Yazar "Orhan, Ibrahim Y." seçeneğine göre listele

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    Designing an alternative reporter system for the GFP reporter system using Escherichia coli BL21 strain
    (Canadian Soc Clinical Investigation, 2015) Orhan, Ibrahim Y.; Karadag, Hizir A.; Bestepe, Furkan; Gul, Fatih; Uctepe, Eyyup; Yilmaz, Burak
    Purpose: Recombinant DNA technology can be used to transfer genetic material to bacteria [1]. To demonstrate that these recombinant bacteria can produce proteins by expressing the added genetic material, reporter systems are indispensable and mandatory [2,3]; hence, the improvement and development of reporter systems play a pivotal role in the progression of experimental method in recombinant DNA technology [2,4]. Methods: Viewing colour changes in the experimental area or on experiemntal subjects is simple, cheap and expedient [2, 5, 6]. In spite of their widespread utilization and the reliability of the consequence data, these reporter systems have some grave disadvantages [2,7,8]. In the absence of alternatives for these reporter systems, despite the serious handicaps and disadvantages, studies in recombinant DNA technology have been constricted by the infeasibility of such reporter systems [9,10]. Results: We focused on an alternative system to ameliorate current problems of common reporter systems - foremost the issue of time. The system in design had to be both potent and inexpensive. The main focus of the study was to design an alternative to the 2008 Nobel prize-winning GFP reporter system. Unlike the function of the GFP reporter system based on synthesizing colour absent in the medium as a means of response, we designed a system based on the degradation of dyes. Conclusion: This novel approach reduced the necessary time to attain a noticeable colour change and increased the certainty of the data.
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    Understanding thermal sensitivity at the molecular level and developing temperature-based systems using RNA Thermometers
    (Canadian Soc Clinical Investigation, 2016) Gul, Fatih; Orhan, Ibrahim Y.; Ceylan, Furkan S.; Akdeniz, Nadir B.; Karadag, H. Abdulkadir
    Purpose: Temperature sensitivity is found in all multicelleular organisms, as well as in most primitive life forms. The ubiquity of this temperature sensitivity is an indicator of its effects at the multicellular, cellular and molecular levels [1]. Previous studies have shown that temperature-based regulation is present in the transcriptional process [2]. RNA Thermometers, temperature-sensitive sequences, have been shown to act on heat-shock genes to regulate temperature-dependant systems in many organisms [3,4]. The goal of this study was to characterize the shifts in the functioning of these RNA Thermometers at various temperatures. In addition, using the principle of transcriptional thermoregulation, an automated temperature-responsive system stimulating inverse endothermic and exothermic enzymatic reactions for heat stabilization was proposed. Methods: The endothermic enzymatic reaction was designated as the breakdown of urea, reflecting the function of urease, and the exothermic reaction was designated as the breakdown of hydrogen peroxide, reflecting the function of catalase [5]. Results: The proposed system was built upon the translation of urease and the inhibition of catalase translation at higher temperatures, and the inverse at lower temperatures. As RNA Thermometers can be used only to drive transcription at higher temperatures, the installation of a lac-regulated 2-way system was suggested. This system would also provide a synthetic solution to thermoregulation and the current systems employed today. This system could be applied where the current thermoregulatory systems prove insufficient and could be further developed and optimized to replace them in the future.