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University of Colorado Denver College of Liberal Arts and Sciences

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Faculty & Staff Directory

Raibatak Das, Ph.D.


Dr. Raibatak Das

Assistant Professor

Email: raibatak.das@ucdenver.edu

Office Location:  SI 4107

Phone:  (303) 556-6595

Fax: (303) 556-4352

2014 Fall Semester Office Hours:  
M & T 3:00p-4:00p
Areas of Expertise:

Mathematical/computational biology, Immune cell signaling,
Microscopy and image analysis.

Ph.D., Chemistry and Chemical Biology, Cornell University, 2005

M.Sc., Indian Institute of Technology, Kanpur, India, 1999

Our lab uses experimental and computational tools to study immune cell signaling.

B cells in our immune system respond to pathogens such as bacteria and fungi by producing antibodies that can bind to these pathogens and facilitate their elimination. We wish to understand how B cells effectively discriminate between foreign and self antigens that bind to B cell receptors (BCRs) on their surface. It is critically important for B cells to mount an immune response to a foreign antigen, and suppress the immune response to a self-antigen. The breakdown of this discrimination is at the heart of a number of autoimmune disorders such as lupus, rheumatoid arthritis, and a majority of lymphomas.

Our goal is to understand the molecular events that comprise the B cell signaling. To do so, we use high resolution microscopy to visualize BCRs and other signaling molecules in B cells. We develop image-analysis tools to quantify the microscopy data, and utilize mathematical and statistical tools to extract meaningful biological information from these data.

Some specific research projects in our lab are described briefly below.


Single-molecule microscopy

One of the most exciting recent developments in cell biology is the emergence of super-resolution microscopy techniques that can achieve essentially single-molecule resolution. One of our goals is to harness the power of these modern microscopy techniques to visualize B cell signaling. We plan to use super-resolution imaging methods to observe single molecule dynamics of BCRs and associated signaling molecules in live cells.

We are also interested in developing computational tools for effectively analyzing the microscopy data. There are a number of exciting research problems in this area, ranging from developing tools for acquiring and processing very large datasets, to automated feature identification and tracking.


Spatial organization of signal transduction

The ability to image signaling molecules with such high resolution opens the door to a number of interesting questions. For example, one of the observations from single molecule studies is that the mobility of receptors is different in different regions of the cell membrane. Changes in receptor mobility influence the kinetics of interactions between signaling molecules, and this is presumed to be one of the ways to regulate signaling. We wish to understand the details of how this spatial organization and regulation is achieved.

 

Mathematical and computational models of B cell signaling

We also develop mathematical models for the signaling events that follow BCR-antigen engagement. These models are guided by data from microscopy and biochemical experiments. We intend to use these models to predict the B cell response to a range of antigens, and to identify points of therapeutic intervention for autoimmune disorders.


Positions available

The Das lab is recruiting motivated undergraduate and graduate students and postdocs who are interested in interdisciplinary research at the interface of Biology, Mathematics and Computational Science. Please email Dr. Das to find out more about research opportunities

Pines M, Das R, Ellis, SJ, Morin, A, Czerniecki, S, Yuan L, Klose M, Coombs D and Tanentzapf G, "Mechanical force regulates integrin turnover in Drosophila in vivo.", Nat Cell Biol, 14:935-943 (2012).

Das R, Nachbar RB, Edelstein-Keshet L, Saltzman JS, Wiener, MC, Bagchi A, Bailey J, Coombs D, Cook J, Hargreaves R, Simon A, "Modeling the effect of gamma-secretase inhibitor on amyloid-beta dynamics reveals significant role of an amyloid clearance mechanism.", Bull Math Biol, 73:230-247 (2011).

Cairo CW, Das R, Albohy A, Baca QJ, Pradhan D, Morrow JS, Coombs D, Golan DE, "Dynamic regulation of CD45 lateral mobility by the spectrin-ankyrin cytoskeleton of T cells." J Biol Chem, 285: 11392-11401 (2010).

Dushek O, Das R, Coombs D, "A role for rebinding in rapid and reliable T Cell responses to antigen." PLoS Comput Biol 5: e1000578 (2009).

Das R, Cairo CW and Coombs D, "A hidden Markov model for single particle tracks quantifies dynamic interactions between LFA-1 and the actin cytoskeleton" PLoS Comput Biol 5: e1000556 (2009).

Dushek O, Das R and Coombs D, "Analysis of membrane-localized binding kinetics with FRAP. Eur Biophys J 37: 627-638 (2008).

Das R, Hammond S, Holowka D and Baird B, "Real-time cross-correlation image analysis of early events in IgE receptor signaling." Biophys J 94: 4996-5008 (2008).

Das R, Baird EJ, Allen S, Baird B, Holowka D, and Goldstein B, "Binding Mechanisms of PEGylated Ligands Reveal Multiple Effects of PEG Scaffold." Biochemistry 47:
1017 -1030 (2008)

Senaratne W, Takada K, Das R, Cohen J, Baird B, Abruña HD and Ober CK, "Dinitrophenyl ligand substrates and their application to immunosensors." Biosens Bioelectron 22: 63-70 (2006).

 


 


BIOL 4764: Biostatistics

BIOL 4050/5050: Biological Modeling