AREAS OF RESEARCH


In this era of specialization, our department is unique in providing excellence in a broad approach to biological research.

Biochemistry


Biochemical Toxicology • Molecular Biochemistry

Faculty

Nülüfer Tülün Güray
Biochemical Toxicology

Research is based on biochemistry, focusing on metabolism and biochemical toxicology. The effect of different molecules on the regulation of biochemical pathways and the cytotoxic effects of drugs and related compounds are the main study topics. Recent research focuses on the effect of different molecules regulating biochemical pathways and the potential use of various nanoparticles in cancer cells.


Orhan Adalı
Molecular Biochemistry

The characterization of the microsomal enzyme systems metabolizing drugs, environmental chemicals, and carcinogens; The clarification of the possible role of flavin monooxygenases in structure and function by employing molecular biology and genetic techniques; Cytochrome P450 (CYP) and flavin monooxygenase (FMO) specific reactions; Identification of proteins in different species and tissues by using antibodies; Multiple Sclerosis and Vitamin D relation; Genotyping and phenotyping of CYP and FMO isoenzymes, paraoxonase, TPMT in human with different disorders; diabetes, stroke, multiple sclerosis and cancer (leukemia); Drug metabolism and disease relation. Pharmacogenetics.

Biotechnology


Nanobiotechnology

Faculty

Hüseyin Avni Öktem
Nanobiotechnology

Homeland Security Applications: Development of new generation portable and fieldable bio-detection platforms and early warning systems. Decontamination Technologies: Development of antimicrobial surfaces for healthcare and security applications. Biosensing Technologies: Immuno and nucleic acid-based detection systems, bioreporters, whole-cell biosensors. Paper Biosensors/Biodetectors: Development of single-use and low-cost paper biosensors for POC applications.

Cancer Biology


Breast Cancer • Colorectal Cancer and Metabolism • Precision Medicine and Drug Resistance • Signal Transduction and Cancer

Faculty

Ahmet Acar
Precision Medicine and Drug Resistance

Precision Medicine and Drug Resistance in Cancer Laboratory aims to understand the underlying mechanisms of drug resistance in cancer. Our goal is to study how cancers evolve and develop resistance to therapies. Acar Lab is interested in developing quantitative 2D/3D co-culture systems with stromal fibroblasts. We leverage single-cell barcoding and next-generation sequencing technologies to delineate actionable mechanisms of drug resistance. To better address patient-specific drug resistance, we establish ex vivo Patient-Derived Organoids (PDOs) as a preclinical model system. Lastly, as a team, we are working on developing and optimizing deep learning models for histopathological WSIs to enable the acquisition, management, and extraction of the information that is crucial to decision-making processes in cancer.


Ayşe Elif Erson Bensan
Breast Cancer

Breast cancer is a major health problem causing significant mortality and morbidity. Our primary focus in the lab is to understand why and how normal mammary cells transform into cancer cells. To begin understanding this complex question, we are interested mainly in mRNAs' 3'-UTRs (untranslated regions). We combine in silico and experimental tools to discover and characterize unconventional isoforms with alternative mRNA 3'-ends in cancer transcriptomes. These isoforms may have functional consequences at the protein level and may explain unknown cases of oncogene activation.


Mesut Muyan
Signal Transduction and Cancer

Our research interest is directed at the understanding of the molecular mechanisms of estrogen hormone action. The flow of estrogen information is primarily conveyed by the transcription factors, estrogen receptors (ERs) α and β. The estrogen-bound ERs primarily mediate many nuclear events that result in gene expressions. Utilizing a multidisciplinary approach that includes biochemistry, molecular, cellular, and tumor biology, we aim to define how estrogen-mediated gene expressions result in changes in the phenotypical features of cells.


Sreeparna Banerjee
Colorectal Cancer and Metabolism

Deregulation in metabolic pathways contributes significantly to cancer progression by meeting the energy needs of a rapidly growing cell population and providing essential metabolites that can help the tumor cells cope with a rapidly changing microenvironment. Using wet lab and data mining, we aim to understand better signal transduction pathways related to enzymes of lipid, protein, and glucose metabolism pathways.

Computational Biology


Comparative and Evolutionary Biology

Faculty

Mehmet Somel
Comparative and Evolutionary Biology

Currently, our work is concentrated on ancient DNA and evolutionary genetics. That includes archaeogenomics of humans and domestic animals and population genomics. We work as part of the METU and Hacettepe Archaeogenomics Team. We have also done comparative genomics and transcriptomics studies, including mechanisms of brain aging, the evolution of aging, mechanisms of neurodegenerative disease, and comparative transcriptomics to study questions in evolutionary biology.

Ecology


Biodiversity Conservation • Ecology of Shallow Lakes • Terrestrial Ecology

Faculty

Cemal Can Bilgin
Biodiversity Conservation

Our laboratory conducts research on a wide range of topics, from population ecology to phylogenetics and spatial ecology. Combining work in the field and in the wet lab provides a better understanding of population-level processes. The species we focus on are usually either under threat, in conflict with humans, or intensively managed due to their economic importance. Recently, we have been utilizing modeling approaches to predict the impact of climate change on vulnerable species and on the protected area network in Turkey. A ringing station to study bird migration, a 60-hive strong apiary for bee research, and up to a hundred nest boxes on the campus grounds are managed to provide long-term data for analyses. We value collaboration with researchers elsewhere and encourage students to become independent and conscientious researchers.


Didem Ambarlı
Terrestrial Ecology

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Meryem Beklioğlu
Ecology of Shallow Lakes

Under the leadership of Prof. Meryem Beklioğlu, Limnology Laboratory explores the ecological structure and function of lake ecosystems and how they are affected by global changes. The research projects of the limnology laboratory are funded internationally (EU-Framework and Horizon 2020) and nationally. The impact of hydrological changes, global warming, and land use are investigated in shallow lakes using experimental and other ecological research approaches. Laboratory and on-site in-situ mesocosm experiments are commonly used to investigate ecosystem processes mechanically. The long-term ecological monitoring and paleoecological methods, which increase temporal resolution by combining the "space for time" method, which increases spatial resolution, are commonly employed in the Limnology laboratory. In all these different research approaches, all trophic groups, including microbial loop (bacteria, heterotrophic flagellate, ciliate), phytoplankton, zooplankton, aquatic plants, and fish biomass and diversity (species diversity, character diversity, functional diversity, etc.) are within the research scope our Limnology Laboratory.

Genetics and Epigenetics


Epigenetics and Cell Fate • Molecular Microbiology and Genetics • Plant Genetics

Faculty

Gülay Özcengiz
Molecular Microbiology and Genetics

Our current research has been focused on (i) Bacillus subtilis regulatory networks with particular involvement of bacilysin biosynthetic (bac) operon to analyse the role of dipeptide antibiotic bacilysin in quorum sensing global regulation, (ii) an integrative transcriptomic and proteomic analysis of an industrial clavulanic acid-overproducing Streptomyces clavuligerus in order to provide insights into the key control points as well as the rational engineering targets for further improvement of clavulanic acid production in this strain, and (iii) development of recombinant vaccines against certain animal and human pathogens, including Pasteurella multocida, Mannheimia haemolytica, Histophilus somni, Bordetella pertussis and SARS-CoV-2.


Nihal Terzi Çizmecioğlu
Epigenetics and Cell Fate

We are interested in the role of chromatin in regulating cell fate decisions. During embryonic development, the zygote undergoes numerous cell division and differentiation events, eventually forming the embryo. The gene expression processes accompanying embryonic development are regulated with high spatial and temporal precision. The chromatin environment affects the accessibility and the activity of target genes. Using embryonic stem cell lineage commitment as an in vitro model for cell fate changes, we are working on the role of chromatin in gene expression regulation. We aim to identify key gene expression pathways and mechanisms using molecular, transcriptomic, and proteomic approaches. Complementing wet lab work, we are also invested in bioinformatic approaches to analyzing and crossreferencing our high-throughput data.


Zeki Kaya
Plant Genetics

The main research activities focus on population genetics of trees, speciation, and evolution of plant species and ancient DNA studies related to crop domestication and evolution.

Immunology


Virology

Faculty

Banu Bayyurt Kocabaş
Virology

Our laboratory is interested in understanding the interactions between microbes and their hosts at the molecular and cellular levels, specifically in terms of the immune system. The first defense mechanism of the immune system is to recognize microbes and respond accordingly. This starts with discrimination of non-self from self. Some receptors, which are known as pattern recognition receptors (PRRs), can recognize patterns of molecules (ligands: PAMP) president in non-self. These receptors are highly regulated and controlled in terms of transcription and translation by different enzymes, proteins, and also post-translational modifications. In case of dysregulation, receptors can be activated by our own molecules and attack our body which can cause deterioration of cells, tissues, and failure of organs. Therefore, we aim to understand the mechanisms of activation, regulation, and control of PRRs and also use ligands in order to activate or suppress innate immunity against cancer, pathogen-induced or autoimmune diseases. Our interdisciplinary background helps us to modify these ligands using biotechnology to elevate the magnitude of the effectiveness of therapy.

Microbiology


Microbial Ecology • Molecular Microbiology and Genetics

Faculty

Ayşe Gül Gözen
Microbial Ecology

Heavy metal and antibiotic acclimation and adaptation of bacterial populations. Total molecular alterations in bacteria upon heavy-metal exposure. Relative expressions of resistance genes upon acclimation to above MIC stress conditions. Investigating gene expression in mutants obtained through UV-induced and spontaneous mutations. Ground stabilization using calcium carbonate precipitating bacteria. Impact of antibiotics on the cognitive abilities of mice through gut microbiota.


Gülay Özcengiz
Molecular Microbiology and Genetics

Our current research has been focused on (i) Bacillus subtilis regulatory networks with particular involvement of bacilysin biosynthetic (bac) operon to analyse the role of dipeptide antibiotic bacilysin in quorum sensing global regulation, (ii) an integrative transcriptomic and proteomic analysis of an industrial clavulanic acid-overproducing Streptomyces clavuligerus in order to provide insights into the key control points as well as the rational engineering targets for further improvement of clavulanic acid production in this strain, and (iii) development of recombinant vaccines against certain animal and human pathogens, including Pasteurella multocida, Mannheimia haemolytica, Histophilus somni, Bordetella pertussis and SARS-CoV-2.

Neurobiology


Molecular and Cellular Neurobiology • Neurobiology of Disease

Faculty

Erkan Kiriş
Neurobiology of Disease

Enhancement of neurotrophin signaling against neurodegenerative diseases. Neurotrophin signaling pathways are considered potential therapeutic targets in many neurodegenerative diseases, including Alzheimer's Disease, due to their roles in neuroprotection, synaptic plasticity, and neurogenesis. Originating from Dr. Kiris' work in Dr. Lino Tessarollo's lab (Neural Development Group at National Cancer Institute at Frederick, NIH, USA), which focused on the in vivo dissection of neurotrophin signaling pathways by targeting specific Trk intracellular domains (Kiris et al., J. Neurosci. 2014), we are interested in the modulation of Trk receptor-mediated signaling against the neurodegenerative process of the diseases.

The molecular mechanism(s) underlying the sex-specific differences observed in neurodegenerative diseases. Previous studies implicate that neurotrophin and estrogen signaling pathways may cross-talk and contribute to the sex-specific differences observed in various neurodegenerative conditions. Our research interests include studies to elucidate direct, functional, sex-specific, integrated effects of neurotrophin and estrogen signaling pathways in health and neurodegenerative diseases using human-induced pluripotent stem cell-derived neuronal models.

Botulinum neurotoxin (BoNT) research and drug discovery. BoNTs target motor neurons and cause the life-threatening disease botulism. Currently, there are no drugs to inhibit these toxins once they are internalized into motor neurons. We have previously established drug screening and experimentation systems using the mouse (Kiris et al., 2011, Stem Cell Research, Kota, et al., 2014, JoVE) and human motor neurons (Kiris et al., 2015, Neurotoxicity Research) derived from embryonic stem cells. In addition to the assay development, our work also focused on identifying mechanism-targeted compounds to identify novel BoNT inhibitors. Currently, we are interested in i) elucidation of critical molecular mechanisms in motor neurons involved in intoxication and recovery, ii) identification of mechanism-targeted compounds to identify novel leads that can be effective against BoNT serotypes responsible for human botulism, and iii) stem cell-based detection technologies for these toxins.


Tülin Yanık
Molecular and Cellular Neurobiology

The primary goal of the molecular and cellular neurobiology laboratory is to elucidate intracellular trafficking, processing, and secretion of neuropeptides and peptide hormones in neuronal cells in normal and disease states. Major areas of interest are understanding molecular mechanisms of psychotic drugs that cause obesity in psychotic patients and human mutations related to obesity.

Plant Biology


Molecular Plant Nutrition • Plant Genetics • Plant Molecular Biology • Plant Nutrition and Biofortification

Faculty

Emre Aksoy
Plant Nutrition and Biofortification

PNB research group works on the uptake, translocation, and signaling of micronutrients and biofortification of crop species. It is also specialized in developing stress-tolerant crops by molecular breeding and genetic engineering. The PNB applies novel genetic and molecular techniques to identify transcription factors, transporters, and gene networks related to stress tolerance in soybean, potato, wheat, quinoa, and Arabidopsis.


Seçkin Eroğlu
Molecular Plant Nutrition

Micronutrient malnutrition is the most widespread nutritional disorder. Micronutrient intake depends mainly on the micronutrient concentration and bioavailability of edible plant parts. We study how plants acquire, transport, and store micronutrients. To elucidate the genes involved in micronutrient homeostasis, we compare Arabidopsis thaliana plants with their mutants, focusing on iron, manganese, and zinc metals. The laboratory's ultimate goal is to contribute to the development of crops fortified with micronutrients to combat malnutrition.


Sertaç Önde
Plant Molecular Biology

Our laboratory has the infrastructure for research in plant tissue culture, plant phylogenetics and population genetics, plant physiology and gene transfer to plants, and recently bioinformatics.


Zeki Kaya
Plant Genetics

The main research activities focus on population genetics of trees, speciation, and evolution of plant species and ancient DNA studies related to crop domestication and evolution.

Structural Biology


Protein-Protein Interactions

Faculty

Çağdaş Devrim Son
Protein-Protein Interactions

Currently, our research focuses on identifying protein-protein interactions by quantitative Förster resonance energy transfer (FRET) measurements and fluorescence intensity ratio (FIR) analysis in live cells. We are interested in G-protein Coupled Receptor (GPCR) dimerization and the effects of post-translational modifications and ligand interactions on receptor dimerization.


Son Güncelleme:
30/12/2022 - 16:27