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

Thesis (Ph. D. in Neuroscience)--Vanderbilt University, Dec. 2005. / Title from title screen. Includes bibliographical references.

Thesis (M.S.)--Brigham Young University. Dept. of Exercise Sciences, 2006. / Includes bibliographical references.

Thesis (Ph. D.)--West Virginia University, 2003. / Title from document title page. Document formatted into pages; contains v, 149 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.

Pulmonary endothelial cell (EC) barrier dysfunction and recovery is critical to the pathophysiology of acute respiratory distress syndrome. Cytoskeletal and subsequent cell membrane dynamics play a key mechanistic role in determination of EC barrier integrity. Here, we characterizAQe the actin related protein 2/3 (Arp 2/3) complex, a regulator of peripheral branched actin polymerization, in human pulmonary EC barrier function through studies of transendothelial electrical resistance (TER), intercellular gap formation, peripheral cytoskeletal structures and lamellipodia. Compared to control, Arp 2/3 inhibition with the small molecule inhibitor CK-666 results in a reduction of baseline barrier function (1,241 +/- 53 vs 988 +/- 64 ohm; p < 0.01), S1P-induced barrier enhancement and delayed recovery of barrier function after thrombin (143 +/- 14 vs 93 +/- 6 min; p < 0.01). Functional changes of Arp 2/3 inhibition on barrier integrity are associated temporally with increased intercellular gap area at baseline (0.456 +/- 0.02 vs 0.299 +/- 0.02; p < 0.05) and thirty minutes after thrombin (0.885 +/- 0.03 vs 0.754 +/- 0.03; p < 0.05). Immunofluorescent microscopy reveals reduced lamellipodia formation after S1P and during thrombin recovery in Arp 2/3 inhibited cells. Individual lamellipodia demonstrate reduced depth following Arp 2/3 inhibition vs vehicle at baseline (1.83 +/- 0.41 vs 2.55 +/- 0.46 mm; p < 0.05) and thirty minutes after S1P treatment (1.53 +/- 0.37 vs 2.09 +/- 0.36 mm; p < 0.05). These results establish a critical role for Arp 2/3 activity in determination of pulmonary endothelial barrier function and recovery through formation of EC lamellipodia and closure of intercellular gaps.

Glioblastoma multiforme (GBM) is an aggressive Grade IV astrocytoma with a poor survival rate. This is largely due to the GBM tumor cells migrating away from the primary tumor site along white matter tracts and blood vessels leading to secondary tumor sites. It is unknown whether the microenvironment nanotopography influences the biomechanical properties of the tumor cells. Although these tumor cells have an innate propensity to migrate, we believe that the nanotopography changes the biomechanical properties to enhance the migratory phenotype. To study this, we used an in vitro polycaprolactone aligned nanofiber film that mimics the nanotopography of the white matter tracts and blood vessels to investigate the mechanical properties of the GBM tumor cells. Our data demonstrate that the cytoskeletal stiffness, traction force, and focal adhesion area are inherently lower in invasive GBM tumor cells compared to healthy astrocytes. Moreover, the tumor cytoskeletal stiffness was significantly reduced when cultured on the aligned nanofiber films compared to smooth and randomly aligned nanofibers films. Analysis of gene expression also showed that tumor cells cultured on the aligned nanotopography upregulated key migratory genes and downregulated key proliferative genes. In addition, cell cycle analysis exhibited a reduced proliferative state on aligned nanofibers, highlighting the dichotomy between proliferation and migration observed in GBM. Finally, focal adhesions of tumor cells were larger and more elliptical when grown on the aligned fibers, suggesting a more migratory state. Therefore, our data demonstrate that the invasive potential is elevated when the tumor cells are cultured on an aligned nanotopography. This in vitro model can further be used to identify the GBM tumor cells’ response in a mimetic in vivo tumor microenvironment and elucidate how the aligned nanotopography transduces into altered gene and protein expression, thus providing a mechanism to target to inhibit the enhanced migratory behavior observed in these cells.

Severing the DNA double helix is a requisite step in the exchange of genetic material between homologous chromosomes in meiosis and between immunoglobulin domains during the generation of immune-receptor diversity. While these DNA transactions are essential for human fertility and the development of the immune system, misrepaired or unrepaired DNA double-strand breaks (DSBs) can lead to chromosome rearrangements or cell death. Indeed, ionizing radiation which generates DSBs in tumors is a cornerstone of cancer therapy. However, tumor cells can tolerate otherwise lethal levels of DNA damage by exploiting DNA repair pathways. Thus, discovering new strategies to selectively inhibit the repair of DSBs remains a major goal in the development of more effective cancer therapies. DSB repair may occur by multiple pathways, and the decision to use one pathway over another is influenced by cell cycle stage, the chromatin state, and the complexity of the inciting lesion. Mammalian cells primarily resolve DSBs by ligating the free ends together during a process termed “non-homologous end joining” (NHEJ). However, chemically modified or damaged DSB ends cannot be directly ligated by the NHEJ machinery. If NHEJ fails, DSBs may be nucleolytically cleaved to generate 3’ single-stranded DNA overhangs via a process called end resection. The resected DNA strands are poor substrates for NHEJ and instead search for homology in the genome to resynthesize the sequence surrounding the break site. This process is termed “homology-directed repair” (HDR). HDR is tightly coupled to cell cycle phase to ensure that resection occurs during late S and G2 when the ideal template, the sister chromatid, may be utilized. Following DNA damage, repair factors accumulate at DSB sites and form microscopically-detectable DNA repair foci. The dynamics of these foci may be observed by time-lapse microscopy making it possible to observe the behavior of breaks undergoing HDR and NHEJ. Interestingly, in yeast and mammalian cells, DNA motion is increased following DSB generation. DNA movements can lead to the clustering of DSBs into a common repair focus. DSB movements are intricately related to repair by HDR and require factors critical for resection initiation and downstream recombination. In contrast, DSBs undergoing NHEJ are relatively immobile. These observations suggest that the commitment of DSB repair to HDR regulates DSB movement and clustering; however, how DSB clustering might promote repair and whether active mechanisms drive this process remain relatively obscure. Recent studies have proposed roles for cytoskeletal proteins in genome organization and chromosomal dynamics. The Arp2/3 complex generates propulsive forces by nucleating a highly branched network of actin filaments. Genotoxic agents trigger actin polymerization in the nucleus. However, how DSB repair pathways might harness nuclear Arp2/3 machinery is unknown. Chapter 1 provides an overview of these pathways including the key steps of DSB repair, the regulation of actin nucleation, and the proteins involved in chromatin mobility. Chapter 1 provides context for the rest of the thesis in which I explore the contribution of nuclear actin polymerization to DSB repair. In Chapter 2, I detail our studies assessing the contribution of the Arp2/3 complex to DSB movement and clustering. Using Xenopus laevis cell-free extracts and mammalian cells, we show that actin nucleation machinery (WASP, Arp2/3, and actin) is recruited to damaged chromatin undergoing HDR. In this chapter, I also investigate how Arp2/3-driven DSB movements specifically promote the dynamics of HDR breaks, while Arp2/3 activity does not influence NHEJ breaks. Finally, I show that reduced DSB movement produces defects in DNA end processing and HDR efficiency, while the efficiency of end-joining is unaffected. I summarize all of these findings in Chapter 3 and discuss their implications for DNA repair, translocation formation, and clinical applications.

Production of infectious retrovirus particles is a complex and poorly-understood process with multiple steps that are often linked to one another. Our aim in this study was to gain better understanding of the path the murine leukemia virus (MLV) structural protein Gag follows to assemble into immature capsid structures, the process of which is central to retroviral assembly and release. Extensive studies of human immunodeficiency virus type 1 (HIV-1) assembly have led to the development of a model proposing that the assembly of immature HIV-1 capsids proceeds sequentially through multiple intermediates, in association with an RNA granule containing some well-conserved cellular factors, such as ATP-binding cassette subfamily E member 1 (ABCE1) and DEAD-box helicase 6 (DDX6). In this work, we provided evidence suggesting that MLV Gag associates with endogenous ABCE1 in human cells expressing assembly-competent MLV, and can be found in at least three high-molecular weight complexes with sedimentation properties highly resembling the HIV-1 assembly intermediates. Furthermore, we assessed the Gag proteins of select assembly-defective MLV mutants in terms of their expression levels, ability to form viral particles, involvement in intracellular complexes, membrane association, and ABCE1 interaction. Our findings were not only consistent with a model of MLV assembly through host-mediated intermediates, but also provided novel information about the effects of various MLV Gag mutations that are associated with defects in particle production.

Cells contain an elaborate cytoskeleton which plays a major role in a variety of cellular functions including: maintenance of cell shape and dimension, providing mechanical strength, cell motility, cytokinesis during mitosis and meiosis and intracellular transport. The cell cytoskeleton is made up of three types of protein filaments: the microtubules, the intermediate filaments and the actin cytoskeleton. These components interact with each other to allow the cell to function correctly. When functioning incorrectly, disruptions to many cellular pathway have been observed with mutations in various cytoskeletal proteins causing an assortment of human disease phenotypes. Characterization of these filament systems in different cell types is essential to the understanding of basic cellular processes and disease causation. The studies in this thesis are concerned with examining specific cytoskeletal tropomyosin-defined actin filament systems in skeletal muscle. The diversity of the actin filament system relies, in part, on the family of actin binding proteins, the tropomyosins (Tms). There are in excess of forty Tm isoforms found in mammals which are derived from four genes: α, β, γ and δTm. The role of the musclespecific Tms in striated muscle is well understood, with sarcomeric Tm isoforms functioning as part of the thin filament where it regulates actin-myosin interactions and hence muscle contraction. However, relatively little known about the roles of the many cytoskeletal Tm isoforms. Cytoskeletal Tms have been shown to compartmentalise to form functionally distinct filaments in a range of cell types including neurons (Bryce et al., 2003), fibroblasts (Percival et al., 2000) and epithelial cells (Dalby-Payne et al., 2003). Recently it has been shown that cytoskeletal Tm, Tm5NM1 defines a cytoskeletal structure in skeletal muscle called the Z-line associated cytoskeleton (Z-LAC) (Kee et al., 2004).The disruption of this structure by over-expression of an exogenous Tm in transgenic mice results in a muscular dystrophy phenotype, indicating that the Z-LAC plays an important role in maintenance of muscle structure (Kee et al., 2004). In this study, specific cytoskeletal Tms are further investigated in the context of skeletal muscle. Here, we examine the expression, localisation and potential function of cytoskeletal Tm isoforms, focussing on Tm4 (derived from the δ- gene) and Tm5NM1 (derived from the γ-gene). By western blotting and immuno-staining mouse skeletal muscle, we show that cytoskeletal Tms are expressed in a range of muscles and define separate populations of filaments. These filaments are found in association with a number of muscle structures including the myotendinous junction, neuromuscular junction, the sarcolemma, the t-tubules and the sarcoplasmic reticulum. Of particular interest, Tm4 and Tm5NM1 define cytoskeletal elements in association with the saroplasmic reticulum and T-tubules, respectively, with a separation of less than 90 nm between distinct filamentous populations. The segregation of Tm isoforms indicates a role for Tms in the specification of actin filament function at these cellular regions. Examination of muscle during development, regeneration and disease revealed that Tm4 defines a novel cytoskeletal filament system that is orientated perpendicular to the sarcomeric apparatus. Tm4 is up-regulated in both muscular dystrophy and nemaline myopathy and also during induced regeneration and focal repair in mouse muscle. Transition of the Tm4-defined filaments from a predominsnatly longitudinal to a predominantly Z-LAC orientation is observed during the course of muscle regeneration. This study shows that Tm4 is a marker of regeneration and repair, in response to disease, injury and stress in skeletal muscle. Analysis of Tm5NM1 over-expressing (Tm5/52) and null (9d89) mice revealed that compensation between Tm genes does not occur in skeletal muscle. We found that the levels of cytoskeletal Tms derived from the δ-gene are not altered to compensate for the loss or gain of Tm5NM1 and that the localisation of Tm4 is unchanged in skeletal muscle of these mice. Also, excess Tm5NM1 is sorted correctly, localising to the ZLAC. This data correlates with evidence from previous investigations which indicates that Tm isoforms are not redundant and are functionally distinct (Gunning et al., 2005). Transgenic and null mice have also allowed the further elucidation of cytoskeletal Tm function in skeletal muscle. Analyses of these mice suggest a role for Tm5NM1 in glucose regulation in both skeletal muscle and adipose tissue. Tm5NM1 is found to colocalise with members of the glucose transport p fibres and analysis of both transgenic and null mice has shown an alteration to glucose uptake in adipose tissue. Taken together these data indicate that Tm5NM1 may play a role in the translocation of the glucose transport molecule GLUT4. In addition to this Tm5NM1 may play a role in adipose tissue regulation, since over-expressing mice found to have increased white adipose tissue and an up-regulation of a transcriptional regulator of fat-cell formation, PPAR-γ. / Doctor of Philosophy (PhD)

Thesis (M.S.)--The University of North Carolina at Greensboro, 2008. / Directed by Paul Steimle; submitted to the Dept. of Biology. Title from PDF t.p. (viewed Mar. 19, 2010). Includes bibliographical references (p. 30-31).