Person: KAZAN, DİLEK
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KAZAN
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DİLEK
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Publication Metadata only Proteomic Analysis of Liver Preservation Solutions Prior to Liver Transplantation(BENTHAM SCIENCE PUBL LTD, 2019) KAZAN, DİLEK; Coskun, Abdurrahman; Baykal, Ahmet Tarik; Oztug, Merve; Kazan, Dilek; Kaya, Ekrem; Emiroglu, Remzi; Yilmaz, Sezai; Dundar, Halit Ziya; Akgoz, Muslum; Berber, Ibrahim; Ak-tas, Hikmet; Bilsel, Gokhan; Karaosmanoglu, Kubra; Cetiner, Banu; Arslan, Cansu; Yurtsever, Ilknur; Yazici, CevatObjective: Transplantation is the preferred treatment for patients with end-stage liver diseases. However, in clinical practice, functional preservation of the liver is a major concern before the transplantation. Although various protective solutions are used (in combination with hypothermia), the functional preservation time for liver is still limited to hours. We analyzed the preservation medium to detect the proteins released from the liver during storage period. Material/Methods: Samples were collected from the pre-transplant preservation mediums of 23 liver donors. For all donors, the cases involved Donation after Brain Death (DBD). 2D-PAGE and LCMSMS methodologies were used to detect the proteins and peptides from the preservation mediums. Results: A total of 198 proteins originating from the liver were detected. Conclusion: The data provide valuable insights into biomarkers that may be used to evaluate organ injury, functional status, and suitability for transplantation. Additionally, the findings could be valuable for the development of new strategies for effective preservation of solid organs prior to transplantation.Publication Metadata only Metabolic Biomarkers and Neurodegeneration: A Pathway Enrichment Analysis of Alzheimer's Disease, Parkinson's Disease, and Amyotrophic Lateral Sclerosis(MARY ANN LIEBERT, INC, 2016) KAZAN, DİLEK; Kori, Medi; Aydin, Busra; Unal, Semra; Arga, Kazim Yalcin; Kazan, DilekNeurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) lack robust diagnostics and prognostic biomarkers. Metabolomics is a postgenomics field that offers fresh insights for biomarkers of common complex as well as rare diseases. Using data on metabolite-disease associations published in the previous decade (2006-2016) in PubMed, ScienceDirect, Scopus, and Web of Science, we identified 101 metabolites as putative biomarkers for these three neurodegenerative diseases. Notably, uric acid, choline, creatine, L-glutamine, alanine, creatinine, and N-acetyl-L-aspartate were the shared metabolite signatures among the three diseases. The disease-metabolite-pathway associations pointed out the importance of membrane transport (through ATP binding cassette transporters), particularly of arginine and proline amino acids in all three neurodegenerative diseases. When disease-specific and common metabolic pathways were queried by using the pathway enrichment analyses, we found that alanine, aspartate, glutamate, and purine metabolism might act as alternative pathways to overcome inadequate glucose supply and energy crisis in neurodegeneration. These observations underscore the importance of metabolite-based biomarker research in deciphering the elusive pathophysiology of neurodegenerative diseases. Future research investments in metabolomics of complex diseases might provide new insights on AD, PD, and ALS that continue to place a significant burden on global health.Publication Metadata only Retro-techno-economic evaluation of acetic acid production using cotton stalk as feedstock(SPRINGER, 2018) SAYAR, AHMET ALP; Sayar, Nihat Alpagu; Kazan, Dilek; Pinar, Orkun; Akbulut, Berna Sariyar; Sayar, Ahmet AlpIn value-added chemical industries, use of agricultural wastes as raw materials remains to be a major challenge in commercialization due to lack of competitiveness with respect to petrochemical processes. This work presents the techno-economic analysis of a novel bioprocessing plant converting 356,400MT/year cotton stalks into 147,000MT/year acetic acid. A production scheme integrating lignin separation with the main bioconversion stages has been proposed. Techno-economic assessment was performed through economic feasibility and retro-techno-economic analysis (RTEA) methods. The RTEA method has been extended to include the estimation of research and development funding for improving economic feasibility. Carbon offset of the proposed technology has been estimated and carbon credit results have been incorporated into the economic feasibility metrics.Publication Metadata only Proteomic insight into phenolic adaptation of a moderately halophilic Halomonas sp. strain AAD12(2011) SARIYAR AKBULUT, BERNA; Ceylan, Selim; Akbulut, Berna Sariyar; Denizci, Aziz Akin; Kazan, DilekA gram-negative, moderately halophilic bacterium was isolated from Çamaltı Saltern area, located in the Aegean Region of Turkey. Analysis of its 16S rRNA gene sequence and physiological characteristics showed that this strain belonged to the genus Halomonas ; hence, it was designated as Halomonas sp. strain AAD12. The isolate tolerated up to 800 mg⋅L(-1) phenol; however, at elevated concentrations, phenol severely retarded cell growth. The increase in lag phase with increasing phenol concentrations indicated that the microorganism was undergoing serious adaptative changes. To understand the physiological responses of Halomonas sp. strain AAD12 to phenol, a 2-dimensional electrophoresis approach combined with mass spectrometric analysis was used. This approach showed that the expression of 14 protein spots were altered as phenol concentration increased from 200 to 800 mg⋅L(-1). Among the identified proteins were those involved in protein biosynthesis, energy, transport, and stress metabolism. So far, this is the first study on phenolic adaptation of a gram-negative, moderately halophilic bacteria using proteomic tools. The results provided new insights for understanding the general mechanism used by moderately halophilic bacteria to tolerate phenol and suggested the potential for using these microorganisms in bioremediation.Publication Metadata only Purification and characterization of a serine alkaline protease from Bacillus clausii GMBAE 42(SPRINGER HEIDELBERG, 2005) KAZAN, DİLEK; Kazan, D; Denizci, AA; Oner, MNK; Erarslan, AAn extracellular serine alkaline protease of Bacillus clausii GMBAE 42 was produced in protein-rich medium in shake-flask cultures for 3 days at pH 10.5 and 37 degrees C. Highest alkaline protease activity was observed in the late stationary phase of cell cultivation. The enzyme was purified 16-fold from culture filtrate by DEAE-cellulose chromatography followed by (NH4)(2)SO4 precipitation, with a yield of 58%. SDS-PAGE analysis revealed the molecular weight of the enzyme to be 26.50 kDa. The optimum temperature for enzyme activity was 60 degrees C; however, it is shifted to 70 degrees C after addition of 5 mM Ca2+ ions. The enzyme was stable between 30 and 40 degrees C for 2 h at pH 10.5; only 14% activity loss was observed at 50 degrees C. The optimal pH of the enzyme was 11.3. The enzyme was also stable in the pH 9.0-12.2 range for 24 h at 30 degrees C; however, activity losses of 38% and 76% were observed at pH values of 12.7 and 13.0, respectively. The activation energy of Hammarsten casein hydrolysis by the purified enzyme was 10.59 kcal mol(-1) (44.30 U mol(-1)). The enzyme was stable in the presence of the 1% (w/v) Tween-20, Tween-40,Tween-60, Tween-80, and 0.2% (w/v) SDS for 1 h at 30 degrees C and pH 10.5. Only 10% activity loss was observed with 1% sodium perborate under the same conditions. The enzyme was not inhibited by iodoacetate, ethylacetimidate, phenylglyoxal, iodoacetimidate, n-ethylmaleimidate, n-bromosuccinimide, diethylpyrocarbonate or n-ethyl-5phenyl-iso-xazolium-3'-sulfonate. Its complete inhibition by phenylmethanesulfonylfluoride and relatively high k(cat) value for N-Suc-Ala-Ala-Pro-Phe-pNA hydrolysis indicates that the enzyme is a chymotrypsin-like serine protease. Km and kcat values were estimated at 0.655 mu M N-Suc-Ala-Ala-Pro-Phe-pNA and 4.21 x 10(3) min(-1), respectively.Publication Metadata only Proteomic response of Escherichia coli to the alkaloid extract of Papaver polychaetum(SPRINGER, 2010) SARIYAR AKBULUT, BERNA; Ozbalci, Cagakan; Unsal, Caglayan; Kazan, Dilek; Sariyar-Akbulut, BernaThe cellular response of Escherichia coli exposed to alkaloids extracted from a biennial endemic plant, Papaver polychaetum, was explored using proteome analysis. Following determination of the minimum inhibitory concentration of the berberine-containing plant extract as 1,250 mu g/mL, E. coli cells were grown in the presence of 750 mu g/mL extract. The response of the bacteria to the extract, with berberine found as the major alkaloid, was analyzed on two-dimensional gels. The differentially expressed proteins in the presence of 750 mu g/mL extract were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. These proteins included those that play vital roles for maintenance such as protein synthesis (elongation factor-Ts), transport (oligopeptide-binding protein A, uncharacterized amino-acid ABC transporter ATP binding protein YECC), energy metabolism (alpha-subunit of ATP synthase, pyridine nucleotide transhydrogenase STHA) and regulation. These results provide clues for understanding the mechanism of the alkaloid extract-induced stress and cytotoxicity on E. coli. The altered proteins can serve as potential targets for development of innovative therapeutic agents.Publication Metadata only Lipase production from Cryptococcus albidus D24 using disposed automotive oil(ELSEVIER SCIENCE BV, 2018) KAZAN, DİLEK; Uras, A.; Pinar, O.; Byk, E.; Buldag; Topal, H.; Yildiz, D. B.; Yalcin, H. T.; Kazan, D.Publication Metadata only Valorization of pea pod, celery root peel, and mixed-vegetable peel as a feedstock for biocellulose production from Komagataeibacter hansenii DSM 5602(SPRINGER HEIDELBERG) KAZAN, DİLEK; Bozdag, Gulnihal; Pinar, Orkun; Gunduz, Oguzhan; Kazan, DilekCurrently, recycling and reuse of wastes to obtain high value-added products are substantial issues for development of sustainable and economic processes. Among these wastes, evaluation of food waste has been received significant attention due to scarcity in undeveloped countries, food security, and environmental problems. In general, this study focused on the investigation of cheap carbon sources and re-utilization of food waste for the production of bacterial cellulose (BC). Therefore, pea pod, celery root peel, and mixed-vegetable peel were evaluated to produce BC from Komagataeibacter hansenii (waste-based Kh-BC) in the present work. Subsequent to the BC production from specified wastes, chemical structure, thermal properties, scanning electron microscope (SEM) analysis, water uptake, and antibacterial activity of BC were analyzed. Among all wastes studied, mixed-vegetable peel and pea pod were positive influencers on BC synthesis and Fourier-transform infrared (FT-IR) spectra of BC membranes produced from wastes were very similar to that obtained from mannitol as a control. Additionally, waste-based Kh-BC has higher biodegradability and thermal stability than the Kh-BC produced from the control medium. Although it has a fragile structure, its water holding capacity and porous structure appear similar to standard BC. Moreover, waste-based Kh-BC could be impregnated with antibiotics to obtain the antibacterial BC membrane. Therefore, the present work showed that vegetable wastes could be valorized for BC production and waste-based Kh-BC is a promising biopolymer candidate for medical and pharmaceutical applications according to its properties.Publication Metadata only Water Miscible Mono Alcohols' Effect on the Proteolytic Performance of Bacillus clausii Serine Alkaline Protease(HUMANA PRESS INC, 2014) KAZAN, DİLEK; Duman, Yonca (Avci); Kazan, Dilek; Denizci, Aziz Akin; Erarslan, AltanIn this study, our investigations showed that the increasing concentrations of all examined mono alcohols caused a decrease in the V (m), k (cat) and k (cat)/K (m) values of Bacillus clausii GMBE 42 serine alkaline protease for casein hydrolysis. However, the K (m) value of the enzyme remained almost the same, which was an indicator of non-competitive inhibition. Whereas inhibition by methanol was partial non-competitive, inhibition by the rest of the alcohols tested was simple non-competitive. The inhibition constants (K (I)) were in the range of 1.32-3.10 M, and the order of the inhibitory effect was 1-propanol > 2-propanol > methanol > ethanol. The Delta G (not equal) and Delta G (not equal) (E -aEuro parts per thousand T) values of the enzyme increased at increasing concentrations of all alcohols examined, but the Delta G (not equal) (ES) value of the enzyme remained almost the same. The constant K (m) and Delta G (not equal) (ES) values in the presence and absence of mono alcohols indicated the existence of different binding sites for mono alcohols and casein on enzyme the molecule. The k (cat) of the enzyme decreased linearly by increasing log P and decreasing dielectric constant (D) values, but the Delta G (not equal) and Delta G (not equal) (E -aEuro parts per thousand T) values of the enzyme increased by increasing log P and decreasing D values of the reaction medium containing mono alcohols.Publication Open Access A two-step purification platform for efficient removal of Fab-related impurities: A case study for Ranibizumab(2023-11-01) PİNAR, ORKUN; SARIYAR AKBULUT, BERNA; KAZAN, DİLEK; Tatli O., Oz Y., Dingiloglu B., Yalcinkaya D., Basturk E., Korkmaz M., Akbulut L., Hatipoglu D., Kirmacoglu C., Akgun B., et al.Antibodies (mAbs) and antibody fragments (Fabs) constitute one of the largest and most rapidly expanding groups of protein pharmaceuticals. In particular, antibody fragments have certain advantages over mAbs in some therapeutic settings. However, due to their greater chemical diversity, they are more challenging to purify for large-scale production using a standard purification platform. Besides, the removal of Fab-related byproducts poses a difficult purification challenge. Alternative Fab purification platforms could expedite their commercialization and reduce the cost and time invested. Accordingly, we employed a strong cation exchanger using a pH-based, highly linear gradient elution mode following Protein L affinity purification and developed a robust two-step purification platform for an antibody fragment. The optimized pH gradient elution conditions were determined on the basis of purity level, yield, and the abundance of Fab-related impurities, particularly free light chain. The purified Fab molecule Ranibizumab possessed a high degree of similarity to its originator Lucentis. The developed purification platform highly intensified the process and provided successful clearance of formulated Fab- and process-related impurities (∼98 %) with an overall process recovery of 50 % and, thus, might be a new option for Fab purification for both academic and industrial purposes.