Computational Biology

Modeling cell-death

Cell-death process, which occurs ubiquitously under normal and healthy conditions, is disturbed in diseased tissues. Cell-death process can be viewed as an outcome of a network of reactions. How does the network dynamically orchestrate the overall cell-death outcome? Can the network be re-wired to reverse the disturbances in the cell-death process? The goal of this project is to understand the cell-death process by developing a kinetic model of the network of reactions and validating with experimental data.

Topic 3 : Metabolic engineering of heterotrophic bacteria (Sugar to chemicals).

-  After the biofuel revolution, there is a need to develop robust technologies for the conversion of sugars to value-added chemicals.

-  The pathway typically involves 3-5 new genes and may additionally require knocking out of a few genes.

Topic 2 : Synthetic biology and metabolic engineering of cyanobacteria (CO2 to chemicals).

-  Cyanobacteria are photosynthetic prokaryotes.

-  We have isolated fast-growing and robust cyanobacteria from Powai lake.

-  We are developing these cyanobacteria as hosts for metabolic engineering.  This involves:

Topic 1 : Global metabolomics to identify markers for pre-diabetes and severity markers for diabetes.

- Diabetes develops over a period of 2-5 years.  Patients benefit immensely if they get a warning sign during this period.

Once developed, diabetes may result in complications.  Currently, available markers do not talk about the severity of the disease.

Molecular Simulations of HIV-2 protein VpX

Our research group is primarily engaged in the investigation of protein dynamics and mechanisms with applications to intrinsic immunity and viral response, HIV therapeutics and enzymatic catalysis. The Ph.D project involves research into a retroviral protein called VpX that enables immunodeficiency retroviruses such as  HIV-2 to counteract the host cell defences.

Open problems in evolutionary biology (experiments and/or theory)

Evolution of life over the last >3.5 billion years has shaped the life forms that we presently see on the planet. Developments in genome sequencing and molecular biology allow us to perform evolutionary experiments in lab, and see in real time, how environment shapes changes in a population. Understanding this relationship between the environment and the changes that take place in the DNA of an organism is the focus of our lab's research. We perform theory and also perform experiments (using yeast and bacteria) to answer questions of interest.

Biochemical signaling network for periodic forcing within sperm flagella.

Sperm motility is critical to fertilization and reproduction in animals. There remain several gaps in the knowledge base about the signaling mechanisms that govern conversion of chemical energy to mechanical work leading to flagellar beating as well as sperm steering and homing. The goal of this study is to build biochemical networks from available literature and propose models that explain and predict sperm motility in response to chemo-attractive molecules. We intend to use of MATLAB® for this project.

Modeling and Simulations of Sorcin, an oncoprotein associated with multi drug resistant cancers.

Sorcin is a calcium binding oncoprotein expressed at high levels in several human tumors such as leukemia, gastric, breast and ovarian cancers.  Sorcin is an essential oncoprotein, which activates and regulates mitosis and cytokinesis. In recent years, there is growing evidence for its role in multi-drug resistant cancers. Our goal is to uncover its working through molecular simulations, understand its role in MDR cancers and attempt to find a druggable way to toggle its activity.