A car mechanic would have a hard time building a car if he or she didn’t know anything about the car’s parts. The same holds true for scientists who want to design or program proteins and microbes. They must first understand the structure, complexity, and interactions of the system they are interested in. For Philip Romero and Ophelia Venturelli — two new assistant professors joining the Department of Biochemistry on July 11 — this idea is what drives their research.
Romero comes to UW–Madison from an assistant professorship at the University of California, Los Angeles, and Venturelli joins from a postdoc at UC Berkeley. Venturelli is interested in the functions of microbial communities and how mathematical models can be used to predict those functions.
Microbes don’t appear in isolation, Venturelli explains, but instead in extremely diverse communities. They interact in a variety of positive and negative processes, competing over limited resources, waging antibiotic warfare by producing toxic chemicals, producing substances other organisms can consume, or even detoxifying the environment. Some of the processes can be helpful to humans, and understanding their underlying mechanisms can help scientists engineer or recreate them to harness their benefits.
“For example, microbes on and inside the human body, which make up the microbiome, have huge implications for human health,” says Venturelli, who earned her Ph.D. at the California Institute of Technology and bachelor’s degree from Stanford. “I’m interested in understanding how those microbial communities function and then how we can design communities to enhance beneficial functions. I am also interested in other broader applications such as the plant microbiome in agriculture and bioenergy.”
While Venturelli is interested in understanding microbes, Romero’s work is similar but focuses on proteins instead. Proteins interest him, he says, because they control almost all processes that take place in cells, such as metabolism, cell-to-cell communication, and DNA replication.
Romero uses new technologies to understand how these proteins function. While in years past it took a lot of time to perform this tedious work, using new experimental methods and technology like machine learning, Romero and his team are able to perform millions of biological experiments. This allows them to extract meaningful information to understand how proteins work.
He worked on applications of this concept in graduate school. For example, he worked on engineering proteins that can act as molecular contrast agents to image neurotransmitters in the brain that could be used to diagnose diseases. He was also involved with projects that would help convert biomass to fuel and developing cancer therapeutics.
“A very long term goal for me is the ability to rationally design proteins to do whatever we can imagine,” Romero says. “This capability would have a tremendous impact across all areas of biology, medicine, and biotechnology. You could pick a disease and then use a computer to rapidly design a therapeutic protein to treat it. You could design custom biocatalysts to interconvert different types of chemicals for industry. The possibilities are really endless once we learn how to design proteins.”
Romero attended Tulane University for his undergraduate studies before working with Frances Arnold at the California Institute of Technology for his Ph.D. At UW–Madison he will also be affiliated with the Department of Chemical and Biological Engineering. Both Romero and Venturelli say they are very excited to join UW–Madison because of the potential for great collaboration in the department and across campus.
“I’m really excited about the strengths of UW-Madison in my research areas, which are biochemistry and also chemical engineering,” Romero says. “And it’s also a very interdisciplinary environment so there’s lots of collaboration across different departments. I’m excited about interacting with people in computer science, chemistry, and electrical engineering. I think it’s that kind of research environment that really attracted me to UW–Madison.”
Venturelli adds she is looking forward to working with students that have interdisciplinary interests in combining engineering principles, microbiology, biochemistry, and mathematical modeling. As an assistant professor in Biochemistry, she will be affiliated with the Department of Bacteriology and the Department of Chemical and Biological Engineering as well.
“I find it to be a very supportive environment for young faculty, the students seem highly motivated, and Madison is a great place to live,” she says. “My research is diverse and I’m excited to interact with faculty and students across many departments at UW.”