(2js) Engineering Biological Systems for Climate Resilience and Human Health: From Proteins to Ecological Communities

The Navaratna Lab

Given the already manifesting threats of climate change and environmental pollution, it is imperative that we develop renewable energy and move away from petroleum extraction and oil-based manufacturing. Plants and green algae remove billions of tons of carbon from the atmosphere and convert it to cellulose and other biopolymers. Fungi and other microorganisms break down this biomass, transforming it into metabolically useful products. A major component of my research program will focus on engineering diverse bacteria, including recently discovered environmental plastic-active microbes, as well as fungi, including white rot fungi capable of lignin degradation, and anaerobic gut fungi found within herbivore rumens. We will combine protein engineering and strain engineering approaches to generate robust and highly active communities of microorganisms for producing valuable bio-based products such as medium and long-chain fatty acids, bioplastics, and biofuels.

Furthermore, microbes in ecologically diverse communities have evolved complex survival strategies, including producing bioactive secondary metabolites. These naturally-derived products have been used by humanity for millennia, and the antibiotics revolution is credited with greatly reducing mortality globally. However, there is broad medical consensus that we are rapidly approaching an antibiotic “cliff”, where microbial drug resistance will render most antibiotic treatments useless. Recently identified pan-drug resistant Candida and Cryptococcus fungi are a looming threat globally. A major focus of my lab will be the high-throughput discovery of antifungal and antibacterial agents. My group will also leverage the power of non-canonical amino acid-based proteomics to gain insight into the mechanisms of persistence and resistance in multi-drug resistant fungi and bacteria.

Research Background

My early training as an undergraduate student in physics and chemical engineering at MIT inculcated in me an appreciation for quantitative biology, using mechanism-based models to gain insight into the behavior of complex phenomena. I developed a stochastic first-reaction model for the pharmacology of multivalent drugs, such as antibodies and contributed to a major study of immune system effects on drug tissue distribution. Later, in my PhD research at the University of Michigan with Professor Greg M. Thurber, I developed new chemical tools to use peptides as molecular imaging agents. Leveraging synthetic biology and chemistry, I created a powerful high throughput screening platform to target disease-relevant protein-protein interactions, applying non-natural amino acid incorporation and affinity sorting to discover potent stapled peptide modulators of the cancer target MDM2. In my current position in the Dr. Michelle O’Malley’s group at UC Santa Barbara, I have worked with large genomics data sets in collaboration with Lawrence Berkeley National Lab and gained further experimental and computational skills. I have been applying these skills towards the genetic engineering of some of nature’s most versatile biomass degraders – anaerobic fungi, and plan to apply these computational and experimental approaches to my own lab’s program.

Teaching Interests

I am eager to teach any core chemical engineering course, having obtained a B.S and PhD in chemical engineering, and serving as a graduate student instructor for undergraduate heat and mass transfer. I have worked extensively with chemical kinetics and transport in my research, so my background makes me especially suited to teach reaction engineering and transport phenomena.

Furthermore, I am excited to develop my own upper undergraduate/graduate course featuring interdisciplinary research at the intersection of engineering and biology. Specifically, next generation sequencing tools have becoming increasingly important in bioprocess for cell line development, and my course will cover the essentials of -omics enabled biotechnology. This course will also cover chemical biology tools to analyze biological systems, including proximity proteomics, unnatural amino acid incorporation for metabolic analysis, and CRISPR-based editing methods, which are all areas that I have experience in.

Building a Diverse and Inclusive Lab and Classroom

I have an extensive background in science communication and have a strong history of mentorship, which I am excited to put into use in training and teaching the next generation of chemical engineers. I am committed to building a diverse and inclusive lab. With the department and my lab, I will develop a program to mentor underrepresented students in surrounding communities, encouraging participation in our group’s research. In my classroom experiences, I have found that the most productive teaching environments mix a variety of pedagogy styles, and I will implement these in my courses. I intend to supplement lectures with group discussions, literature reports, and encourage extensive student participation.