TÜBİTAK Support for GTU Academics
January 3, 2024-Office of Press and Public Relations
The scientific evaluation results of the TÜBİTAK-ARDEB 2023 2nd Term 1001 Projects have been announced.
The Scientific and Technological Research Council of Turkey (TÜBİTAK) has revealed the recipients of support within the framework of the "1001-Scientific and Technological Research Projects Funding Program" for the 2nd term of 2023. Six projects from Gebze Technical University (GTU) have been entitled to receive scientific support and it has been decided that the other six projects can apply without waiting for the next term.
The academics from GTU whose projects have been decided to receive scientific support, along with project details, are as follows:
Dr. Abu Musa MD Talimur Reza from the Department of Molecular Biology and Genetics, Faculty of Science at GTU, leads the project titled "Effect of Targeted tRNA Manipulation to Control the Expression of MYC, an 'Undruggable' Proto-Oncogene and Master Transcription Factor."
Project details: Ribosomes, which collaborate with different transfer RNA (tRNA) molecules, play a role in protein synthesis. If we consider ribosomes as factories for protein production, then tRNAs should be thought of as suppliers of raw materials (amino acids) for protein synthesis. In other words, messenger RNA (mRNA) molecules are deciphered by ribosomes with the help of tRNAs carrying anti-codons to produce proteins. There are unique tRNAs for each codon (a three-nucleotide sequence representing a specific amino acid). If specific tRNA molecules corresponding to a particular codon are not available, decoding the codon's message becomes impossible, and the protein synthesis process is hindered. In fact, a single amino acid can be represented by multiple codons. However, all codons representing an amino acid are not used with equal frequency in mRNAs encoding proteins: a specific mRNA encoding a protein may use some codons abundantly while using other codons very rarely or not at all. This phenomenon is known as codon bias.
In the proposed research, codon bias is planned to be used as an advantage to control the expression of genes encoding proteins that are difficult to target or 'undruggable.' The target gene in this study is MYC, the main transcription factor and the most important proto-oncogene discovered to date (over 50% of cancers show overexpression of the MYC oncogene). Interestingly, despite tremendous efforts to control it, MYC continues to be an undruggable gene due to unique features such as the lack of binding sites for conventional small molecules, lack of accessibility for antibodies, and unique nuclear localization.
In this proposed project, the aim is to use codon bias to control the expression of MYC, which is an undruggable gene. Specifically, the availability of the most frequently used anticodon tRNAs for deciphering MYC mRNA will be examined. According to our analysis, tRNA-Ser-GCT and tRNA-Gln-CTG are two excellent candidate tRNA isoacceptor families, corresponding codons of which make up ~10% of the MYC mRNA molecule, much higher than the average usage of these codons in other genes. As mentioned earlier, specific anticodon tRNAs are suppliers of specific amino acids. Therefore, limiting the presence of an anticodon tRNA will restrict the availability of that specific amino acid in mRNA molecules that have used the corresponding codons. This will eventually disrupt the synthesis of the associated protein(s). The plan is to limit the availability of tRNA-Ser-GCT and/or tRNA-Gln-CTG to restrict the expression of MYC. This approach is expected to be highly effective: scarcity leads to the downfall of the most dependent. Here, MYC is the most dependent due to the frequent usage of codons corresponding to tRNA-Ser-GCT and tRNA-Gln-CTG.
Dr. Hülya Akdemir-Koç from the Department of Molecular Biology and Genetics, Faculty of Science at GTÜ, leads the project titled "Production and Characterization of Complex Anthocyanins as Natural Food Dyes through Metabolic Engineering Pathway in Escherichia coli Cultures."
Project details: Today, the food industry is actively seeking natural pigments that can be used as alternatives to synthetic dyes. Anthocyanins, due to their coloring properties and beneficial effects on health, emerge as the strongest candidates to replace synthetic dyes. In fermented beverages like wine, the condensation of anthocyanins with various microbial metabolites results in the formation of pyranoanthocyanins. When looking at the colors of widely occurring natural pigments, blue-colored pigments are rare. Therefore, the production of new, natural blue colorants is considered a priority for the food industry. Within the scope of this proposed project, the aim is to design a production model for the microbial synthesis of blue-colored portisins and red-orange-colored vitisins. The pyranoanthocyanin molecules we plan to produce have a more stable structure than anthocyanin precursors, and there is no literature on the microbial-based production of blue-colored portisin anthocyanins to date. Furthermore, this project will serve as an excellent example of a microbial co-culture-based approach for the production of complex natural products like pyranoanthocyanins, which do not originate from a linear metabolic pathway.
Dr. Sadiye Velioğlu from the Institute of Nanotechnology at GTU, leads the project titled "Investigation of the Separation Potentials of Mxene Membranes Specific to the Paint and Pharmaceutical Industries for Economic Growth and a Sustainable Environment."
Project details: The release of significant amounts of organic solvents used in various chemical processes in the petrochemical, pharmaceutical, paint, food, and paper industries poses a major threat to the environment and living organisms. Organic Solvent Nanofiltration (OSN) membranes for the purification and recovery of organic solvents have demonstrated their potential, especially in the paint and pharmaceutical industries, over the past few years. The paint industry, being the largest user and emitter of organic solvents, has started incorporating OSN-focused membrane technology to both generate profits and minimize environmental damage. The pharmaceutical industry, which holds the pulse of the economy, has also begun to prefer OSN membranes in recent years due to their low energy consumption and high selectivity in obtaining high-value products that need to be separated from organic solvents. Membranes synthesized from inorganic materials, especially those in the form of two-dimensional (2D) nanosheets, hold great promise for OSN technology. This is because their ultra-thin thickness results in low mass transfer resistance, leading to high permeability, and their size-selective interlayer distance contributes to high separation efficiency. The performance of the MXene family, a 2D nanomaterial discovered in the last decade, in purifying organic solvents has been shown to be superior to other existing 2D nanomaterials through limited studies. The primary goal of this project is to purify Ti3C2Tx from the rapidly advancing MXene family, which has found numerous applications, for the separation and purification of paints and drugs from organic solvents, and to determine the performance of solvent recovery. The project's findings, particularly the discovery of an OSN membrane with superior separation performance, will contribute to the development of both OSN membrane technology and the industries using this technology, such as the paint and pharmaceutical industries. This contribution will play a crucial role in making the environment and the economy more sustainable.
Dr. Hilal Yılmaz, a postdoctoral researcher at the Department of Environmental Engineering at GTU, leads the project titled "Investigating the Effect of Recombinant Cell and Gene Augmentation for Bioremediation of PET Polymer Degradation."
Project Details: This project involves the development of recombinant cells for the degradation of PET (polyethylene terephthalate) waste and conducting research on the behavior of these recombinant cells in their natural environment.
The increasing global plastic pollution is considered a serious threat to the environment and biodiversity in recent times. It is known that there is a significant amount of plastic, with 399,000 tons, including 69,000 tons as microplastics, in the oceans alone, causing the death of thousands of animals each year. The burning of plastics also releases more toxic products such as dioxin furan, mercury, and polychlorinated biphenyls.
Bioremediation, which involves the removal of leaking oil, various toxic pollutants, or heavy metals from the environment, is a widely accepted and cost-effective environmentally friendly approach globally. An approach that includes the inoculation of microorganisms involved in bioremediation in the contaminated area has gained prominence recently. Researchers have identified the mechanism of PET degradation by microorganisms, and Ideonella sakaiensis has been documented in the literature as the microorganism that performs PET degradation most rapidly. I. sakaiensis has the potential to break down PET waste causing widespread environmental pollution by producing valuable monomers with its PETase and MHETase enzymes.
Within the scope of the project, effective microorganisms that can be used for the removal of persistent plastics known in nature will be obtained. Additionally, important information will be obtained about the natural behaviors of plasmids and the impact of gene augmentation on bioremediation.
Dr. Abdulkadir Koçak, from the Department of Chemistry, Faculty of Science at GTU, leads the project titled "Development of Calculation Methods for Binding/Solubility Free Energies and Other Physicochemical Properties Using Artificial Neural Networks in Drug Design."
