No description available.

No description available.

No description available.

<p><em>Chlamydia pneumoniae </em>is a Gram-negative, obligate intracellular bacterium which shares its unique biphasic developmental cycle, genus-specific lipopolysaccharide, and complement fixation antigen with the other <em>Chlamydia</em> species. Intracellular bacteria, like <em>Chlamydia</em>, require strategies to invade host cells, evade host detection, commandeer host processes, and absorb nutrients in order to support their developmental cycle and survive. The type III secretion (T3S) system meets these needs by transporting bacterial effector proteins across the bacterial membrane and through the host cell membrane. The T3S system in <em>C. pneumoniae </em>is composed of approximately twenty different proteins, whose encoding genes are dispersed throughout ten operons in the <em>Chlamydia</em> genome. CdsD (<em>Cpn0712</em>), a basal body protein component of the T3S apparatus, is suggested to localize to the inner membrane and anchor other T3S structural components of the inner membrane ring. However, the cytoplasmic N-terminal domain contains two putative forkhead-associated (FHA) domains which may play an additional functional role in cellular signalling. This large hypothetical inner-membrane protein is poorly characterized in <em>C. pneumoniae </em>and the role of the predicted phospho-threonine binding, N-terminal FHA domains has yet to be elucidated. Herein, we provide evidence that CdsD has a high affinity for five cytoplasmic (CdsQ, CdsL, CdsN, PknD and SycH) and one periplasmic (CdsF) T3S-associated proteins. We also provide the first evidence that the phosphorylation of CdsD may permit the phosphorylation-dependent oligomerization or interaction with other phosphorylated components of the T3S apparatus. Future research will clarify the role of phosphate signalling in the T3S virulence mechanism. Ultimately, this may lead to a greater understanding of signalling mechanisms that regulate the secretion of bacterial effectors into host eukaryotic cells.</p> / Master of Science (MSc)

No description available.

No description available.

Diabetes is growing public health problem in the United States. Both in Type 1 and Type 2 diabetes, the deterioration of glycemic control over time is largely due to insulin secretory dysfunction and significant loss of functional β-cells. As such, the search for novel agents that promote β-cell survival and preserve functional β-cell mass are one of the essential strategies to prevent and treat the onset of diabetes. Genistein, a flavonoid in legumes and some herbal medicines, has various biological actions. It was recently shown that dietary intake of foods containing genistein improves diabetes in both experimental animals and humans. However, the potential anti-diabetic mechanisms of genistein are unclear. In the present study, we first investigated the effect of genistein on β-cell insulin secretion and proliferation and cellular signaling related to these effects in vitro and in vivo. We then determined its anti-diabetic potential in insulin-deficient and obese diabetic mouse models. The results in our study showed that exposure of clonal insulin secreting (INS1E) cells or isolated pancreatic islets to genistein at physiologically relevant concentrations (1-10 μM) enhanced glucose-stimulated insulin secretion (GSIS), whereas insulin content was not altered, suggesting that genistein-enhanced GSIS is not due to a modulation of insulin synthesis. This genistein's effect is protein tyrosine kinase- and KATP channel-independent. In addition, genistein had no effect on glucose transporter-2 expression or cellular ATP production, but similarly augmented pyruvate-stimulated insulin secretion in INS1E cells, indicating that genistein improvement of insulin secretion in β-cells is not related to an alternation in glucose uptake or the glycolytic pathway. Further, genistein (1-10 μM) induced both INS1 and human islet β-cell proliferation following 24 h of incubation, with 5 μM genistein inducing a maximal 27% increase. The effect of genistein on β-cell proliferation was neither dependent on estrogen receptors, nor shared by 17β-estradiol or a host of structurally related flavonoid compounds. Pharmacological or molecular intervention of PKA or ERK1/2 completely abolished genistein-stimulated β-cell proliferation, suggesting that both molecules are essential for genistein action. Consistent with its effect on cell proliferation, genistein induced cAMP/PKA signaling and subsequent phosphorylation of ERK1/2 in both INS1 cells and human islets. Furthermore, genistein induced protein expression of cyclin D1, a major cell-cycle regulator essential for β-cell growth. Dietary intake of genistein significantly improved hyperglycemia, glucose tolerance, and blood insulin levels in both insulin deficient type 1 and obese type 2 diabetic mice, concomitant with improved islet β-cell proliferation, survival, and mass. These changes were not due to alternations in animal body weight gain, food intake, fat deposit, plasma lipid profile, or peripheral insulin sensitivity. Collectively, these findings provide better understanding of the mechanism underlying the anti-diabetic effects of genistein. Loss of functional β-cell mass through apoptosis is central to the development of both T1D and T2D and islet β-cell preservation and regeneration are very important components of β-cell adaptation to increased apoptosis and insulin resistance and therefore holds promise as a treatment for this disease. In this context, these findings may potentially lead to the development of novel low-cost natural agents for prevention and treatment of diabetes. / Ph. D.

Researchers of <i>Clostridium perfringens</i>, a Gram-positive anaerobic pathogen, were lacking a tightlyregulated, inducible promoter system in their genetic toolbox. We constructed a lactose-inducible plasmid-based system utilizing the transcriptional regulator, BgaR. Using the <i>E. coli</i> reporter GusA, we characterized its induction in three different strains of <i>C. perfringens</i>. We then used a newly-developed mutation system to create in-frame deletion mutants in three genes with homology to Type IV pilins, and we used the promoter system described above to complement the mutants. We analyzed each pilin for localization and expression, as well as tested each of the mutants for various phenotypes frequently associated with type IV pili (TFP) and type II secretion systems. PilA2, PilA3, and PilA4 localized to the poles of the cells. PilA2 was expressed in the wildtype when <i>C. perfringens</i> was grown on agar plates, and the PilA3 mutant lacked a von Willebrand factor A domain-containing protein in its secretome. We used our promoter system to express GFP-tagged versions of the TFP ATPase homologues and view them in cells growing on surfaces. We saw that PilB1 and PilB2 co-localized nearly all of the time, while a portion of PilT was independent of the PilB proteins. PilT appeared necessary for the localization of PilB, and it localized independently of TFP proteins in <i>Bacillus subtilis</i>. PilT's typical localization in <i>Bacillus subtilis</i> was disrupted when the GTPase and polymerization activity of cell division protein FtsZ was blocked, suggesting that PilT associates with cell division proteins. / Master of Science

The opportunistic pathogen Pseudomonas aeruginosa ranks among the leading causes of nosocomial infections.  The type III secretion system (T3SS) aids acute P. aeruginosa infections by injecting potent cytotoxins (effectors) into host cells to suppress the host's innate immune response.  Expression of all T3SS-related genes is strictly dependent upon the transcription factor ExsA.  Consequently, ExsA and the biological processes that regulate ExsA function are of great biomedical interest.  The ExsA-ExsC-ExsD-ExsE signaling cascade ties host cell contact to the up-regulation of T3SS gene expression.  Prior to T3SS induction, the antiactivator protein ExsD binds to ExsA and blocks ExsA-dependent transcription by interfering with ExsA dimerization and promoter interactions.  Upon host cell contact, ExsD is sequestered by the T3SS chaperone ExsC, resulting in the release of ExsA and an up-regulation of the T3SS. ExsA is an AraC/XylS-type transcriptional regulator and belongs to a subfamily of activators that regulate the T3SS in a variety of Gram-negative pathogens.  These regulators are characteristically difficult to purify due to the low solubility of their C-terminal DNA binding domains.  A new method for purifying ExsA was developed and produced ExsA with improved solubility.  The interaction of ExsA and its PexsD promoter was examined using fluorescence anisotropy.  An in vitro transcription assay was developed and it was determined that ExsA is sufficient to activate T3SS transcription. Next, the ExsD--ExsA inhibitory mechanism was examined.  It was demonstrated for the first time that ExsD alone is sufficient to inhibit ExsA-dependent transcription in  vitro without the aid of any other cellular factors.  More significantly and contrary to previously published results, it was discovered that independently folded ExsD and ExsA are capable of interacting, but only at 37 degrees C and not at 30 degrees C.  Guided by the crystal structure of ExsD, a monomeric variant of the protein was designed to demonstrate that ExsD trimerization prevents ExsD from inhibiting ExsA-dependent transcription at 30 degrees C. To further elucidate the ExsD-ExsA inhibitory mechanism, the ExsD-ExsA interface was examined.  ExsD variants were generated and used to determine which region of ExsD interacts with ExsA.  Interestingly, ExsD was also found to bind DNA, although it is unclear whether or not this plays a role in ExsA inhibition.  Fully understanding the mechanism by which ExsD inhibits ExsA may enable the development of drugs that target ExsA in order to shut down the T3SS, thereby eliminating P. aeruginosa infection. / Ph. D.

In this thesis we study modeling and simulation approaches for multiscale biochemical systems. The thesis addresses both modeling methods and simulation strategies. In the first part, we propose modeling methods to study the behavior of the insulin secretion pathway. We first expand the single cell model proposed by Bertram et. al. to model multiple cells. Synchronization among multiple cells is observed. Then an unhealthy cell model is proposed to study the insulin secretion failure caused by weakening of mitochondria function. By studying the interaction between the healthy and unhealthy cells, we find that the insulin secretion can be reinstated by increasing the glucokinase level. This new discovery sheds light on antidiabetic medication. In order to study the stochastic dynamics of the insulin secretion pathway, we first apply the hybrid method to model the discrete events in the insulin secretion pathway. Based on the hybrid model, a probability based measurement is proposed and applied to test the new antidiabetic remedy. In the second part, we focus on different simulation schemes for multiscale biochemical systems. We first propose a partitioning strategy for the hybrid method which leads to an efficient way of building stochastic cell cycle models. Then different implementation methods for the hybrid method are studied. A root finding method based on inverse interpolation is introduced to implement the hybrid method with three different ODE solvers. A detailed discussion of the performance of these three ODE solvers is presented. Last, we propose a new strategy to automatically detect stiffness and identify species that cause stiffness for the Tau-Leaping method, as well as two stiffness reduction methods. The efficiency is demonstrated by applying this new strategy on a stiff decaying dimerization model and a heat shock protein regulation model. / Ph. D.