Prof. Dr. Ali Osman BELDUZ
Ali Osman Belduz received a Bachelor of Science in Biology in 1985 from Karadeniz Technical University. In the same year, he started to work as a research asssitant in the Department of Biology, Karadeniz Technical University. Then, he was awarded a scholarship to do studies in the area of Molecular Biology in the USA. His graduate work at Texas Tech University focused on interactions of cAMP with the cAMP receptor protein (CRP) of Escherichia coli. He completed his Doctor of Philosophy degree in Biology majoring Molecular Biology at Texas Tech University.
In February 1996, he was awarded a six month fellowship (NATO-B2) from the Scientific and Technical Research Council of Turkey to work in Prof. J.E.G. McCarthys laboratory in the National Centre for Biotechnology, Braunschweig, Germany. He has continued working on selenocysteine binding factor project for two more years at UMIST with a fellowship from the Wellcome Trust, UK.
He has published so many articles in peer-reviewed respective journals. He is acquainted with the many key techniques essential for studying gene cloning, expression, protein isolation, allosteric interactions, RNA-protein interactions, bacterial systematics, applied and environmental microbiology. He has not only run several research projects granted by TUBITAK, State Planning Organization (DPT) and Karadeniz Technical University Scientific Research Projects Unit as Principal Investigator but also involved in either reseacher or advisor in so many of projects as well.He has identified so many novel bacteria from different environments of Turkey; and characterized mostly thermostable enzymes from these novel microbial organisms; and improved the same characteristics of recombinant enzymes by mutagenesis; and involved in or supervised so many plant or animal systematics.
He has been a chairman for the Department of Biology and founding chairman of the Technology Transfer Office of Karadeniz Technical University.
His current research interests are;
1) Improving the stability and optimum temperatures of some lignolytic enzymes like xylanase, ferulic asit esterase, lignin peroxidase because longer thermal and pH stabilities and higher optimum temperatures decrease the running costs in enzyme utilizing industy like paper pulp processing.
2) Bioremediation and toxicity reduction of pulp and paper mill effluents by newly isolated indigenous microbial strains because the wastewater produced by industrial operations (i.e., pulp and paper industry) has a significant impact on the environment. Large amount of chemicals especially, sodium hydroxide, solvents and chlorine compounds during paper manufacturing processes are utilized and also consisting of potentially toxic chlorinated compounds, suspended solids, tannins, resin acids and sulphur compounds along with lignins are released. He aims to bioremediate and detoxify wastewater effluent from pulp and paper mills by screening and identifiying indigenous microbial strains.
3) Investigating inhibitors from either plants or natural products against replicative DNA polymerase and reverse transcriptases for the purpose of preventing or curing bacterial or viral infections because specific inhibitors against Gram (-) or Gram (+) bacteria or RNA viruses (i.e., HIV) may help preventing or curing of infections.
4) Exploring novel enzymes used for the economic production of Resistant Starch (RS) because Resistant Starch belongs to the group of dietary fibers with many health benefits prominently including the control of risk of diabetes mellitus type II, cardiovascular diseases, colorectal cancer, gastrointestinal abnormalities, and assist in metabolism of lipids and glucose. Resistant starch in comparisons to the traditional fibers has several dominant functional and physiological favorable characteristics.
5) Working out on the understanding of encapsulin structure and function and highlighting exciting open questions of physiological significance because the biological purpose of encapsulation in most organisms remains unknown.
6) Studying on industrial production of recombinant of plant plant-growth stimulator (Harpin) from Erwinia amylovora because it provides healtier and higher amount of yields by stimulating the growth and defense systems of so many plant species. It is non toxic and environmentaly friendly.
Dr. Ali Osman KILIC
Dr. Kiliç graduated from the Biology Department, Atatürk University, Erzurum, Turkey, in 1981. He completed his Master's degree in 1987 at Ondokuz Mayis University (Samsun, Turkey) and his doctorate in 1994 at Oklahoma State University in Microbiology and Molecular Genetic (Stilllwater, Oklahoma (USA). After two years of post-doctoral work at the University of Missouri-Kansas City (USA), he began his career as an Assistant Professor in the Department of Microbiology and Clinical Microbiology at the School of Medicine, Karadeniz Technical University in 1996 (Trabzon, Turkey). Dr. Kiliç was appointed as Associate Professor in 1998 and continued to work in the same institution until 2000. He took a Research Assistant Professor position at the Collage of Dentistry, University of Illinois at Chicago until 2005. In 2005-2010, he worked as a project manager of Healthcare Domain at Air Liquide, and in 2010-2012 he was a senior group leader at Biologics and Vaccines department of Pharmaceutical Product Development Company. Dr. Kiliç joined the Department of Medical Microbiology at School of Medicine, Karadeniz Technical University in 2013. Currently, he holds a faculty position as professor at the same institution. Dr. Kiliçs academic work focused mainly on multi-drug resistance, bacteriophage biology, biofilms and quorum sensing.
Dr. Remziye NALCACIOGLU
Remziye Nalcacioglu received her Bachelor of Science degree in Biology from Karadeniz Technical University, Trabzon, Turkey (1996). She received her Master of Science (MSc) degree in 1998 and her Doctor of Philosophy (PhD) in 2003 at Karadeniz Technical University, Faculty of Science, Department of Biology. She studied as research assistant at the same department during her MSc and PhD studies. She became an Assistant Professor in 2004, Associate Professor in 2011, and, Professor in 2017, at Karadeniz Technical University.
In 2002, she received a six month fellowship (NATO-B2) from the Scientific and Technical Research Council of Turkey to work in Virology Lab, Wageningen Agricultural University, The Netherlands. She studied in the same lab for 6 months with a grant from Wageningen Graduate School Production Ecology & Resource Conservation (PE&RC) and another 6 months from the Fellowship Programme of the Netherlands Ministry of Agriculture (IAC) in 2004. In 2008 she obtained a post doc grant from TUBITAK for 6 months.
She has published so many articles in peer-reviewed respective journals. She has experience on many techniques including gene cloning, expression, protein isolation, cell culture techniques, transcription factors, genomic, proteomic and bioinformatic. She has not only run several research projects granted by TUBITAK, State Planning Organization (DPT) and Karadeniz Technical University Scientific Research Projects Unit as Principal Investigator but also involved in either researcher or advisor in so many of projects as well.
Her scientific interest covers especially the understanding of the complexity of insect virus molecular structures and insect immunity against virus infections. Her current work focuses on iridovirus molecular biology, enhancing the infectivity of iridoviruses, gene function analysis.
Dr. Sabriye CANAKCI
Sabriye ÇANAKÇI received a Bachelor of Science in Biology in 1993 from Karadeniz Technical University. In 1994, she started to work as a research assistant in the Department of Biology, Karadeniz Technical University. She completed her Doctor of Philosophy degree in Biology majoring Molecular Biology at Karadeniz Technical University.
She has published so many articles in peer-reviewed respective journals. She is acquainted with the many key techniques essential for studying gene cloning, expression, protein isolation, allosteric interactions, RNA-protein interactions, bacterial systematics, applied and environmental microbiology. She has not only run several research projects granted by TUBITAK, and Karadeniz Technical University Scientific Research Projects Unit as Principal Investigator but also involved in either researcher or advisor in so many of projects as well.
She has identified so many novel bacteria from different environments of Turkey; and characterized mostly thermostable enzymes from these novel microbial organisms;
and improved the same characteristics of recombinant enzymes by mutagenesis.
Her current research interests are;
1) Improving the stability and optimum temperatures of some lignolytic enzymes like xylanase, ferulic asit esterase, lignin peroxidase because longer thermal and pH stabilities and higher optimum temperatures decrease the running costs in enzyme utilizing industry like paper pulp processing.
2) Bioremediation and toxicity reduction of pulp and paper mill effluents by newly isolated indigenous microbial strains because the wastewater produced by industrial operations (i.e., pulp and paper industry) has a significant impact on the environment. Large amount of chemicals especially, sodium hydroxide, solvents and chlorine compounds during paper manufacturing processes are utilized and also consisting of potentially toxic chlorinated compounds, suspended solids, tannins, resin acids and sulphur compounds along with lignins are released. She aims to bioremediate and detoxify wastewater effluent from pulp and paper mills by screening and identifying indigenous microbial strains.
Dr. Zihni DEMIRBAG
He received his Bachelor degree of Science in Biology from Fırat University, Elazığ, Turkey (1986). He assisted with teaching and research at Karadeniz Technical University, Trabzon, Turkey (1986-1987). He went to Texas Tech University, Lubbock, TX, USA, in 1988, and completed his Doctor of Philosophy in Biology, emphasizing microbiology, in May, 1993. He had been a teaching assistant at Texas Tech University, taught in General Microbiology Laboratory. He became an Assistant Professor in 1993, Associate Professor in 1996, and, Professor in 2002, at Karadeniz Technical University.
He had a 4-month post graduate research support from UNESCO on the baculovirus expression vector system at Wageningen Agricultural University, The Netherlands, 1995. He had a 4-month post graduate research support by OECD on the analysis of the potential immediate-early promoter sequences of iridovirus, Texas Tech University, Department of Biology, Lubbock, TX, USA, 1999. He also associated with researches on the molecular aspects of poxviruses as a visiting professor for one year at Department of Molecular Genetics and Microbiology, School of Medicine, University of Florida, Gainesville, FL, USA, 2004. He has been working on the molecular aspect of insect viruses.
He heads a well-equipped microbiology and molecular biology laboratory deals with insect pathogens. Over the past two decades, his research group has focused on studies on the biology and biotechnological applications of insect pathogens (viruses, bacteria, fungi, protists, nematodes) determined from soil samples and dozens of insects distributed in Turkey.
His current work focuses on the detection, isolation and characterization of the viruses infecting noxious insects. He is also interested in understanding the molecular mechanisms and intracellular components involved in the virology of the large dsDNA genome insect viruses including baculoviruses, iridoviruses and poxviruses specifically focusing on virus-host interactions, transcriptional regulation, DNA replication, genomics, proteomics, viral protein functions, localizations and interactions.
Insect viruses are used as microbial control agent for insect pest management purposes, as laboratory research tools for production of recombinant proteins and for protein display, and as potential vectors for human gene therapy. For these reasons, he has been focusing on the molecular biology of three type species of different groups of insect viruses including baculovirus, iridovirus and entomopoxvirus. They are Autographa californica nuclear polyhedrosis virus (AcNPV), Chilo iridescent virus (CIV) and Amsacta moorei entomopoxvirus (AMEV).
Dr. Ahmet YASAR
Our work is based on methodology. In these studies, it is aimed to produce alternatives to the methods used both in analytical field and synthesis field. Developed methods are published in various journals. It is also aimed at marketing the output and products obtained. For this purpose, a company was established in 2014.
Our company has developed up to 4 valuable chemicals and is ready for sale. The products we develop are products that are used in Chemistry, Health Sciences and Biotechnology.
The first product we developed is a dye used for imaging DNA and Polymerase Chain Reaction (PCR) devices. Ethidium bromide and Sybrgreen are used as an imaging DNA dyes. Ethidium bromide is the most commonly used dye. Because it is soluble in water and easy to use. But it's a very cancerous chemical. Even breathing is very dangerous. Sybrgreen is a water-insoluble dye that is difficult to use and dissolves in DMSO. It is both very expensive, so it is not very preferred. The paint we have developed is a safe dye.
Our second product is fingerprint detection paint on non-porous surfaces used safely. This study was carried out with the cooperation of Trabzon Security Directorate Police Station. The body traces developed after the Super Glu method applied to the non-porous surfaces were observed with visible light and fluorescent light in the staining with solution prepared with the staining agent. This dyestuff can be used instead of Rhodamime 6G and Ardrox dyestuffs. The Rhodamine 6G method should be carcinogenic, non-inhaled and not exposed to the skin. Edema in the lungs, red mite effects may appear with effects on the mucous membrane of the eyes, throat and nasal respiratory tract and gastrointestinal system.
The Ardrox method has central nervous system and neural effects in the respiratory system. Causes redness and flaking on skin. When taken in high doses, loss of consciousness, convulsions and respiratory arrest were observed. There have been many cases of sudden deaths when they were pulled out.
The Ninhydrin method applied to porous surfaces and the super glu method applied to nonporous surfaces are the most used methods in the Fingerprint Development Laboratory which are sensitive to old traces. Our dye is still a safe dye. it analyses is done. Another feature of the paint we develop is the ability to observe body traces both in visible light and in fluorescence light.
Our third product is an alternative acid-base indicator to the litmus paper, which is a commonly used acid-base indicator in laboratories. Litmus paper is one of the acid-base reagents used in chemistry. It is used to distinguish acids and bases in solutions. Litmus is red when it comes in contact with acid, and blue when it comes in contact with base. In the acid-base indicator developed by our company, yellow is obtained by acid solution and orange by base solution.
Dr. Hacer MURATOGLU
She graduated Department of Biology at Karadeniz Technical University in 2002. She performed a PhD study at the Laboratory of Virology at Karadeniz Technical University, and defended her thesis about Amsacta moorei entomopoxvirus (AMEV) in 2010. She performed a recombinant AMEV lacking protein kinase gene within the scope of doctoral thesis, and compared it with the ancestral virus. Because protein kinase genes of AMEV coded regulator enzymes of the other viral proteins, she is working about these important genes for insect control of AMEV by molecular techniques since that time. She is interested in genes encoding viral adhesion proteins, viral matrix proteins, and immunogenic virus proteins, and producing monoclonal antibodies against viral proteins as well as protein kinases.
She is continuing her career Department of Molecular Biology and Genetic (MBG) at same University. She is serving as vice president of department of MBG.
She is interest in Entomopathogens, Molecular virology, Viruses, Entomopoxviridae, Insect control, Vaccine development, Biotechnology.
Dr. Cihan INAN
He received his Bachelor degree of Education in Biology from Karadeniz Technical University, Trabzon, Turkey (2010). He received his Master degree of Molecular Biology and Genetics from İstanbul University, İstanbul, Turkey (2010-2012). For his master thesis titled Proteomic Analyses in Yellow Rust Resistant Wheat (Triticum aestivum L.) he worked on a COST project by TUBITAK MAM Genetic Engineering and Biotechnology Institute. After that he received his PhD degree of Biology from Karadeniz Technical University, Trabzon, Turkey (2012-2017). In his PhD thesis he worked on Functional and Structural Analysis of Amsacta moorei entomopoxvirus Putative Glycosyltransferase Gene (AMV248) as a part of TUBITAK 1001 project executed by Professor Demirbag. He became an Assistant Professor in 2017, at Karadeniz Technical University, Faculty of Science, Department of Molecular Biology and Genetics.
His current work focuses on insect viruses especially large dsDNA genome instect viruses such as poxviruses and baculoviruses.
Insect virus-host cell attachment & entry mechanisms: Viruses use different attachment and entry mechanisms depending on hosts. His researches focused on determining attachment proteins and entry mechanisms using Amsacta moorei entomopoxvirus (AMEV) genome information. For this purpose he is especially focused on attachment proteins AMV248 and AMV217 and also entry fusion complex.
Genome analysis & bioinformatics: As a member of Demirbag research group, he is aimed to illuminate viral genome sequences retrieved by their group. For this purpose he is especially focused on Baculovirus genomes.
Proteomics: To understand functions of proteins he is focused on prediction of 3D structure of proteins, generating mutations and virus-ligand, ligand-macromolecule molecular docking experiments.
Cell culture techniques: While AMEV can be propogated in cell culture he is interested in generating recombinant viruses lacking some important proteins, adding some genes for expanding virus host spectrum and using virus as viral therapy vector.
Also he is interested in mammalian cell culture and applications.
Dr. Gokhan YILDIZ
My primary research interest is identification of molecular biological, genetic and epigenetic alterations during development and progression of liver cancer; and development of novel diagnostic and therapeutic approaches for liver cancer through targeting these altered molecular processes.
So far, we have successfully determined a diagnostic molecular gene signature test, which is able to distinguish non-tumour cirrhosis and early liver cancer with high accuracy (Yildiz, G. et al., 2013). We have also identified mutation frequencies of human telomerase reverse transcriptase (hTERT) gene promoter mutations, which are the most common mutations in liver cancer, using human DNA samples from three different continents and in vitro samples (Cevik, D. et al., 2015). In addition, we have determined novel molecular players responsible for high chemotherapeutical resistance of liver cancer cells (Ferroudj, S. et al., 2016) and a novel anti-cancer small molecule for the selective therapy of liver cancer (Mustufa, M.A. et al., 2016).
I also perform research studies on identification of genetic and biological mechanisms of inherited rare diseases, as my recently emerged secondary research interest, since I have joined Karadeniz Technical University.
Dr. Tuba DINCER
I did my PhD at Bilkent University, Molecular Biology and Genetics department. During my PhD studies, I analysed the functions of the nuclear matrix protein C1D. In an attempt to identify C1Ds function, I have employed the yeast two-hybrid assay to screen a B-lymphocyte cDNA library to reveal the interacting proteins with C1D. As a consequence of this screen, we found that most of the isolated cDNA clones encode mainly proteins involved in DNA recombination, DNA repair, and transcription. We chose one of the proteins involved in DNA double strand break and V(D)J recombination and performed functional assays to understand the biological significance of this interaction (Erdemir T. 2002; Journal of Cell Science 115, 207-216). The second part of my PhD project was based on another approach to identify the biological function of C1D. Because of the high homology between yeast and mammalian C1D proteins, S. cerevisiae was used as a model organism to reveal the function of C1D gene. C1D gene was knocked-out in yeast and the phenotypic and functional consequences of disruption of the yeast C1D gene was analysed (Erdemir T. 2002; Molecular Microbiology, Volume 46, Issue 4, Pages 947-957). We established a novel in vivo assay to analyse the efficiency of homologous recombination in yeast. During my PhD studies I became familiar with yeast based techniques, recombinant DNA technology and protein assays.
I did my post-doctoral studies in Samuel Lunenfeld Research Institute, Toronto, Canada, in a TGFβ signalling lab under the supervision of Prof. Dr. Jeff Wrana. During my post-doctoral studies, I worked on projects that analyses the role of TGFβ signaling on heart development, metastasis and cytokinesis (von Both I. 2004,Developmental Cell Volume 7, Issue 3, Pages 331-345) ( Viloria-Petit AM. 2009, Proc Natl Acad Sci U S A. Volume 106 Issue 33, pages14028-33).
When I came back to Turkey, I joined to Medical Biology team in KTÜ Medical Faculty. In our department, my colleagues have expertise in genetic linkage analyses and they used to associate the genes responsible from rare diseases. Here, I combine my background that based on cell signalling and identification of protein functions with their expertise in molecular genetics. Since I have started, we have established a functional laboratory for analysis of proteins, RNA and cellular functions such as cell cycle, apoptosis, cell signalling and transcription activation etc. In Turkey, there are not so many labs that connect genetic studies with functional assays. Human Genome Project is ended. Now we know the genes but we dont know the function of proteins they encode. In our department, first we associate the gene with a disease and then we try to identify the function of the product of this gene. Basically, we try to find answers to questions such as why mutation on this gene cause the disease, what are the cellular events underneath and what can be the solutions. We cant find the cure to treat diseases if we dont know its molecular basis. Therefore, our ultimate goal is to understand the function of disease associated gene. By this way, it will be possible to design therapeutic approaches. Recently, we published a paper which summarizes our scope (Dinçer T., 2017, Eur J Hum Genet. 2017;25(10):1118-1125). In this paper, we identified a novel mutation in PLK4 gene which is associated with Seckel syndrome and we suggested a novel function of PLK4 protein in DNA damage response.
Dr. Ugur UZUNER
The long term goal of Uzuner lab is to develop and provide the large-scale production of solid, cost-effective and high-demand industrial bio-products which are applicable in pharmacy, medicine, agriculture, bioremediation, food industry and biofuel bioprocesses. The major research initiatives focus predominantly on the development of potential recombinant drugs, enzymes, proteins, cosmetics and anticarcinogenic monoclonal antibodies.
Among ongoing research projects of Uzuner lab, one foremost direction is homology modeling of biotechnologically crucial enzymes such as xylanases, laccases, alkaline proteases, polyphenol oxidases, and peroxidases and engineer them for enhanced thermostability and application-oriented pH improvements. We do perform in silico comprehensive and residue-based 3D structure analyses of enzymes of interest in order to establish information-driven and cost-effective enzyme engineering surveys. The engineered recombinant biocatalysts are then integrated into various expression and production systems like E. coli, different yeast; Saccharomyces cerevisiae, Pichia pastoris and fungal hosts; Trichoderma reesei and Aspergillus niger. In other words, the enzymes of interest are engineered through rational design and supporting computational analyses for enhanced characteristics which make them more desired and applicable in industrially crucial processes.
The second direction of Uzuner lab is to perform large-scale and low-cost production of cosmetics ingredients, effective molecules, anticarcinogenic, value-added peptides and proteins in various microalgae hosts. We routinely perform nuclear transformation and molecular analysis of industrially essential model microalgae strains such as Chlamydomonas reinhardtii, Chlorella vulgaris, C. sorokiniana, Dunaliella salina and similar. Key and promising large projects are available for interested researchers.
The third direction of Uzuner lab is to develop biologically useful and low-cost biocontrol agents against plant pathogens such as bacteria, fungi and insects. We currently examine the development of highly robust biological control agents against fungal biotrophs causing powdery mildew and downy mildew diseases on corylus nuts; Corylus avellana and its close relatives.
The fourth immense and pivotal direction is to foster the bioremediation of waste waters from various power plants such as textile factories, heavy metal mining, olive oil production and paper pulp bleaching systems. We further focus on developing the biologically resist microorganisms to break down the instantly released municipal waste waters, lessen the toxic effects of heavy metals, alleviate environmental pollution and integrate multiple processing systems to efficiently produce byproducts, green fuels, electricity and biologically applicable organic manures out of such processes.