Thesis (Ph. D. in Biomedical Engineering)--Vanderbilt University, Aug. 2007. / Title from title screen. Includes bibliographical references.

Thesis (Ph. D.)--University of Chicago, Committee on Genetics, June 2003. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Marty Shankland. Vita. Includes bibliographical references.

Thesis (M. Med. Sc.)--University of Hong Kong, 2006.

Thesis (Ph.D.)--University of Delaware, 2008. / Principal faculty advisors: Babatunde Ogunnaike, Dept. of Chemical Engineering; and Boris N. Kholodenko, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University. Includes bibliographical references.

published_or_final_version / Medicine / Master / Master of Philosophy

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Communication is a ubiquitous component of life. While complexity and sophistication vary, both unicellular and multicellular organisms constantly interact with their environment. Unicellular organisms, once thought to be asocial, have since been demonstrated to display a multitude of social interactions and hierarchies. For example, quorum sensing enables a bacterial population to modulate gene expression in response to cell-population density, initiating social behavior and the exchange of resources. In eukaryotes, unicellular ascomycete fungi use mating GPCRs to detect secreted peptide pheromones, initiating changes in gene expression required for mating. An overview of communication in unicellular organisms is presented in Chapter 1. In general, these communication systems are characterized by a high degree of fidelity, and as such have been harvested by synthetic biologists to organize communication in synthetic systems. Quorum sensing modules have been employed for pattern formation and to coordinate biosynthesis processes across a community. However, fungal mating remains underutilized as a source of synthetic biology tools. In this dissertation, we leverage fungal mating G-protein-coupled receptors (GPCRs) and their peptide ligands to build responsive yeast systems. We use genome-mining to identify additional fungal peptide-GPCR pairs, which are then characterized in the yeast Saccharomyces cerevisiae. In Chapter 2, we exploit the high specificity and sensitivity of fungal mating GPCRs to design a yeast whole-cell biosensor that produces a visible output in response to detection of peptide biomarkers. In Chapter 3, we genome-mine additional peptide-GPCR pairs and use them as orthogonal signaling channels to build synthetic yeast communities. Finally, in Chapter 4, we use these synthetic yeast communities to provide sense-and-respond capabilities to an Engineered Living Material (ELM).

Cellular differentiation is the cornerstone of metazoan development. Cell-cell signaling mechanisms are responsible for the specification of many cell fates. The response of a particular cell to a given signal is highly context dependent allowing signaling mechanisms to be reused to produce a variety of different outcomes. The EGFR and LIN-12/Notch signaling pathways are well-conserved across metazoan species and govern many fate-specification events. The specification of C. elegans Vulval Precursor Cells (VPCs) offers a powerful system to investigate how these signaling mechanisms specify cell-fates, and previous studies of VPC fate patterning have identified several forms of crosstalk between these two critical signaling mechanisms. In this thesis, I investigate how input from both the EGFR and LIN-12/Notch signaling pathways is integrated by the VPCs. I provide evidence that VPCs respond to the relative levels of LIN-12/Notch and EGFR signaling. I show that LIN-1/Elk1 is critical for VPCs to adopt discrete cell fates. In addition, I show that the Mediator components SUR-2/Med23 and the CDK-8 kinase module (CKM), in cooperation with LIN-1/Elk1, are required for an EGFR-mediated resistance to LIN-12/Notch activity. I also used CRISPR/Cas9 techniques to generate endogenous, fluorescently-tagged LAG-1 proteins. Characterization of tagged LAG-1 accumulation in the VPCs and in the somatic gonad show that LAG-1 is present in all VPCs at low levels in a lin-12/Notch independent manner. Activation of LIN-12/Notch is correlated with higher levels of LAG-1 accumulation compared to cells that do not have activated LIN-12/Notch. These findings suggest a potential autoregulation mechanism for lag-1 in certain contexts. They also suggest that endogenously tagged LAG-1 may be a useful molecular marker of LIN-12/Notch activation.

Physical factors in the environment of a cell regulate cell function and behavior and are involved in the formation and maintenance of tissue. There is strong evidence that substrate rigidity plays a key role in determining cell response in culture. Previous studies have demonstrated the importance of rigidity in numerous cellular processes including migration and adhesion and stem cell differentiation. Immune cells have been shown to respond differently to surfaces having different rigidities. Atypical response to rigidity is also a characteristic of cancerous cells. Understanding the mechanisms that support cellular rigidity sensing can lead to new tissue engineering strategies and potential new therapies based on rigidity modulation. A new technique was developed for the creation of biomimetic surfaces comprising regions of heterogeneous rigidity on the micro- and nanoscale. The surfaces are formed by exposing an elastomeric film of polydimethylsiloxane (PDMS) to a focused electron beam to form patterned regions of micro- and nanoscale spots. This thesis involves the formation of theses surfaces, characterization of their physical and chemical properties as a consequence of the electron beam exposure and investigation of how cells behave when plated on these surfaces. Cellular response to different patterns of heterogeneous rigidity is performed for several cell types. Human mesenchymal stem cells plated upon electron beam-exposed PDMS in a pattern of spots with diameters ranging from 2 µm to 100 nm display differential focal adhesion co-localization to the exposed features, depending on both rigidity and feature size. This behavior persists as the area of the exposed regions is reduced below ~1 µm. On spots with diameters of ~ 250 nm and smaller, focal adhesion co-localization is lost. This supports the notion that there is a length scale for cellular rigidity sensing, with the critical length in the range of a few hundred nanometers. When the heterogeneous rigidity surfaces are applied to CD4+ T cells, accumulations of proteins including TCR and pCasL on the exposed features are observed as a function of feature size. The pCasL appeared to significantly accumulate on 2 µm spots; For spots ~ 1 µm and below, cells appeared unable to identify the rigid regions. Further, Ca2+ release, a functional indicator of immunoresponse, is significantly enhanced on mixed-rigidity patterned PDMS relative to both soft and hard PDMS. Possible signaling pathways of TCR activation have been verified on e-beam exposed PDMS substrates with heterogeneous rigidity. These results are suggestive of possible new approaches to adoptive immunotherapy based on rigidity modulation. Studies on breast cancer cells indicate that on patterned substrates, sub-cellular processes are also significantly modulated. Integrin recruitment is enhanced on the rigid regions. Understanding the role of geometry in cellular rigidity response will point the way toward revealing its functional response and will shed light on the mechanistic underpinnings of this process.