The integrin Mac-1 (αMβ2, CD11b/CD18) is an important adhesion receptorexpressed on macrophages and neutrophils. It plays a crucial role in phagocytosis, cell-cell fusion, and cell migration. αMβ2 is also the most promiscuous integrin with over 100 known ligands that span a broad range of physical and chemical attributes, many of which bind to the inserted (I) domain from the αM subunit. The interaction of αMI-domain with cytokine pleiotrophin (PTN) were determine. PTN is a cationic protein known to induce Mac-1- mediated adhesion and migration in cells. The data showed that PTN’s interaction with αMI-domain contains both divalent cation-dependent and independent mechanisms. In particular, PTN’s N-terminal domain has weak interactions with the N/C-termini side of αMI-domain using a metal-independent mechanism. However, stronger interaction is achieved through the chelation of the divalent cation in the metal ion-dependent adhesion site of active αMI-domain by PTN’s acidic residues. Although many acidic residues in PTN can act as the chelator, active αMI-domain’s interaction with PTN’s E98 plays an especially important role. NOE, chemical shift perturbation (CSP) data, and mutagenesis studies showed residues near E98 are at the binding interface and the E98 mutation greatly reduced binding affinity between two proteins. Interestingly, the CSP and MD simulation data showed the binding interface can be supported by the interaction of PTN’s H95 with the acidic clusters D242, E244, and D273 from αMI-domain, while PTN’s E66 form electrostatic interaction with R208 and K245 from αMI-domain. The determined recognition motif of αMI-domain for its ligands is (H/R/K)xxE. The ability to accommodate the longer distance between E and (H, R, K) compared to the zwitterionic motif RGDii explained how αMβ2 can interact with a large repertoire of ligands and be versatile in its functional portfolio.

Adsorption of fibrinogen on various surfaces, including biomaterials, dramatically reduces the adhesion of platelets and leukocytes. The mechanism by which fibrinogen renders surfaces non-adhesive is its surface-induced self-assembly leading to the formation of a nanoscale multilayer matrix. Under the applied tensile force exerted by cellular integrins, the fibrinogen matrix extends as a result of the separation of layers which prevents the transduction of strong mechanical forces, resulting in weak intracellular signaling and feeble cell adhesion. Furthermore, upon detachment of adherent cells, a weak association between fibrinogen molecules in the superficial layers of the matrix allows integrins to pull fibrinogen molecules out of the matrix. Whether the latter mechanism contributes to the anti-adhesive mechanism under the flow is unclear. In the present study, using several experimental flow systems, it has been demonstrated that various blood cells as well as model HEK293 cells expressing the fibrinogen receptors, were able to remove fibrinogen molecules from the matrix in a time- and cell concentration-dependent manner. In contrast, insignificant fibrinogen dissociation occurred in a cell-free buffer, and crosslinking fibrinogen matrix significantly reduced cell-mediated dissociation of adsorbed fibrinogen. Surprisingly, cellular integrins contributed minimally to fibrinogen dissociation since function-blocking anti-integrin antibodies did not significantly inhibit this process. In addition, erythrocytes that are not known to express functional fibrinogen receptors and naked liposomes caused fibrinogen dissociation, suggesting that the removal of fibrinogen from the matrix may be caused by nonspecific low-affinity interactions of cells with the fibrinogen matrix. These results indicate that the peeling effect exerted by flowing cells upon their contact with the fibrinogen matrix is involved in the anti-adhesive mechanism.

Mucosal membranes represent a major site of pathogen transmission and cancer development. Enhancing T cell migration to mucosal surfaces could improve immune-based therapies for these diseases, yielding better clinical outcomes. All-trans-retinoic acid (ATRA) is a biologically active form of vitamin A that has been shown to increase T cell migration to mucosal sites, however its therapeutic use is limited by its toxicity potential and unstable nature. ATRA-related compounds with lower toxicity and higher stability were assessed for their ability to induce similar immune migration effects as ATRA, using in vitro and in vivo model systems. Chapter 2 summarizes the first project, in which synthetic, ATRA-like compounds called rexinoids were used to modulate T cell expression of mucosal homing proteins chemokine receptor 9 (CCR9) and integrin alpha 4 beta 7 (α4β7), and alter their physical migration in vitro. Several rexinoids independently mimicked the activity of ATRA to enhance protein expression and migration, while others worked synergistically with subtoxic doses of ATRA to produce similar results. Furthermore, rexinoid administration in vivo was well-tolerated by animal models, a finding not seen with ATRA. Chapter 3 focuses on the second project, where plasmids containing ATRA-synthesizing proteins were assessed for their in vivo ability to act as mucosal vaccine adjuvants and enhance T cell migration to mucosal sites during DNA vaccination. Though increased mucosal migration was seen with use of the adjuvant plasmids, these findings were not determined to be significant. Immune-mediated protection following viral challenge was also not determined to be significant in animal models receiving both vaccine and adjuvant plasmids. The data shows that several novel rexinoids may possess enhanced clinical utility compared to ATRA, lending support for their use in immunotherapeutic approaches towards mucosal maladies. While the potential mucosal vaccine adjuvants did not show great significance in enhancing T cell migration or viral protection, further optimization of the model system may produce better results. This work helps advance knowledge of immune cell trafficking to afflicted mucosal regions. It can be used as a basis for understanding migration to other body areas, as well as for the development of better immune-based treatments.

Macrophage fusion resulting multinucleated giant cells (MGCs) formation is associated with numerous chronic inflammatory diseases including the foreign body reaction to implanted biomaterials. Despite long-standing predictions, there have been attempts to use live-cell imaging to investigate the morphological features initiating macrophage fusion because macrophages do not fuse on clean glass required for most imaging techniques. Consequently, the mechanisms of macrophage fusion remain poorly understood. The goal of this research project was to characterize the early and late stages of macrophage multinucleation using fusogenic optical quality substrate. Live-cell imaging with phase-contrast and lattice-light sheet microscopy revealed that an actin-based protrusion initiates macrophage fusion. WASpdeficient macrophages and macrophages isolated from myeloid cell-specific Cdc42-/- mice fused at very low rates. In addition, inhibiting the Arp2/3 complex impaired both the formation of podosomes and macrophage fusion. Analyses of the late stages of macrophage multinucleation on biomaterials implanted into mice revealed novel actin-based zipper-like structures (ZLSs) formed at contact sites between MGCs. The model system that was developed for the induction of ZLSs in vitro allowed for the characterization of protein composition using confocal and super-resolution microscopy. Live-cell imaging demonstrated that ZLSs are dynamic formations undergoing continuous assembly and disassembly and that podosomes are precursors of these structures. It was further found that E-cadherin and nectin-2 are involved in ZLS formation by bridging the plasma membranes together. ii Macrophage fusion on implanted biomaterials inherently involves their adhesion to the implant surface. While biomaterials rapidly acquire a layer of host proteins, a biological substrate that is required for macrophage fusion is unknown. It was shown that mice with fibrinogen deficiency as well as mice expressing fibrinogen incapable of fibrin polymerization displayed a dramatic reduction of macrophage fusion on biomaterials. Furthermore, these mice were protected from the formation of the dense collagenous capsule enveloping the implant. It was also found that the main cell type responsible for the deposition of collagen in the capsule were mononuclear macrophages but not myofibroblasts. Together, these findings reveal a critical role of the actin cytoskeleton in macrophage fusion and identify potential targets to reduce the drawbacks of macrophage fusion on implanted biomaterials.

CD47 is a cell surface receptor expressed on many cells in the body. It has many immune functions such as marking host cells as “self” and the activation of apoptosis through phagocytosis. Mac-1 is a major integrin on myeloid cells and has been implicated in several different macrophage immune functions. Previous studies from Dr. Ugarova’s lab demonstrated CD47 may form a complex with Mac-1 through the cis-interaction and could regulate Mac-1-dependent macrophage functions. To localize the binding site for Mac-1 in CD47, the extracellular domain of CD47 IgV was isolated as GST-fusion protein from E. coli cells. The recombinant fusion protein is being used in current studies with cell adhesion assays and immunoprecipitation to determine the complementary binding site in Mac-1.

My thesis consisted of both a self-directed study and a creative project. I worked with Dr. Michael Grabow, an endodontist of 20 years, to understand the scientific and technical aspects of root canal therapy. The first phase of the thesis was a review of dental biology, tooth development, morphology, physiology, radiology, and endodontics. The second phase was the creative project in which I learned the technical process of performing a root canal. In this phase, I observed Dr. Grabow execute root canal therapy on live patients and extracted teeth (obtained from an oral surgeon). I then completed root canals of my own on extracted teeth, under the instruction and oversight of Dr. Grabow.

Cell fusion is a process that occurs in normal cells as well as in pathological cells. This process does not occur spontaneously, fusogens are required to mediate the process. Syncytin is one of the proteins that was determined to have fusogenic properties. Syncytin is a newly discovered transmembrane protein that is generally expressed in mammalian placenta and it is known for its role in cell fusion during placentation. The recent studies in Ugarova’s laboratory suggest syncytin is expressed in macrophages, thus it may be involved in macrophage cells fusion. This paper provides a literature review of syncytin protein; it also contains an experimental study conducted to determine syncytin expression on both RNA and protein level. The study was conducted on RNA and protein isolated from macrophages isolated from mouse peritoneum. Agarose gel electrophoresis and Western blot analysis were used to determine syncytin expression on RNA and protein level respectively. Using these methods, syncytin expression was determined at different time points during macrophage fusion. The results show that syncytin is not expressed in freshly isolated macrophages, but its expression is initiated during macrophage adhesion in the presence of IL-4.

A novel clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) tool for simultaneous gene editing and regulation was designed and tested. This study used the CRISPR-associated protein 9 (Cas9) endonuclease in complex with a 14-nucleotide (nt) guide RNA (gRNA) to repress a gene of interest using the Krüppel associated box (KRAB) domain, while also performing a separate gene modification using a 20-nt gRNA targeted to a reporter vector. DNA Ligase IV (LIGIV) was chosen as the target for gene repression, given its role in nonhomologous end joining, a common DNA repair process that competes with the more precise homology-directed repair (HDR).

To test for gene editing, a 20-nt gRNA was designed to target a disrupted enhanced green fluorescent protein (EGFP) gene present in a reporter vector. After the gRNA introduced a double-stranded break, cells attempted to repair the cut site via HDR using a DNA template within the reporter vector. In the event of successful gene editing, the EGFP sequence was restored to a functional state and green fluorescence was detectable by flow cytometry. To achieve gene repression, a 14-nt gRNA was designed to target LIGIV. The gRNA included a com protein recruitment domain, which recruited a Com-KRAB fusion protein to facilitate gene repression via chromatin modification of LIGIV. Quantitative polymerase chain reaction was used to quantify repression.

This study expanded upon earlier advancements, offering a novel and versatile approach to genetic modification and transcriptional regulation using CRISPR/Cas9. The overall results show that both gene editing and repression were occurring, thereby providing support for a novel CRISPR/Cas system capable of simultaneous gene modification and regulation. Such a system may enhance the genome engineering capabilities of researchers, benefit disease research, and improve the precision with which gene editing is performed.

Traumatic brain injury (TBI) is a serious health problem around the world with few available treatments. TBI pathology can be divided into two phases: the primary insult and the secondary injury. The primary insult results from the bump or blow to the head that causes the initial injury. Secondary injury lasts from hours to months after the initial injury and worsens the primary insult, creating a greater area of tissue damage and cell death. Many current treatments focus on lessening the severity of secondary injury. Secondary injury results from the cyclical nature of tissue damage. Inflammatory pathways cause damage to tissue, which in turn reinforces inflammation. Since many inflammatory pathways are interconnected, targeting individual products within these pathways is impractical. A target at the beginning of the pathway, such as a receptor, must be chosen to break the cycle. This project aims to identify novel nanobodies that could temporarily inactivate the CD36 receptor, which is a receptor found on many immune and endothelial cells. CD36 initiates and perpetuates the immune system's inflammatory responses. By inactivating this receptor temporarily, inflammation and immune cell entry could be lessened, and therefore secondary injury could be attenuated. This project utilized phage display as a method of nanobody selection. The specific phage library utilized in this experiment consists of human heavy chain (V_H) segments, also known as domain antibodies (dAbs), displayed on M13 filamentous bacteriophage. Phage display mimics the process of immune selection. The target is bound to a well as a means of displaying it to the phage. The phage library is then incubated with the target to allow antibodies to bind. After, the well is washed thoroughly to detach any phage that are not strongly bound. The remaining phage are then amplified in bacteria and run again through the same assay to select for mutations that resulted in higher affinity binding. This process, called biopanning, was performed three times for this project. After biopanning, the library was sequenced using Next Generation sequencing (NGS). This platform enables the entire library to be sequenced, as opposed to traditional Sanger sequencing, which can only sequence single select clones at a time thereby limiting population sampling. This type of genetic sequencing allows trends in the complementarity determining regions (CDRs) of the domain antibody library to be analyzed, using bioinformatics programs such as RStudio, FastAptamer, and Swiss Model. Ultimately, two nanobody candidates were identified for the CD36 receptor.

Vaccinia virus (VV) is a prototype virus of the Orthopox viruses. The large dsDNA virus composed of 200kbp genome contains approximately 200 genes and replicates entirely in the cytosol. Since its use as a live vaccine against smallpox that leads to the successful eradication of smallpox, Vaccinia has been intensely studied as a vaccine vector since the large genome allows for the insertion of multiple genes. It is also studied as a molecular tool for gene therapy and gene functional study. Despite its success as a live vaccine, the vaccination causes some mild to serious bur rare adverse events in vaccinees such as generalized Vaccinia and encepharitis. Therefore, identification of virulence genes and removal of these genes to create a safer vaccine remain an important tasks. In this study, the author seeks to elucidate the possible relationship between immune evading proteins E3 and B19. VV did not allow double deletions of E3 and B19, indicating the existence of a relationship between the two genes.