Theses and Dissertations from UMD
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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM
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Item Electrogenetic communication structures to encode, propagate, and decode information through synthetic biology(2022) VanArsdale, Eric S; Bentley, William E; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Cellular communication, the exchange of information between cells, is a process in which cues are encoded, propagated, and decoded through shared chemical and physical semantics. This general process forms the basis for homeostatic decision-making to which the cell dedicates substantial resources. Central to these processes are abstract communication structures each which serve a defined role and create semantic compatibility. “Transmitters” relay messages away from the source, the “channel” propagates the message through a network, and “receivers” are the terminal site of relay. When a particular semantic code of a message is not fit to the structure it must interact with there is a loss in communication capacity. Overcoming this barrier requires transformation of semantic variants to fit the context of a particular communication channel. For bioelectronics, communication structures must interconvert electron-oriented codes, such as current and voltage, into molecularly-oriented codes, such as genetic inducers and molecular gradients. Here, I present the creation of a redox electrogenetic communication channel which contains the principal transmitter, channel, and receiver structures, each of which is made through the combination of electrochemistry, materials science, and synthetic biology. Each of these structures is the focus of separate sections within my dissertation. First, I will present receiver structures that convert molecular information into electrochemical redox signals. These systems are comprised of engineered bacteria that recognize molecular cues and catalytically synthesize redox-active components that are received using electrochemistry. Second, I will present transmitter structures that encode electronic inputs into redox-active inducers that are perceived by genetic circuits. These circuits interact with the message to ensure faithful replication of the message and constitute electrogenetic noise suppression at the single-cell level and second messenger homogenization on the population level. Lastly, I will present channel propagation which links transmitter and receiver structures. These systems link the prior two sections and network communication into a greater context of biological control. I will demonstrate these interactions through controlled production of small molecules, on-demand cell lysis, and restructuring of cell consortia. Together, these methodologies constitute a bioelectronic communication paradigm that can directly mediate information exchange between electronic and molecular formats. Future application of these communication structures will enable logic-driven control systems and computer-learning models in a medical and environmental internet of bionano-things and true cybernetic integration.Item DESIGN OF ENZYME CASCADE AND CRISPR-CAS9 NETWORKS FOR ENABLING BIOELECTRONIC COMMUNICATION(2017) Bhokisham, Narendranath; Bentley, William E; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)There is an increasing emphasis on building closed loop systems in human health where real time monitoring and analysis is connected to feedback and treatment. Building such systems requires bridging the information loop across the different signal modalities of biology and electronics. In this work, I have created two different networks at biology-electronic interface to enable the communication from biology to electronics and vice versa. The first network is a multi-step enzyme cascade assembled on a microchip to enable conversion of biologic information into electro-chemical information. I first devised a modular construction approach using microbial transglutaminase (mTG) based conjugation chemistry where multiple enzyme components are assembled on an abiotic surface in a ‘plug and play’ fashion. Integration of bio-components with electronics requires a scaffold material for functionalization of the bio-electronic interface. To address this challenge, I engineered a self-assembling Tobacco Mosaic Virus-Virus Like Particle into a 3D scaffold displaying desired functional groups at the interface. Using the 3D scaffolds and mTG mediated conjugation chemistry, I assembled a synthetic 3-enzyme cascade on a microchip for conversion of methyl cycle intermediates into homocysteine, an electrochemically readable molecule. The modular construction approach and the scaffold materials that I developed can enable facile assembly of multi-subunit bio-components and diversify the range of metabolites that can be detected on a microchip for use in biosensing applications. Next, I focused on mediating communication from electronics to specific genes in the genome of biological systems. An electrogenetic promoter that is responsive to the electrical stimuli was reported in E. coli. In this work, I integrated the precise gene targeting capabilities of the CRISPR-Cas9 system with the electrogenetic promoter to target specific host transcriptional processes. I displayed temporal silencing of several host defense mechanisms against the electrical signals resulting in an overall positive feedback for electrogenicity in E. coli. A more sophisticated control of host transcriptional processes by the CRISPR-Cas9 system is a valuable addition to the existing electrogenetic toolbox, one that could enhance the interoperability of electrogenetic systems and mediate bio-electronic communication between strains and species.