CMU gets grant to study HIV

AIDS is one of the most devastating pandemics to have been recorded in history, affecting humans of all ages and from all parts of the world. Recently, the World Health Organization estimated that AIDS has killed more than 25 million people since it was first recognized. It is no wonder that scientists around the world are working quickly to find a cure for such a destructive virus.

Judith Klein-Seetharaman is one such scientist who is active in HIV research. She currently is teaching at Royal Holloway, University of London, where she is a neuroscience professor and head of the Center for Biological Sciences. She was a research scientist in the Language Technologies Institute at Carnegie Mellon University, where she studied computational biolinguistics, and her research on HIV will also be conducted at Carnegie Mellon.

Many organizations around the world have noted the damage caused by infections like AIDS and tuberculosis, and have been supporting research for their cure. Recently, the Bill and Melinda Gates Foundation awarded 104 research grants to explore unconventional and novel methods to improve global health.
The grants are worth $100,000 each, and were awarded to scientists from 22 countries around the world.

Out of nearly 4000 proposals, Klein-Seetharaman’s was selected as one of the 104 to receive the grant. Klein-Seetharaman aims to analyze sequences of signal transduction pathways, which are intercepted by HIV so they do not function as they should. Signal transduction pathways are the signaling mechanisms in a cell that help the cell respond to different stimuli.

HIV interferes with the cellular signaling system causing the host cells to make more copies of HIV. Klein-Seetharaman explained it was similar to the virus hijacking a cell.
As stated in the general project summary, “[Klein-Seetharaman’s research] aims to use advanced computational methods to predict parallel pathways that can be found and used to circumvent the points of HIV interception.”

Klein-Seetharaman explained, “Predicting the human proteins that interact with HIV and predicting the human proteins that interact with other human proteins are two biological functions that are critical to our project.”

Using computational tools, she will find new signal transduction pathways associated with human proteins and study how HIV and other pathogens interact with these proteins.
Klein-Seetharaman wants to apply algorithms that were produced from earlier studies of molecules to HIV, focusing on certain membrane proteins. She also hopes to find alternate pathways which have the same endpoint as those affected by HIV. Activating these may counter the HIV-affected pathways.

She plans to use methods developed for understanding human languages to understand molecular language. This idea was started in 2001 when the Human Genome Sequence was published, and Klein-Seetharaman and a team of researchers decided to link genes to their protein functions.

She explained, “We proposed that we can map the gene sequences to protein structure and function in the same way words map to meaning in human language.”
This research is very different from previous research because, as Klein-Seetharaman said, “It is general.” She explained, “We will find novel drug targets using a new approach generally referred to as systems biology — instead of restricting ourselves to a few proteins, we analyze the whole set of proteins.”

Klein-Seetharaman aims at targeting the way HIV interacts with cells, and not just manipulating one protein in the pathway to prevent HIV infection. Through her research, she hopes to find a list of human proteins that will be novel anti-HIV drug targets.

Dr. Tachi Yamada is the president of the Gates Foundation’s Global Health Program. “I congratulate each individual who took the initiative to share their idea with us to help fight the world’s most serious diseases,” he said in an article from Medical News Today. “The number of creative approaches we received exceeded our highest aspirations.”

The resources at Carnegie Mellon have been valuable for conducting research. The large variety of expertise that Carnegie Mellon has to offer is very beneficial to the project. Klein-Seetharaman noted the importance of collaboration and the sharing of ideas. “Our collaborations with computer scientists at Carnegie Mellon University are important components of the project,” she said.

Klein-Seetharaman is hopeful that her project and many others will be beneficial for health in developing countries, and will be ready for real-world applications. “I’m very excited. We found something that’s held relevant. It’s nice to support the connection from fundamental to applied research.”