, therefore their research is important. The fact that absorption takes place from the root hair makes the observations necessary. The inadequacy of traditional methods requires the development of new methods to ensure their observations, especially during root studies. The fact that chip systems have the features that can overcome the problems has caused plant researches by using this method. The fact that environmental factors can be imitated in chip systems paves the way for abiotic stresses to work. Although abiotic stresses have been studied extensively on plants, seed germination and subsequent root extension and root hair formation have not been studied in detail except for the model organism (Arabidopsis thaliana). The use of chip system for plant studies of scientists have begun the 21st century is also reveals the need to do more work in this area. Researchers show that they are excited about the advantages they bring to the system and that necessary studies will be carried out in other side branches. It is thought that more research will be done by using chip systems after a short time. By using chip systems, a suitable environment for seed growth can be provided and environmental conditions can be simulated. By creating the desired controlled environment, it is possible to create a system which results in less time and less cost in order to replace the inconvenient and expensive method.Master Thesis Lab-on-a-chip devices for drug screening(Izmir Institute of Technology, 2019) Gökçe, Begüm; Pesen Okvur, Devrim; Çağır, AliBreast cancer is one of the cancers with the highest incidence and mortality rates in women in Turkey as well as in the world. Tumor micro environment comprises of cancer and normal cells, extracellular matrix, soluble biological and chemical factors. Research has shown that cell shape, adhesion, migration, response to growth factors and drugs are different in 2D and 3D culture. Today, only 8 out of 100 anti-cancer clinical trial gives effective results. 3D cell culture systems have shown to be a necessary step between in vitro, in vivo and clinical studies. Therefore, it is necessary to better understand the interactions of cancer cells with their micro environment, for which new cell culture setups are required. The most apparent disadvantage of widely used 3D cell culture setups is the lack of stromal cells. The systems to be developed should both provide a 3D environment and comprise multiple cell types. The drug screen in 3D tri-culture method with a lab-on-a-chip device, that will be developed in this study will be able to answer these needs. Cell lines that represent different breast cancer types alone or together with stromal cells were cultured in 3D in the to be developed lab-on-a-chip; by determining the effects of drugs with different targets on the viability and distribution of cells, a drug screening method is developed.Master Thesis Fungal Biotransformation of Novel 20(27)- Octanor Cycloastragenol and Biological Activities of the Purified Metabolites(Izmir Institute of Technology, 2019) Duman, Seda; Bedir, Erdal; Çağır, AliBiotransformation is the chemical modifications performed by enzymes or living organisms. The difficulty and high cost of enzyme isolation and purification makes it more advantageous to use whole cell systems as biocatalysts. Microbial biocatalysts are particularly interesting in the modification of complex molecules such as steroids and triterpenoids, which can catalyze stereo- and regio- selective reactions that are difficult or impossible to perform with chemical reactions. Specially, ability of endophytic microorganisms to produce specific enzymes for adaptation to their environment by tolerating toxic defense metabolites, makes them interesting for biotransformation studies. Telomeres are nucleotide structures located at the end of chromatids shortening with each cell division. Telomerase is a reverse transcriptase enzyme, and it helps to replenish telomere ends that are truncated by aging and stress factors. The telomerase activators (TA) with their potentials are suggested encouraging agents for healthy aging, and they are projected to generate a huge market in the future. Cycloastragenol is the only natural product in the sector marketed as a potent telomerase activator. In this study, by using endophytic fungi, the biotransformation studies were performed on 20(27)-octanor cycloastragenol. As a result, 14 biotransformation products, were isolated by chromatographic studies, and the structures of the metabolites were established by spectral methods. Based on the literature survey, 13 compounds turned out to be new for nature. Seven metabolites were screened for telomerase activation. In these screenings, metabolites showed telomerase activation ranging from 5.43 to 12.36 fold at doses ranging from 0.1 to 30 nM compared to the control cells treated with DMSO.Master Thesis Investigating Immunomodulator Mechanisms of Astragalus Saponins(Izmir Institute of Technology, 2018) Yakuboğulları, Nilgün; Yakuboğulları, Nilgün; Bedir, Erdal; Sağ, DuyguAdjuvants are chemical/biological substances that are used in vaccines to increase immunogenicity of antigens. Astragaloside VII (AST VII), a triterpenoid saponin isolated from Astragalus species, stimulates Th1 mediated immune response with antigen specific antibody response. The main goals of this thesis are synthesis of immunologically active analogs of AST VII and identifying immunomodulatory mechanism of actions of AST VII. The impact of AST VII and its synthesized analogs (dicarboxylic AST VII: DC-AST VII and dodecylamine conjugated AST VII: DAC-AST VII) on the cytokine release profile of human whole blood cells (hWB), dendritic cell maturation and subsequently T cell activation were analyzed by using flow cytometry and ELISA. IL-1 and IL-17A cytokines were substantially induced on hWB following treatments of the compounds. The most potent compounds were: DAC-AST VII (3.32 fold) for production of IL-1, AST VII (5.05 fold) for production of IL-17A. AST VII was more effective than DAC-AST VII (7.52 fold versus 1.34) in IL-1 production in BMDCs (bone marrow derived dendritic cells). The co-stimulation with AST VII and LPS enhanced dendritic cell maturation and activation by upregulating MHC II, CD86 and CD80, as well as IL-12 induction. All compounds were able to activate CD4+ and CD8+ T cells via increasing CD44 expression. Inflammasome activation may have a role in AST VII induced IL-1 secretion, dendritic cell maturation and T cell activation. However, more detailed molecular mechanism studies are warranted to substantiate our findings and to put forward signaling pathways involved.Master Thesis Green Synthesis of Metal Nanoparticles and Their Applications as Plasmonic Substrates(Izmir Institute of Technology, 2018) Elveren, Beste; Arslan Yıldız, Ahu; Yıldız, Ümit HakanGold nanoparticles (GNPs) have been widely used in diagnostic, tissue engineering, and drug delivery fields, in the last decades. Generally, reducing gold salts to zero valent gold has been accomplished by harsh chemicals and strong reducing agents, which cause toxicity and eventually limiting the bioapplications. Green synthesis is a newly developing methodology to synthesize GNPs. Especially natural products and plants extracts are commonly preferred for green synthesis based on their natural content. Biological molecule-capped GNPs, are more biofriendly and biocompatible nano-materials that can be used for varied applications.1-3 Sensor applications; varying from biosensing to environmental analysis, are an important field that GNPs were intensively utilized.4-5 Cyanide ion (CN-) has been considered as one of the main pollutants of water, because of its rapid discharge. CN- is currently being used in industry such as; polymer synthesis6, noble metal mining7, pest control8, plastics production etc., at large scale. However, there is an unmet need for CN- detection and monitoring. Colorimetric detection of CN- that utilizes GNPs has been done by several researchers.9-10 However, in all these studies reduction of GNPs were done by strong reducing agents. Green synthesis of GNPs eliminates the toxic side-products that can be harmful to both environment and human health. To overcome this problem green synthesized GNPs were used to establish the sensor platform, which can be further employed for CN- detection. Oxidation of GNPs in the presence of cyanide molecules is a direct-forward, colorimetric and optical method that requires no toxic chemicals; therefore it is a greener approach towards CN- detection in water resources.Master Thesis Comparison Od Side Effects of Anti-Cancer Drugs in 2d and 3d And, Classical and Cell-On Cultures(Izmir Institute of Technology, 2016) Kankale, Deniz; Pesen Okvur, Devrim; Çağır, AliThe studies that aim to assess the effects of drugs developed against cancer at the cellular level use multiwell plates. However, these classical systems fail to reproduce the in-vivo like microenvironment necessary for realistic assessment. In addition, classical cell culture systems use high amount of materials increasing cost. On the other hand, lab-on-a-chip systems use minimal volumes of reagents and more importantly can mimic the in-vivo microenvironment via spatial and temporal control. Furthermore, it is known that cell response to drugs can be very different in 2D and 3D cell culture setups. Doxorubicin is a widely used anticancer drug. Here, doxorubicin uptake by highly metastatic human breast cancer cell line MDA-MB-231 and normal mammary epithelial cell line MCF10A were investigated using 2D and 3D, classical and cell-on-a-chip cultures. Drug uptake at 24, 48 and 72 hours various concentrations of the drug determined by measuring signal intensities from fluorescence microscopy images of cells. For cell viability assay, cells were stained with dapi and two cell lines were compared in systems. According to results, it was observed that 3D cell culture environment in chip provides more in-vivo like environment with less reagent consumption and cell viability is not correlated only with drug uptake.Master Thesis Development of Antibacterial Polymer Based Nanocomposite Materials(Izmir Institute of Technology, 2015) Abatay, Ezgi; Arslanoğlu, Alper; Tanoğlu, MetinHuman beings are often infected by microorganisms such as bacterium, mold, yeast, virus, etc. in the living environment. It became a requirement and a necessity to create sterile fields in areas. Composite stones are one of the main materials that can be used for the contact surfaces in indoor and outdoor places due to their being of highly resistant to abrasives, chemicals and impacts. Research has been intensive in antibacterial material containing various inorganic substances. The aim of this thesis is investigating the antibacterial effect of inorganic substances such as silver, zinc oxide, calcium oxide, titanium oxide and magnesium oxide on stone products. This study also deals with the silver doped zinc oxide powder and their antibacterial efficacies. Stone product is formed of mainly two type compound which are quartz aggregates as reinforced and filler and thermoset polyester resin as matrix. The manufacturing process begins with selection of raw quartz materials. They are crushed and blended in the ratio of 90 % quartz aggregates to 10% polyester matrix and other additives such as antibacterial agent, pigment. These united constituents are used for production of composite stones by applying those combined vacuum, vibration and pressing processes which are named as vibropress, simultaneously. Following it, they are subjected to surface preparation and polishing processes. In this study, mechanical, thermal, and morphological properties of the particles, polyester matrix and stone product were investigated. Antibacterial efficacies of these were investigated based on colony-count method against gram negative (E.coli) and gram positive (Bacillus subtilis) bacteria. Silver-containing stone samples showed best antibacterial property about ninety-nine percent reduction.Master Thesis Test of Biomaterials in Biological Systems(Izmir Institute of Technology, 2001) Sudağıdan, Mert; Güneş, HaticeCeramic, metallic, polymeric and composite materials are generally used as biomaterials in order to improve human health. In addition to desired mechanical properties of biomaterials, biocompatibility is important in the treatment or replacement of body parts. Prior to the introduction of new biomaterials to the market, detailed biological tests are carried out to prevent any undesired side effects in the body. Both in vitro and in vivo tests are applied initially which is followed by the evaluation with clinical trials of the biological safety and performance.The aim of this study was to examine some biomaterials in biological systems.For this purpose, the effects of ceramic, metallic, polymeric and ceramic composite materials with different chemical and surface properties on the viability of peripheral blood mononuclear cells (PBMC) by trypan blue exclusion method, on the proliferation of PBMC by incorporation of bromodeoxyuridine to DNA in the proliferating cells and the activation of PBMC by MTT test were investigated. Furthermore, the effects of biomaterials on the secretion of proinflammatory cytokines (IL-1. and IL-6) from PBMC were examined by using ELISA kits. The alteration of conductivity and pH in different solutions were determined to elucidate dissolution properties of ceramic pellets. In addition, AMES test (Salmonella typhimurium reverse mutation test) for the determination of mutagenic potentials and the agar diffusion method for examination of anti-bacterial effects of biomaterials were applied. Adhesion of pathogenic bacteria to the surface of biomaterials was investigated by staining bacteria and examining under the optical microscope.Except for HA 800 C pellets, all samples showed positive results for biocompatibility compared to the controls without biomaterials. The dissolution of HA 800 °C pellets in the culture medium changed the ionic environment that led to a decrease in the viability, proliferation and activation of PBMC. However, BSA-coated HA 800 °C pellets increased the cell viability with respect to uncoated HA 800 °C pellets. Polished metallic samples and other metallic and polymeric samples showed high percent cell viabilities during 48 hours. After 72 hours, most probably because of released ions and particles to the environment, a decline in the viabilities of PBMC was determined. A negative correlation between increasing extract concentration and the cell viability was observed for all ceramic samples especially after 48 and 72 hours treatments.Cytokine secretion analysis after treatment of PBMC with biomaterials indicated that HA 800 °C, HA-Alumina 1250 °C and HA-Zirconia 1250 °C pellets led to a decrease in IL-1. secretion and BSAcoated HA 800 °C pellets in the presence of LPS. Stainless steel, titanium alloy and cirulene pellets caused low levels of IL-1. secretion. In addition, BSA-coated HA 800 °C pellets increased IL-6 secretion compared to uncoated pellets. In metallic samples, low IL-6 levels were obtained with and without LPS stimulation.Moreover, the proliferation and activation of PBMC in the presence of biomaterials were evaluated. HA 800 °C, HA-Alumina 1250 °C and HA-Zirconia 1250 °C samples had inhibitory effects on the proliferation of PBMC in the presence of Con A. In the activation of PBMC, HA 800 °C and HA 900 °C samples showed the lowest values at all incubation periods. Moreover, other ceramic samples showed lower cell activation than the control cultures after 48 and 72 hours treatments. In addition, the cell activation was observed at 24 hours after treatment with the ceramic extracts at low concentrations.Furthermore, investigation of dissolution properties of ceramic samples indicated that only HA 800 °C pellets led to significant increases in the conductivity of cell culture medium and deionized water. Moreover, a slight increase in the pH levels of solutions was obtained in the presence of HA 800 °C samples, but not in the other samples.Finally, none of the extracts of biomaterials in PBS had mutagenic effect on Salmonella typhimurium TA100 strain when they were compared to the mutagenic material (sodium azide) and the negative controls. In addition, all tested ceramic powders, ceramic pellets, metallic and polymeric materials had no anti-bacterial effects on both gram-negative strains (E. coli, P. aeruginosa, K. pneumonia, Proteus spp.) and gram-positive strains (S. aureus and S. pyogenes). In bacterial adhesion studies, it was found that surface roughness and other surface properties play important roles for attachment, adhesion and formation of biofilm by bacteria on the surface of material.As a result, although the ceramic samples sintered at low temperatures resulted in a decrease in the viability of PBMC, all tested biomaterials showed positive results for in vitro biocompatibility evaluation.Master Thesis Structural Investigation of Isopropanol and Alkaline Ph-Induced Trypsin Gel and Thin Flim and Its Biotechnological Applications(Izmir Institute of Technology, 2011) Karaçiçek, Bilge; Ceylan, ÇağatayTrypsin is a biologically and industrially important member of serine protease family. Gelation forms a three dimensional network structure through the interaction of protein molecules among themselves and also with the environment. The aim of the study was the investigation of structural and the functional properties of bovine pancreatic trypsin after gelation and aggregation processes. The phase behaviour of trypsin was determined for different protein concentration, NaOH concentration and CaCl2 concentrations. In addition, the effect of sucrose addition to gelation time was observed. Increasing protein concentrations caused a decrease in gelation time. Increasing NaOH concentrations resulted in a decrease in gelation time. In low CaCl2 concentrations gelation was observed but in high CaCl2 concentrations aggregation was observed. The gels were resolubilized in water. Trypsin stability studies showed that there was a nearly 50% specific activity loss after the gelation process. According to FTIR studies β–sheet structure in 1637 cm-1 band disappeared in trypsin gel and trypsin aggregates. Increases in α–helix structure in 1651 cm-1 in trypsin gel with sucrose and aggregate with and without sucrose were observed. Iodoacetamide was shown to delay in gelation indicating the importance of intermolecular disulfides in the gelation process. The QCM studies showed that the film formed after gelation had absorbtion ability to different gases (benzene, carbon monoxide, carbon dioxide, dichloromethane, hydrogen peroxide and propanol) and can be used for gas sensing purposes. GI-XRD studies showed that trypsin thin film did not contain any crystalline structures.