FACULTY OF ARTS AND SCIENCESDEPARTMENT OF BIOLOGICAL SCIENCES: BIOLOGY/MOLECULAR BIOLOGY & GENETICS


Research

    Research at the Department of Biology, METU


    In this era of specialization, the METU Biology Department is unique in providing excellence in a broad and comprehensive approach towards biological research.

    The faculty, graduate students, and undergraduates carry out research encompassing a wide array of disciplines ranging from molecular biology and genetics to biomaterials and tissue engineering, nanotechnology, microbiology, immunology and vaccine development, molecular biophysics, ecology, evolutionary biology and conservation. Collaborative national and international networks, both within the Department and Turkey and internationally, allow for the sharing of ideas and technology, thereby greatly enhancing research potential and productivity in our country.

    Research areas include the following:


    Aquatic Ecology and Limnology 

    Research in aquatic ecology and limnology focuses on the impact of hydrology, nutirents and climate change in ecology of shallow lakes. Long-term bio-monitoring and paleoecology using multiple proxies (including cladocere, pigments, diatoms, and plant macro-fossils) to focus on temporal resolution, to enhance spatial resolution snap-shot sampling with space time substitute have been commonly utilized to understand the effects of multiple stressors on ecology of Turkish shallow lakes. In-situ mesocosms and laboratory experiments have been undertaken for hypothesis testing to improve our understanding. Whole catchment and lake basin analyses and modellings to understand the tight links between land use and water quality have also been undertaken. Restoration of shallow lakes using such as biomanipulation is also within main research interest that Lake Eymir restoration through biomanipulation has been undertaken to develop understanding how efficient the method is in Mediterranean climatic regions.

    The Limnology Laboratory is fully equipped for analyzing physical, chemical, biological and peleoecological constituents in lake water samples. Furthermore, permanent facilities for mesocosms experiments with 16 tanks are also available. The Limnology laboratory has undertaken research through several EU-FP and TUBITAK funded large projects.

    Contact: Dr. Meryem Beklioğlu 

    www.limnology.bio.metu.edu.tr

     

    Biochemistry

    Current research in this field is concentrated on the purification of enzymes of medical and industrial importance, enzyme kinetics, enzyme structure and function, properties of conjugation enzymes, membrane proteins; protein-protein, hormone-receptor and drug-DNA interactions. 

    Biochemical and genetic studies on the mechanisms of the regulations of the enzymes of xenobiotic metabolism: CYPs, GSTs, FMO and NATs, and also on antioxidant enzyme systems, oxidative stress, drug metabolism, molecular pharmacology, medicinal plant-drug interactions, genetic polymorphisms of enzymes and various disease relations are studied with recent techniques in well equipped laboratories.

    Contacts: Dr. Orhan Adalı and Dr. Tülin Güray

    Biomaterials

    The studies include the design and preparation of biomaterials, materials for application to humans. These involve biodegradable and biostable implants, drug delivery systems and most importantly, tissue engineered products. Nano and micro sized particles are being developed for use in delivery of growth factors, anticancer and other bioactive agents. Liposomes are a part of this nano/microparticle group and most recently they were designed for delivery of agents for the treatment of damaged skin and also as light-sensitive release systems for subcutaneous use. Construction of tissue substitutes by "tissue engineering" approach involves use of animal and human cells and among the tissues studied in the group are bone, cartilage, meniscus, small diameter blood vessels, oral mucosa and peripheral nerve. Novel techniques like rapid prototyping, electrospinning and microCT are being used in the construction and characterization of these constructs.

    Contact: Dr. Vasıf Hasırcı

    http://biomat.metu.edu.tr/

    http://biomaten.metu.edu.tr/

    Cancer Biology

    In Gündüz’s lab the molecular mechanisms of drug resistance against chemotherapeutic agents, reversal of resistance by means of chemical agents, by gene silencing or by targeting of cancer drugs through nano carriers are studied.

    Contact: Dr. Ufuk Gündüz

    In the Erson Lab the primary interest is in identifying mechanisms that lead to the transformation of normal cells into cancer cells. Genomic instability is a common characteristic of breast cancers and such chromosomal instability regions harbor copy number alterations of coding and non-coding genes including microRNA genes. Thus, the research in our laboratory seeks to reveal how such specific oncogene and tumor suppressor candidates may contribute to the breast cancer pathogenesis.

    Contact: Dr. A. Elif Erson-Bensan

    http://users.metu.edu.tr/erson/

    Cancer is a multistep process and in addition to genetic mutations and DNA damage, an inflammatory milieu often leads to its progression. The focus of Banerjee Lab is on inflammatory pathways that lead to the development of colorectal cancer. Our research emphasizes on bioactive lipids and enzymes of the arachidonic acid pathway and their interplay with the inflammatory transcription factor nuclear factor kappa B and its target proteins. For our latest publications and open positions, please visit our webpage.

    Contact: Dr. Sreeparna Banerjee

    http://users.metu.edu.tr/banerjee/

    Conservation Biology

    The Biodiversity and Conservation Lab carries out research on a wide range of topics, from population ecology to phylogenetics and spatial ecology, but with a strong conservation perspective. The species we focus on are usually either under threat, in conflict with humans or intensively managed due to their economic importance. A noninvasive DNA lab, GIS and RS capabilities, and field equipment are available at the lab.

    Contact: Dr. Can Bilgin

    http://users.metu.edu.tr/cbilgin/

    Research in Togan’s lab include i) methods in priority setting for the conservation of domestic animals on the basis of their genetic diversity, utility, endengarement and ii) monitoring the conserved flocks of domestic animals to maximize the efficiency of conservation efforts are under consideration.

    Contact: Dr. İnci Togan

    Research in the Kence Lab includes the conservation of several threatened and endangered wild mammal species of Turkey.  Some of the studies in this area are (i) the assessment of genetic variation within and among populations, (ii) management of genetic variation through captive breeding and reintroduction programs, (iii) identification of genetic structure of natural and managed populations and (iv) phylogenetic analysis through the use of molecular markers (mostly mtDNA genes and satellite sequences). 

    Contact: Dr. Aykut Kence

    Ecological Genetics

    The primary area of research in the Kence lab is the identification of genetic and morphological variation within and among natural populations and to give ecological and evolutionary explanations for the responsible factors. In this area, our research generally centres on the honey bee (Apis mellifera L.) races found in Turkey. We are using a variety of molecular techniques (allozymes, RAPDs, Inter SSRs, SNPs and microsatellites), geometric morphometrics and perform field experiments including common garden tests on honey bees. We are currently trying to breed Muğla honey bees for hygienic behavior. A second research theme in this area focuses on some fish species, particularly on ray-finned fishes (Pseudophoxinus spp.). 

    Contacts: Dr Aykut Kence

    Evolutionary Biology

    There are multiple labs working on wide array of research topics in evolutionary biology. 

    Evolutionary Genetics 

    We explore variation, selection, adaptation,  genetics and evolution of  stress responses in general. In particular, gene-environment interactions are being tested in insect model organisms,  Musca domestica L.,  and Apis mellifera L., in the form of resistance to toxic chemicals, resistance mechanisms to pests and pathogens at various levels; molecules, individual, and population levels. Enzymes, mtDNA, microsatellites, and more recently SNPs are used for detection of variation and its consequences on the success of these invertebrates. Application of these genetic tools to vertebrate animals such as Gazella was also done for detection of variation and conservation.  

    Contact: Dr Meral Kence

    Immunology

    Research in immunology laboratory focuses on activators of the innate immune system including Toll-like receptor (TLR) ligands and their therapeutic applications. Particularly, different strategies to improve the delivery and boost the activity of TLR ligands and small-molecule immune modulators are investigated. 

    Contact: Dr. Mayda Gürsel

    Mathematical and Theoretical Biology

    Mathematical models and computer simulations are used to address the open questions at the interface of ecology and evolutionary biology.

    Contact: Dr. Ayşegül Birand

    http://users.metu.edu.tr/birand/labpage/Labs_Home.html

    Microbial Ecology

    Research in the microbial ecology laboratory involves the studies on bacterial populations of soil and aquatic environments.

    Contact: Dr. Ayşegül Gözen

    Molecular Biology of Archaea

    Our research has primarily focused on molecular mechanisms underlying protein thermostability; functional, structural and regulatory analyses of molecular machines (i.e., proteasome and molecular chaperonines, small heat-shock proteins); improving stability and activity of enzymes with potential medical uses through rational design and using molecular chaperones; molecular basis of stress response in thermoacidophilic archaea, Thermoplasma volcanium as the model organism.

    Contact: Dr. Semra Kocabıyık

    Molecular and Cellular Biophysics

    In Severcan’s lab research includes; lipid-lipid, protein-lipid and drug-lipid interactions in biological membranes, structure-function and stability of proteins,  investigation of the molecular basis of diseases (cancer, diabetes, obesity and neurological disorders)  and therapeutic and protective role of drugs and chemical agents, Medical screening and diagnostics by vibrational spectroscopy and microscopic imaging,  Application of biophysical techniques such as vibrational spectroscopy Electron Spin Resonance and Fluorescence  Spectroscopy and calorimetry on different branches of biology such as  ecotoxicology, microbiology and food area. These studies are performed on animal/human tissues and membranes, body fluids, and cells. 

    Contact: Dr. Feride Severcan 

    http://www.biophysics.metu.edu.tr

    Research carried out in Son’s lab include Fluorescence microscopy, FRET studies and protein-protein interaction by Bimolecular fluorescence complementation (BiFC) techniques can be applied to biological samples.  

    Contact: Dr. Çağdaş D. Son

    http://users.metu.edu.tr/cson/

    Molecular Microbiology, Microbial Genetics and Proteomics


    Proteomics of Bacillus subtilis to further analyze the role of dipeptide antibiotic biosynthesis in quorum sensing global regulation/Proteome dynamics of heavy metal stress response in Phanerochaete chrysosporium/Proteomics and immunoproteomics of Bordetella pertussis/Development of DNA and subunit vaccines against pasteurollosis/Pathway engineering to improve clavulanic acid and cephamycin C biosynthesis in Streptomyces clavuligerus and transcriptional regulation of cephamycin C biosynthetic gene cluster are among the particular interests of our working team. 

    Contact: Dr Gülay Özcengiz

    http://molmicrobio.metu.edu.tr

    Molecular Endocrinology

    The dynamic regulation of hormone target tissue physiology relies on transient fluctuations in the levels of endocrine messengers, called hormones. These messengers are sensed by target organs to regulate a complex array of convergent and divergent signaling pathways which orchestrate cellular proliferation, differentiation and death of cells. Molecular endocrinology laboratories are using multidisciplinary approaches that include biochemistry, molecular, cellular, and tumor biology to better understand the physiology and pathophysiology of target tissues.

    Research in the Molecular Neuroendocrinology Lab is focusing on studying cellular mechanism of processing and trafficking neuro/hormones to understand human diseases related to defects in hormone and neuropeptide targeting, synaptic transmission, neurodegeneration, diabetes, and obesity. Emerging studies suggest that neuroendocrine and hypothalamic changes in these diseases; therefore, studies addressing the points using experimental models such as cell lines, primary cell cultures, and animal models and material from patients are ongoing in the research group.  Techniques used in the laboratory include immunocytochemistry, ELISA, Western blots, HPLC, RT-PCR, basic molecular biology and immunohistochemistry.

    Contact: Dr Tülin Yanık. 

    Research in Nuclear Hormone Receptor laboratory is focusing on the structure-function of nuclear receptors, intracellular signaling routes, mechanisms of gene expressions as well as on the development of novel receptor-based modalities for the prevention and treatment of target tissue cancers.  

    Contact: Dr. Mesut Muyan 

    Nanobiotechnology R&D Lab

    Our lab conducts basic and applied research and development activities in the following areas: 

    Biosensing technologies: Application of nanobiotechnological approaches in molecular diagnosis and disease treatment. Gold nanoparticles, DNA chips (Bio chips), lab on a chip applications, array platforms, aptamer technologies and nucleic acid based diagnostic technologies are among our research interest.

    Renewable energy: Energy production form biological and solar systems are the main focus of research with particular emphasis on algal systems. 

    Contact: Dr Hüseyin Avni Öktem 

    Neurobiology

    Neurobiology Laboratory is applying multidisciplinary approaches (behavioral, morphological, pharmacological and molecular) to the studies on brain and behavior. The main research areas are: Experimental Brain Research, Psychopharmacology, and Behavioral Neuroscience. Research topics include studies on the molecular basis of individual variation in episodic-like memory in a random animal population; the variation in learning skills and strategies as well as morphological and biochemical correlates of learning and memory during the postnatal development and aging; studies on alcohol teratogenity and on the  effects of adult alcohol intake and alcohol withdrawal; and recently, validation of animal models of human neurological diseases such as Parkinson’s disease. The techniques used include a variety of behavioral tasks aided by a computerized video-tracking system (Etho-Vision 3.1, Noldus Technology), Stereotaxic apparatus (Stoelting Co) for subcortical lesions or intracerebral drug infusions, Leica DM4000 microscope with digital DM4000 camera and MicroBrightField Stereo-Investigator software enabling stereological/morphometric studies of the brain tissue. The laboratory has a long-lasting cooperation with GATA, Medical Pharmacology and Embryology and Histology Departments, and overseas with the School of Medicine, Center for Neuroscience, UC Davis, USA.

    Contact: Dr. Ewa Doğru

    Pharmaceutical Biotechnology Laboratory

    The aims of the Pharmaceutical Biotechnology laboratory, incorporating yeast genetics and molecular biology and mammalian cell culture technology are the following. Cloning of genes coding for human therapeutic proteins. Construction of stable mammalian and yeast cell lines for permanent gene expression. Scale up of production of the cell-expressed human therapeutic proteins in bioreactors and fermentors and their purification. Quality control of human medicinal products derived by recombinant DNA technology according to European Pharmacopoeia regulations. Discovery and development of natural antitumor agents. Isolation and characterization of novel antifungal proteins with little or no toxicity toward mammalian cells and a low tendency to elicit resistance.

    Contact: Dr. Fatih İzgu

    Plant Biotechnology

    Genetic manipulation of crop plants via Agrobacterium, particle bombardment and electroporation techniques. Target plant species include tobacco, legumes and cereals.

    Contacts: Dr Meral Yücel and Dr Hüseyin Avni Öktem

    http://plantbiotech.metu.edu.tr/

    Plant Genetics 

    Molecular genetics of trees and crops, conservation of genetic resources of crop and tree species, population genetics of forest trees, molecular breeding of forest trees (especially poplar and willow), organogenesis and somatic embryogenesis in forest trees, molecular phylogenetics-speciation and ancient DNA in plants are studied in fully equipped DNA and Plant tissue culture laboratories.

    Contacts: Dr. Zeki Kaya and Dr. Sertaç Önde

     

    Plant Systematics Laboratory

    The laboratory carries out research in the fields of plant taxonomy & systematics, morphology & anatomy, ecology and conservation biology. The current research activities include the following topics: systematics of the tribe Triticea (Gramineae) in Turkey; taxonomic revision of Plumbaginaceae in Turkey; the revision of Salvia (Labiatae) in Turkey and ecosystem modeling by means of GIS.

     

    Contact: Dr. Musa Doğan

    Population Genetics

    In Togan’s population genetics laboratory, admixture rates among the peoples of Anatolia, evolutionary history of Anotolian shepherd dogs and Turkish native sheep breeds have been studied by using molecular genetics and bioinformatics tools. With the newly acquired ancient DNA laboratory, time and direction of human/ domestic animal migrations are estimated more precisely. Other topics of interest have been the evolutionary history of fish (brown trout, sword fish) and speciation within the European anchovy.  

    Contact: Dr. İnci Togan