Person: TOKSOY ÖNER, EBRU
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TOKSOY ÖNER
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Publication Metadata only Evaluation of industrial Saccharomyces cerevisiae strains for ethanol production from biomass(PERGAMON-ELSEVIER SCIENCE LTD, 2012) KASAVİ, CEYDA; Kasavi, Ceyda; Finore, Ilaria; Lama, Licia; Nicolaus, Barbara; Oliver, Stephen G.; Oner, Ebru Toksoy; Kirdar, BetulFive industrial Saccharomyces cerevisiae strains were evaluated for their suitability for strain improvement for future use in ethanol production processes. Principal components analysis of growth-related and production-related fermentation parameters of the 5 strains grown on glucose demonstrated the superiority of the Y9 strain in terms of its rapid growth and highest ethanol yields on both biomass and glucose. The growth and ethanol production performances of these strains on various agro-industrial wastes (including sugar beet pulp, starch and sugar beet molasses) and biological residues (including carrot, tomato and potato peel) were also determined. Ethanol tolerance studies, using both solid and liquid cultures, revealed the remarkable abilities of the BC187 and Y9 strains to survive and grow at high ethanol concentrations. Suspension cultures were found to be highly tolerant to 78.80 g L-1 ethanol however their growth ability showed a distinct decrease with increasing ethanol concentration such that only (1-2)% of the control growth was observed in media containing 118.20 g L-1 ethanol. The importance of choosing the appropriate S. cerevisiae strain to be used in ethanol production was clearly established with this study. Fermentation performances of the cultures under different cultivation conditions pointed to the fact that the choice of strain will not only depend on the ethanol tolerance but also on the preferential utilization of the carbon resources of biological residues. (c) 2012 Elsevier Ltd. All rights reserved.Publication Metadata only Real imaging and size values of Saccharomyces cerevisiae cells with comparable contrast tuning to two environmental scanning electron microscopy modes(JOHN WILEY & SONS INC, 2007) TOKSOY ÖNER, EBRU; Misirli, Zulal; Oener, Ebru Toksoy; Kirdar, BetulThe combined application of electron microscopy (EM) is frequently used for the microstructural investigation of biological specimens and plays two important roles in the quantification and in gaining an improved understanding of biological phenomena by making use of the highest resolution capability provided by EM. The possibility of imaging wet specimens in their native states in the environmental scanning electron microscope (ESEM) at high resolution and large depth of focus in real time is discussed in this paper. It is demonstrated here that new features can be discovered by the elimination of even the least hazardous approaches in some preparation techniques, that destroy the samples. Since the analysis conditions may influence the morphology and the extreme surface sensitivity of living biological systems, the results obtained from the same cultured cell with two different ESEM modes (Lvac mode and wet mode) were compared. This offers new opportunities compared with ESEM-wet/Lvac-mode imaging, since wet-mode imaging involves a real contrast and Gives an indication of the changes in cell morphology and structure required for cell viability. In this study, wet-mode imaging was optimized using the unique ability of cell quantities for microcharacterization in situ giving very fine features of topological effects. Accordingly, the progress is reported by comparing the results of these two modes, which demonstrate interesting application details. In general, the functional comparisons have revealed that the fresh unprocessed Saccharomyces cerevisiae cells (ESEM-wet mode) were essentially unaltered with improved and minimal specimen preparation timescales, and the optimal cell viability degree was visualized and also measured quantitatively while the cell size remained unchanged with continuous images.Publication Open Access A system based network approach to ethanol tolerance in Saccharomyces cerevisiae(BMC, 2014-12) KASAVİ, CEYDA; Kasavi, Ceyda; Eraslan, Serpil; Arga, Kazim Yalcin; Oner, Ebru Toksoy; Kirdar, BetulBackground: Saccharomyces cerevisiae has been widely used for bio-ethanol production and development of rational genetic engineering strategies leading both to the improvement of productivity and ethanol tolerance is very important for cost-effective bio-ethanol production. Studies on the identification of the genes that are up-or down-regulated in the presence of ethanol indicated that the genes may be involved to protect the cells against ethanol stress, but not necessarily required for ethanol tolerance. Results: In the present study, a novel network based approach was developed to identify candidate genes involved in ethanol tolerance. Protein-protein interaction (PPI) network associated with ethanol tolerance (tETN) was reconstructed by integrating PPI data with Gene Ontology (GO) terms. Modular analysis of the constructed networks revealed genes with no previously reported experimental evidence related to ethanol tolerance and resulted in the identification of 17 genes with previously unknown biological functions. We have randomly selected four of these genes and deletion strains of two genes (YDR307W and YHL042W) were found to exhibit improved tolerance to ethanol when compared to wild type strain. The genome-wide transcriptomic response of yeast cells to the deletions of YDR307W and YHL042W in the absence of ethanol revealed that the deletion of YDR307W and YHL042W genes resulted in the transcriptional re-programming of the metabolism resulting from a mis-perception of the nutritional environment. Yeast cells perceived an excess amount of glucose and a deficiency of methionine or sulfur in the absence of YDR307W and YHL042W, respectively, possibly resulting from a defect in the nutritional sensing and signaling or transport mechanisms. Mutations leading to an increase in ribosome biogenesis were found to be important for the improvement of ethanol tolerance. Modulations of chronological life span were also identified to contribute to ethanol tolerance in yeast. Conclusions: The system based network approach developed allows the identification of novel gene targets for improved ethanol tolerance and supports the highly complex nature of ethanol tolerance in yeast.