Berna Sarıyar Akbulut                                         

Marmara University          .

Department of Bioengineering          .

c

 

berna.akbulut-at-marmara.edu.tr

Tel: + 90 212 3480292 / 721
Fax: + 90 212 3450126

Go to course pages

 

Degrees

PhD, Chemical Engineering, Bogaziçi University, Istanbul- Turkey, 2003
MSc,   Chemical Engineering, Bogaziçi University, Istanbul- Turkey, 1997
BSc,    Chemical Engineering, Bogaziçi University, Istanbul- Turkey, 1995

 

Employment
2011 - present      Assoc. Prof. Department of Bioengineering, Marmara Univ.

2007 - 2011             Asst. Prof. Department of Bioengineering, Marmara Univ. 
2003 - 2007        Asst. Prof. Department of Chemical Eng., Marmara Univ. 
1996 - 2003           Teaching/Research Asst., Department of Chemical Eng., Bogazici Univ.
 

 

Appoinments
 

2008-2011                Member of the executive board of the faculty.


 

Visiting scientist

Visiting Scholar, Department of Bioengineering, Rice Univ. Houston – TX 2000
Institute of Biology, Humboldt University, Berlin – Germany 2004

 

 

Peer reviewer
Applied Microbiology and Biotechnology
Biochemical Engineering Science
Bioinformatics

 

 

Invited speaker
 

Beta-Lactamase Inhibition.

Biotechnology for Economic Development by COMSTECH. 16-18 February 2011. Islamabad, Pakistan.

 

Peptide Inhibitors of beta-Lactamase.

Turkish German Workshop on Biotechnology and Bioengineering 21-22 September 2010. Aachen, Germany.

 

Proteomik Yöntemler ile Bitkisel Ilaçların Etkilerinin Arastırılması.

Proteomik Arastırmaları: Temel Bilgiler ve Uygulama Örnekleri. 10-11 Aralık 2009 ISTANBUL.

 

Beta-Laktamaz Inhibitörü Gelistirmede Yeni Bir Yaklasım.

20. Ulusal Biyoloji Kongresi. 21-25 Haziran 2010 DENIZLI.

 

Mikroorganizma tanılamada biyo-istatiksel yöntemler.

Enzim Saflastırmada Temel Yöntemler, Uygulamalı Lisansüstü Egitim Kursu, TUBITAK-GMBE.

Temmuz 2006,  Agustos 2007,  Haziran/Temmuz 2008.

 

 

Projects

 

Extremophiles as source of natural products useful for biotechnological applications: Studies of osmoregulation strategies by engineering tools. TUBITAK: MAG-110T174.

Production of industrial enzymes intended for feed industry. TUBITAK: KAMAG-107G246. 

Investigation of the cell-uptake and in-vivo inhibition potential of inhibitory peptides using computational and experimental methods. TUBITAK: MAG-109M229.

Investigation of cellular differentialtion by integration of OMICs data. Marmara University Scientific Research Project: FEN-A-130511-0157.  

The analysis of metabolic capabilities under stress conditions using biosystems engineering principles. TUBITAK: MAG-108M597, completed.

Peptide based inhibitor design against beta-lactamase. TUBITAK: MAG-108M644, completed.

Microbial adaptation to stress conditions using an integrative modelling and experimental approach. Marmara University Scientific Research Project: FEN-C-YLP-171209-0342, completed.

Investigation of peptide inhibitor binding to beta-lactamase. Marmara University Scientific Research Project: FEN-C-YLP-181208-0290, completed.

Investigation of the metabolic pathways of halophilic microorganisms by metabolic engineering: Marmara University Scientific Research Project: FEN-C-DRP-181208-0286, completed.

Investigation of the effect of antimicrobial agents on microorganisms. Marmara University Scientific Research Project: FEN-C-YLP-060308-0041, completed.

Experimental and molecular modeling studies for antimicrobial peptide design. Bogazici University Scientific Research Project: 06A501, completed.

The translocation of thermostable glucose isomerase using bacterial SEC and TAT mechanisms. Marmara University Scientific Research Project: FEN-BGS-100105-0063, completed.

Investigation of the effect of environmental conditions on newly isolated halophilic microorganisms by proteomics. TUBITAK: MAG 104M236, completed.

 

 

Publications

Ceylan S, Yilan G, Sarıyar Akbulut B, Poli A, Kazan D. Interplay of adaptive capabilities of Halomonas sp. AAD12 under salt stress. Journal of Bioscience and Bioengineering, in press.

Uzyol KS, Sarıyar Akbulut B, Denizci AA, Kazan D (2012). Thermostable α-amylase from moderately halophilic Halomonas sp. AAD21. Turk J Biol, in press. doi: 10.3906/biy-1106-7.

Selim Ceylan, Berna Sarıyar Akbulut, Aziz Akın Denizci, Dilek Kazan. Proteomic insight into phenolic adaptation of a moderately halophilic Halomonas sp. strain AAD12. Can J Microbiol, 57: 295-302 (2011).

Cagakan Ozbalci, Caglayan Unsal, Dilek Kazan, Berna Sariyar-Akbulut. Proteomic response of Escherichia coli to the alkaloid extract of Papaver polychaetum. Ann Microbiol, 60: 709-717 (2010).

Sariyar Akbulut B. Discriminant Function Analysis Based on Principal Components for Rapid Discrimination of Metabolic Capabilities of New Isolates. Chem Biochem Eng Q, 24 (1): 119-127 (2010).

Utkur F.O., Sariyar Akbulut B, Hortacsu A. Cellular distribution of activity for three enzymes with maltose binding protein as fusion partner and the structural implications. Turk J Chem, 33: 1-13 (2009).

Sariyar Akbulut B. Rapid differentiation of new isolates with MALDI-TOF mass spectrometry via discriminant function analysis based on principal components. Korean J Chem Eng, 26(6): 1645-1651 (2009).

Sarıyar B, Dilgimen Salman A, Ceylan S, Perk S, Denizci AA, Kazan D. RAPID METABOLOME ANALYSIS: Preliminary phenotypic characterization of newly isolated microorganisms by footprinting. Archieves of Microbiology 2008, 189, 19-26.

Berna Sarıyar, Sinem Perk, Ugur Akman, Amable Hortacsu. Monte Carlo sampling and principal component analysis of flux distributions yield topological and modular information on metabolic networks. Journal of Theoretical Biology, 242(2): 389-400, (2006).

Pınar Ozkan, Berna Sariyar, F. Ozde Utkur, Ugur Akman, Amable Hortacsu. Metabolic flux analysis of recombinant protein overproduction in Escherichia coli. Biochemical Engineering Journal, 22: 167–195 (2005).

Ka-Yiu San, George N. Bennett, Susana J. Berríos-Rivera, Ravi V. Vadali, Yea-Tyng Yang, Emily Horton, Fred B. Rudolph, Berna Sariyar, and Kimathi Blackwood. Metabolic Engineering through Cofactor Manipulation and Its Effects on Metabolic Flux Redistribution in Escherichia coli. Metabolic Engineering, 4: 182–192 (2002).

 

 

Presentations

 

AC Serdaroglu, B Ayan, B Sariyar Akbulut, N Ozer. Distribution of Amino Acids in Extremophiles. Istanbul Conference on Mathematical Methods and Modeling in Life Sciences and Biomedicine, Istanbul, Turkey, 2011.

Selim Ceylan, Gülsah Yılan, Berna Sarıyar Akbulut, Dilek Kazan, Analysis of the osmolyte strategy of the moderately halophilic Halomonas sp. AAD12. The 12th International Conference on Systems Biology (ICSB), 28 August-1 September 2011, Heildelberg/Mannheim, Germany.

Kübra Karaosmanoglu, Dilek Kazan, Berna Sariyar Akbulut. Proteomic Analysis of the Effect of Berberine on Escherichia coli. Mass Spectrometry in Biotechnology and Medicine. Dubrovnik, Croatia, 3-9 July 2011.

Ihsan Ömür Akdag, Berna Sarıyar Akbulut, Elif Özkırımlı Çlmez, Peptide transport across the lipid bilayer. The International Congress on Bioinformatics and Biomics, May 18-22, 2011, Kusadası.

Nilay BUDEYRI, Naze Gül AVCI, Elif OZKIRIMLI OLMEZ, Berna SARIYAR AKBULUT. In-vitro Inhibitory Effect of BLIP Derived Peptides on TEM-1 b-Lactamase. 35th FEBS Congress - Molecules of life. June 26 – July. 1, 2010 in Gothenburg, Sweden.

Çagakan Özbalcı, Kübra Karaosmanoglu, Isıl Aksan Kurnaz, Dilek Kazan, Berna Sarıyar Akbulut. Comparative Transcriptome and Proteome Analysis for the Effect of Berberine. 35th FEBS Congress - Molecules of life. June 26 – July. 1, 2010 in Gothenburg, Sweden.

Hilal Mangaoglu, Naze Gül Avcı, Berna Sarıyar Akbulut, Dilek Kazan. Optimization of cellulase production by newly isolated Bacillus sp. 35th FEBS Congress - Molecules of life. June 26 – July. 1, 2010 in Gothenburg, Sweden.

Nilay BÜDEYRI, A. Ezgi AKKAYA, Celal CEYLAN, Naze Gül AVCI, Gizem BULDUM, Özlem KOCAMAN, Natali YÜZARI, Elif ÖZKIRIMLI ÖLMEZ, Berna SARIYAR AKBULUT. TEM-1 Beta-Laktamaz Ligand Etkilesiminin Incelenmesi. 9.Ulusal Kimya Mühendisligi Kongresi-UKMK 2010. 22-25 Haziran 2010. Gazi Üniversitesi Ankara.

Pınar KANLIKILIÇER, Nilay BÜDEYRI, Berna Sarıyar AKBULUT and Elif ÖZKIRIMLI ÖLMEZ. INVESTIGATION OF TEM-1 AND SHV-1 BETA LACTAMASE LIGAND BINDING. Lara, Antalya, Turkey. April 20-22, 2010

Çagakan Özbalcı, Çaglayan Ünsan, Dilek Kazan, Berna Sarıyar AKBULUT. Berberine vs. P. polychaetum alkaloit extract for antimicrobial activity. BioMivroWorld 2009. 2-4 December Lisbon, Portugal.

N Budeyri, E Ozkirimli Olmez, B Sariyar Akbulut. Investigation of in-vitro and in-vivo Beta-Lactamase Inhibition by Beta-Lactamase-Inhibitor-Protein Based Peptides. BioMivroWorld 2009. 2-4 December Lisbon, Portugal.

G. Avcı, H. Mangaoglu, D. Kazan, B. S. Akbulut. Optimization of growth media for economical β-glucanase production by Bacillus sp. BioMivroWorld 2009. 2-4 December Lisbon, Portugal.

Selim Ceylan, Berna S. Akbulut, Dilek Kazan. Proteome Analysis of the Responses to Phenol Concentration Variations in Moderately Halophilic Bacteria Halomonas sp.MU12. BioMivroWorld 2009. 2-4 December Lisbon, Portugal.

Hilal Mangaoglu, Tugba Bahcivan, Naze Gül Avcı, Berna Sarıyar Akbulut. Yeni Izole Edilen Bacillus sp Suslarının Ekstrem Kosullara Dayanıklı ß-Glukanaz Üretiminin Incelenmesi. 21.Ulusal Biyokimya Kongresi, 28-31 Ekim 2009 Istanbul Askeri Müzesi, Istanbul.

Gizem BULDUM, Burcu BULAK. Bacillus licheniformis BA17 Alkalen Proteazının Metal Iyonları Varlıgında Termal Inaktivasyon ve Organik Çözücü Varlıgındaki Inaktivasyon Kinetiklerinin Incelenmesi. 21. Ulusal Biyokimya Kongresi, 28-31 Ekim 2009 Istanbul Askeri Müzesi, Istanbul.

 Aslı Dedeagaç, Kristen Smith, Mayumi Fujitani, Çaglayan Ünsal, Berna Sarıyar, David R. Kaplan, Isıl Aksan Kurnaz (2009). Pediatric Nöroblastomlara Karsı Olası Ilaç Adaylarının Taranması. 8. Ulusal Sinirbilimleri Kongresi. 18-22 Nisan 2009. Abant Izzet Baysal Üniversitesi, Bolu.

Pınar Kanlıkılıçer, Nilay Büdeyri, Berna Sarıyar Akbulut, Amable Hortaçsu, Elif Özkırımlı Ölmez (2009). Dynamic Analysis of β-Lactamase Ligand Recognition. Biophysical Society's 53rd Annual Meeting February 28 - March 4, Boston, Massachusetts – USA.

Pınar Kanlıkılıçer, A. Ezgi Akkaya, Elif Ölmez Özkırımlı, Berna Sarıyar Akbulut, Amable Hortaçsu (2008) In-vivo Binding of TEM-1 β-Lactamase and β-Lactamase Inhibitory Protein (BLIP) Complex. IV. National Bioengineering Congress Izmir-TURKEY, October 15-18.

Nilay Büdeyri, Pınar Kanlıkılıçer, Berna Sarıyar Akbulut, Amable Hortaçcu, Elif Özkırımlı Ölmez (2008). Dynamic Analysis of b-Lactamase Ligand Recognition. ECCB’08 European Conference on Computational Biology, Cagliari, Sardinia-Italy September 22-26.

Nilay Büdeyri, Berna Sarıyar, Dilek Kazan (2008) The optimization of beta-galactosidase production by Halomonas sp. using response surface methodology. UKMK-8, 8th National Chemical Engineering Congress, Malatya-TURKEY, 26-29 Agustos.

Nilay Büdeyri, Berna Sarıyar Akbulut, Elif  Özkırımlı Ölmez, Amable Hortaçsu (2008) Dynamic Analysis of beta-Lactamase Ligand Recognition. HIBIT, Istanbul.

Çagakan Özbalcı, Çaglayan Ünsal, Dilek Kazan, Berna Sariyar-Akbulut (2008) Proteomic approach to understand antimicrobial effect of Papaver polychaetum alkaloids. HIBIT, Istanbul. B. Sarıyar Akbulut, A. Salman Dilgimen, S. Ceylan, S. Perk, A. A Denizci, D. Kazan. Preliminary Identification Of Moderately Halophilic Microorganisms Through Metabolic Footprinting. 31st FEBS Congress, Molecules in Health and Disease, 24-29 June 2006, Istanbul, TURKEY.

FO Bayraktar, B Sarıyar, A Hortaçsu. Experimental and Theoretical Studies to Determine the Effect of Protein Characteristics on Translocation of Fusion Proteins in E. coli. 31st FEBS Congress, Molecules in Health and Disease, 24-29 June 2006, Istanbul, TURKEY.

KS Uzyol, B Sarıyar, D Kazan. a-Amylase Production from food waste by using newly isolated Halomonas sp., 31st FEBS Congress, Molecules in Health and Disease, 24-29 June 2006, Istanbul, TURKEY.

B Sarıyar, A Hortaçsu. Mathematical Modeling of the Sec Pathway and Its Application to Maltose Binding Protein-Glucose Isomerase Fusion Protein. Euresco Conferences: Protein Targeting, SPA-Belgium, 26 September-1 October, 2003.

A Hortaçsu, P Özkan, B Sarıyar, U Akman. Metabolic Flux Analysis of the Cellular Response of E. coli to Heterologous Protein Overproduction. Systeomics 2002, San Franscisco, California, USA, November 3-6, 2002.

K-Y San, GN Bennett, SJ Berríos-Rivera, RV Vadali, B Sariyar, K Blackwood. Metabolic Engineering through cofactor manipulation and its effects on metabolic flux redistribution in Escherichia coli, Metabolic Engineering III, Colorado Springs, Colorado, November 22-27, 2000.

B Sarıyar, B Kırdar, A Hortaçsu. Production of Extracellular Thermostable Glucose Isomerase in E. coli. 2nd European Symposium on Biochemical Engineering Science (ESBES-2), Porto-Portugal, September 16-19, 1998.

B Sarıyar, B Kırdar, A Hortaçsu. Cloning of Thermostable Glucose Isomerase in E. coli, 8th European Congress on Biotechnology (ECB-8), Budapest-Hungary, August 17-21, 1997.