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Glycogen Synthase Kinase-3αß is an enzyme that is involved in cell cycle regulation by promoting the degradation of cyclin D1 and cycling D3 in cells. Special emphasis is placed in its regulatory role in B cells, as there it is evidence that suggests that this protein is inhibited during germinal center formation, where B cells undergo proliferation, somatic hypermutation and class switch recombination. By inducing DNA recombination via the Cre/lLxP recombination system and utilizing tamoxifen as a Cre activity inducer, B cells were culture in 40LB cells to form induced germinal center in vitro. Flow cytometry analysis suggests that in the absence of GSK-3 αß B cells proliferate extensively in germinal centers and being the process of class switch recombination. Although the results of this study are in accord with current theory, more experiments and research need to be made to validate the conclusions set forth in this study.

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Protein regulatory networks are the hallmark of many important biological functionalities. Two of these functionalities are mammalian cell cycle progression and near-perfect adaptive responses. Modeling and simulating these functionalities are crucial stages to understanding and predicting them as systems-level properties of cells. In the context of the mammalian cell cycle, the timing of DNA synthesis, mitosis and cell division is regulated by a complex network of biochemical reactions that control the activities of a family of cyclin-dependent kinases. The temporal dynamics of this reaction network is typically modeled by nonlinear differential equations describing the rates of the component reactions. This approach provides exquisite details about molecular regulatory processes but is hampered by the need to estimate realistic values for the many kinetic constants that determine the reaction rates. To avoid this problem, modelers often resort to "qualitative" modeling strategies, such as Boolean switching networks, but these models describe only the coarsest features of cell cycle regulation. In this work, we describe a hybrid approach that combines features of continuous and discrete networks. The model is evaluated in terms of flow cytometry measurements of cyclin proteins in asynchronous populations of human cell lines. Using our hybrid approach, modelers can quickly create quantitatively accurate, computational models of protein regulatory networks found in various contexts within cells. Large-scale protein regulatory networks, such as the one that controls the progression of the mammalian cell cycle, also contain small-scale motifs or modules that carry out specific dynamical functions. Systematic characterization of smaller, interacting, network motifs whose individual behavior is well known under certain conditions is therefore of great interest to systems biologists. We model and simulate various 3-node network motifs to find near-perfect adaptation behavior. This behavior entails that a system responds to a change in its environmental cues, or signals, by coming back nearly to its pre-signal state even in the continued presence of the signal. We let various topologies evolve in their parameter space such that they eventually stumble upon a region where they score well under a pre-defined scoring metric. We find many such parameter sample sets across various classes of topologies. / Ph. D.

Indiana University-Purdue University Indianapolis (IUPUI) / Stem cell factor (SCF) mediated c-Kit signaling, and downstream activation of Phosphatidylinositol-3 Kinase (PI-3K) is critical for multiple biological effects mediated by mast cells. Mast cells express multiple regulatory subunits of PI-3Kinase, including p85α, p85β, p50α and p55α. In the present study, we have examined the relationship between p85α and p85β subunit in mast cell development and show that loss of p85α in mast cell progenitors impairs their growth, maturation and survival whereas loss of p85β enhances this process. To further delineate the mechanism (s) by which p85α provides specificity to mast cell biology, we compared the amino acid sequences between p85α and p85β subunits. The two isoforms share significant structural homology in the two SH2 domains, but show significant differences in the N-terminal SH3 domain as well as the BCR homology domain. To determine whether the c-Kit induced reduction in growth of mast cells is contributed via the N-terminal SH3 or the BCR homology domain, we cloned and expressed the shorter splice variant p50α, and various truncated mutant versions of p85α in p85α deficient mast cells. We demonstrate both invitro and invivo that while the SH3 and the BH domains of p85 are dispensable for mast cell maturation; they are essential for normal growth and survival. In contrary to existing dogma on redundant functional role of PI-3K regulatory subunits, this study proves that p85α and p85β regulatory subunits of PI-3K have unique roles in mast cell development. We prove that p85α deficiency impairs the expression of multiple growth, survival and maturation related genes whereas p85β deficiency inhibits c-Kit receptor internalization and degradation. This novel finding on negative role of p85β in mast cell development has significant clinical implication, as this knowledge could be used to develop treatments for mast-cell-associated leukemia and mastocytosis.

Cul3 forms E3 ubiquitin ligase complexes that regulate a variety of cellular processes. This dissertation describes Cul3's role in several of these pathways and provides new mechanistic details regarding the role of Cul3 in eukaryotic cells. Cyclin E is an example of a protein that is regulated in a Cul3-dependent manner. Cyclin E is a cell cycle regulator that controls the beginning of DNA replication in mammalian cells. Increased levels of cyclin E are found in some cancers, in addition, proteolytic removal of the cyclin E N-terminus occurs in some cancers and is associated with tumorigenesis. Cyclin E levels are tightly regulated and controlled in part through ubiquitin-mediated degradation initiated by one of two E3 ligase complexes, Cul1 and Cul3. Cul1 mediated degradation of cyclin E is triggered by cyclin E phosphorylation, however the mechanism Cul3 uses to ubiquitinate cyclin E is poorly understood. In order to gain a better understanding of how Cul3 mediates cyclin E destruction we identified the degron on cyclin E that is important in Cul3 dependent degradation. In addition, we show this degron is lacking in LMW cyclin E (found in abundance in breast cancer), providing a novel mechanism for how these cyclin E modifications result in increased cyclin E levels by avoiding the Cul3 degradation pathway.