Articles

2018

Begum Alaybeyoglu, Berna Sariyar Akbulut, Elif Ozkirimli (2018). pVEC hydrophobic N‐terminus is critical for antibacterial activity. J Pep Sci. 2018;e3083.

Fatma Gizem Avci, Nihat Alpagu Sayar, Berna Sariyar Akbulut (2018). An OMIC approach to elaborate the antibacterial mechanisms of different alkaloids. Phytochemistry 149 (2018) 123-131.

2017

Pinar, O., Karaosmanoğlu, K., Sayar, N.A., Kula, C., Kazan, D. and Sayar, A.A., 2017. Assessment of hazelnut husk as a lignocellulosic feedstock for the production of fermentable sugars and lignocellulolytic enzymes. 3 Biotech, 7(6), p.367.

Begum Alaybeyoglu, Bilge Gedik Uluocak, Berna Sariyar Akbulut, and Elif Ozkirimli (2017). The effect of a beta-lactamase inhibitor peptide on bacterial membrane structure and integrity: a comparative study. J Pept Sci. 2017 May;23(5):374-383. doi: 10.1002/psc.2986. Epub 2017 Mar 16.

Dilara Ayyildiz, Kazim Yalcin Arga, Fatma Gizem Avci, Fatma Ece Altinisik, Caglayan Gurer, Gizem Gulsoy Toplan, Dilek Kazan, Katharina Wozny, Britta Brügger, Bulent Mertoglu, Berna Sariyar Akbulut (2017). Transcriptomic analysis displays the effect of (-)-roemerine on the motility and nutrient uptake in Escherichia coli. Curr Genet. 2017 Aug;63(4):709-722. doi: 10.1007/s00294-016-0673-4. Epub 2016 Dec 24.

2016

Begum Alaybeyoglu, Berna Sariyar Akbulut & Elif Ozkirimli (2016). Insights into Membrane Translocation of the Cell-Penetrating Peptide pVEC from Molecular Dynamics Calculations, Journal of Biomolecular Structure and Dynamics, Journal of Biomolecular Structure and Dynamics. 17:1-12.

Nilay Budeyri Gokgoz, Fatma Gizem Avci, Kubra Karaosmanoglu Yoneten, Begum Alaybeyoglu, Elif Ozkirimli, Nihat Alpagu Sayar, Dilek Kazan, and Berna Sariyar Akbulut (2016). Response of Escherichia coli to Prolonged Berberine Exposure. Microbial Drug Resistance. DOI: 10.1089/mdr.2016.0063

Fatma Gizem Avci, Fatma Ece Altinisik, Didem Vardar Ulu, Elif Ozkirimli  Olmez & Berna Sariyar Akbulut (2016). An evolutionarily conserved allosteric site modulates beta-lactamase activity. Journal of Enzyme Inhibition and Medicinal Chemistry. 31:sup3, 33-40.

Coskun, A., Baykal, A.T., Kazan, D., et al. Proteomic Analysis of Kidney Preservation Solutions Prior to Renal Transplantation (2016). PLOS ONE, accepted for publication.

Kori, M, Aydın, B., Unal, S., Arga, K.Y., Kazan, D., (2016) Metabolic Biomarkers and Neurodegeneration: A Pathway Enrichment Analysis of Alzheimer's Disease, Parkinson's Disease, and Amyotrophic Lateral Sclerosis, OMICS A Journal of Integrative Biology, 20 (11), DOI: 10.1089/omi.2016.0106

Bal, E., Pinar, O., Kazan, D., Ozturk, H.U., Sayar, A.A., (2016) Immobilization of alpha-amylase from Bacillus subtilis SDP1 isolated from the Rhizosphere of Acacia cyanophila Lindey, Electronic Journal of Biology, 12:2, 115-121.

2015

Ceylan, S., Kazan, D. (2015).  Pyrolysis kinetics and thermal characteristics of microalgae Nannochloropsis oculata and Tetraselmis sp.  Bioresource Technology, 187(7), 1-5., Atıf Sayısı: 5, Doi: 10.1016/j.biortech.2015.03.081.

Öztürk HU, Sariyar Akbulut B, Ayan B, Poli A, Denizci AA, Utkan G, Nicolaus B and Kazan D (2015). Moderately Halophilic Bacterium Halomonas sp. AAD12: A Promising Candidate as a Hydroxyectoine Producer. J Microb Biochem Technol. 7(5), 262-268.  

Yilmaz, D.E., Sayar, N.A., 2015. Organic solvent stable lipase from Cryptococcus diffluens D44 isolated from petroleum sludge. Journal of Molecular Catalysis B: Enzymatic, 122: 72-79.

Yoruk, H.M., Sayar, N.A., 2015. Topological analysis of carbon flux during multi-stress adaptation in Halomonas sp. AAD12. Electronic Journal of Biotechnology, 18: 480-485.

Nilay Büdeyri Gökgöz, Simay Yalaz, Naze Gül Avcı, Gizem Buldum, Elif Özkırımlı Ölmez, Berna Akbulut (2015). Investigation of the in vivo interaction between β-lactamase and its inhibitor protein. Turk J Biol. 39, 485-92.

Nilay Budeyri Gokgoz and Berna Sariyar Akbulut (2015). Proteomics Evidence for the Activity of the Putative Antibacterial Plant Alkaloid (-)-Roemerine: Mainstreaming Omics-Guided Drug Discovery. OMICS A Journal of Integrative Biology. 19(8), 478-89.

Begum Alaybeyoglu, Berna Sariyar Akbulut and Elif Ozkirimli (2015). A novel chimeric peptide with antimicrobial activity. Journal of Peptide Science. 21(4), 294–301.

Ozen, R., Sayar, N.A., Durmaz-Sam, S., Sayar, A.A., 2015. A sigmoidal model for biosorption of heavy metal cations from aqueous media. Mathematical Biosciences, 265: 40-46.

2014

Kubra Karaosmanoglu, Nihat Alpagu Sayar, Isil Aksan Kurnaz, and Berna Sariyar Akbulut (2014). Assessment of Berberine as a Multi-target Antimicrobial: A Multi-omics Study for Drug Discovery and Repositioning. OMICS A Journal of Integrative Biology. 18: 1.

Sayar, N.A., Durmaz-Sam, S., Kazan, D., Sayar, A.A., 2014. Schizosaccharomyces pombe and its Ni(II)-insensitive mutant GA1 in Ni(II) uptake from aqueous solutions: a biodynamic model. Applied Microbiology and Biotechnology, 9 8:6859–6869.

Öztürk Hasan Ümit, Denizci A.A., Ogan, A., Kazan, D., (2014).  A Maltooligosaccharide Producing alpha-Amylase from Bacillus subtilis SDP1 Isolated from Rhizosphere of Acacia cyanophylla Lindley.  FOOD BIOTECHNOLOGY, 28(4), 309-332.,

Dilgimen, A.S., Arga, K.Y., Erdmann, V.A., Wittmann-Liebold, B., Denizci, A.A. and Kazan, D. (2014) Comparison of Protein Expression Profiles of Novel Halo Halomonas smyrnensis AAD6T and Halomonas salina DSMZ 5928T. Natural Science, 6, 628-640. 

Sayar, N.A., Durmaz-Sam, S., Kazan, D., Sayar, A.A., (2014) Schizosaccharomyces pombe and its Ni (II)-insensitive mutant GA1 in Ni(II) uptake from aqueous solutions: a biodynamic model, ,  Appl Microbiol Biotechnol, DOI 10.1007/s00253-014-5740-5.

Duman, Y., Kazan, D., Denizci, A.A., Erarslan, A., (2014). Water Miscible Mono Alcohol’s Effect on the Proteolytic Performance of Bacillus clausii Serine Alkaline Protease, Appl Biochem Biotechnol, 172, 469-486, 10.1007/s12010-013-0525-3

2013

Sayar, N.A., Durmaz-Sam, S., Odabasi, G., Sayar, A.A., 2013. Biosorption of Co (II) by Schizosaccharomyces pombe: kinetic and thermodynamic studies for process design. Bioprocessing & Biosystems, 3(3):1-8.

Poli, A., Nicolaus, B., Denizci, A.A., Yavuzturk, B., Kazan, D. (2013). Halomonas smyrnensis sp. nov., a moderately halophilic exopolysaccharide-producing bacterium from Çamaltı Saltern Area, Turkey. Int J Syst Evol Microbiol, 63. doi: 10.1099/ijs.0.037036-0

2012

Ceylan S, Yilan G, Sarıyar Akbulut B, Poli A, Kazan D (2012). Interplay of adaptive capabilities of Halomonas sp. AAD12 under salt stress. Journal of Bioscience and Bioengineering, 114:1, 45-52.

Kamil Serkan Uzyol, Berna Sarıyar Akbulut, Aziz Akın Denizci, Dilek Kazan (2012). Thermostable alpha-Amylase from Moderately Halophilic Halomonas sp. AAD21. Turk J Biol. 36, 327-338.

Öztürk, N.C., Kazan, D., Denizci, A.A., Erarslan, A., (2012) The influence of copper on alkaline protease stability toward autolysis and thermal inactivation, Eng. Life Sci., 12, No. 5, 1–10 1

2011

Durmaz-Sam, S., Sayar, N.A., Topal-Sarikaya, A., Sayar, A.A., 2011. Biosorption of Ni (II) by Schizosaccharomyces pombe: kinetic and thermodynamic studies. Bioprocess and Biosystems Engineering, 34: 997-1005.

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

2010 and earlier

Çağakan Ozbalci, Çağlayan Unsal, Dilek Kazan, Berna Sariyar-Akbulut. (2010). Proteomic response of Escherichia coli to the alkaloid extract of Papaver polychaetumAnn. Microbiol. 60: 709 – 717.

Sarıyar-Akbulut, B. (2010). Discriminant Function Analysis Based on Principal Components for Rapid Discrimination of Metabolic Capabilities of New Isolates. Chemical and Biochemical Engineering Quarterly (CABEQ). Chem. Biochem. Eng. Q. 24(1): 119–127.

N.A. Sayar, B.H. Chen, G.J. Lye, J.M. Woodley, 2009. Process modelling and simulation of a transketolase mediated reaction: analysis of alternative modes of operation. Biochemical Engineering Journal, 47 (1-3): 10-18.

N.A. Sayar, B.H. Chen, G.J. Lye, J.M.Woodley, 2009. Modelling and simulation applications to a transketolase mediated reaction: Sensitivity analysis of kinetic parameters. Biochemical Engineering Journal, 47 (1-3): 1-9.

N.A. Sayar, M. Filiz, A.A. Sayar, 2009. Extraction of Co (II) and Ni (II) from concentrated HCl solutions using Alamine 336. Hydrometallurgy, 96(1-2): 148-153.

N.A. Sayar, A.A. Sayar, M. Filiz, 2009. Simulation and optimisation-oriented modeling considerations for the extraction of Ni (II) from its acidic aqueous chloride solutions into Alamine 336-m-xylene systems. Hydrometallurgy, 96(3-4): 280-284.

Özde F. Ütkür, Berna Sarıyar Akbulut, Amable Hortaçsu (2009). Cellular Distribution of Activity for Three Enzymes with Maltose Binding Protein as Fusion Partner and the Structural Implications. Turk J Chem. 33: 1 – 13.

B. Sarıyar-Akbulut (2009). Rapid Differentiation of New Isolates with MALDI-TOF Mass Spectrometry via Discriminant Function Analysis based on Principal Components. Korean Journal of Chemical Engineering. 26(6): 1645 – 1651.

Denizci A.A., Kazan D., Erarslan A., (2009) Bacillus marmarensis sp. nov., an alkaliphilic, protease-producing bacterium isolated from mushroom compost., IJSEM., doi:ijs.0.012369-0

Kazan D., Bal H., Denizci A.A., Ozturk N.C., Ozturk U., Dilgimen A.S., Ozturk D.C., Erarslan A., Studies on Alkaline Serine Protease Produced by Bacillus clausii GMBE 22, Preparative Biochemistry and Biotechnology, 39(3):289-307.

Ozturk, D., Kazan, D., Denizci, A.A., Grimoldi, D., Secundo, F., Erarslan, A., (2009) Water Miscible Mono Alcohols Effect on the Structural Conformation of Bacillus clausii GMBAE 42 Serine Alkaline Protease, Journal of Molecular Catalysis B: Enzymatic doi:10.1016/j.molcatb.2009.02.017    

Öztürk, S., Morgan-Özeren, M., Salman-Dilgimen,A., Denizci, A.A.,S Arıkan, B., Kazan, D., (2009). Alkaline serine protease from halotolerant Bacillus licheniformis BA17. Annals Microbiology, 59 (1) 1-8.

Sarıyar-Akbulut, B., Dilgimen, A.S., Ceylan, S., Perk, S., Kazan, D. (2008). Preliminary phenotypic characterization of newly isolated halophilic microorganisms by footprinting: a rapid metabolome analysis. Archives of Microbiology 189:16-29.

Yagız, F., Kazan, D., Akin, N.A., Biodiesel production from waste oils by using lipase immobilized on hydrotalcite and zeolites,  Chemical Engineering Journal Volume 134, Issues 1-31 November 2007Pages 262-267.

Ates, O., Toksoy Oner, E., Arıkan, B., Denizci, A.A., Kazan, D., (2007) Isolation And Identification Of Alkaline Protease Producer Halotolerant Bacillus licheniformis Strain BA17, Annals Microbiology, 57 (3), 369-375.

N.A. Sayar, M. Filiz, A.A. Sayar, 2007. Extraction of Zn(II) from aqueous hydrochloric acid solutions into Alamine 336-m-xylene systems. Modelling considerations to predict optimal operational conditions. Hydrometallurgy, 86(1-2): 27-36.

B.H. Chen, N.A. Sayar, U. Kaulmann, P. Dalby, J.M. Ward, J.M. Woodley, 2006. Reaction modelling and simulation to assess the integrated use of transketolase and omega-transaminase for the synthesis of an aminotriol. Biocatalysis and Biotransformations, 24(6): 449-457.

M. Filiz, N.A. Sayar, A.A. Sayar, 2006. Extraction of cobalt (II) from aqueous hydrochloric acid solutions into Alamine-336-m-xylene mixtures. Hydrometallurgy, 81(3- 4): 167-173.

B. Sariyar, S. Perk, U. Akman, A. Hortacsu (2006). 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.

Filiz, M; Sayar, AA (2006).  Extraction of titanium(IV) from aqueous hydrochloric acid solutions into alamine 336-m-xylene mixtures Chemical Engineering Communications. 193(9):1127-1141.

P. Özkan, B. Sariyar, Ö. Utkur, U. Akman and A. Hortaçsu (2005). Metabolic Flux Analysis of Recombinant Protein Overproduction in Escherichia coli, Biochemical Engineering Journal, 22, 167-195.

Kazan, D., Denizci, A., Kerimak, Ö.M.N.,  Erarslan, A., “Purification and characterization of a serine alkaline protease from Bacilllus clausii GMBAE42” J.Ind. Microbiol Biotechnology, 32, 335-344 (2005).

B. Sariyar and A. Hortacsu (2004). Expression and translocation of glucose isomerase as a fusion protein in E. coli, Enzyme and Microbial Technology, 35(2-3), 105-112.

Denizci, A., Kazan, D., Abeln, E. C. A., Erarslan, A., Newly ısolated Bacillus clausii GMBAE42: an alkaline protease producer capable to grow under higly alkaline conditions”, Applied Microbiology and Biotechnology, Journal of Applied Microbiology, 96, 320-327 (2004).      

B. Sariyar and A. Hortaçsu (2004). Mathematical Modeling of Sec Pathway Mechanism in Escherichia coli: A case study for periplasmic translocation of maltose binding protein-glucose isomerase fusion protein, Chemical Engineering Science, 59(5), 1027-1038.

San K-Y., Bennet, G.N., Berrios-Rivera, S.J., Vadali, R.V., Yang, Y.T., Horton E., Rudolph, F.B., Sariyar, B. and Blackwood, K., (2002). Metabolic Engineering through Cofactor Manipulations and Its Effects on Metabolic Flux Redistribution in Escherichia coli, Metabolic Engineering 4, 182-192.

Coskuner Öztürk, D., Kazan, D., Erarslan, A., Stabilization and functional properties of Esherichia coli penicillin G acylase by cocalent conjugation of anionic polisaccaride carboxymethylcellulase, World Journal of Microbiology and Biotechnology, 18, 881-888 (2002).

Ercelen, S., Kazan, D., Erarslan, A., Demchenko, A.P., On the exiced-state energy transfer between tryptophan residues in proteins: the case of penicillin acylase, Biophysical Chemistry, 90, 203-217 (2001).                                        

Kazan, D., Erarslan, A., The identification of catalytically essential amino acid residues of penicillin G acylase obtained from a mutant of  Escherichia coli ATCC 11105, Process Biochemistry, 36, 861-867, (2001).

Kazan, D., Erarslan, A., Effect of dextrans polymers on the stability of soluble Escherichia coli penicillin G acylase., J. Chem. Tech. Biotech.,74, 1157-1164, (1999).      

Kayaman, N., Kazan, D., Erarslan, A., Okay, O., Structure and protein separation efficiency of poly(N-isopropylacrylamide) gels: Effect of synthesis conditions., J. Appl. Polymer Sci., 67, 805-814, (1998).

Kazan, D., Ertan, H., Erarslan, A., Stabilization of Escherichia coli penicillin G acylase against thermal inactivation by cross-linking with dextran-dialdehyde polymers., Appl. Microbiol. Biotechnol., 48, 191-197, (1997).                                                

Ertan, H., Kazan, D., Erarslan, A., Cross-linked stabilization of Escherichia coli penicillin G acylase against pH by dextran-dialdehyde polymers., Biotechnology Techniques, 11, 225-229, (1997).

Kazan, D., Erarslan, A., Stabilization of Escherichia coli penicillin G acylase by polyethylene glycols against thermal inactivation., Appl. Biochem. Biotechnol., 62, 1-13, (1997). Kazan, D., Erarslan, A., Influence of polyhydric compounds on the pH stability of penicillin G acylase obtained from a mutant of Escherichia coli ATCC 11105., Process Biochemistry, 31, 691-697, (1996).                                          

Kazan, D., Ertan, H., Erarslan, A., Stabilisation of penicillin G acylase against pH by chemical cross-linking., Process Biochemistry, 31, 135-140, (1996).              

Kazan, D., Çamurdan, A., and Hortaçsu, A., The Effect of Glucose Concentration on the Growth Rate and some Intracellular Components of a Recombinant Escherichia coli Culture., Process Biochemistry, 30, 269-273, (1995)     

Senol, A; Sayar, AA (1995). Liquid-Liquid Equilibriaof some water plus Tetrahydrofurfuryl Alcohol plus solvent Ternaries at 293.2+/-0.1 K AND 101.3+/-0.8 KPA Fluid Phase Equilibria 106(1-2): 169-183

Senol, A; Alptekin, G; Sayar, AA (1995)(LIQUID PLUS LIQUID) EQUILIBRIA OF SOME (WATER PLUS TETRAHYDROFURAN PLUS SOLVENT) TERNARIES AT THE TEMPERATURE (293.2+/-0.1) K AND PRESSURE (101.3+/-0.7) KPA. JOURNAL OF CHEMICAL THERMODYNAMICS  Volume: 27   Issue: 5   Pages: 525-529  

Sayar, AA (1992). ON THE CONSISTENCY OF SEMAC EQUATIONS – REPLY FLUID PHASE EQUILIBRIA  Volume: 81   Issue: 1-2   Pages: 347-348  

Arda, N; Sayar, AA (1992). LIQUID LIQUID EQUILIBRIUM OF WATER + 2-PROPANOL + 2,2,4-TRIMETHYLPENTANE TERNARY AT (293.2+/-0.1)- K. FLUID PHASE EQUILIBRIA  73  (1-2):  129.

Arda, N; Sayar, AA (1992). (LIQUID+LIQUID) EQUILIBRIA OF (WATER+TETRAHYDROFURAN+1-METHYLCYCLOHEXANOL) AND OF (WATER+TETRAHYDROFURAN+2-METHYLBUTYL ETHANOATE) AT THE TEMPERATURE (293.16+/-0.30)-K AND PRESSURE (101.325+/-0.070) KPA. JOURNAL OF CHEMICAL THERMODYNAMICS 24(2): 145-149.

Sayar, AA; Tatlı, B; Dramur, U (1991). LIQUID LIQUID EQUILIBRIA OF THE WATER + ACETIC-ACID + CYCLOHEXYL ACETATE TERNARY. JOURNAL OF CHEMICAL AND ENGINEERING DATA  36(4): 378-382

Sayar, AA (1991) ON THE ISOBARIC VAPOR-LIQUID-EQUILIBRIUM OF THE CYCLOHEXANOL-PHENYLMETHANOL BINARY AT 101.325 +/- 0.067 KPA FLUID PHASE EQUILIBRIA 6(3): 341-354  

Sayar, AA (1991). LIQUID LIQUID EQUILIBRIA OF SOME WATER + 2-PROPANOL + SOLVENT TERNARIES JOURNAL OF CHEMICAL AND ENGINEERING DATA 36(1): 61-65

Sayar, AA (1989) A SEMI-EMPIRICAL MOLECULAR ACTIVITY-COEFFICIENT MODEL WITH IRREGULAR PARAMETER DISTRIBUTION CHEMICAL ENGINEERING COMMUNICATIONS 80: 127-134


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