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Q: Why are you so interested in cancer research?
A: I find cancer biology to be like a puzzle, which is very interesting to me. I’m interested in cancer as a whole and what makes it metastasize.
Q: How did you end up at HudsonAlpha?
A: I grew up in Patiala, a small city in India. In 2003, I was working on a master’s degree in Biotechnology in India when I learned about some interesting research being done with anti-cancer drugs from natural products at UAHuntsville by Dr. William Setzer, chair of the chemistry department at the time. I contacted Dr. Setzer to learn more about the research. During our discussion, he ended up inviting me to come to UAHuntsville (University of Alabama, Huntsville) to continue my research.
I took him up on his offer and came to Huntsville in January 2004. I worked for two and a half years screening products from Costa Rica in various cancer lines, looking for the effect of the chemicals on the cells.
In early 2007, I started working at HudsonAlpha. I worked for one and a half years with the UAHuntsville Charger Products program, and with two HudsonAlpha resident associate companies, Open Biosystems and AGI, on developing cell arrays.
Q: You have recently reached a milestone in your career. Can you explain?
A: I am happy to say that I received my Ph.D. in biotechnology science and engineering from UAHuntsville in July.
Q: What kind of research do you do at HudsonAlpha?
A: I am currently working on the ENCODE project as a postdoc in Dr. Myers’ lab at HudsonAlpha. [ENCODE, the ENCyclopedia Of DNA Elements, was launched in 2003 to develop efficient ways of identifying and precisely locating all of the protein-coding genes, non-protein-coding genes and other functional components in the human genome. The goal of ENCODE is to develop the parts list of biologically functional elements and subsequently determine the signals that activate or silence each of the parts, identifying how such signals interact with each other and the environment.]
Specifically, I am working on transcription factors, which are proteins that serve as the regulators of the gene expression in a cell. A transcription factor can regulate the expression of one or many genes, by binding at specific sites on the DNA at the start of a gene and signaling the cellular machinery to start expressing a gene at a certain point. These proteins are extremely important for normal functioning of a cell.
Understanding which transcription factor is regulating which set of genes is very important to better understand the state of a cell. It can help identify genes that are specific to a disease or normal functioning of the cell. Specific diseases can even arise not from DNA changes in the gene itself, but from changes in how transcription factors regulate the output of that gene. The ENCODE project is measuring where transcription factors are bound throughout our entire genetic code, so that we can better understand their normal functions.
In my experiments, I am blocking the expression of one transcription factor at a time in a cell, which means significantly reducing the amount of that protein present in a cell at a given time. This means the protein is not available to bind to its normal place at the start of a gene. These experiments will tell us which of the binding sites identified by the ENCODE project are functional binding sites and which genes are regulated by a particular transcription factor. We want to know if expression levels of genes throughout the cell are changed with respect to the blocked transcription factor, or only specific genes. Do these genes respond similarly in all cell types, and if not then what is the difference? The answers may help us determine new treatments for disease and will certainly shed light on how cells function.
Q: What have you learned while at HudsonAlpha?
A: Working at HudsonAlpha has exposed me to functional genomics — the idea of looking at the genome — and to a collaborative environment that is not always present in an academic setting. Being involved in the institute will definitely help me in the future. It has also exposed me to companies that are doing patient-targeted research like AGI and the opportunity to have Dr. Doug Ross, co-founder of AGI, as my Ph.D. advisor.