Current project

Systems analysis of innate immune response in response to molecules containing pathogen associated molecular patterns (PAMPs) and danger associated molecular patterns (DAMPs)

details to follow …

Past Projects

Ribosomes as Translational Control Elements

Cells, the biological units of life, live in a constantly changing environment. They adapt to these changes by detecting the environmental cues and, subsequently, using the information encoded in their DNA to synthesize new proteins. To do that, first, the information in the DNA is encoded into a special class of RNA molecules called messenger RNAs, or mRNAs, which in turn is decoded into a protein sequence. I am interested in the last step of this process, the translation of mRNA into a protein sequence. The central player in this process is a large complex of RNA and proteins called ribosomes. Ribosome with the help of accessory factors reads the code from the mRNAs to synthesize a new protein.

There are many different types of ribosomes in a cell that differ in their protein or RNA composition. In 2002 in a paper published in PNAS, two scientists Vincent Mauro and Gerald Edelman proposed a hypothesis called ribosome filter hypothesis, which says that the different types of ribosomes prefer to synthesize different proteins. For my thesis project, I have designed experiments to test the ribosome filter hypothesis using budding yeast Saccharomyces cerevisiae as my model system. I reasoned that a cell needs an assortment of different proteins if it is fed glucose, whose synthesis would require a specific mixture of ribosomes. The same cell would require a different assortment of proteins if it is fed glycerol, which in turn would require a different mixture of ribosomes.  Therefore, the populations of different  ribosomes, would exist in an equilibrium and the equilibrium would change with the changes in the environment.

Using state of the art quantitative liquid chromatography tandem mass spectrometry based techniques, isobaric tags for relative and absolute quantitation (iTRAQ) and multiple/selected reaction monitoring (MRM/SRM), I have found that it is indeed the case. Using a combination of yeast genetics, molecular biology and a novel quantitative mass spectrometry approach, I am trying to decipher which ribosome prefers to make which protein.

I hope one day my research would lead to the development of new drugs. For example, let us imagine we need to stop the synthesis of one protein to cure cancer. A drug based upon my research would be able to inactivate the ribosome that synthesizes the cancer causing protein, thus killing the cancer cells and curing cancer with minimal side effects.

Systems Analysis of the Proteome and the Transcriptome in Myotonic Dystrophy

Myotonic dystrophy (DM) is the most common form of hereditary muscular dystrophy in adults characterized by progressive muscle weakness and slow relaxation of muscles among other symptoms. The are two types of myotonic dystrophy; Type I or DM1 and Type II or DM2. DM1 is caused by the expansion of CTG repeat element in myotonic dystrophy protein kinase (DMPK) gene. DM2 is cause by CCTG repeat expansion in the first intron of cellular nucleic acid binding protein (CNBP, also known as zinc finger 9 or Znf9). It has been proposed that DM is caused by RNA toxicity caused by expression of expanded repeat elements. However, the exact mechanism by which RNA toxicity causes the disease is less clear. Additionally, all the factors having a role in DM have not yet been identified.

We are quantifying the proteome and the transcriptome of skeletal muscles from DM patients and healthy individuals to inventory the list of factors involved in DM and build mathematical models to study the disease mechanism. We are using isobaric tag for relative and absolute quantitation (iTRAQ) labeling and liquid chromatography tandem mass spectrometry to quantify the proteome of skeletal muscles. We are quantifying the transcriptome using RNA-Seq.

(This work is being done in collaboration with Nripesh Prasad in the Shawn Levy lab at Hudsonalpha Institute for Biotechnology and Rahul in the Brian Ingalls lab at the University of Waterloo)