Chemical and Biomolecular Engineering at Illinois

Arnab Mukherjee advancing research in antibiotic resistance, protein imaging

Arnab Mukherjee, a finalist for the 2013 Lemelson Illinois award, has demonstrated his versatility and interdisciplinary prowess as both a student and researcher at the University of Illinois.

A native of India, Mukherjee graduated from the Indian Institute of Technology in Madras with bachelor and master of science degrees in biotechnology. Although he is trained as a biologist, he is also versed as a chemical engineer.

“I come from a biological background, but I try to incorporate engineering principles to biological systems,” Mukherjee said. “Similar to what computer engineers do with electrical circuits, I enjoy taking components and putting them together piece by piece to build biological machines that can make lives easier in the future.”

Arnab Mukherjee
Arnab Mukherjee

Mukherjee’s first introduction to innovation and technology came as a result of trying to meet one of the “five grand challenges in engineering” in a program sponsored by General Electric more than a decade ago. He helped conceptualize a design for computer keyboards to meet the needs of people with motor disabilities.

“One patient was able to successfully navigate to a web page in under a minute as opposed to 10 minutes or longer, that they often require,” Mukherjee said.

Mukherjee has been working as a graduate research student with chemical engineering assistant professor Charles Schroeder for the past five years.

It was in listening to a talk from another U of I professor, Paul Kenis, head of chemical and biomolecular engineering, that he conceived an idea to use a microfluidic technology originally developed by Kenis and coworkers, to design a diagnostic platform for screening antibiotic susceptibilities in bacterial infections.

Due in large part to its overuse, experts say that within the next decade or two, the world is at risk of running out of any effective antibiotics to treat bacterial infections. This is due to bacteria gaining resistance to antibiotics at an alarming rate. The primary research goal is to utilize microfluidic chips as diagnostic tools to screen a patient’s sample against antibiotics and quickly provide information on what drugs or combination of drugs would work best against the infection.

“What I believe our technology will enable us to do is significantly slow down this rampant abuse and misuse of antibiotics, especially in developing nations,” Mukherjee said. “In those places they are very much above the counter. That will help us buy more time to develop a completely new class of drugs.”

While Mukherjee proposed the idea, the research project is a collaborative effort. The Kenis lab provides the microfluidics expertise, while the Schroeder lab contributes microbiological, imaging, and bioengineering knowledge. Mukherjee has since passed on the work of the project to researchers in the Kenis lab.

Meanwhile, Mukherjee has focused much of his attention to a project to “expand the biological imaging toolbox through molecular engineering of photoreceptor proteins,” where he is the lead researcher through the Schroeder lab. One of the benefits of the project will be the development of imaging technologies to study hypoxic environments, such as solid tumors, which are often the starting points of cancer.

“I realized that medicine relies a lot on looking at what goes on inside your body,” Mukherjee said. “The more you’re able to look and observe, the better your treatment is. Existing imaging technologies fail to image environments that lack oxygen. This campus helped me realize that the world is more anaerobic than aerobic.”

Arnab Mukherjee was one of eight finalists for the 2013 Lemelson Illinois Prize.
Arnab Mukherjee was one of eight finalists for the 2013 Lemelson Illinois Prize.

In other words, because cancerous tumors are really anaerobic (there is no oxygen in them) and current imaging methods require the use of oxygen, those imaging techniques fail in studying those tumors. Mukherjee is looking at naturally occurring biological light sensing molecules or photoreceptors to see if they have fluorescent characteristics in hopes of using them to study cancer cells.

“If we take these photoreceptors and use molecular cloning and protein engineering to convert them into fluorescent proteins they will glow,” Mukherjee explains. “Therefore if you put them in cells irrespective of if oxygen is present, they will light up which will allow you to track what’s going on inside the cell with absolute precision.

“Overall, my research seeks to substantially advance biological imaging with broad implications for biofuels production, cancer therapy and real-time monitoring of anaerobic ecosystems such as the human and rumen gut microbiomes and antibiotic-resistant infections,” he adds in his research essay.

Mukherjee’s research has already resulted in the discovery of new and improved fluorescent biomolecules that are suitable for a wide range of applications in anaerobic environments as well as under relatively harsh conditions typically encountered in industrial bioproduction platforms. Some of these findings were recently published in the Journal of Biological Engineering and PLOS ONE (see references). Mukherjee has another busy year of study and research ahead with plans to finish his PhD in 2014 and pursue a career in academia with an emphasis on research.

“I like taking technologies that are used for something else and trying to reapply them for a different application,” Mukherjee said. “I would love to find a place where I can conduct similar research in an academic setting.”

Mukherjee, A., Walker, J., Weyant, K.B., Schroeder, C.M. Characterization flavin-based fluorescent proteins: an emerging class of powerful fluorescent probes. PLOS ONE. 8:5. (2013) doi:10.1371/journal.pone.0064753
Mukherjee, A., Weyant, K.B., Walker, J., Schroeder, C.M. Directed evolution of bright mutants of a flavin-binding fluorescent protein from Pseudomonas putida. Journal of Biological Engineering. 6:20. (2012). doi: 10.1186/1754-1611-6-20
Writer: Mike Koon, writer/editor, Engineering Communications Office, University of Illinois at Urbana-Champaign.