Person: SARIYAR AKBULUT, BERNA
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SARIYAR AKBULUT
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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 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 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.Publication Metadata only Transcriptomic analysis displays the effect of (-)-roemerine on the motility and nutrient uptake in Escherichia coli(SPRINGER, 2017) SARIYAR AKBULUT, BERNA; Ayyildiz, Dilara; Arga, Kazim Yalcin; Avci, Fatma Gizem; Altinisik, Fatma Ece; Gurer, Caglayan; Toplan, Gizem Gulsoy; Kazan, Dilek; Wozny, Katharina; Bruegger, Britta; Mertoglu, Bulent; Akbulut, Berna SariyarAmong the different families of plant alkaloids, (-)-roemerine, an aporphine type, was recently shown to possess significant antibacterial activity in Escherichia coli. Based on the increasing demand for antibacterials with novel mechanisms of action, the present work investigates the potential of the plant-derived alkaloid (-)-roemerine as an antibacterial in E. coli cells using microarray technology. Analysis of the genome-wide transcriptional reprogramming in cells after 60 min treatment with 100 mu g/mL (-)-roemerine showed significant changes in the expression of 241 genes (p value < 0.05 and fold change > 2). Expression of selected genes was confirmed by qPCR. Differentially expressed genes were classified into functional categories to map biological processes and molecular pathways involved. Cellular activities with roles in carbohydrate transport and metabolism, energy production and conversion, lipid transport and metabolism, amino acid transport and metabolism, two-component signaling systems, and cell motility (in particular, the flagellar organization and motility) were among metabolic processes altered in the presence of (-)-roemerine. The down-regulation of the outer membrane proteins probably led to a decrease in carbohydrate uptake rate, which in turn results in nutrient limitation. Consequently, energy metabolism is slowed down. Interestingly, the majority of the expressional alterations were found in the flagellar system. This suggested reduction in motility and loss in the ability to form biofilms, thus affecting protection of E. coli against host cell defense mechanisms. In summary, our findings suggest that the antimicrobial action of (-)-roemerine in E. coli is linked to disturbances in motility and nutrient uptake.Publication Metadata only Proteomics in industrial biotechnology(CURRENT BIOLOGY LTD, 2011) SARIYAR AKBULUT, BERNA; Ceylan, Selim; Ozbalci, Cagakan; Akbulut, Berna Sariyar; Kazan, DilekPublication Metadata only What Are the Multi-Omics Mechanisms for Adaptation by Microorganisms to High Alkalinity? A Transcriptomic and Proteomic Study of a Bacillus Strain with Industrial Potential(MARY ANN LIEBERT, INC, 2018) SAYAR, AHMET ALP; Kaya, Fatma Ece Altinisik; Avci, Fatma Gizem; Sayar, Nihat Alpagu; Kazan, Dilek; Sayar, Ahmet Alp; Akbulut, Berna SariyarAlkaliphilic organisms are among an industrially important class of extremophile microorganisms with the ability to thrive at pH 10-11.5. Microorganisms that exhibit alkaliphilic characteristics are sources of alkali-tolerant enzymes such as proteases, starch degrading enzymes, cellulases, and metabolites such as antibiotics, enzyme inhibitors, siderophores, organic acids, and cholic acid derivatives, which have found various applications in industry for human and environmental health. Yet, multi-omics mechanisms governing adaptation to high alkalinity have been poorly studied. We undertook the present work to understand, as a case study, the alkaliphilic adaptation strategy of the novel microorganism, Bacillus marmarensis DSM 21297, to alkaline conditions using a multi-omics approach that employed transcriptomics and proteomics. As alkalinity increased, bacteria remodeled the peptidoglycan layer by changing peptide moieties along with the peptidoglycan constituents and altered the cell membrane to reduce lipid motility and proton leakiness to adjust intracellular pH. Different transporters also contributed to the maintenance of this pH homeostasis. However, unlike in most well-known alkaliphiles, not only sodium ions but also potassium ions were involved in this process. Interestingly, increased pH has triggered the expression of neither general stress proteins nor gene encoding proteins associated with heat, salt, and nutrient stresses. Only an increase in the expression of oxidative stress related genes was evident. Endospore formation, also a phenomenon closely linked to stress, was unclear. This questioned if high pH was a real stress for B. marmarensis. These new findings, corroborated using the multi-omics approach of the present case study, broaden the knowledge on the mechanisms of alkaliphilic adaptation and might also potentially offer useful departure points for further industrial applications with other microorganisms.Publication Metadata only Production of industrial enzymes for feed industry(ELSEVIER SCIENCE BV, 2012) SARIYAR AKBULUT, BERNA; Sogut, Melis S.; Ozturk, Nurcin C.; Ozturk, H. Umit; Pinar, Orkun; Ipek, Fatih M.; Cayir, Ebru; Gokce, Abdulmecit; Karasu, Deniz; Ozturk, Dilek C.; Ozturk, Yavuz; Denizci, A. Akin; Ozturk, Bengu; Bahar, Banu; Avci, Naze G.; Ayan, Burak; Kazan, Dilek; Duman, Yonca A.; Sargin, Sayit; Karacanli, Sevket; Mizrak, Cengizhan; Catli, A. Ugur; Kucukyilmaz, Kamil; Guvenmez, Hatice K.; Arikan, Burhan; Bozkurt, Mehmet; Seyhan, Ferda; Akbulut, Berna S.; Erarslan, A. Altan; Ongen, Gaye; Dincer, Sadik; Yenice, Engin; Mandaci, SevnurPublication Metadata only Thermostable alpha-amylase from moderately halophilic Halomonas sp AAD21(TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEY, 2012) SARIYAR AKBULUT, BERNA; Uzyol, Kamil Serkan; Akbulut, Berna Sariyar; Denizci, Aziz Akin; Kazan, DilekThe moderately halophilic Halomonas sp. strain AAD21, which produces extracellular thermostable alpha-amylase, was isolated from the Camalti Saltern area located in Izmir, Turkey. NaCl, carbon, and nitrogen sources in the growth medium were optimized to enhance alpha-amylase yield. The highest enzyme yield was measured in the presence of 20% NaCl with peptone as the nitrogen and starch as the carbon sources in the fermentation broth. This microorganism was also found to utilize waste potato peel as a carbon source for alpha-amylase production. Concentrations of carbon and nitrogen sources were optimized using a statistical approach, and alpha-amylase activity increased from 4.07 U mL(-1) min(-1) to 26.25 U mL(-1) min(-1). Maximum alpha-amylase production was achieved at the end of 48 h of growth in the presence of 20% NaCl, 4.12% starch, 1.0% peptone, 0.2% KCl, 2% MgSO4 center dot 7H(2)O, and 0.03% trisodium citrate pentahydrate. The optimum pH and temperature of the alpha-amylase were found to be 7.0 and 50 degrees C, respectively. The alpha-amylase synthesized by Halomonas sp. AAD21 was also thermostable. Crude alpha-amylase did not lose its original activity after 2 h of incubation at 50 degrees C and 60 degrees C, and it retained 70% of its original activity after 120 min of incubation at 90 degrees C.Publication Metadata only Techno-economic analysis of caffeine and catechins production from black tea waste(ELSEVIER, 2019) SARIYAR AKBULUT, BERNA; Sayar, Nihat Alpagu; Sam, Selcen Durmaz; Pinar, Orkun; Serper, Damla; Akbulut, Berna Sanyar; Kazan, Dilek; Sayar, Ahmet Alpy This work establishes a proof of concept level economic assessment of a novel commercial production scheme for caffeine and catechins from black tea waste collected in the north-eastern region of Turkey. A base case in which dichloromethane (DCM) is used as the product extracting agent and an alternative greener case where DCM is replaced with environmentally friendlier ethyl acetate (EA) were designed and modelled on Superpro Designer platform. Profitability analyses were conducted for both cases, each treating 30,000 MT/year of black tea waste. Under the base case scenario, the Net Present Value (NPV) was calculated as 16,249,000 USD whereas the alternative scenario gave an NPV of 4,379,000 USD with corresponding payback times of 5.64 and 6.79 years. A novel techno-economic evaluation method involving the metamodeling of Superpro Designer models via Kriging and subsequent multi-objective optimization is incorporated into the economic assessment and applied to the two cases in order to optimize selected dominant process variables. Optimal values for dominant operating process variables were found using 3-D graphs simulating the combined effects of these variables on NPV. Results showed that the base case has a greater potentiality to generate profit. However, the greener case could be implemented if it is supported on environmental and toxicity issues considering the potential health and pollution preventive benefits. The present work demonstrates how the integration of novel conceptual design, modelling, and optimization approaches can foster broader evaluation of bioprocesses utilizing negative-value agro-wastes for the production of value-added chemicals. (C) 2019 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.