Indiana University-Purdue University Indianapolis (IUPUI) / Drug-drug interactions (DDIs) refer to situations where one drug affects the pharmacokinetics or pharmacodynamics of another. DDIs represent a major cause of morbidity and mortality. A common adverse drug reaction (ADR) that can result from, or be exacerbated by DDIs is drug-induced myopathy. Identifying DDIs and understanding their underlying mechanisms is key to the prevention of undesirable effects of DDIs and to efforts to optimize therapeutic outcomes. This dissertation is dedicated to identification of clinically important myopathic DDIs and to elucidation of their underlying mechanisms. Using data mined from the published cytochrome P450 (CYP) drug interaction literature, 13,197 drug pairs were predicted to potentially interact by pairing a substrate and an inhibitor of a major CYP isoform in humans. Prescribing data for these drug pairs and their associations with myopathy were then examined in a large electronic medical record database. The analyses identified fifteen drug pairs as DDIs significantly associated with an increased risk of myopathy. These significant myopathic DDIs involved clinically important drugs including alprazolam, chloroquine, duloxetine, hydroxychloroquine, loratadine, omeprazole, promethazine, quetiapine, risperidone, ropinirole, trazodone and simvastatin. Data from in vitro experiments indicated that the interaction between quetiapine and chloroquine (risk ratio, RR, 2.17, p-value 5.29E-05) may result from the inhibitory effects of quetiapine on chloroquine metabolism by cytochrome P450s (CYPs). The in vitro data also suggested that the interaction between simvastatin and loratadine (RR 1.6, p-value 4.75E-07) may result from synergistic toxicity of simvastatin and desloratadine, the major metabolite of loratadine, to muscle cells, and from the inhibitory effect of simvastatin acid, the active metabolite of simvastatin, on the hepatic uptake of desloratadine via OATP1B1/1B3. Our data not only identified unknown myopathic DDIs of clinical consequence, but also shed light on their underlying pharmacokinetic and pharmacodynamic mechanisms. More importantly, our approach exemplified a new strategy for identification and investigation of DDIs, one that combined literature mining using bioinformatic algorithms, ADR detection using a pharmacoepidemiologic design, and mechanistic studies employing in vitro experimental models.

Indiana University-Purdue University Indianapolis (IUPUI) / Signal Transducer and Activator of Transcription 3 (Stat3) is a transcription factor expressed in bone and joint cells that include osteoblasts, osteocytes, osteoclasts, and chondrocytes. Stat3 is activated by a variety of cytokines and growth factors, including IL-6/gp130 family cytokines. These cytokines not only regulate the differentiation of osteoblasts and osteoclasts, but also regulate proliferation of chondrocytes through Stat3 activation. In 2007, mutations of Stat3 have been confirmed to cause a rare human immunodeficiency disease – Job syndrome which presents skeletal abnormalities like: reduced bone density (osteopenia), scoliosis, hyperextensibility of joints, and recurrent pathological bone fractures. Changes in the Stat3 gene alter the structure and function of the Stat3 proteins, impairing its ability to control the activity of other genes. However, little is known about the effects of Stat3 mutations on bone cells and tissues. To investigate the in vivo physiological role of Stat3 in bone homeostasis, osteoblast/osteocyte-specific Stat3 knockout (KO) mice were generated via the Cre-LoxP recombination system. The osteoblast/osteocyte-specific Stat3 KO mice showed bone abnormalities and an osteoporotic phenotype because of a reduced bone formation rate. Furthermore, inactivation of Stat3 decreased load-driven bone formation, and the disruption of Stat3 in osteoblasts suppressed load-driven mitochondrial activity, which led to an elevated level of reactive oxygen species (ROS) in cultured primary osteoblasts. Stat3 has been found to be responsive to mechanical stimulation, and might play an important role in mechanical signal transduction in osteocytes. To investigate the role Stat3 plays in mechanical signaling transduction, osteocyte-specific Stat3 knockout (KO) mice were created. Inactivation of Stat3 in osteocytes presented a significantly reduced load-driven bone formation. Decreased osteoblast activity indicated by reduced osteoid surface was also found in osteocyte-specific Stat3 KO mice. Moreover, sclerostin (SOST) protein which is a critical osteocyte-specific inhibitor of bone formation, its encoded gene SOST expression has been found to be enhanced in osteocyte-specific Stat3 KO mice. Thus, these results clearly demonstrated that Stat3 plays an important role in bone homeostasis and mechanotransduction, and Stat3 is not only involved in bone-formation-important genes regulation in the nucleus but also in mediation of ROS and oxidative stress in mitochondria.

Indiana University-Purdue University Indianapolis (IUPUI) / Adaptive optics-optical coherence tomography (AO-OCT) is a non-invasive method of imaging the human retina in vivo. It can be used to visualize microscopic structures, making it incredibly useful for the early detection and diagnosis of retinal disease. The research group at Indiana University has a novel multi-camera AO-OCT system capable of 1 MHz acquisition rates. Until this point, a method has not existed to process data from such a novel system quickly and accurately enough on a CPU, a GPU, or one that can scale to multiple GPUs automatically in an efficient manner. This is a barrier to using a MHz AO-OCT system in a clinical environment. A novel approach to processing AO-OCT data from the unique multi-camera optics system is tested on multiple graphics processing units (GPUs) in parallel with one, two, and four camera combinations. The design and results demonstrate a scalable, reusable, extensible method of computing AO-OCT output. This approach can either achieve real time results with an AO-OCT system capable of 1 MHz acquisition rates or be scaled to a higher accuracy mode with a fast Fourier transform of 16,384 complex values.

The main purpose of this project is to develop new functionalities for the Solicitation Management System (SMS) to support the Office of Technology Transfer and Commercialization (OTTC), California State University San Bernardino (CSUSB) and the Center for the Commercialization of Advanced Technology (CCAT), San Diego State University (SDSU) for the 2008 solicitation, which opened on 28 Jan 2008. SMS is a system built to facilitate the processing of grant proposal solicitations. The SMS was first built in 2004 and was primarily used by the OTTC, CSUSB for its solicitation activities. The new version of the SMS is more user friendly, so that it is easier for users to use and comprehend. The purpose of this software is to aid the processing of a solicitation for organizations that conduct solicitations for grant proposals.

Indiana University-Purdue University Indianapolis (IUPUI) / Histone acetylation has been linked to developmental changes in gene expression and is a validated drug target of apicomplexan parasites, but little is known about the roles of individual histone modifying enzymes and how they are recruited to target genes. The protozoan parasite Toxoplasma gondii (phylum Apicomplexa) is unusual among invertebrates in possessing two GCN5-family lysine acetyltransferases (KATs). While GCN5a is required for gene expression in response to alkaline stress, this KAT is dispensable for parasite proliferation in normal culture conditions. In contrast, GCN5b cannot be disrupted, suggesting it is essential for Toxoplasma viability. To further explore the function of GCN5b, we generated clonal parasites expressing an inducible HA-tagged form of GCN5b containing a point mutation that ablates enzymatic activity (E703G). Stabilization of this dominant-negative form of GCN5b was mediated through ligand-binding to a destabilization domain (dd) fused to the protein. Induced accumulation of the ddHAGCN5b(E703G) protein led to a rapid arrest in parasite replication. Growth arrest was accompanied by a decrease in histone H3 acetylation at specific lysine residues as well as reduced expression of GCN5b target genes in GCN5b(E703G) parasites, which were identified using chromatin immunoprecipitation coupled with microarray hybridization (ChIP-chip). We also demonstrate that GCN5b interacts with AP2-domain proteins, which are plant-like transcription factors in Apicomplexa. The interactions between GCN5b, AP2IX-7, and AP2X-8 were confirmed by reciprocal co-immunoprecipitation and revealed a “core complex” that includes the co-activator ADA2-A, TFIID subunits, LEO1 polymerase-associated factor (Paf1) subunit, and RRM proteins. The dominant-negative phenotype of ddHAGCN5b(E703G) parasites, considered with the proteomics and ChIP-chip data, indicate that GCN5b plays a central role in transcriptional and chromatin remodeling complexes. We conclude that GCN5b has a non-redundant and indispensable role in regulating gene expression required during the Toxoplasma lytic cycle.

Indiana University-Purdue University Indianapolis (IUPUI) / Telomere maintenance is a critical component of genomic stability. An increasing body of evidence suggests BRCA1, a tumor suppressor gene with a variety of functions including DNA repair and cell cycle regulation, plays a role in telomere maintenance. Mutations in BRCA1 account for approximately half of all hereditary breast and ovarian cancers, and the gene is silenced via promoter methylation and loss of heterozygosity in a proportion of sporadic breast and ovarian cancers. The objective of this study was to determine whether GRN163L, a telomerase inhibitor, currently in clinical trials for the treatment of cancer, has enhanced anti-cancer activity in BRCA1 mutant breast/ovarian cancer cell lines compared to wild-type cancer cells. BRCA1 mutant cancer cells were observed to have shorter telomeres and increased sensitivity to telomerase inhibition, compared to cell lines with wild-type BRCA1. Importantly, GRN163L treatment was synergistic with DNA-damaging drugs, suggesting potential synthetic lethality of the BRCA1 cancer subtype and telomerase inhibition In a related study to examine the roles of BRCA1/2 in telomere maintenance, DNA and RNA extracted from peripheral blood were used to investigate the age-adjusted telomere lengths and telomere-related gene expression profiles of BRCA1 and BRCA2 individuals compared to individuals who developed sporadic cancer and healthy controls. BRCA1 mutation carriers and breast cancer patients showed the shortest average telomere lengths compared to the other groups. In addition, distinct genomic profiles of BRCA mutation carriers were obtained regarding overexpression of telomere-related genes compared to individuals who developed sporadic or familial breast cancer. In summary, telomerase inhibition may be a viable treatment option in BRCA1 mutant breast or ovarian cancers. These data also provides insights into further investigations on the role of BRCA1 in the biology underlying telomere dysfunction in cancer development.

Indiana University-Purdue University Indianapolis (IUPUI) / Spore photoproduct lyase (SPL) is a radical SAM (S-adenosylmethionine) enzyme that is responsible for the repair of the DNA UV damage product 5-thyminyl-5,6-dihydrothymine (also called spore photoproduct, SP) in the early germination phase of bacterial endospores. SPL initiates the SP repair process using 5'-dA• (5'-deoxyadenosyl radical) generated by SAM cleavage to abstract the H6proR atom which results in a thymine allylic radical. These studies provide strong evidence that the TpT radical likely receives an H atom from an intrinsic H atom donor, C141 in B. subtilis SPL. I have shown that C141 can be alkylated in native SPL by iodoacetamide treatment indicating that it is accessible to the TpT radical. Activity studies demonstrate a 3-fold slower repair rate of SP by C141A which produces TpTSO2 - and TpT simultaneously with no lag phase observed for TpTSO2- formation. Additionally, formation of both products shows a Dvmax kinetic isotope effect (KIE) of 1.7 ± 0.2 which is smaller than the DVmax KIE of 2.8 ± 0.3 for the WT SPL reaction. Removal of the intrinsic H atom donor by this single mutation disrupts the rate-limiting process in the enzyme catalysis. Moreover, C141A exhibits ~0.4 turnover compared to the > 5 turnovers in the WT SPL reaction. In Y97 and Y99 studies, structural and biochemical data suggest that these two tyrosine residues are also crucial in enzyme catalysis. It is suggested that Y99 in B. subtilis SPL uses a novel hydrogen atom transfer pathway utilizing a pair of cysteinetyrosine residues to regenerate SAM. The second tyrosine, Y97, structurally assists in SAM binding and may also contribute to SAM regeneration by interacting with radical intermediates to lower the energy barrier for the second H-abstraction step.

Indiana University-Purdue University Indianapolis (IUPUI) / The tight-binding model that has been used for many years in condensed matter physics, due to its analytic and numerical tractability, has recently been used to describe light propagating through an array of evanescently coupled waveguides. This dissertation presents analytic and numerical simulation results of light propagating in a waveguide array. The first result presented is that photonic transport can be achieved in an array where the propagation constant is linearly increasing across the array. For an input at the center waveguide, the breathing modes of the system are observed, while for a phase displaced, asymmetric input, phase-controlled photonic transport is predicted. For an array with a waveguide-dependent, parity-symmetric coupling constant, the wave packet dynamics are predicted to be tunable. In addition to modifying the propagation constant, the coupling between waveguides can also be modified, and the quantum correlations are sensitive to the form of the tunneling function. In addition to modifying the waveguide array parameters in a structured manner, they can be randomized as to mimic the insertion of impurities during the fabrication process. When the refractive indices are randomized and real, the amount of light that localizes to the initial waveguide is found to be dependent on the initial waveguide when the waveguide coupling is non-uniform. In addition, when the variance of the refractive indices is small, light localizes in the initial waveguide as well as the parity-symmetric waveguide. In addition to real valued disorder, complex valued disorder can be introduced into the array through the imaginary component of the refractive index. It is shown that the two-particle correlation function is qualitatively similar to the case when the waveguide coupling is real and random, as both cases preserve the symmetry of the eigenvalues. Lastly, different input fields have been used to investigate the quantum statistical aspects of Anderson localization. It is found that the fluctuations in the output intensity are enhanced and the entropy of the system is reduced when disorder is present in the waveguides.

Indiana University-Purdue University Indianapolis (IUPUI) / This work is focused on developing viable self-healing coatings, especially considering the viability of the coating in a commercial context. With this in mind, finding low cost healing agents, with satisfactory healing and mechanical properties as well as adapting the healing system for use in coatings was required. Seven potential healing agents were evaluated and an air-drying triglyceride (linseed oil) was identified as the candidate healing agent. Different encapsulation techniques were evaluated and ureaformaldehyde microcapsules were chosen as the candidate encapsulation technique. Self-healing coatings were fabricated using urea-formaldehyde encapsulated linseed oil. EIS, SEM and TGA technologies were used to evaluate mechanical performance, corrosion resistance, and self-healing performance.

Indiana University-Purdue University Indianapolis (IUPUI) / More than a decade ago, it was shown that non-Hermitian Hamiltonians with combined parity (P) and time-reversal (T ) symmetry exhibit real eigenvalues over a range of parameters. Since then, the field of PT symmetry has seen rapid progress on both the theoretical and experimental fronts. These effective Hamiltonians are excellent candidates for describing open quantum systems with balanced gain and loss. Nature seems to be replete with examples of PT -symmetric systems; in fact, recent experimental investigations have observed the effects of PT symmetry breaking in systems as diverse as coupled mechanical pendula, coupled optical waveguides, and coupled electrical circuits. Recently, PT -symmetric Hamiltonians for tight-binding lattice models have been extensively investigated. Lattice models, in general, have been widely used in physics due to their analytical and numerical tractability. Perhaps one of the best systems for experimentally observing the effects of PT symmetry breaking in a one-dimensional lattice with tunable hopping is an array of evanescently-coupled optical waveguides. The tunneling between adjacent waveguides is tuned by adjusting the width of the barrier between them, and the imaginary part of the local refractive index provides the loss or gain in the respective waveguide. Calculating the time evolution of a wave packet on a lattice is relatively straightforward in the tight-binding model, allowing us to make predictions about the behavior of light propagating down an array of PT -symmetric waveguides. In this thesis, I investigate the the strength of the PT -symmetric phase (the region over which the eigenvalues are purely real) in lattices with a variety of PT - symmetric potentials. In Chapter 1, I begin with a brief review of the postulates of quantum mechanics, followed by an outline of the fundamental principles of PT - symmetric systems. Chapter 2 focuses on one-dimensional uniform lattices with a pair of PT -symmetric impurities in the case of open boundary conditions. I find that the PT phase is algebraically fragile except in the case of closest impurities, where the PT phase remains nonzero. In Chapter 3, I examine the case of periodic boundary conditions in uniform lattices, finding that the PT phase is not only nonzero, but also independent of the impurity spacing on the lattice. In addition, I explore the time evolution of a single-particle wave packet initially localized at a site. I find that in the case of periodic boundary conditions, the wave packet undergoes a preferential clockwise or counterclockwise motion around the ring. This behavior is quantified by a discrete momentum operator which assumes a maximum value at the PT -symmetry- breaking threshold. In Chapter 4, I investigate nonuniform lattices where the parity-symmetric hop- ping between neighboring sites can be tuned. I find that the PT phase remains strong in the case of closest impurities and fragile elsewhere. Chapter 5 explores the effects of the competition between localized and extended PT potentials on a lattice. I show that when the short-range impurities are maximally separated on the lattice, the PT phase is strengthened by adding short-range loss in the broad-loss region. Consequently, I predict that a broken PT symmetry can be restored by increasing the strength of the short-range impurities. Lastly, Chapter 6 summarizes my salient results and discusses areas which can be further developed in future research.