Academic degrees and work experience

Assoc. Prof. - Istanbul Technical University, Faculty of Science & Letters, Dept of Molecular Biology & Genetics, Istanbul, Turkey (May 2006-

Assist. Prof. - Istanbul Technical University, Faculty of Science & Letters, Dept of Molecular Biology & Genetics, Istanbul, Turkey (December 2001- May 2006)

Postdoctoral research associate – Division of Biochemistry, Biocenter, University of Basel,

Basel, Switzerland (2000-2001)

Research and teaching assistant – Institute of Biotechnology, Swiss Federal Institute of Technology, ETH-Zurich, Zurich, Switzerland (1996-2000)

Research and teaching assistant – Bogazici University, Dept. of Chemical Engineering, Istanbul, Turkey (1994-1996)

Ph.D. degree (Dr. sc. nat. ETH Zurich) -  Institute of Biotechnology, Swiss Federal Institute of Technology, ETH-Zurich, Zurich, Switzerland (2000)

M.Sc. degree -  Bogazici University, Dept. of Chemical Engineering, Istanbul, Turkey (1996)

B.Sc. degree -  Bogazici University, Dept. of Chemical Engineering, Istanbul, Turkey (1994)

B.Sc. degree (Double Major Program) -  Bogazici University, Dept. of Molecular Biology & Genetics , Istanbul, Turkey (1995)

High school education – Istanbul (Erkek) Lisesi (1983-1990)

Area of Interest

·         Evolutionary engineering of industrially important microorganisms

·         Investigation of the molecular mechanism of yeast (Sachharomyces cerevisiae) stress resistance, particularly heavy metal stress and industrially important stress types

·         Metabolic engineering and inverse metabolic engineering, systems biology

·         Molecular biomimetics, nanobiotechnology

·         Molecular medicine: investigation of the effects of ischemia-reperfusion and ischemic preconditioning of kidney on gene expression

·         Environmental biotechnology: biochemical storage and stress metabolism of activated sludge model organisms, polyhydoxyalkanoate production, identification of microbial communities using molecular methods 

Projects

·         Evolutionary engineering of industrial stress-resistant yeast Saccharomyces cerevisiae and characterization of the stress resistance mechanism at a molecular level, TÜBİTAK Career Project, 105T314, principal investigator, (May 2006-

·         Novel sustainable bioprocesses for the European colour industries, proposal number: 505899, European Union 6^th Framework Integrated Project (IP), SME 2, researcher, (2004-  

·         Production of nanotechnological functional materials using biomimetics, Turkish State Planning Organization (DPT), 2004K120540,researcher, (2004-

·         Directed evolution of industrially important microorganisms, Istanbul Technical University Research Funds, project no: 30108, principal investigator, (2002-2005) 

·         The effects of substrate composition and feeding patterns on biochemical storage, TUBITAK-YDABAG project no: 102Y060, principal investigator, (2002- 2005)

·         Investigation of the effects of stress conditions caused by heavy metals on the metabolism of activated sludge, TUBİTAK-YDABAG 102Y071, researcher, (2002-2005)

Publications  

A.  Papers in SCI- journals

·         Insel, G., Celikyilmaz, G., Ucisik-Akkaya, E., Yesiladali, K, Cakar, Z.P., Tamerler, C., Orhon, D. 2007. Respirometric evaluation and modeling of glucose utilization by Escherichia coli under aerobic and mesophilic cultivation conditions. Biotechnol. Bioengin. 96: 94-105.

·         Akar, A., Ucisik Akkaya, E., Yesiladali, S.K., Celikyilmaz, G., Ubay Cokgor, E., Tamerler, C., Orhon, D.,

      Cakar, Z.P. 2006. Accumulation of polyhydroxyalkanoates by Microlunatus phosphovorus under various

      growth conditions. J. Ind. Microbiol. Biotechnol. 33: 215-220. 

·         Cakar, Z.P., Seker, U.O.S., Tamerler, C., Sonderegger, M., Sauer, U. 2005. Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res. 5: 569-578.

·         Chatenay-Rivauday, C., Cakar, Z.P., Jeno, P., Kuzmenko, E.S., Fiedler, K. 2004.  Caveolae: biochemical analysis. Mol. Biol. Rep. 31: 67-84.

·         Kuzmenko, E.S., Djafarzadeh, S., Cakar, Z.P., Fiedler, K. 2004.  LDL transcytosis by protein membrane   diffusion. Int. J. Biochem. Cell Biol. 36: 519-534.

·         Fiaux, J., Cakar, Z.P., Sonderegger, M., Wuethrich, K., Szyperski, T., Sauer, U. 2003. Metabolic flux profiling of the yeasts Saccharomyces cerevisiae and Pichia stipitis. Eukaryotic Cell. 2: 170-180.

·         Maaheimo, H., Fiaux, J., Cakar, Z. P., Bailey, J. E., Sauer, U., Szyperski, T. 2001. Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional ¹³C labeling of common amino acids. Eur. J. Biochem. 268: 2464-2479.

·         Cakar, Z. P., Sauer, U., Bailey, J. E., Mueller, M., Stolz, M., Wallimann, T., Schlattner, U. 2000. Vacuolar morphology and cell cycle distribution are modified by leucine limitation in auxotrophic Saccharomyces cerevisiae. Biol. Cell 92: 629-637.

·         Cakar, Z. P., Sauer, U., Bailey, J. E. 1999. Metabolic engineering of yeast: the perils of auxotrophic hosts. Biotechnol. Lett. 21: 611-616.

B.  Proceedings / oral presentations in international conferences

·         Alkim, C., Yilmaz, B., Vata, C.K., Tamerler, C., Sarikaya, M., Francois, J., Benbadis, L., Cakar, Z. P. 2007. Riboflavin-producing cobalt-resistant Saccharomyces cerevisiae obtained by evolutionary engineering, 3^rd European Federation of Biotechnology Conference, Physiology of Yeasts and Filamentous Fungi (PYFF3), oral presentation, abstract book, page no: T38, June 13-16, 2007, Helsinki, Finland.

·         Akar, A., Ucisik Akkaya, E., Yesiladali, S.K., Celikyilmaz, G., Ubay Cokgor, E., Orhon, D., Tamerler, C.,

      Cakar, Z.P. 2004. Growth physiology and biochemical storage characteristics of Microlunatus phosphovorus , a model organism for activated sludge systems. Environmental Biotechnology-ESEB 2004, (editor: W. Verstraete), proceedings, page no: 737-740, April 25-28, 2004, Oostende, Belgium.

C. Proceedings / oral presentations in national conferences

·         Altintas, A., Alkim, C., Aloglu, T., Turanli, B., Yilmaz, B., Cakar, Z.P. 2007. The effects of Vitamin B and cultivation conditions on growth physiology and stress resistance of wild type and mutant yeasts, Molecular Biology & Genetics Student Congress, oral presentation, abstract book, page no: 22, September 8-11, 2007, Istanbul Technical University, Istanbul, Turkey.

·         Ucisik Akkaya, E., Akar, A., Celikyilmaz, G., Yesiladali, S.K., Ubay Cokgor, E., Tamerler, C., Orhon, D., Cakar, Z.P. 2004. Investigation of biochemical storage properties of Escherichia coli, a common activated sludge microorganism, Nature and Environment, 5^th National Ecology and Environment Congress, proceedings, page no: 459-466, October 5-8, 2004, Bolu, Turkey.

·         Birol, G., Cakar, Z. P., Onsan, Z. I., Kirdar, B. 1996. A study on the influence of substrate concentration in secretion of alpha amylase and glucoamylase separately or as bifunctional fusion proteins by yeast, 13^th National Biochemistry Congress (with international participation), Turkish Society of Biochemistry,    Antalya, Turkey.

D. Poster presentations (abstracts) in international conferences

·         Terzioglu, E., Kahveci, M.U., Cakar, Z.P., Selcuki, C. 2007. Computational conformational analysis of MXCXXC motif of ATX1 in Saccharomyces cerevisiae, Drugs Fut., 32 (Suppl. A): 6^th AFMC International Medicinal Chemistry Symposium, PB-44, Istanbul, Turkey. 

·         Kahveci, M.U., Terzioglu, E., Cakar, Z.P., Selcuki, C. 2007. Computational conformational analysis of REXLE motif of iron permease FTR1 in Saccharomyces cerevisiae, Drugs Fut., 32 (Suppl. A): 6^th AFMC International Medicinal Chemistry Symposium, PB-45, Istanbul, Turkey. 

·         Yilmaz, U., Alkim, C., Turanli, B., Tokman, N., Akman, S., Tamerler, C., Sarikaya, M.,  Cakar, Z.P.  2007. Evolutionary engineering for biomimetics: selection of chromium-resistant yeast under pulse stress conditions, abstract book, page no: P39, Molecular Biomimetics & Bionanotechnology-II, Protein-based Materials & Systems for Engineering & Medicine, International Workshop, May 23-25, 2007, Istanbul Technical University (ITU-MOBGAM), Istanbul, Turkey.

·         Yilmaz, U., Alkim, C., Turanli, B., Tokman, N., Akman, S., Tamerler, C., Sarikaya, M.,  Cakar, Z.P.  2007. Evolutionary engineering for biomimetics: selection of chromium-resistant yeast under continuous stress conditions, abstract book, page no: P40, Molecular Biomimetics & Bionanotechnology-II, Protein-based Materials & Systems for Engineering & Medicine, International Workshop, May 23-25, 2007, Istanbul Technical University (ITU-MOBGAM), Istanbul, Turkey.

·         Karabulut, C., Alkim, C., Tokman, N., Akman, S., Tamerler, C., Sarikaya, M., Cakar  Z.P. 2007. Evolutionary engineering of copper-resistant yeast under pulse stress conditions, 3^rd European Federation of Biotechnology Conference, Physiology of Yeasts and Filamentous Fungi (PYFF3), Abstract book, page no: P27, June 13-16, 2007, Helsinki, Finland.

·         Vata, C.K., Tektas, O., Yilmaz, B., Sachs, M., Akcetin, Z., Cakar  Z.P. 2007. Predominant effect of ischemic preconditioning on short-term reperfusion following ischemia, abstract book, page no: 294, abstract no: 70, II. Congress of Molecular Medicine, March 24-26, 2007, Istanbul, Turkey.

·         Tektas, O., Gursoy, G., Yuzuak, Z., Alkim, C., Ucisik-Akkaya, E., Vata, C.K., Cakar Z.P., Akcetin, Z. 2007. Gene expression patterns in rat kidneys upon ischemia-reperfusion, with ischemic and heat-preconditioning: a microarray and RT-PCR study, abstract book, page no: 296, abstract no: 73, II. Congress of Molecular Medicine, March 24-26, 2007, Istanbul, Turkey.

·         Turanli, B., Alkim, C., Tokman, N., Akman, S., Tamerler C., Sarikaya, M., Cakar  Z.P. 2006. Evolutionary engineering for biomimetics: selection of cobalt-resistant yeast under continuous stress conditions, Molecular Biomimetics & BioNanoTechnology, Protein-based Materials & Systems for Science & Technology, International Workshop, abstract book, page no: P37, November 12-14, 2006, Istanbul Technical University (ITU-MOBGAM), Istanbul, Turkey. 

·         Alkim, C., Turanli, B., Karabulut, C., Yilmaz, U., Tokman, N., Akman, S., Tamerler C., Sarikaya, M., Cakar  Z.P. 2006. Evolutionary engineering for biomimetics: selection of cobalt-resistant yeast under pulse stress conditions, Molecular Biomimetics & BioNanoTechnology, Protein-based Materials & Systems for Science & Technology, International Workshop, abstract book, page no: P2, November 12-14, 2006, Istanbul Technical University (ITU-MOBGAM), Istanbul, Turkey. 

·         Ergun, A., Basar, F., Yesiladali, S. K., Cakar, Z. P., Tamerler, C. 2006. Decolorization of textile dyes by the white-rot fungus Coriolopsis polyzona MUCL 38443, Oxizymes in Oeiras, 3^rd European Meeting in Oxizymes, abstract book, page no: P42, September 7-9, 2006, Oeiras, Portugal.

·         Alkim, C., Turanli, B., Karabulut, C., Yilmaz, U., Tokman, N., Akman, S., Tamerler C., Sarikaya, M., Cakar  Z.P. 2006. Evolutionary engineering of cobalt-resistant yeast under pulse stress conditions, ESBES 6, 6th European Symposium on Biochemical Engineering Science, abstract book, page no: 194, August 27-30, 2006, Salzburg, Austria.

·         Turanli, B., Alkim, C., Tokman, N., Akman, S., Tamerler C., Sarikaya, M., Cakar  Z.P. 2006. Evolutionary engineering of cobalt-resistant yeast under continuous stress conditions, ISEB ESEB JSEB 2006, International Conference on Environmental Biotechnology, , abstract book, page no: 48, July  9-13, 2006, Leipzig, Germany.

·         Toktay, B., Seker,U.O.S., Turanli, B., Asimgil, H., Keshavarz, T., Tamerler, C., Cakar, Z.P. 2005. Directed evolution of Ophiostoma piliferum for lipase production, 3^rd International Conference on Analysis of  Microbial Cells at the Single Cell Level, abstract book , page no: 78, PIV.22, Semmering, Austria. 

·         Aloglu, T., Tamerler, C., Sauer, U., Cakar, Z.P. 2005. Evolutionary engineering of osmotolerant Saccharomyces cerevisiae, 12^th European Congress on Biotechnology, Copenhagen, Denmark, J. Biotechnology, Vol. 118, Suppl. 1., S9.

·         Ucisik Akkaya, E., Ozturk, T., Ajredin, N., Celikyilmaz, G., Yesiladali, S.K., Tamerler, C., Orhon, D., Cakar, Z.P. 2005.The effects of anaerobic-aerobic cycles on polyhydroxybutyrate storage mechanism of Paracoccus pantotrophus, a model organism of activated sludge systems, 10. European Ecological Congress, abstract book, page no: 509, Kusadasi, Turkey.   

·         Seker,U.O.S., Akce, H., Tamerler, C., Sauer, U., Cakar, Z.P.  2004. High levels of trehalose in multiple-stress resistant Saccharomyces cerevisiae obtained by evolutionary engineering. PYFF 2 Meeting, Physiology of Yeasts and Filamentous Fungi, abstract book, page no: 111, March 24-28, 2004, Anglet, France.

·         Seker,U.O.S., Akce, H., Tamerler, C., Sauer, U., Cakar, Z.P.  2003. Directed evolution of multiple-stress resistant Saccharomyces cerevisiae. 11^th European Congress on Biotechnology, abstract book, page no: 102, August 24-29, 2003, Basel, Switzerland.

·         Toktay, B., Seker, U.O.S., Turanli, B., Keshavarz, T., Tamerler, C., Cakar, Z.P. 2003. Improvement of lipase production in Ophiostoma piliferum via evolutionary engineering and media optimization .11^th European Congress on Biotechnology, abstract book, page no: 97, August 24-29, 2003, Basel, Switzerland.

·         Ucisik Akkaya, E., Akar, A., Yesiladali, S.K., Celikyilmaz, G., Tamerler, C., Orhon, D., Cakar, Z.P. 2003. A physiological and morphological study on the growth and biochemical storage of activated sludge model organisms. 11^th European Congress on Biotechnology, abstract book, page no: 139, August 24-29, 2003, Basel, Switzerland.

·         Celikyilmaz, G., Akar, A., Yesiladali, S.K., Ucisik Akkaya, E., Yazgan Karatas, A., Cakar, Z.P., Orhon, D.,  Tamerler, C. 2003 The effects of heavy metal stress on the metabolism of various activated sludge bacteria. 11^th European Congress on Biotechnology, abstract book, page no: 139, August 24-29, 2003, Basel, Switzerland.

·         Chatenay-Rivauday, C., Cakar, Z. P., Kuzmenko, E., Jenoe, P., Fiedler, K. M. 2000. A complex of actin, caveolin-1, and dynamin in caveolae. Mol. Biol. Cell 11: 2000 Supp. S. The American Society for Cell Biology  (ASCB), Fortieth Annual Meeting, San Francisco, USA.

·         Cakar, Z. P., Sauer, U. 2000. Evolutionary Engineering of Multiple-Stress Resistant Saccharomyces cerevisiae. Biotechnology 2000, The World Congress on Biotechnology,  Berlin, Germany.

·         Chatenay-Rivauday, C., Cakar, Z. P., Buehler, H., Kuzmenko, E., Hristoskova, S., Fiedler, K. 2000. Caveolae: a multiprotein complex?, European Life Scientist Organisation (ELSO) 2000 Meeting, Geneva, Switzerland.

·         Cakar, Z. P., Sauer, U., Fiaux, J., Szyperski, T., Wuethrich, K., Bailey, J. E. 1999. Intracellular carbon flux analysis and metabolic engineering of yeast: the perils of auxotrophic hosts, VAAM (Vereinigung fuer Allgemeine und Angewandte Mikrobiologie) Conference, Jahrestagung, Goettingen, Germany.

E. Poster presentations (abstracts) in international conferences

·         Ucisik Akkaya, E., Celikyilmaz, G., Yesiladali, S.K., Tamerler, C., Orhon, D., Cakar, Z.P 2005. Investigation of growth physiology and storage characteristics of Escherichia coli, a common activated sludge microorganism, in a sequencing batch reactor. 14^th National Biotechnology Congress, abstract book, page no: 502, Eskisehir, Turkey.

·         Celikyilmaz, G., Yesiladali, S.K., Ucisik Akkaya, E., Akar, A., Yazgan Karatas, A., Ubay Cokgor, E., Cakar, Z.P., Orhon, D.,  Tamerler, C. 2004. The effects of heavy metals on the respiratory metabolism of Escherichia coli, 5^th National Ecology and Environment Congress, abstract book, page no: 159, October, 5-8, 2004, Bolu, Turkey.

·         Turanli, B., Toktay, B., Seker, U.O.S., Tamerler, C., Cakar, Z.P. 2003. Evolutionary engineering of stress resistance of industrially important microorganisms, 13^th Biotechnology Congress, abstract book, page no: 223, August 25-29, 2003, Canakkale, Turkey.

Courses taught

·         MBG 512 Mikrobiyel Metabolizma (Microbial Metabolism), Istanbul Technical University (ITU)

·         ENB 503E Metabolic Concepts in Environmental Sciences, ITU 

·         MBG 617 Biyoteknolojide Son Gelismeler (Recent Developments in Biotechnology), ITU

·         BIO 211E Cell Biology, ITU

·         BIO 321 Mikrobiyoloji (Microbiology), ITU

·         BIO 492E Graduation Project, ITU

·         MBG 535 Laboratuvar Arastirmasi (Laboratory Research), ITU

·         Tutorial: Introduction to Biology , Biocenter, University of Basel, 2000-2001

Administrative Responsibilities

·         Vice Chair, Dept. of Molecular Biology & Genetics, Istanbul Technical University, (December 2006-

·         Vice Director,  Istanbul Technical University, Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM)  (2004-December 2006)

·         Istanbul Technical University, Faculty of  Science & Letters, Double Major Program Commission Member  (2002-

·         Istanbul Technical University, Faculty of  Science & Letters, Internal and External Student Transfer Commission Member  (2005-

·         Istanbul Technical University, Dept. of Molecular Biology & Genetics, Strategic Planning Commission Member (2005-

·         Istanbul Technical University, Dept. of Molecular Biology & Genetics, Student Technical Training Commission Member (2003-2005)

Awards and Scholarships

·         Evolutionary engineering of industrial stress-resistant yeast Saccharomyces cerevisiae and characterization of the stress resistance mechanism at a molecular level, TÜBİTAK CAREER Project, 105T314, principal investigator, (May 2006-

·         Plastics Technology Research Development and Education Foundation (PAGEV), Plastics Technologies Research Honorable Mention Award, 2005.

·         Post-doctoral grant as research assistantship, the Swiss National Science Foundation, Biocenter (Biozentrum), University of Basel, 2000-2001.

·         Doctoral grant for Ph.D. study, as research and teaching assistantship, Swiss Priority Programme (SPP) in Biotechnology, ETH-Zurich, Institute of Biotechnology, Swiss Federal Institute of Technology, 1996-2000.

·         Doctoral grant for Ph.D. study in Germany, DAAD (German Academic Exchange Service), kindly rejected, 1996.

·         Highest GPA, honor list, Bogazici University, Dept. of Molecular Biology & Genetics, 1995.

·         Second highest GPA, honor list, Bogazici University, Dept. of Chemical Engineering, 1994.

Editorial activities

·         Editorial board member of the Journal of Applied Biological Sciences (JABS) (2007-

·         Contributes as a referee to various journals listed in Science Citation Index (SCI) : Biotechnology & Bioengineering, Applied Biochemistry & Biotechnology, Coloration Technology, (2005-

·         Contribution as panelist and referee to TUBITAK project evaluations (2007)

·         Contribution as referee to Istanbul Technical University Scientific Research project applications (2006)