A Scientist's Life: Deirdre Lyons

Deirdre Lyons is an assistant professor at the Center for Marine Biotechnology and Biomedicine at Scripps Institution of Oceanography at UC San Diego. She received her bachelor’s degree in biology from Mount Holyoke College in 2002 and her PhD from UC Berkeley in 2008. She joined Scripps Oceanography in 2016. In 2021, she received a CAREER Award from the National Science Foundation.
 

explorations now: What do you do for a living?

Deirdre Lyons: I have the best job in the entire world. I get to run a lab and do research and teach and be with young, interesting, intelligent people all day long. I do that because I'm a developmental biologist. I study how sperm and egg come together and make a new cell. I study how that one cell carries the instructions inside it to build a multicellular organism that can be as big as sequoias or whales – and you and me.

en: What are some of the main questions in your field?

DL: Some of the big questions in the field of developmental biology are how cells become different from one another. Every cell in your body holds the same genomic information. The DNA information is largely the same in almost every cell in your body, but of course we have different body parts like hands versus eyes. Developmental biology is trying to understand how cells become different from one another. That is something that we can never say that we've solved completely when we only look at a small number of organisms. 

Most of what we know about how that process works is based on studies in model system organisms that are terrestrial. So, one active area of research is trying to expand the types of organisms that we study cell differentiation in, especially marine organisms, which have traditionally been difficult to keep in the lab or have not had genetic manipulations available. The advent of CRISPR technology allows us to edit their genomes. Reduced costs for sequencing their genomes allows us to know what the DNA content is.

It used to be that people assumed that organisms looked different from one another because they possess different genes. And so if we were able to look at enough of them, we would find the genes, for instance, what makes a mollusc and what makes a sea star and what makes you a human, and that it would be pretty easy to figure out what genes control differences.

But it turns out after decades of being able to sequence genomes that we all possess about the same number of genes and most categories of genes are shared among all organisms. The thing that makes us different from one another is really how the genes interact with one another.

We have learned from comparing those genomes that many of the genes we know about being involved in development or cellular processes are shared between organisms. The basic metabolism that allows your cells to function is shared between all organisms. Then if you look at what we would call developmental regulatory genes or cell-specification genes – what makes an eye gene versus a gene that controls hand development – it turns out that even organisms that don't have eyes or hands have the genes that we know are involved in eye development and hand development in humans.

Another thing that my lab is really interested in looking at is that every time you sequence an organism’s genome, there are other genes that are unique to that organism, but since they're unique to that organism, those genes have never really been studied in great detail. So we're going to look at what we call those novel genes and see whether they have anything to do with making organisms different from one another.

We want to understand the natural world and all the variations in the way life has formed. Especially in a time when we are looking at environments crumbling and disappearing in real time, we need to understand the full diversity of how life exists on this planet in this time when it might be going away quickly.
 

en: What are you working on right now?

DL: We have a number of projects I'm really excited about. One of them is to understand brain development in nudibranchs, which are a type of sea slug. Based on what is already known about neural function and behavior in these animals, we want to understand the developmental origins of those neurons. We are studying a newly described species of nudibranch and trying to understand its genome and the genes that get turned on in the brain. We collaborate with neuroscientists who seek to manipulate those neurons to see if we can understand how their behavior is controlled.

Another set of experiments in the lab that I'm excited about is making live-image movies of embryos. We can inject mRNAs that code for fluorescently-tagged proteins. And that allows us to label the cells in an embryo, and then we can make time-lapse movies of them dividing and differentiating, and the cells moving around. This gives us a really important window into understanding how cells behave and thus understanding the genes that control those different behaviors.

A third project is trying to understand what we call gene regulatory networks. Individual genes don't necessarily only function on their own. The proteins they make interact with other proteins. We're using that to understand how the mollusc shell is made. When you think of a mollusc, you might think of a snail or a clam, and one of its defining features is the shell that is around it. You might pick those up on the beach in front of Scripps if you visit. And it's amazing that although we know a lot about shells from paleontology and from a biomaterials perspective, we really don't know very much about how they form in development and what individual proteins that make up that shell are doing. That’s part of my NSF CAREER award to try and understand how the mollusc shell is made.
 

en: What are some of the tools you use in your research?

DL: In developmental biology, there's a saying that all of the experiments that people do can fall into one of three categories. We call them “show it, lose it, move it.” So what that means is when we want to understand how a process works, like how an organism builds a structure, or has a behavior, we want to find the genes that make proteins that allow that process to happen.

We work with live organisms and embryos. We also make movies of those embryos. So we use a lot of fluorescence microscopy and live imaging. Sometimes we preserve those embryos and stain them with certain chemicals to highlight parts of the cells. We do a lot of investigation of where proteins and mRNAs are localized in the embryo. That’s the “show-it” part.

The “lose-it” part means you interfere with the function of that gene and ask if that gene is taken away, what types of structures or abilities of an embryo are lost? The most exciting tool for this is CRISPR. The innovation of CRISPR is that it's a way to specifically edit genomes of virtually any organism on the planet. That has really opened the door for people to study any organism they want. My lab is working on developing tools like CRISPR for a wider range of organisms, especially marine organisms.

Then the “move-it” part is if you think you know what that gene does, you could say, ‘if I put this gene in an ectopic place, or an extra place, or put extra amounts of this gene into an organism, would I get more of that structure?’ So those are the three types of experiments we do.
 

en: What got you into this field?

DL: I thought I was going to go to college to study history and then be a lawyer someday, because I like to talk and be in front of people. But I walked into the wrong biology class by accident as part of my general education classes at a liberal arts school and the teacher who was teaching the biology class turned out to be a Darwin scholar. He was a historian of science and he was telling us about how cephalopods have independently evolved really high intelligence. And it was really fascinating to me to understand the evolutionary history of where different organisms come from. And that set me on my path to studying evolutionary developmental biology.
 

en: Why did you want to come to Scripps Oceanography?

DL: I wanted to come to Scripps to work with some of the great colleagues that I have here. For instance, my colleague Amro Hamdoun and I are collaborating to work on a local sea urchin species for which we've sequenced its genome. His group has been able to grow them for their entire life cycle in the lab. Now we are working on making them transgenic, which means we modify their genome – for example by marking a protein with a fluorescent tag so that we can observe it in real time – and keep those genetically modified organisms in the lab.  

One of the things that I love about being a professor and working at UC San Diego is being able to work with such incredibly talented undergraduates. For instance, my undergraduate Course-assisted Undergraduate Research Experience lab, or CURE, is an NSF-funded program where I invite students into a lab class where we give them authentic research experience. It’s similar to a summer research internship, but we do it during the school year and the students and I collaborate to come up with individual and novel research questions that we answer over the course of the 10-week quarter.

I've been to a number of marine labs over my career and they're always beautiful and a place where people revere the ocean. And I always knew I wanted to be at a marine lab, but many marine labs are quite remote and hard to get to. In contrast, Scripps is one of the few urban marine labs in the country and was just the perfect place for me.