Yonatan Chemla, a bioengineering researcher at the Massachusetts Institute of Technology, will join the Department of Bioengineering at The Robert Mehrabian College of Engineering in March 2027. Chemla is a bioengineer who has an interdisciplinary background spanning molecular biology, synthetic biology, and regulatory policy. At UC Santa Barbara, he will work to integrate advances in mRNA biology, genetic engineering, machine learning, and hyperspectral imaging with engineering principles to support new solutions for human and environmental health. His research is guided by the goal of making synthetic biology work beyond the lab, enabling engineered biological systems to operate safely and effectively in complex real-world environments, whether sensing and remediating pollution in soil or working inside the human body as living cell therapeutics.

Chemla received his PhD from Ben-Gurion University, in Israel, where he used genetic code expansion, cell-free systems, and biophysical modeling to study bacterial ribosomal translation — work that laid the foundation for his efforts in mRNA design. As the recipient of a Human Frontier Science Program Postdoctoral Fellowship, Chemla worked with Christopher Voigt at MIT to develop novel tools to measure and control gene expression in complex and non-model systems, including hyperspectral reporters that enable gene expression to be detected remotely across large environmental scales, with the goal of creating technology that allows engineered cells to function as real-world tools. 

Last year, Chemla received the National Institutes of Health K99 Pathways to Independence Award, which he will use to integrate his doctoral and postdoctoral research, pursuing mRNA design that can support environmental sustainability and human health safely and effectively, whether applied to engineered environmental microbes or human cells.

We spoke with Chemla in June.

Q: How did you get interested in bioengineering?

Yonatan Chemla: I grew up in Jerusalem at the edge of the forest, and I was always fascinated by how amazing trees are, and animals, and the nature around us. When I learned that you could start engineering those things, I realized that’s what I wanted to do. Then, for my PhD research at Ben-Gurion University, I studied molecular biology and biological engineering of messenger RNA molecules.

For those who aren’t familiar with the process, DNA is the blueprint in the cell of an organism. It’s then transcribed into messenger RNA, or mRNA, and it is the mRNA that controls how much of a protein is produced by dictating the kinetics by which ribosomes bind and initiate their translation. I was fascinated by the question of how the mRNA sequence can control ribosomes binding to the mRNA, how mRNA initiates and terminates translation, and how they release the ribosomes.

The way to answer these questions is to engineer new synthetic, wild, weird mRNAs to try to understand how the ribosome behaves. In the process, we discovered new mechanisms by which the mRNA structure controls some of these processes. We used these insights to improve our ability to produce recombinant, or engineered, proteins in bacterial cells. My PhD really crystalized for me the power of biological engineering and synthetic biology to both understand and engineer nature.

Q: I’ve read that, along with engineering mRNA, you’re also thinking about the safety of introducing engineered organisms into the environment. Could you talk about that?

YC: This is actually something I’ve been thinking about since I started doing bioengineering research. There’s an international competition for synthetic biology called iGEM (International Genetically Engineered Machine), and as an undergraduate at Ben-Gurion University, I decided to start the first-ever team from our university. Our project was around the question of safety in biological engineering. This was in 2013, and bioengineering was becoming increasingly powerful in the lab. We didn’t have — and we largely still don’t have today — the design principles to move these organisms outside the lab safely. But if that became possible, we thought, once a genetically engineered organism was introduced into the environment, how would we keep it under control? So we developed these fun little genetic safety switches that will eliminate a released microbe after a pre-programmed number of generations as our project, and we went to the iGEM finals and got the best presentation award. 

This question came back to haunt me in my postdoc. I worked with Chris Voigt at MIT, and he was doing a lot of frontier science on these questions of how we release genetically engineered organisms into the environment. I was initially continuing to work in mRNA design, but Chris immediately pushed me to do more. So I began to look at when we release an organism into the environment: what happens to the environment, and what happens to the organism? How do we track this? How do we understand this? There’s surprisingly little understanding of this process, despite the fact that we humans have been releasing microbes into the environment for millennia when we make wine, ferment food, fertilize our fields, or do wastewater treatment.

Q: What is bringing you to UCSB?

YC: I think the number one thing was the people I met there. I was very attracted to the scientific culture I saw there, which felt very different from other places, in a good way — collegial, collaborative, supportive, adventurous, playful. It’s a big university, but it feels like a village, a close-knit community, which is how I like to do science. 

There are the wonderful new facilities, ExFAB (BioFoundry for Extreme and Exceptional Fungi, Archaea and Bacteria) and the Mammalian BioFoundry, which will both be very useful and important for several of my research tracks. And of course, the beauty, the weather. I thought Santa Barbara would be a great place to raise my kids. 

Q: What will your research here be focused on?

YC: I’m working around three main pillars, one being the continuation of my research with mRNA. I have an NIH grant to look at questions around how ribosomes bind to mRNA, such as how the sequence of the mRNA itself controls the affinity of the binding. It sounds very technical, but it’s extremely important for our ability to do precise genetic engineering of any organism. 

A second pillar is the interactions between organisms, particularly engineered organisms, and their environment. The third pillar is what I call hyperspectral biology, and that’s going to be a major theme in my lab. I want to use the fact that each molecule in nature that absorbs light has a unique signature of how it does that, and use that fact to create tools, methods, molecules, and instruments that will enable us to make the invisible biological world visible and observe living systems across entire environments in ways that were previously impossible.

We’ve been using light to look at molecules for a hundred years, but what’s new is our ability to use imaging to do that. Instead of having to do limited measurement in a lab with elaborate methodologies, with hyperspectral imaging we can see unique signatures of a light absorbed in a picture that we take directly outside, directly in the field, or directly in the human body. We can measure an almost continuous spectrum of light reflected from every pixel in a picture. In my lab, we are going to measure thousands of natural molecules to learn how they absorb light, then create computational models with machine learning to predict how new molecules can absorb light.

Understanding this will help us to find molecules that absorb light in a unique way. We could genetically engineer these molecules into living cells, and then we’d be able to monitor, image, or use them as biosensors, in scales and environments that we could not do before, because we could track their unique light signature. Today, most biological measurements require collecting samples and bringing them back to the laboratory. Our goal is to move biology from the test tube to the landscape, enabling measurements across fields, forests, coastlines, and entire ecosystems.

In my postdoc, we have already demonstrated that engineered microbes can be detected in soil from drones and even satellites. Looking ahead, I am excited to explore how hyperspectral biology could enable a new generation of environmental biosensors, help monitor ecosystem health, and ultimately provide a way to observe and understand the living world at scales that biology has never been able to access before.

Although these pillars may seem distinct, they all serve one goal: to develop the engineering principles needed to design, measure, and control biological systems outside the highly controlled conditions of the laboratory.

Q: What potential applications do you see emerging from this research?

YC: Generally, I like to be application agnostic; I want to develop the basic engineering design principles without collapsing those principles into a specific application. However, often there are serendipitous projects that emerge, and I do think one of the first use cases for this research will be in biosensing and environmental remediation. I’m most passionate about cleaning up the environment through bioengineering, and we could use the tools we develop both to see where pollution is, and then to remediate it. 

Beyond advancing our understanding of the world through engineering, my primary motivation is the belief that environmental biotechnology, broadly defined, can help address some of the most urgent challenges facing society. Chief among these is pollution, particularly synthetic chemical pollution from plastics and other petrochemicals, pesticides, and PFAS, all of which continue to accumulate. I believe engineered biology is one of the most promising technologies with the potential to tackle these problems effectively.