Research
The projects listed below are conducted by our team.
Investigation of Cell Viability and Localization in Chitosan-Coated Carbon Quantum Dots Synthesized from Turkish Coffee Waste (TUBİTAK 2209-A)
Project Leaders: Selcen Umay Barutçugil, Elif Demir
Consultant: Res. Asst. Beste Dipçin, Assoc. Prof. Bükem Tanören
Quantum dots (QDs) are semiconductor nanocrystals which can be organic (carbon-based) or inorganic based. They have unique properties such as good chemical and photostability and autofluorescence. QDs have low toxicity, biocompatible types named carbon dots (CDs). The most preferred carbon dots are carbon quantum dots (CQDs) which have tunable size. These CQDs can be synthesized sustainably from waste; this synthesis from waste for recycling purposes is called green synthesis.
In literature, the microwave-assisted pyrolysis technique is used to synthesize CQDs from biowastes, such as coffee beans, powder, or fruit. However, in this project, the microwave-assisted pyrolysis technique is going to be used to synthesize CQDs from Turkish coffee ground waste for the first time in our knowledge. These synthesized CQDs are going to be coated with chitosan for enhancing cellular uptake since it is a cationic and biodegradable natural polymer. Even though studies regarding chitosan coating CQDs in the literature, coating CQDs synthesized from Turkish coffee ground waste with this aim has not been observed. In Turkey, Turkish coffee is one of the most consumed beverages, due to that, lots of Turkish coffee ground waste are produced, that’s why the lack of using this waste as a raw material in the green synthesis of CQDs and its use in cytotoxicity research has been identified beneficial.
In this project, chitosan-coated CQDs will be used which will be synthesized from Turkish coffee ground waste with different roasting levels. It is aimed to investigate physical and chemical characteristics of the obtained materials, as well as the effect of chitosan coating of the CQDs on the viability and localization of cancer and healthy cells.
Within this scope, CQDs which will be synthesized from different roasting levels of turkish coffee ground waste will be characterized via fluorescence microscopy, UV-VIS spectrophotometry, FT-IR, DLS, TEM, SEM, EDS, Zeta potential. According to the result of this characterization, the most optimum roasting level will be selected for chitosan-coating and in vitro testing.
To investigate the effect of chitosan-coating for cell viability and localization, chitosan-coated or not-coated CQDs are going to be used in HepG2 and MCF-7 cell lines, as the target cells, and HEK293 as control cells. For cell viability, all cell lines are going to be treated with different concentrations of chitosan-coated or not-coated CQDs for 24h. According to IC50 results, which will be detected with CCK-8 assay, the cellular localization of the CQDs will be assesed with a fluorescent microscope for different incubation times (0, 1, 2, 3, 4, 6, and 24h).
This project aims to contribute to the literature by evaluating the results obtained within the scope of the project regarding the synthesis of Turkish coffee grounds waste through recycling and its presentation as a new raw material for green coffee grounds synthesis. Furthermore, it is believed that the materials to be produced in this project have the potential to contribute to the national and international market as products due to their high potential for use in many application areas such as bioimaging, biosensors, optoelectronic devices, clean energy sources, etc.
Investigation of the Effect of PEG Molecular Weight on Cell Viability and Cellular Localization on PEGylated Carbon Quantum Dots (TUBİTAK 2209-A)
Project Leaders: Selin Tan, Onur Mohamed Haniffa
Consultant: Res. Asst. Beste Dipçin, Assoc. Prof. Bükem Tanören
Quantum dots (QDs) are semiconductor nanocrystals that are known for their distinctive optical and electronic properties. These QDs can either be organic or inorganic-based. When compared with inorganic quantum dots, carbon quantum dots (CQDs) are less cytotoxic, more biocompatible, and exhibit long-lasting fluorescence, which makes them highly attractive for imaging in biological systems.
Polyethylene glycol (PEG) is a widely used polymer, particularly in biomedical applications. Thanks to its hydrophilic nature, PEG is highly soluble in water and is considered biocompatible. It is commonly used in drug delivery systems and bioimaging. The molecular weight of PEG varies broadly with its chain length (approximately 200–10,000,000 g/mol). Previous studies have shown that PEGylation can alter the physicochemical properties of inorganic or organic materials, as well as their cytotoxicity and intracellular localization, depending on PEG molecular weight. However, how the physicochemical characteristics of PEGylated CQDs change with different PEG molecular weights—and how this, in turn, affects cell viability (cytotoxicity) and cellular localization—has not yet been investigated, representing a gap in the literature.
To address this gap, in this project CQDs will be coated separately with PEG of different molecular weights and evaluate how PEG molecular weight influences the materials' physicochemical properties, cell viability, and intracellular localization.
CQDs will be synthesized from sulfuric acid and acetone using the hot-bubble synthesis (HBBBS) method. The CQDs will then be individually coated with four different PEGs that vary in molecular weight (PEG-2, PEG-4, PEG-6, and PEG-10). The resulting materials will be characterized by zeta potential analysis, FT-IR, UV–Vis spectroscopy, DLS, SEM, TEM, EDS, and fluorescence microscopy. In addition , the characterized materials will be applied to HEK293 cells, and the impact of coating with PEG of different molecular weights on CQD cytotoxicity will be evaluated using the CCK-8 assay, while intracellular localization will be examined by fluorescence microscopy.
The outcomes of this project are expected to help identify the most suitable PEG molecular weight for PEGylation in CQD–based applications, thereby contributing to the literature. Moreover, given the high potential of the developed materials for use in a range of applications—particularly bioimaging—they may also have promise for commercialization in national and international markets.
Classification and Segmentation of Nasopharyngeal Carcinoma Using Machine Learning Models from Head and Neck Computer Tomography Images (Acibadem University General Research Projects Support Program)
Project Leaders: Bora Güvendiren
Consultant: Lect. PhD Seda Nilgün Dumlu, Prof. Ata Akın, Prof. Dr. Enis Özyar, Assoc. Prof. Bükem Tanören
In this work, a machine learning algorithm is created from radiomics features with the intent of classifying and segmenting NPC tumor from computer tomography (CT) images. CT images of 73 patients were preprocessed and prepared before tumor classification and segmentation, then the performance of the model was evaluated by comparing the results with those identified by radiation oncologists. After obtaining the results, on average, 95% accuracy score was obtained for the NPC classification and a 0.75 Jaccard score was obtained for the segmentation parts of the algorithm. The algorithm was concluded to be capable of classifying the NPC tumor from the CT images, but lacked performance when it came to segmentation.
Investigation of Antimicrobial Effects of Different Quantum Dots on Standard Microorganism Strains Alongside Laboratory Collection Strains and Imaging of Them with Fluorescent Microscope (TUSEB-B)
Project Leaders: Res. Asst. Beste Dipçin, Bora Güvendiren
Consultant: Assoc. Prof. Bükem Tanören, Prof. Dr. Zühtü Tanıl Kocagöz, Assoc. Prof. Kadriye Kızılbey, Asst. Prof. Özgül Gök Özatay
In this project it is aimed to synthesize doped, and sustainable carbon quantum dots (from coffee and tea wastes) and silver indium sulfate quantum dots to test their potential as antimicrobial agents in both standard bacteria strains and multidrug-resistant bacteria strains (ESKAPE microorganisms) alongside standard and multidrug-resistant fungi. Also, to understand how quantum dots present antimicrobial effects, molecular dynamic (MD) simulation of the microorganism membrane and their interaction with the quantum dots will be done.
Carbon Quantum Dot Synthesis With Hot Bubble Synthesis (HBBBS) Method and Its Characterization (Acibadem University General Research Projects Support Program)
Project Leaders: Res. Asst. Beste Dipçin, Bora Güvendiren
Consultant: Assoc. Prof. Bükem Tanören, Assoc. Prof. Kadriye Kızılbey, Dr. Selçuk Birdoğan
This project is about synthesizing carbon quantum dots (C-dots) from 98% sulfuric acid, pure acetone, and sodium hydroxide with a newly developed method, hot bubble synthesis (HBBBS) method, and understanding the chemical and physical properties of C-dots alongside characterizing them by UV-Vis Spectrophotometry, Fourier Transform Infrared Spectroscopy (FT-IR), Transmission Electron Microscope (TEM), Scanning Electron Microscope (SEM), Dynamic Light Scattering (DLS), Zeta Potential analysis, and fluorescence microscopy.
Formation of TTR Gene Targeted Nanoparticles Investigating the Effect of Them on Transthyretin Protein Production and Cell Viability Alongside Observation of Their Cell Localization Utilizing Confocal Microscope (TUSEB-A)
Project Leader: Res. Asst. Beste Dipçin
Consultant: Assoc. Prof. Bükem Tanören, Assist. Prof. Özgül Gök Özatay
Genetic transthyretin amyloidosis (hATTR) is a genetic rare disease that occurs because of mutation(s) in the TTR gene that has become endemic in a few countries and causes the protein structure of transthyretin to deteriorate. This disease causes a complex, multifunctional system disorder that affects many systems, especially the nervous and cardiovascular systems. In the treatment of the disease, liver transplantation, transthyretin protein stabilizing drugs, and gene-targeted drugs are used. Gene silencing using the RNA interference (RNAi) mechanism is one of the most preferred methods in gene-targeted drug delivery systems. Gene therapies based on gene silencing by RNA interference hold great potential for the treatment of hATTR. Within the scope of this project, conjugation of PEG, HIV-1 Tat peptide, and carbon quantum dot to chitosan polymer, physical encapsulation of the obtained coating to the TTR gene-targeted siRNA molecules into the formed chitosan complex, characterization and optimization of the nanoparticle, measurement of cytotoxicity of the resulting nanoparticle in cell lines are aimed. It is planned to observe the cell localization utilizing a confocal microscope and to investigate the changing transthyretin (TTR) protein levels in the cells with Protein Immunoblot (Western Blot). In addition, stabilization and drug release analyzes of the nanoparticle will be performed. Obtained nanoparticles’ analysis and characterization will be done with Fourier Transform Infrared Spectrophotometer (FT-IR), Transmission Electron Microscope (TEM), Scanning Electron Microscope (SEM), Zeta analysis, Nanodrop, agarose gel electrophoresis Dynamic Light Scattering Spectrometer (DLS) and Liquid Chromatography - Mass Spectrometry - Mass Spectrometry (LC-MSMS) instrument. With the findings obtained in the project, it is aimed to produce a gene therapy that can be used in the treatment of hATTR.
Investigation of the Effects of the PEGylation of Carbon Quantum Dots and Peptide Interactions on the
Cell Viability, Apoptosis, and Cellular Localization (Acibadem University General Research Projects Support Program)
Project Leader: Res. Asst. Beste Dipçin
Consultant: Assoc. Prof. Bükem Tanören, Assoc. Prof. Kadriye Kızılbey, Assist. Prof. Nazlı Keskin, Assist. Prof. Özgül Gök Özatay
The goal of this project is to synthesize biocompatible bioimaging agents (carbon quantum dots) and to observe how PEGylation and peptide interactions effect the cell toxicity, cellular localization of the carbon quantum dots, and their effects on apoptosis which is a programmed cell process. The theranostic potential of bare and PEGylated/peptide physically absorbed carbon quantum dots will be tested in breast cancer and human embryonic kidney cells.
Development of a C-Shaped Transcranial Magnetic Stimulation Device and Magnetic Targeted Drug Delivery Combined Therapy in Animal Models of Neurophysiological Disorders
Project Leaders: Şevval Yıldız, Mert Parmaksızoğlu, Batuhan Güneş
Consultants: Prof. Dr. Jakub Antczak, Assoc. Prof. Bükem Tanören, Assist. Prof. Melis Yavuz, Dr. Ferit Tiryaki
Epilepsy significantly diminishes patients' quality of life, and preventing seizures remains challenging. This project aims to enhance antiepileptic drug delivery systems and Transcranial Magnetic Stimulation (TMS), both of which show promise but face clinical challenges. Antiepileptic drugs can prevent seizures by regulating neurons, but conventional delivery methods often lack efficiency, fail to target specific areas, and can accumulate in the blood-brain barrier, causing toxicity. TMS, which uses magnetic fields to prevent seizures, also faces issues with precise targeting and efficacy, and lacks standardized methodologies for in vivo and in vitro experiments.
The main objective of this project is to develop three types of drug-based nanoparticles for in vitro testing. These nanoparticles will be evaluated with a C-coil-based TMS device developed during the project. The goal is to increase the efficacy of TMS treatment and establish a novel therapeutic approach that reduces the effects of epileptic seizures. The effectiveness of the new TMS device and antiepileptic drug therapy will be tested through cell migration experiments, ensuring their potential for future research and clinical applications.
Investigation of The Effects of L-Arginine on Atherosclerotic Plaque Patients' Saphenous Vein and IMA Grafts
Project Leaders: Res. Asst. Beste Dipçin, Ahmet Turan Keskintaş, Fatemeh Ataei
Consultants: Assoc. Prof. Bükem Tanören, Prof. Dr. Murat Uğurlucan
In this project, it is aimed to investigate the effects of L-arginine on the morphology and the collagen content of the internal mammarian artery (IMA) and saphenous vein grafts that were collected from atherosclerotic plaque patients utilizing a cryostat microtome, fluorescence microscope, and a scanning acoustic microscope (SAM). Also, it is aimed to check how L-arginine affects the elemental composition of the grafts utilizing the EDS analysis. It is believed that with the outcomes of this project, L-arginine's potential as a new treatment option for the disease can be enlightened and can lead to further scientific research.