Browsing by Author "Dereli, Elif."

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    An integrated appoach to investigate tor signaling mechanism in Saccharomyces Cerevisiae
    (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Social Sciences, 2013., 2013.) Dereli, Elif.; Kırdar, Betül.
    Target of rapamycin (TOR) signaling, a conserved mechanism from yeast to human, is the major regulator of cell metabolism and growth. Rapamycin, an immunosuppressive and anti-proliferative drug, and caffeine, a widely used psychoactive drug, target and inhibit TOR function. In this study the long-term administration effects of 2 nM rapamycin and 5 mM caffeine, together with oxygen availability and acidity as well as the rapamycin dosage (2 nM or 200 nM) on yeast transcriptional and metabolic responses were comparatively investigated. For this purpose batch cultivations of yeast cells were carried out in the absence and presence of rapamycin and caffeine with different levels of oxygen availability and pH. Batch cultivations were conducted under micro-aerated conditions where pH was maintained at 5.5 to investigate the effects of the rapamycin dosage. The analysis of the transcriptional responses of yeast cells to the long term presence of rapamycin revealed that long term administration of low dose of rapamycin resulted in more subtle changes in transcriptional responses of yeast causing a partial TOR inhibition than the administration of high dose. However both low and high doses of rapamycin resulted in a set of transcriptional changes mimicking nutrient starvation responses of yeast cells and they both induced autophagy and altered membrane trafficking. Low dose of rapamycin was still effective at the transcriptome level by leading metabolism to autophagy but this dose may not be enough to block the proliferation of aggressive tumors. The effects of caffeine in the long term administration resulted in a wider set of transcriptional changes resembling the high dose of rapamycin treatment; high dose of rapamycin or caffeine suppressed the growth-related processes and increased the energy requirement of the cells. pH was observed to be more decisive parameter on the transcriptional responses of the cells than the oxygen level and both oxygen availability and pH should be carefully evaluated during rapamycin or caffeine treatment.
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    Studies on the role of HAP4, MIG1 and MIG2 in transcriptional control network of Saccharomyces Cerevisiae
    (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2007., 2007.) Dereli, Elif.; Kırdar, Betül.
    In this study, transcriptional responses of HAP4, MIG1, MIG2 and GSM genes to transient perturbations under glucose and nitrogen limited conditions were investigated in order to understand glucose sensing and signaling pathways in yeast. For this purpose six sets of chemostat experiments with pulse injections were performed with three homozygous deletion strains (ho /ho , mig1 /mig1 and mig2 /mig2 ) of Saccharomyces cerevisiae BY4743. Growth characteristics and metabolite profiles for glucose, ethanol, ammonia and glycerol were compared. mig1 /mig1 and mig2 /mig2 strains produced higher biomass than ho /ho under glucose limitation. Absence of MIG2 did not affect the glucose repression mechanism as much as MIG1. mig2 /mig2 produced the lowest biomass under nitrogen limitation. The glucose concentration was the highest in ho /ho in nitrogen limited chemostat cultivation. The expression profiles of HAP4, MIG1, MIG2 and GSM1 were determined via real time rt-qPCR. HAP4, MIG1, MIG2 and GSM1 were up-regulated under glucose limitation in ho /ho . Deletion of MIG1 or MIG2 resulted in repression of HAP4 and GSM1 under glucose limitation. After the glucose pulse injection GSM1 was activated after HAP4 in mig1 /mig1 and this provided further evidence that GSM1 is regulated by HAP complex. GSM1 showed similar expression levels with HAP4 both in ho /ho and mig2 /mig2 throughout the glucose limited cultivations. This indicated a possible role of GSM1 in regulation of respiratory pathway of yeast together with HAP4. Deletion of MIG1 diminished the up-regulation of MIG2 under nitrogen limitation.