
This is the study of biology as an integrated system of genetic, protein, metabolite, cellular, and pathway events that are continually changing and inter-related. Gene expression data provide information on pathways relevant to the metabolic models. Although genes yield informative clues to diseases, they do not contain functional information. Disease mechanisms can stem from genetic and environmental causes. The importance of studying biology as a system rather than one gene or protein at a time has become increasingly relevant with the advent of high throughput genomic and proteomic technologies. A systems approach can help explain why some genes respond to a particular environmental stimulus, while others do not.
In this project, metabolic engineering will be applied to further our mechanistic understanding of diseases, such as Type II diabetes, Parkinson's and Alzheimer diseases. The objective of this project is to quantify the pathway alterations in response to environmental mediators. Knowledge of in-vivo flux distributions in cells at different physiological states is of increasing importance by providing "cellular" targets for evaluation as predictors of the disease.
Tissue engineering technology allows design of cellular co-culture systems and manipulation of the cellular microenvironment to reflect in vitro the metabolism in vivo. Nonparenchymal cells can aid parenchymal cells to maintain functions, but they can also mediate deleterious effects. An advantage of this technique, upon which we will capitalize, is the ability to control the cell seeding density and the spatial orientation and placement of different cell types. Tissue engineering permits engineering of cell-cell architecture and cell-cell interactions of nonparenchymal and parenchymal cells to better reflect metabolism in vivo.
Current delivery systems bring one type of biomolecule, e.g., one protein or one gene, at a time to the targeted site. We are developing platforms to integrate polymers with biomolecules, such as aptamers, to deliver multiple biomolecules to a targeted pathway or site.
Kidambi, S ., Lee, I, and Chan, C., “Directed deposition of cells and macromolecules using salt tunable m-dPEG acid patterns on polyelectrolyte multilayers”, (2007) Langmiur, (in press).
Srivastava, S., Li, Z., Yang, X., Yedwabnick, M., Shaw, S., and Chan, C., “Identification of genes that regulate multiple cellular processes/ responses in the context of lipotoxicity in hepatoma cells”, (2007) BMC Genomics, 8:364. Link to publication
Patil, S., Melrose, J., and Chan, C., “Involvement of astroglial ceramide in palmitic acid-induced Alzheimer-like changes in primary neurons”, (2007) European Journal of Neuroscience. 26(8):2131-41. Link to publication
Kidambi, S., Lee, I, and Chan, C., “Patterned Co-culture of Neurons and Astrocytes on Polyelectrolyte Multilayer Films for Studying Astrocyte Mediated Oxidative Stress in Neurons”, (2007) Advanced Functional Materials (in press).
Srivastava, S. and Chan, C., “Application of Metabolic Flux Analysis to Identify the Mechanisms of Free Fatty Acid Toxicity to Human Hepatoma Cell Line, HepG2”, (2007) Biotechnology and Bioengineering, 2007 Jul 5; [Epub ahead of print] . Link to publication
Jin, R. , Si, L., and Chan, C., “A Bayesian Framework for Knowledge Driven Regression Model In Micro-array Data Analysis”, International Journal of Data Mining and Bioinformatics (IJDMB) (in press).
Li, Z. , Srivastava, S., Yang, X., Mittal, S., Sheng, L., and Chan, C., “A Three Stage Integrative Pathway Search (TIPS ©) framework to identify toxicity relevant genes and pathways”, (2007) BMC Bioinformatics, June 14; 8(101):1-17. Link to publication
Jin, R. , Si, L., and Chan, C., “A Bayesian Framework for Knowledge Driven Regression Model In Micro-array Data Analysis”, International Journal of Data Mining and Bioinformatics (IJDMB) (in press).
Li, Z. , Srivastava, S., Yang, X., Mittal, S., Sheng, L., and Chan, C., “A Three Stage Integrative Pathway Search (TIPS ©) framework to identify toxicity relevant genes and pathways”, (2007) BMC Bioinformatics, June 14; 8(101):1-17.
Li, Z., Srivastava, S., Mittal, S., Norton, P., Resau, J., Haab, B, and Chan, C., “A Hierarchical Approach Employing Metabolic and Gene Expression Profiles to Identify Pathways that Confer Fatty Acid and TNF-α Cytotoxicity in HepG2 Cells”, (2007) BMC Systems Biology, 1(21), 1-15. Link to publication
Kidambi, S., Udpa, N., Schroeder, S.A, Lee, I, and Chan, C., “Cell Adhesion on Polyelectrolyte Multilayer Coated Poly(dimethylsiloxane) Surfaces with Varying Topographies”, Tissue Engineering, (2007) 13(8):2105-17. Link to publication
Kidambi, S ., Sheng, L., Toner, M., Yarmush, M., Lee, I, and Chan, C., “Patterned Co-culture of Primary Hepatocytes and Fibroblasts using Polyelectrolyte Multilayer Templates”, Macromolecular Bioscience, (2007) (3): 344 - 353. Link to publication
Srivastava, S. , and Chan, C., “Hydrogen peroxide and hydroxyl radicals mediate palmitate-induced cytotoxicity to hepatoma cells: relation to MPT”, (2007) Free Radical Research, 41(1):38-49. Link to publication