Browsing by Subject "Cell engineering"
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Item Embargo Biotechnological drug platforms(Bilkent University, 2023-11) Ahan, Recep ErdemBiopharmaceuticals, also known as biotechnological drugs, have revolutionized the treatment of many diseases by providing access to new mechanisms of action that can target the underlying biological processes behind the diseases. Technological advancement in biological sciences opens new paths to uncover new biopharmaceutical modalities in nature as well as to augment the existing modalities new functions. The implementation of engineering principles i.e., synthetic biology approaches have been transforming biopharmaceutical research wherein “smart” therapeutics are developed and deployed for treatment of previously intractable diseases. However, there are still unmet clinical needs that require novel and advanced biopharmaceuticals. In this thesis, I explored different biopharmaceuticals to characterize and/or advance their capabilities for diverse indications. Firstly, we have developed a prophylactic agent from the lectin protein, griffithsin, as for ancestral and the emerged strains of SARS-CoV-2. Secondly, we have advanced genetic technologies to engineer the probiotic Escherichia coli (E. coli) strain, Nissle 1917 (EcN), for therapeutical purposes. We developed a stable recombinant DNA transfer system based on cryptic plasmids of EcN. Furthermore, a synthetic protein secretion system was envisioned and functionally validated in EcN to shuttle therapeutical proteins to diseases site. Finally, peptide tags for extracellular protein secretion as well as a cell surface protein display system were developed for Lachnospiraceae species which are parts of the healthy human gut microbiome. The technologies and methodologies described herein will pay the way for inventing and/or discovering novel biopharmaceuticals to treat current and future diseases.Item Open Access Engineering sensorial delay to control phototaxis and emergent collective behaviors(American Physical Society, 2016-01) Mijalkov, M.; McDaniel, A.; Wehr, J.; Volpe, G.Collective motions emerging from the interaction of autonomous mobile individuals play a key role in many phenomena, from the growth of bacterial colonies to the coordination of robotic swarms. For these collective behaviors to take hold, the individuals must be able to emit, sense, and react to signals. When dealing with simple organisms and robots, these signals are necessarily very elementary; e.g., a cell might signal its presence by releasing chemicals and a robot by shining light. An additional challenge arises because the motion of the individuals is often noisy; e.g., the orientation of cells can be altered by Brownian motion and that of robots by an uneven terrain. Therefore, the emphasis is on achieving complex and tunable behaviors fromsimple autonomous agents communicating with each other in robust ways. Here, we show that the delay between sensing and reacting to a signal can determine the individual and collective long-term behavior of autonomous agents whose motion is intrinsically noisy. We experimentally demonstrate that the collective behavior of a group of phototactic robots capable of emitting a radially decaying light field can be tuned from segregation to aggregation and clustering by controlling the delay with which they change their propulsion speed in response to the light intensity they measure. We track this transition to the underlying dynamics of this system, in particular, to the ratio between the robots' sensorial delay time and the characteristic time of the robots' random reorientation. Supported by numerics, we discuss how the same mechanism can be applied to control active agents, e.g., airborne drones, moving in a three-dimensional space. Given the simplicity of this mechanism, the engineering of sensorial delay provides a potentially powerful tool to engineer and dynamically tune the behavior of large ensembles of autonomous mobile agents; furthermore, this mechanism might already be at work within living organisms such as chemotactic cells.Item Open Access Enhanced Performance of Nanowire-Based All-TiO2 Solar Cells using Subnanometer-Thick Atomic Layer Deposited ZnO Embedded Layer(Pergamon Press, 2015) Ghobadi, A.; Yavuz, H. I.; Ulusoy, T. G.; Icli, K. C.; Ozenbas, M.; Okyay, Ali KemalIn this paper, the effect of angstrom-thick atomic layer deposited (ALD) ZnO embedded layer on photovoltaic (PV) performance of Nanowire-Based All-TiO2 solar cells has been systematically investigated. Our results indicate that by varying the thickness of ZnO layer the efficiency of the solar cell can be significantly changed. It is shown that the efficiency has its maximum for optimal thickness of 1 ALD cycle in which this ultrathin ZnO layer improves device performance through passivation of surface traps without hampering injection efficiency of photogenerated electrons. The mechanisms contributing to this unprecedented change in PV performance of the cell have been scrutinized and discussed.