Anamika Sarkar, Ph.D.
Assistant Scientist, Department of Pharmacology and Systems Therapeutics
E-mail: anamika.sarkar@mssm.edu
Mailing Address
One Gustave L. Levy Place, Box 1215 New York NY 10029
Training and Education
Postdoctoral Fellow (2004 – 2005) Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, USA
Postdoctoral Fellow (2000 - 2004) Bioengineering, University of Washington, Seattle, USA
Ph.D. (2000) Applied Mathematics, Indian Institute of Technology Delhi, New Delhi, India
Research Assistant (1992-1994) Indira Gandhi National Open University, New Delhi, India
M.Sc. (1992) Applied Mathematics, Indian Institute of Technology Delhi, New Delhi, India
Current Research
Regulation of Interferonβ in Dendritic cells in response to viral infection
When a mammalian system is attacked by pathogens like viruses, bacteria, fungi, it demonstrates a complex and dynamic immune response, involving various immune cells, such as Dendritic cells, T- and B-cells. Different types of Toll-like receptors, on Dendritic cell membrane, have the capacity to recognize specific pathogens and hence leading to an intricate intracellular signal transduction processes, involving protein- protein interactions and gene transcriptions. Among other pathogens, viral DNA has the capability to invade the cell membrane and multiply inside the cell in the cytoplasm of Dendritic cells. As an initial response to the recognition of the presence of viruses, either by receptor-ligand binding or intracellular signaling events, it results in an innate immune response by increasing the production of interferon β (IFN β) mRNA. The gene transcription of IFNβ leads to the production of IFNβ protein and then to an autocrine loop by binding to the receptor and hence amplification of the signal. My interest is to understand such dynamic processes from systems biology approaches. The protein-protein reaction kinetics is represented mathematically as ordinary differential equations with proper kinetic parameters, acquired either from the literature or from experimental results obtained in the laboratories through collaborations. The number of signaling components in the connection network will be large enough to identify different feedback loops present as sub-networks in the large signaling network. My interest is to find the contribution of these feedback loops towards the dynamic outcome when Dendritic cells are stimulated with viral infections.
Effect of cell shape and size on the local biochemical regulation
Cell shapes and sizes regulate biochemical reactions locally. One of the distinct examples of such biological phenomenon is synapse formation in the tips of the dendrites of neuron cells. My interest is to explore the relationship between two/three dimensional shapes of the cells on the kinetics of intracellular biochemical reactions, in presence of stimulus.
Selected Publications
Sarkar A, Wist A, Iyengar R. Signaling networks in biology. In Wiley Encyclopedia of Chemical Biology. John Wiley & Sons, Inc. 2008.
 
Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R. Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks. Cell. 2008 May 16;133(4):666-80.
Sarkar A, Meila M, Franza RB. IkappaB, NF-kappaB Regulation Model: Simulation Analysis of Small Number of Molecules. EURASIP J Bioinform Syst Biol. 2007:25250.
Sarkar A, Beard DA, Franza BR. Effect of binding in cyclic phosphorylation-dephosphorylation process and in energy transformation. Math Biosci. 2006 Jul;202(1):175-93.
Sarkar A, Franza BR. A logical analysis of the process of T cell activation: different consequences depending on the state of CD28 engagement. J Theor Biol. 2004 Feb 21;226(4):455-66.
Sarkar A, Jayaraman G. The effect of wall absorption on dispersion in oscillatory flow in an annulus: application to catheterized artery. Acta Mechanica. 2004 Nov;172(3-4):151-167.
Sarkar A, Jayaraman G. Non linear analysis of oscillatory flow in the annulus of an elastic tube - application to catheterized artery. Physics of Fluids. 2001 Oct;13(10):2901-2911.
Sarkar A, Jayaraman G. Correction to flow rate – pressure drop relation in coronary angioplasty - steady streaming effect. J Biomech. 1998 Sep;31(9):781-91.
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