Browsing by Subject "Systems Biology"
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Item Pathways, Networks and Therapy: A Boolean Approach to Systems Biology(2012-07-16) Layek, RitwikThe area of systems biology evolved in an attempt to introduce mathematical systems theory principles in biology. Although we believe that all biological processes are essentially chemical reactions, describing those using precise mathematical rules is not easy, primarily due to the complexity and enormity of biological systems. Here we introduce a formal approach for modeling biological dynamical relationships and diseases such as cancer. The immediate motivation behind this research is the urgency to find a practicable cure of cancer, the emperor of all maladies. Unlike other deadly endemic diseases such as plague, dengue and AIDS, cancer is characteristically heterogenic and hence requires a closer look into the genesis of the disease. The actual cause of cancer lies within our physiology. The process of cell division holds the clue to unravel the mysteries surrounding this disease. In normal scenario, all control mechanisms work in tandem and cell divides only when the division is required, for instance, to heal a wound platelet derived growth factor triggers cell division. The control mechanism is tightly regulated by several biochemical interactions commonly known as signal transduction pathways. However, from mathematical point of view, these pathways are marginal in nature and unable to cope with the multi-variability of a heterogenic disease like cancer. The present research is possibly one first attempt towards unraveling the mysteries surrounding the dynamics of a proliferating cell. A novel yet simple methodology is developed to bring all the marginal knowledge of the signaling pathways together to form the simplest mathematical abstract known as the Boolean Network. The malfunctioning in the cell by genetic mutations is formally modeled as stuck-at faults in the underlying Network. Finally a mathematical methodology is discovered to optimally find out the possible best combination drug therapy which can drive the cell from an undesirable condition of proliferation to a desirable condition of quiescence or apoptosis. Although, the complete biological validation was beyond the scope of the current research, the process of in-vitro validation has been already initiated by our collaborators. Once validated, this research will lead to a bright future in the field on personalized cancer therapy.Item Quantitative Modeling and Estimation in Systems Biology using Fluorescent Reporter Systems(2013-12-10) Bansal, LoveleenaBuilding quantitative models of biological systems is a challenging task as these models can consist of a very large number of components with complex interactions between them and the experimental data available for model validation is often sparse and noisy. The focus in this work is on modeling and parameter estimation of biological systems that are monitored using fluorescent reporter systems. Fluorescent reporter systems are widely used for various applications such as monitoring gene expression, protein localization and protein-protein interactions. This dissertation presents various techniques to facilitate modeling of biological systems containing fluorescent reporters with special attention given to challenges arising due to limited experimental data, simultaneous monitoring of multiple events and variability in the observed response due to phenotypic differences. First, an inverse problem is formulated to estimate the dynamics of transcription factors, a crucial molecule that initiates the transcription process, using data of fluorescence intensity profiles obtained from a fluorescent reporter system. The resulting inverse problem is ill-conditioned and it is solved with the aid of regularization techniques. The main contribution is that, with the presented technique, any complex dynamics of transcription factors can be estimated using limited data of fluorescence measurements. The technique has been evaluated using simulated data as well as experimental data of a GFP reporter system of STAT3. Second, an experimental design formulation is developed to facilitate the use of multiple fluorescent reporters, with overlapping emission spectra, in the same experiment. This work develops a criterion to select the fluorescent proteins for simultaneous use such that the accuracy in the estimated contributions of individual proteins to the overall observed intensity is maximized. This technique has been validated using mixtures of different E. coli strains which express different fluorescent proteins. Finally, a population balance model of a cell population containing a fluorescence reporter system is developed to describe the variability in the observed fluorescence in cells. Factors such as rate of fluorescent protein formation as well as partitioning of the fluorescent protein on cell division have been taken into account to describe the dynamics of fluorescence intensity distributions in the cell populations. The model has been used to obtain preliminary hypotheses to explain the difference in response of HeLa cells containing the Tet-on expression system on stimulation by different levels doxycycline. Thus, this work describes techniques for building robust predictive models of biological systems such as regularization for solving ill-posed estimation problems, experimental design techniques as well as using population balance modeling to model complex multi-scale dynamics. Moreover, while the examples discussed here are motivated for fluorescent reporter systems, the developed techniques can be used for different kinds of linear or non-linear dynamic biological systems.Item A systems pharmacology approach to discovery of drugs to ameliorate oxidant stress in human endothelial cells(2015-05) Bynum, James Andrew, Jr.; Stavchansky, Salomon; Bowman, Phillip D; Kerwin, Sean M; Cui, Zhengrong; Williams, Robert OIschemia is characterized by reduced blood flow to an area of the body which can then cause cellular injury through the generation of reactive oxygen species (ROS), activation of inflammation, and induction of apoptosis. Although rapid reestablishment of flow is required to prevent organ death, the reperfusion phase of this injury can cause its own deleterious effects often exacerbating the initial insult. The combined action of the two injuries is termed ischemia/reperfusion (I/R) injury. Oxidative stress that results from ischemia/reperfusion injury is a common pathological condition that accompanies many human diseases including stroke, heart attack and traumatic injury. In addition, neurodegenerative diseases including Parkinson’s, Alzheimer’s, and Huntington’s disease appear to involve oxidative stress. Although actively investigated by the medical and pharmaceutical industry; limited progress has been made to ameliorate I/R injury and to date there is no drug approved for treatment for I/R injury. Therapeutic approaches to treat I/R injury have included the administration of compounds to scavenge ROS or induce protective pathways or genetic responses. It was previously reported that caffeic acid phenethyl ester (CAPE), a plant-derived polyphenol, displayed cytoprotective effects against menadione (MD)-induced oxidative stress in human umbilical vein endothelial cells (HUVEC), and the induction of heme oxygenase-1 (HMOX1), a phase II enzyme, played an important role for CAPE cytoprotection. In an effort to improve this cytoprotection, other phase II enzyme inducers were investigated and, 2-cyano-3,12 dioxooleana-1,9 dien-28-imidazolide (CDDO-Im) and 2-cyano-3,12-dioxooleana-1,9-dien-28-oyl methyl ester (CDDO-Me), were found to be potent inducers with a rapid onset of action. CDDO-Im and CDDO-Me, synthetic olenane triterpenoids, developed as anticancer agents were compared to CAPE revealing that CDDO-Im was a more potent inducer of Phase II enzymes including HMOX1 and provided better cytoprotection than CAPE. Gene expression profiling showed that CDDO-Im was more potent inducer of protective genes like HMOX1 than CAPE and additionally induced heat shock proteins. To better understand the mechanism of action of CDDO-IM, a gene expression time-course was undertaken to identify early initiators of the transcriptional response preceding cytoprotection. Application of systems pharmacology identified molecular networks of cell mediating processes.