Natalie Kuldell (00:02):
Hi, Jenn. It’s good to see you.
Jenn Brophy (00:05):
Hi, Natalie. It’s good to see you too.
Natalie Kuldell (00:07):
Thank you for joining on this conversation. I’ve been really lucky to know you for a couple of years now, and I’m probably as excited as anyone to hear about what you’re currently doing. So, maybe you can say who you are and where you are and what your job is.
Jenn Brophy (00:27):
Yeah. Okay. So I’m Jenn Brophy, I’m a new assistant professor of Bioengineering at Stanford. My lab just opened four months ago and we are setting up a new synthetic biology lab.
Natalie Kuldell (00:41):
It’s amazing. So, what was one of the first things you bought as a setup for a synthetic biology lab?
Jenn Brophy (00:48):
Pipettes. Actually a lot of pipettes. Yeah, it turned out there were a few that were already in the lab that we didn’t know about. But you can really never have too many. <Laugh>
Natalie Kuldell (01:02):
You will always find a use for them. I am sure. So, a synthetic biology lab. So, um, gosh, I could ask you about Stanford. I could ask you about that. So, maybe I’ll ask about both what attracted you to going to Stanford to do synthetic biology?
Jenn Brophy (01:18):
Yeah. So Stanford has a really unique kind of collection of researchers. That was great for me. So we do plant synthetic biology and there are sort of fewer institutions that have a really strong plant biology research groups and synthetic biology research groups, but Stanford had both. And so I thought that would be a great place to set up the lab because the students and postdocs that come to work with me will be able to get influence from both the plant biology community and the synthetic biology community.
Natalie Kuldell (01:51):
That sounds amazing. So plant synthetic biology is not, I’d say one of the biggest branches of synthetic biology right now, or maybe not the most advanced of all the synthetic biology branches. So what is it that you’re working on there? The field seems to be wide open.
Jenn Brophy (02:07):
Yeah, so, during my postdoc, I developed some synthetic genetic circuits in plants and we used those to reprogram the way that plant roots grow. And I am interested in continuing to do that and to move sort of from the model that we were working with. So this plant is kind of like the E coli of the plant world. Everybody does their experiments in this one because it’s fast to grow and it’s easy to introduce new DNA into, but nobody eats it. Nobody grows it as a crop. Um, and so what we would love to do is take sort of the synthetic biology tools to build circuits from this model plant into crop species, and then to kinda loop back in some of the bacteria that live in and around plants in order to help those plants survive because bacteria are kind of easier synthetic biology models or targets.
Natalie Kuldell (03:03):
Yeah. Is that what is shown on your board behind you are roots?
Jenn Brophy (03:08):
Yeah, there’s kind of a weird collection of like DNA constructs and then root tips and sort of by engineering expression in root tips, we’re hoping to change kind of whole root phenotypes. So these are theories but we haven’t tested most of them yet. <Laugh>
Natalie Kuldell (03:28):
Well, you have your pipettes, so you’re gonna be on your way. I’m sure.
Jenn Brophy (03:33):
I’d say like most of them are still in the boxes, but we have gotten out a few.
Natalie Kuldell (03:38):
Awesome, I think that diagram behind you just captures so much, right? The molecular piece, the programming piece, the species from the plants to bacteria to phenotypes. It’s just awesome.
Jenn Brophy (03:55):
Yeah. I mean, I think that’s one of the reasons why we haven’t seen as advanced of synthetic biology in plants as we have in like unicellular organisms, like bacteria, because in addition to the DNA that you introduce changing a single cell’s behavior, you have the cells working in kind of concert with each other to change what the whole plant does and predicting based on what DNA you give it, how the whole organism will respond is really hard. Um, and yeah, definitely a barrier to engineering. If you don’t have an idea what your DNA is gonna do, you have less ideas for how to engineer it, but our understanding of those things has been improving over the last several decades by a lot of really great molecular biology work in plants. And, so we’re kind of taking advantage of some of that.
Natalie Kuldell (04:48):
So what I hear is that it is the big wave that you are just catching and that’s awesome that you are there. And, also that you are a very brave person to be able to be trying such unchartered territory. It’s fabulous. But you had done some as a postdoc, you say, would you wanna say a little bit about where you were postdoc and what you did?
Jenn Brophy (05:08):
Yeah, so I was actually also a postdoc at Stanford. I was in a different department. So, my lab’s in bioengineering, I did my postdoc in biology, which is actually not just a different department. It’s a different school within Stanford. There’s the school of engineering and then the School of Humanities and Sciences. So it does feel like a really different job to have moved, but at the same time, when I walk around campus, I see some familiar faces, which is nice. Um, the lab that I worked in as a postdoc, studies root development and the impact that a root system has on a plant’s ability to survive in a drought. Um, so it was really helpful to work there, to have this idea of how changes in a root system really affect its ability to survive and to learn how to look at plants and determine did I do something helpful or something not helpful. Right.
Natalie Kuldell (06:06):
Mine just turned brown. That’s all I know is that mine just turned brown when they don’t like what I’ve done.
Jenn Brophy (06:12):
I mean, so do most of mine, I have two decorative plants in my office, but that is it because I’m scared to have more and have people judge me when they come in.
Natalie Kuldell (06:26):
Yeah, I get that.
Jenn Brophy (06:27):
Yeah, but well, phenotyping is hard, right? How do you know if what you’ve introduced is helping a plant do better or not – if your engineering is helping? And so this postdoc lab was really helpful in helping me figure out some of that.
Natalie Kuldell (06:44):
That’s very, very wonderful. And you came to it from MIT. So that is where I got to know you first. So, I know you did synthetic biology at MIT. So, do you want to say just a few words about that?
Jenn Brophy (06:58):
Yeah. The lab that I worked in at MIT is one of the world leading experts on synthetic genetic circuits. And so when I first joined, I did a small-ish project on, kind of methods of tuning expression levels that would help you tune synthetic genetic circuits that they functioned well. Um, but I actually joined this lab at sort of a strange time. The lab was moving from, UCSF over to MIT. And I was the first MIT student that joined, actually before the lab physically got there. And that made me have to find a different space to start to work in. And I got a co-advisor for my PhD who, you know, really had no interest in synthetic biology or in circuits, but was a fantastic microbiologist and geneticist. And he influenced my work a lot because he was sort of like, okay, well, that’s cool in E. coli, but you know, we work in this gram positive bacteria and there are so many other types of bacteria that are doing important things. And so towards the end of my PhD, we tried to address some of that. And I developed this tool working with kind of both advisors that would allow you to deliver pieces of DNA to undomesticated gram positive bacteria. So if you were to take a sample from somewhere, could you engineer the bacteria that are there?
Natalie Kuldell (08:32):
So, I mean, I’m hearing a pattern here of you finding these complimentary support networks, whether it’s advisors or departments and bringing them together in novel ways, and ways that most people would agree have to get done, but not everybody is willing to jump on and try to get to happen. So, backing up, I guess a little bit further, have you always sort of had that, I don’t know cross-disciplinary or multidisciplinary interest?
Jenn Brophy (09:08):
Um, that’s hard to answer. I’m not sure I ever really thought about that in that way until grad school. But when I was in high school, what I was really interested in was math and art.
Natalie Kuldell (09:23):
So I would say yes then.
Jenn Brophy (09:25):
Yeah. But I never thought about it like that. I kind of thought, these are the two things that I like, and I kind of went on this mission and undergrad to find classes that fit those interests. And funnily enough ended up in biology because of the kind of visual aspects of biology, like how beautiful some of the organisms that we were studying and my intro biology class, which was sort of a requirement for everybody and found engineering through the math sides and ended up actually not deliberately, but by my junior year, realizing I needed to declare a major and looking at what the classes I took fit at Berkeley and chose bioengineering based on that.
Natalie Kuldell (10:13):
Yeah. You may be the first person to reverse engineer a bioengineering degree as an undergraduate.
Natalie Kuldell (10:23):
I think that’s awesome. And, you know, I think there are a lot of scientists who do have interest in the arts and interest in creative endeavors and it is not true that scientists are only focused on math and numbers and data. There is a creative and, I don’t know, intuitive side to science, would you say?
Jenn Brophy (10:46):
Yeah, totally. I think that’s because you often, especially with biology, you can’t know exactly how – you can have a guess – but you can’t know exactly how a system works or how it may behave. And so you kind of intuit your way occasionally to an answer. Yeah.
Natalie Kuldell (11:05):
So when you look for students to come into your lab, now that you’re a new professor there and starting off your lab, what are you looking for?
Jenn Brophy (11:13):
Mostly enthusiasm. We’re interested, or I’m interested in applying some of this plant engineering work towards sustainability problems. And so we’re looking for students with a kind of passion for sustainability and interest in plants, which can be, you know, a little more frustrating to grow than bacteria. Um, and yeah, I guess, a willingness to take a chance on a new lab. I think that’s also kind of scary depending on what point in your career you’re at. But, I mean, so far just been meeting with everybody who seems interested in trying to determine if we can find projects that we both want to pursue.
Natalie Kuldell (11:57):
I think it sounds great. You know, I would absolutely believe that you will have people lining up to join you and the really important work that you’re doing. If we were to look ahead a year from now, what would a year from now, like total success look like for you?
Jenn Brophy (12:20):
Ooh, well, we will be totally set up, our growth chambers would have healthy growing plants in them. And I’m hoping, you know, we have a collection of people who are working on some plant synthetic biology – kind of helping each other figure out the best ways, fastest ways maybe to do this engineering in plants.
Natalie Kuldell (12:43):
I think that that is a very realistic goal. I would be surprised if a year from now, that’s not where you’re at, Jenn. I wish you every success. I think the work you’re doing is so important. I think you’re exactly the right person to be doing it. I’m just so excited to see what comes next for you.
Jenn Brophy (13:02):
Thanks, Natalie. I’m excited too.
Natalie Kuldell (13:03):
Thank you for being here today to talk about your work.
Jenn Brophy (13:07):
Thanks for having me.