Siobhan Brady
Description: Siobhan Brady is a Professor of Plant Biology and Principle Investigator of the Brady Lab at the University of California, Davis. Her work looks at the differences in spatial temporal development of cells in plant roots by studying transcriptional networks. In this episode we talk about her research on roots, nitrogen processes, and flooding in plants. Additionally we discuss the possibilities of breeding drought tolerant plants, enhancing nitrogen uptake, and protecting crops from parasitic plants.
Websites:
Publications:
A High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns
Running A Research Group in the Next Generation
Evolutionary Flexibility in Flooding Response Circuitry in Angiosperms
Resources:
Promoting Root Microbes for Integrated Striga Eradication (PROMISE)
Articles:
Getting to the Root of Food Production: Siobhan Brady Receives Faculty Research Award
Gene Network Lets Plant Roots Handle Nitrogen
Grains in the Rain: Study Opens the Door to Flood-Resistant Crops
Show Notes:
[0:00:05] Introduction and Background: From Canada to Davis
[0:03:28] Transition to Duke University and Dream Job at Davis
[0:06:20] Variation in Root Systems and Adaptation to Different Environments
[0:09:11] Genetics: Unraveling the Genes and Making Mutants
[0:13:59] Findings from Tomato Research: Contrasting Domesticated and Wild Species
[0:15:28] The Exodermis: A Barrier in Wild and Domesticated Species
[0:16:33] Subarin Production for Drought Tolerance in Plants
[0:18:31] Root Development and Environmental Stress
[0:24:52] Understanding the Intellectual Property Process
[0:28:08] Importance of Nitrogen for Plants and the Nitrogen Cycle
[0:32:56] Eutrophication: Impact on Water Organisms
[0:34:29] The Classification of Fertilizer Use in Organic Farming
[0:34:49] Soil Functions and Nitrogen Mobilization in Agriculture
[0:44:02] Introduction to PROMIS project and its partners
[0:47:03] Striga Hijacking the Process
[0:47:35] Strigalactone signal and parasitic plant-host root interaction
[0:50:23] Physical barriers in xylem and other cell layers to block striga
[0:53:33] Foreign genetics and the removal of Cas9 protein
[0:56:22] Transitioning to a new stage of lab research
[0:57:36] Exploring Climate Change and Plant Stressors
[1:00:40] Finding Research Opportunities and Developing Research Skills
Unedited AI Generated Transcript
Introduction and Background: From Canada to Davis
Brent:
[0:05] Welcome, Professor Siobhan Brady, thank you for coming on today.
Siobhan:
[0:08] Thank you so much for inviting me.
Keller:
[0:10] We'd love to start off by hearing a little bit more about your story.
How'd you get to Davis and what got you interested in plants?
Siobhan:
[0:16] Okay, so how did I get to Davis? It was a long, long path.
So I did my, I'm from Canada, so from a small, very, very, very small town in Ontario, which which is a province of Canada.
I did my undergraduate and my PhD work at the University of Toronto.
And we had a lot of lab courses when we were in Toronto.
Unfortunately, unlike here, you don't have as many in your bio classes.
And from my very first year, we did a plant biology lab. We worked on grasses that were metal tolerant.
And I thought that was super fascinating. And then at the same time, we also worked on, we had labs that worked on molecular biology.
And at the time actually, so Eduardo Blumwald, I don't know if you know him, he's a professor here. So he moved from University of Toronto to Davis.
His lab worked on transporters of this particular class called ABC transporters.
And some of those transporters have been associated with changes in like mineral transport and then others in some cases with metal transport, I believe. And so I just like the idea ofputting those two together.
And I thought that, yeah, plants were super exciting. I was amazed by everything that they could do.
And then in my PhD, so I did undergraduate research work when I was working on plant-pathogen interactions.
[1:44] So I started in my second year. They had, uh, programs that were focused on bringing students in, in their second year, which is the sophomore year here, right?
And, uh, and again, like I made lots of mistakes, I sucked, uh, but I really like if I'm doing something wrong, doing it better.
And so I just kept working on that. Uh, and by the time I was in my fourth year, I was a very weird person in that I decided that I I wanted to be a professor in plant molecular biology,which is usually not how things are done.
So I picked a research lab for my PhD. His name is Professor Peter McCourt.
[2:28] His lab worked on plant hormone interactions, and I really wanted to work in his lab because it was one of my worst biology classes, his genetics class in terms of my GPA, but Iloved the way that he thought, and he was really, really good at teaching students to think critically.
So I worked in his lab. I started working on plant roots. I could look at roots all the time under a microscope. I loved them so much.
The sequence of the plant Arabidopsis Thaliana had just been published in 2000.
And there was so much data available that it just seemed like you could do anything that you wanted.
And then I met my husband who's a software engineer and he and I were super geeky and loved talking about genome sequences and how to mine useful information.
And then we started, so I loved genomics at that point and I started to get really interested in systems biology.
Transition to Duke University and Dream Job at Davis
[3:28] And so then I made the transition from after my PhD, moving to Duke University where I worked with an expert in plant systems biology. His name is Philip Benfie.
Worked there for about three and a half years and then I got offered the job here in Davis and I started in January 2009.
[3:50] And like Davis was my dream school to work at because it's one of the best in the world in terms of plant biology.
And there's also a woman named Catherine Esaw who did a lot of research here and she works on, or she worked on plant developmental biology.
And I had read her textbooks in my undergraduate classes.
And so, yeah, I was just thrilled.
Brent:
[4:13] That's amazing.
Siobhan:
[4:14] I was super excited. I had my dream job and then that's how I ended up here.
Brent:
[4:19] And then you started to say that you focus a lot on the roots.
Correct. What makes up the root of a plant?
Siobhan:
[4:26] Okay, so, a root, so.
Most plants make a root.
You can usually see them when you take a seed and you germinate it.
You probably did it when you were in elementary school, putting a seed into a paper towel, so you can see the root emerging first usually.
And then if you look at the root and you start to make sections through it, every root is the same. So it's made up of different cell layers.
So, imagine you have like a circle and a circle inside a circle and a circle inside a circle and a circle inside a circle.
Those are all different cell types in the root. It always has that same patterning.
And so, that's if you like make a section through it, like you're cutting a carrot round, you know.
And then if you look along the length of the root, so the stem cell population, the population that gives rise to all of those cells, that's all at the tip always, and then that's the part that'sgrowing down.
Every root is exactly the same in that particular way.
And then the root system is formed by other roots that are coming off of the primary root.
So that's that first root that's just coming out of the seed.
So they branch off, and then those roots themselves can produce more roots.
And then that's how you get the root system.
Brent:
[5:54] Okay.
Keller:
[5:55] In what role do the roots play other than absorbing nutrients from the soil?
Siobhan:
[6:00] Mechanical support. They're also critical in transporting water, so the majority of, that a plant needs to survive comes from below ground, which is through the roots.
Brent:
[6:11] And then what would be some of the variation you see? Because I kind of find it hard to believe that all plants have the same root system.
Is there some variation?
Variation in Root Systems and Adaptation to Different Environments
Siobhan:
[6:20] Yeah, that's a really great question and the focus of our research, which is there's such a diversity of plant roots that exist on this earth.
So, and that variation I think is also responsible for allowing plants to grow in different environments.
So at its like most basic level, so I described like the primary root system, but you can also have in corn as an example, in other grasses you can have adventitious roots that come off of,well, first they come off of like the bottom part of the stem.
Brent:
[7:00] Is it the meristem?
Siobhan:
[7:01] That's not the meristem. Yeah, that's, so it's just the stem.
Brent:
[7:05] Okay.
Siobhan:
[7:06] So right at like the stem root junction, you can have some roots coming off of there. Those are called adventitious roots.
And then you can also have crown roots and brace roots.
And brace roots are if you ever like, if you go out and do like the corn maze Halloween, for instance, and you're going through all the cornfields, you can see that there are these roots thatform a circle at kind of the base of the stalk and then they anchor, they further anchor the plant into the ground.
That's a trait that's really heavily bred for because if you have lots of wind or rain, it can keep the plant standing up. So...
[7:48] That's different types of what we call root system architecture.
But then what my lab works on is the differences in root cell type patterning.
So I said there are always those circles of cells, like one inside each other.
Generally, like there's generally the same types of cells, but in some cases there's many more of a particular type of cell, like in Arabidopsis, this model plant we work on.
For instance, there's like one layer called a cortex, but then in other plant species, there can be, you know, anywhere from two to like eight or even 11 or 13 cortex layers.
So we want to understand what makes those layers different from each other.
And in many cases, those cells can, they've found ways to adapt to the environment.
So they produce really particular features that protect the plants from its external environment.
Like it can help prevent water loss, for instance, by producing a particular type of wall, or it can keep oxygen inside if plants are being flooded, or it could help in like salt uptake.
There's all different kinds of ways in which they can be modified, and we don't really understand what all those ways are.
Brent:
[9:07] And then, is that where your work with genetics comes in?
Genetics: Unraveling the Genes and Making Mutants
Siobhan:
[9:11] Yes, that is definitely where my work with genetics comes in, so we're interested in the genes that control the development of the plant root, and specifically the development ofcertain cell types, and now even individual cells.
And so, our first job is to try to figure out what the genes are that are found in each of those different cell types or cells, and then we, Next, in order to figure out what they actually do, wemake mutants of them.
And then we look to see what the cells look like afterwards. How do you make a mutant?
Brent:
[9:54] So we look to see their phenotypes.
Siobhan:
[9:55] Ha!
So you, well, if you're lucky enough, you work in a plant that has them already available to you, like through a resource center.
So there's a resource center in San Diego, for instance, that produced a lot of different mutants that we get to use for Arabidopsis.
[10:16] Okay, so that's if you're lucky. But the different ways in which they make mutants in the past was by either like you take seeds and you expose them to a really harsh chemical likeethyl methane sulfonate or to ionizing radiation.
And then you'll have mutations in the DNA and they'll figure out where, well ideally other people will have figured out where those mutations are, but if not, you can figure it out yourself.
You can also have mutants where there's transposons, so pieces of DNA that have jumped randomly into the genome or have jumped into regions that you know ahead of time, and thatcan disrupt the genes.
And then now with CRISPR-Cas9, we can make, well, we ideally want to make really precise mutations in individual genes.
So that's like the genetics part of it. And then once we've identified those genes, we then want to start to map the pathways of those genes, which gene turns on another gene, that gene,what its target is.
And so, we like building these giant networks because each gene doesn't act in isolation.
So we've also developed ways to be able to look at what those networks are and to use those networks to predict how that cell type is responding to the environment.
And then we test those hypotheses, again, using mutants.
Brent:
[11:42] CB.
Keller:
[11:42] And are you building these models within certain model organisms or are you testing a bunch of different varieties? DR.
Siobhan:
[11:49] Right. So when I started, it was in a specific organism.
So it was in Arabidopsis, which is this little weed whose genome was sequenced.
And then as I started my own lab, we started working in tomato.
So I don't know if you're familiar with, have you ever heard of the Tomato Genetics Resource Center? No, I don't think so.
It's another center on campus that you guys are getting familiar with all the different centers in the state of California.
[12:18] So the Tomato Genetics Resource Center was started by this gentleman named Charlie Rick.
And he went on these, to me, crazy field expeditions field expeditions down the coast of South America.
And he collected a range of different tomato species, particularly it's the wild species that he collected a lot of that grow in again all these crazy environments where nothing is perfect.
[12:49] So we had this tomato genetics resource center here and there were other people in my department who were working on tomato and they convinced me to look at the roots and Idid. And now like 70% of my lab works on tomato roots.
And then the other organism that we work on is sorghum.
So sorghum by color, which is a grass that's grown in Asia and Sub-Saharan Africa.
And even here now, like again, at that like the maze, there's like the maze over on 113, I can't remember the name of of it, but they had like a sorghum field.
I have kids, we go to mazes a lot. And so they grow sorghum there, and it's also like one of these niche, like hipster-ish kind of plants in a well that they have in Davis where you can makeflour and things like that.
But it's a staple grain for a lot of Asian countries and Sub-Saharan African countries.
Brent:
[13:51] And then what are some of the findings from the tomato work? Okay.
Findings from Tomato Research: Contrasting Domesticated and Wild Species
Siobhan:
[13:59] So, oh, so many.
Like 10 to 12 years worth of findings. So let me see where to start.
I'll give you like my big picture findings.
So first, we started comparing this domesticated species. So just like your regular tomato that you eat, there's a processing tomato variety called M82.
And we compared that to a wild tomato species, which is found in coastal deserts of South America with like very, very little water, very little nutrients.
And so those roots look very different. So the domesticated like M82 root, it grows, you know, the root grows straight and down and in this regular way that we expect.
But the wild species root, it's very short, and it grows off at an angle.
It has a different response to gravity. And so, We've identified potential genes that control that, So using quantitative genetics.
More importantly for the rest of our lab's research, we looked at the cell types in those roots and the ways in which those cell types were patterned.
And we found a lot of differences in those patterns.
And so, we've studied that a little bit further.
The Exodermis: A Barrier in Wild and Domesticated Species
[15:28] In the wild species, there is this cortex layer that I mentioned before called the exodermis.
It's actually it's present in both the domesticated species and the wild species.
But in the wild species, it produces this barrier that's called Subarin.
It's like you can find Subarin's present in high levels in oak, in cork oak, for instance, or like in cork and like a fancy beer or wine bottle.
And so, there's a ton of it in those exoderma cells and it's on all the time.
So, in control conditions and drought stress conditions.
But in the M82 species, it is only formed when the plants are exposed to drought.
Okay. So, we found a lot of genes that control the production of the Subarin in both species.
And then we've shown in the domesticated species that.
Subarin Production for Drought Tolerance in Plants
[16:33] The production of Subarin is necessary for a plant's response to drought.
So the idea is that if you have a plant that produces different levels of Subarin, you know, if you have more Subarin then it should be drought tolerant.
And less Subarin, it'll be drought sensitive. And so we can use this as a tool to try to breed more drought tolerant plants.
Brent:
[16:58] Okay, and then would the production of Subarin when it's not in a drought cause issues?
Siobhan:
[17:04] That's a really good question. Likely yes, because it forms this really strong barrier. And so if you have a strong barrier being produced, it's hard for cells to divide or continue togrow.
So there'll probably be a penalty in terms of root growth, so it'll be harder for the root to grow.
And then those genes that control Subarin biosynthesis, they also play a role often in the development of the fruit. So, you have your fruit skin, which is pretty strong.
So, Subarin or a relative of a molecule that's a relative of Subarin is also found in those fruits.
So, it could also influence fruit ripening and hardiness.
Brent:
[17:47] CB.
Keller:
[17:48] Okay. And does soil type play into this at all? If you had two of the same plants and you edited them the same way, but placed them like one in Davis where you have very clayeysoil and one somewhere else, would they respond differently? BT.
Siobhan:
[18:00] Yes, in all likelihood. And that's kind of a really big tension.
You've stumbled on this really big tension between people who do a lot of basic plant research, like basic plant molecular biology and genetics like I grew up doing and like my labgenerally does, compared to people who actually breed plants for human consumption.
Root Development and Environmental Stress
[18:31] Because the environment plays an enormous role in terms of root development, and so what you find in the lab in a greenhouse is generally not what you would observe in, in, forinstance, soils with different types, much less regions with different temperatures, or soils with different mineral nutrient content, or microbes, or all the rest of it.
So they're really, really highly responsive to environmental stress.
That's what makes them so amazing.
So, what we try to do is to look for genes that control processes in ways that don't necessarily change across different environments.
Or, like in the case of drought, or that they change in exactly the same way in different conditions.
Like meaning like control and and then water-limited conditions.
Keller:
[19:31] You mentioned earlier the cell patterns of formation. Does that relate to the transcriptional networks or is that distinct?
Siobhan:
[19:36] Yes. So when I talked about the gene pathways and the genes that we look at, we are really, we love mapping gene networks.
So like genes that control other genes. And so we work specifically on transcription factors and their targets.
And so transcription factors are proteins that can bind to target regions of DNA, and then they can interact with other machinery to control transcription to either increase it or to decreaseit.
And then the transcription produces these transcripts, and the transcripts go on and code for proteins that are generally the ones that are doing the stuff that are required for life.
And so, we like to map transcriptional networks for individual cell types.
And we'd like to continue to do so in the future, even within individual cells.
Brent:
[20:32] How do you go about mapping?
Siobhan:
[20:34] The networks?
Brent:
[20:35] Yes.
Siobhan:
[20:36] Yeah. So I'll try to explain it kind of generally, conceptually.
So we've we've developed a way or we translated a way from work in worms and C. elegans so that we can map interactions between transcription factors and their targets in yeast.
And so yeast is great because yeast can grow in just days as opposed to plants which like Arabidopsis can grow in six to weeks, tomato like three to six months.
So we can look for the interactions between.
We produce a huge amount of transcription factors of each individual transcription factor within a genome, and then we take the promoters of genes and we hook them up to differentreporters that'll tell us whether or not, that promoter is enough to make the gene be turned on or turned off to be transcribed or not to be transcribed.
And then we introduce the transcription factor and that promoter with what we call a reporter, we introduce those entities together.
And then with that reporter, we can read out if that interaction occurs or not.
Brent:
[22:00] So is it basically the reporter, you track the movement of the reporter and then that tells you to where it ended up going in that.
Siobhan:
[22:08] So not the movement of the reporter, but just like the activity.
Like, is the yeast blue or is it not blue? And that'll tell us if it's blue, that means that the transcription factor interacted with the promoter.
And it'll just give us that like yes or no.
In yeast, it's able to do that. And so we do that like on repeat for every transcription factor, like 2,000 within the Arabidopsis genome, then with individual promoters.
So that's how we map them. And then we'll map it for an individual cell type by only including transcription factors which are expressed in a particular cell type, and then looking forpromoters of genes that are also only expressed or found in that cell type.
Keller:
[22:54] CB is temporal data taken for this?
Siobhan:
[22:57] BT. No. And so, yeah, temporal data is really important.
So this method in yeast is a way that you can relatively quickly get an idea of what possible interactions can occur.
But then in the plant, we want to look to see how those interactions can change over time. And that's like definitely more complicated. Yeah. Okay.
Keller:
[23:21] One sec.
Brent:
[23:21] Yeah. I think that mic is, Has it fallen a bit?
Siobhan:
[23:25] Maybe. Is that better?
That should be perfect. Okay. Yeah.
Brent:
[23:39] I have a, sip of my coffee. There we go. So then you mentioned a bit earlier the difference between working in the lab and those type of plants versus the ones we use in the field orto actually grow.
How do you hope to see your work in the lab translate or how can it translate?
Siobhan:
[24:05] Yeah. That is, so first of all, that's something that I had never even imagined that my research could do when I was like growing up as a scientist because I only worked on this plantto rabidopsis.
So my work is now starting to really impinge pinch into translational research.
So like working on Subarin for instance, and then this other barrier called Ligden that's produced, those barriers are considered to be an area of interest for breeding plants that are moreable to handle diverse like climate stressors.
Understanding the Intellectual Property Process
[24:52] So first we started the whole process whole process just by working with at UC Davis, they have an innovation access team that handles intellectual property and kind of walks youthrough what intellectual property is, how just like the whole process works, like how do you even start to define what intellectual property is and whether or not it would be of marketinginterest, meaning that like if you file a patent on a particular gene that controls Subarin, would there be a company that would be interested in purchasing that patent or using that patentand licensing the technology?
And then what I've realized is that they're really only interested in these genes if they can see a really clear way in which they can translate that into a plant that can be grown in the field.
And so, the companies have a lot of different ways in figuring that out, a lot of which I'm not exactly sure of how it works, but they have ways.
And then what we also do on the side now is that we're trying to create plant lines in M82, which is this background, it's a processing tomato, but it's not anything that's grown currently byany farmers like in the Central Valley. And so we are...
[26:20] We're going to try to make our plants that can do that, plant it in the field.
And then if it produces the trait that we're interested in, then at least we have evidence that it can work in this particular tomato variety.
And then we can provide more evidence to the companies that this could be of use.
And then maybe they'd be interested in licensing the technologies that that we've generated.
Brent:
[26:44] So when you make the patent, is it for a plant or a specific part of the genome that you've edited?
Siobhan:
[26:52] For a specific part of the genome. And then there's a lot of different pieces of evidence that you provide to show that this gene can do something that is of commercial importance.
CB.
Keller:
[27:09] So the process starts kind of with working with the companies also see like what you should lean towards or does it start with an idea and then tested once it's tested presented?Where exactly does that?
Siobhan:
[27:21] BT. So it's not with the idea, it's with a demonstration of an idea or of a principle on showing that it works.
So that's the first part. And then the companies, well, first the lawyers will decide here at UC Davis, they'll decide whether or not it's worth pursuing.
And then it's up to the companies to then further decide if they're interested in licensing that.
Brent:
[27:50] So kind of taking a step back, and can we go into your work with how plants interact with nitrogen? So.
And maybe just start that off. What is the nitrogen cycle and why is nitrogen so important for plants?
Importance of Nitrogen for Plants and the Nitrogen Cycle
Siobhan:
[28:08] The nitrogen cycle, like and I had to look that up in my son's fifth grade biology.
So, but like the nitrogen cycle is all about the nitrogen that you have that exists on earth and how that nitrogen can be used.
Nitrogen is critical for growth of every single living organism, right? So it's a core component of protein, so you need to have nitrogen in order to produce proteins.
And as such, right? I mean, like if you're trying to eat super healthy, sometimes you may just like eat a lot of high protein food and less carbs, there's like issues with that, right? But thenitrogen is important there.
[28:48] So from the perspective of plant roots, so they do play a critical role in the uptake of nitrogen.
So all of the nitrogen that we take as humans in some form comes from the plants.
Even if it's like from eating meat, that like the cow, for instance, has eaten grass or clover or whatever that has actually nitrogen in it and the animals metabolize that nitrogen.
So we have microbes in the soil that assist with nitrogen fixation.
And then plant roots are also responsible for nitrate assimilation.
So taking up the nitrogen and usable forms into the plant.
So that's nitrogen and how it works. And so we're really interested in genes that control the process in roots from a transcriptional perspective.
Brent:
[29:47] So does the nitrogen fixation happen at the root level?
Siobhan:
[29:51] Yeah, so for instance, like you have rhizobia that are nitrogen fixing bacteria.
And so then they interact with the plant in a symbiotic relationship.
So they can fix nitrogen, interact with the root. The root can take up the nitrogen and then the root gives the microbe something else that it needs to survive.
Brent:
[30:14] And then when you start to edit the genome of the plant, does that basically allow the plant to say take up more nitrogen or is it like a higher yield of what the bacteria gives off?
Siobhan:
[30:30] Is that what the- So we aren't really working with nitrogen fixing bacteria, but I can tell you about.
We're interested in. So we're interested in finding transcription factors that can change the expression levels of genes that are involved in nitrate assimilation.
So converting the nitrogen to a form that will be fed directly into central metabolism for the plant.
And so, yeah, so we want to identify those critical regulators, those critical transcription factors that can increase this process.
And then you like really, again, also your questions are great.
So you zeroed in on the really important part, which is that just because you have a transcription factor that can increase the production of these genes involved in nitrogen metabolism, itdoesn't necessarily mean that that nitrogen is in a form that can be taken up into the parts of the plants that we use as food.
And so, you also have to measure like changes in nitrogen use efficiency.
And so, that's how the nitrogen can be taken up and how it can be used and also how it can be used to at the very end produce like seeds or fruit or whatever that have increased levels ofnitrogen. Yeah.
Keller:
[31:52] So, this could be a way of reducing fertilizer use.
Siobhan:
[31:56] Yes, exactly. So, we definitely want to rely a lot less on nitrogen from fertilizer, which is applied in excess, and which, you know, also pollutes like our waterways and soil andeverything else.
Brent:
[32:10] Could you maybe expand a bit more on like what excess nitrogen does to the environment? Sure.
Siobhan:
[32:15] And I can do it in my like broad kind of perspective as a person who, who understands this to a basic, well maybe not so basic degree, a general understanding.
So if you have excess nitrogen in the environment, particularly in the case of water, so the nitrogen will be leached out into the groundwater, which can go into like lakes for instance orriverways.
Which I'm using like as my Canadian example because I grew up by a lake.
Eutrophication: Impact on Water Organisms
[32:56] And so we can see this all the time.
And so when you have that increase in nitrogen, that nitrogen is used by will be other organisms in the water that can't capture available sunlight, for instance, and they can't grow.
And then there's fish who can't necessarily acquire the oxygen that they need to be able to survive.
And that whole process is called eutrophication.
And then there's also ways that it affects soil. And so this is really, really important, particularly and like the Central Valley and the areas in the state of California that are really, that areagricultural producers, where you have a huge amount of nitrogen in the soil, and it's stored in ways that are really harmful for particularly like, as an example, like small children.
So you can have nitrites, for instance, and huge levels of nitrites in the groundwater that are taken up, for instance, in like carrots.
And if you have like a baby and you're feeding the baby mushed up carrots, and those carrots have high levels of nitrites, then it can cause really horrible effects on, for instance, like heartfunction in infants.
[34:21] So those are like two different ways in which they have really horrible downstream consequences.
The Classification of Fertilizer Use in Organic Farming
Brent:
[34:29] Yeah. And then would that fertilizer use still be classified under organic possibly?
Because if you're thinking about the end user trying to prevent the nitrites or other things like that, what's the best way to go about that?
Soil Functions and Nitrogen Mobilization in Agriculture
Siobhan:
[34:49] So I don't, again, I'll answer in my general, in my way that I understand generally, which is that if you can find ways for the soil to use, it's just like natural functions, right? Likeyou consider it as a whole ecosystem.
If you can find ways to mobilize that nitrogen within the soil so that the plant can take it up better without the addition of additional nitrogen, then that's better.
It's better for the environment, but you also want to do it in a way that doesn't harm the ecosystem.
So for instance, like you could, so there's a balance with everything, right? So I don't, you know, like, I...
[35:40] Don't think that if you want to be able to support a massive agricultural ecosystem like that, for instance, in the state of California, that you're ever going to be able to completely getrid of the use of nitrogen in fertilizer.
It's still needed to be able to produce enough food that we can grow in a cost-effective manner.
But there are certainly ways in which we can and try to improve the ways that plants need nitrogen so that you have less of a requirement for those really high amounts of nitrogen.
Keller:
[36:20] And have the plants that have been edited in the lab for nitrogen fixation, have those reached commercial markets yet?
Siobhan:
[36:26] No.
Keller:
[36:27] Is that on the horizon or is that?
Siobhan:
[36:29] No.
Keller:
[36:30] Okay.
Siobhan:
[36:31] It's written about in grant proposals. But yeah, it's about at that level.
Keller:
[36:37] Yeah. And then you also mentioned earlier flooding and how that could impact plants. Could you talk a little bit about that research?
Siobhan:
[36:44] Right, okay. So flooding is also a big problem with climate change.
So in the same way that like here, for instance, oh, yeah, I mean like California's a perfect example, right? Like we have historic, you know, seven-year droughts and then we have periodsof time, like this winter and spring, where just like there's been constant flooding.
And again, it's plant roots that are really the first responders to those stresses.
So with flooding, you have plants which aren't able to get oxygen because their roots are exposed to huge amounts of water and they aren't able to access the oxygen that they need tosurvive.
And we were involved in a project that had a lot of different collaborators.
So, ones in, so our.
[37:40] Our whole consortium consists of myself, of Neelima Sinha, who is a professor in the Department of Plant Biology, Julia Bailey-Ceres, who is at UC Riverside, and then RogerDeal, who's at Emory University in Atlanta.
And so in that project, we wanted to see how plant roots respond to flooding, to excess water.
[38:06] And we did so by looking at roots at like different levels of gene regulation to see if there were similar ways in which they did it and if there were different ways in which they didit.
And so the similar ways could tell us if the plant, If you go back way in like history, you know, hundreds of thousands of years ago, if there's just like a core way in which they respond tothat stress, that's the same.
And then we could look at a plant like rice, which has just the way that it grows, right?
Like it grows in a patty, for instance. If you go over the causeway, you can see the rice growing probably, like, well, I think everything's a little bit different now because of the flooding.
But like, right about now or the next like month or two you could start to see the rice growing in water-filled paddies.
And so those roots have figured out a way to respond to the flooding by activating particular programs that allow it to grow really, really well and actually thrive in that type ofenvironment.
So we were also looking at ways in which those plants respond favorably, and then you have the information that you need at that point to see if you can figure out how to change a plantto become more able to withstand that flooding.
Brent:
[39:33] What was that favorable change?
Siobhan:
[39:35] Oh, there it is. It's like a kind of general.
We found some really general changes, and it's changes that occurred across hundreds or thousands of genes at a time.
So the plants were able to open their chromatin, to make their DNA much more accessible, in a really dramatic way.
They were able to really open their chromatin, their DNA to make it accessible.
And they were able to really quickly ramp up the expression of genes that they typically respond with in terms of changing what transcripts are produced.
So Rice did that really, really well.
And then the other species like this wild tomato species that I talked about, it basically did nothing.
It had a very like low-level response, but it did change the amount of like nuclear RNA that was produced, but still in like a really like piddly kind of manner. So, yeah.
Keller:
[40:51] And with the flooding, is the main issue the lack of oxygen going to the plants, or is it disease that's formed as a result of, you know, like root mold or things like that?
Siobhan:
[41:02] So both, but the first, so we looked at the most immediate response, which is the immediate change in oxygen levels, but absolutely it changes everything, right?
Like it changes the microbial ecosystem that's around the roots, their particular functions, you have neighboring plants which have started to rot, yeah, you have a lot of issues.
Keller:
[41:27] Yeah. And is rice the only plant that naturally responded favorably to flooding or are there other?
Siobhan:
[41:33] Oh, there are lots of other like, like wetland species, for instance, that, that, or like even, you know, like mangroves, which I find to be fascinating, right?
Those kinds of plants, they only grow in, in wet environments.
And so, but we use these plants for which there's more for our research, for which there's more resources available, like genetic resources available that but we can manipulate.
Brent:
[41:58] And then is there a possibility of taking say whatever rice is able to do and applying that to a different plant?
Siobhan:
[42:05] That's what we'd love to do, yeah.
Brent:
[42:08] Do you think it will work?
Siobhan:
[42:12] I think it's definitely possible. I think that you have to think of the most clever way to do it possible in a way that like you asked before in a way that doesn't interfere with the otheraspects of plant growth. So without a penalty.
Brent:
[42:30] Because do you fully understand the mechanism for which the response occurs?
Siobhan:
[42:36] So it's really, so there's one gene that was, so that Pam Ronald and Julia, so Pam Ronald here at UC Davis and Julia Bailey-Cerez worked on called Snorkel.
And so we definitely know a lot about how that gene works and how it controls the submergence response.
But there's a lot of other genes that also control the response.
And so, any response to a stress like that requires other genes.
And so, yeah, there are a lot of ways in which you can change the response, potentially in other plants, but you have to try everything out first, which requires more basic research.
I'm not sure if I answered your question. Did I? Yeah? No, I think so.
Brent:
[43:21] The original question?
Siobhan:
[43:22] I think so.
Brent:
[43:22] Okay. Because, would it be more editing what is already there or would it be like taking CRISPR and adding it into?
Siobhan:
[43:32] From a basic research perspective, you'd maybe do both, taking things away and adding things, but for an agricultural perspective, like if you think about having plant species be, orplant varieties being able to be grown within the U.S., than editing is the better way to do it, like taking things away. CB.
Brent:
[43:52] Yeah.
Keller:
[43:54] And then kind of one last part of your overall research that we want to touch on is your work for PROMIS.
Could you go into that a little bit?
Introduction to PROMIS project and its partners
Siobhan:
[44:03] BT. Yeah. So PROMIS is, so it stands for, let me make sure I get this right, promoting microbes for integrated striga eradication.
I'm pretty sure that's right.
So this is a Bill and Melinda Gates funded project with many different partners.
So UC Davis through my lab, a company called AgBiome which is in North Carolina.
We have partners at the Ethiopian Institute for Agricultural Research in Holeta, Ethiopia.
And then a lot of collaborators in the Netherlands. So at the University of Amsterdam, NEO which is the Dutch Institute for Ecology. the lead on that project.
The Westerdijk Institute, which is an institute that specializes on fungi.
Okay, so those are all the players.
And our goal is to identify microbes that interfere with this interaction of a parasitic plant with striga.
Okay, so what is a parasitic plant? So in this case the parasitic plant that we work with is called witchweed and it's Striga hermonthica is its scientific name.
[45:18] And in Sub-Saharan Africa for instance where there's very little water, so sorghum in particular is really quite dramatically affected although like maize or millet are also affected.
So what happens is that you can just see if you plant the sorghum, you know, after like five or six leaves are produced that the plant starts to look really sick and wilts.
And then you have this other green plant that comes up and that produces these beautiful flowers, but the sorghum itself has died.
[45:49] And so, this witchweed, the striga, it produces lots of little teeny tiny seeds.
And the teeny tiny seeds fall down. They look like dust, like little pepper flakes. They live in the soil for sometimes up to 30 years.
And so, this parasitic plant, so it needs sorghum to survive or it needs a host to survive.
And so, sorghum, again, as an example, when it grows in the soil, it generally can grow pretty well in environments where there isn't a lot of water or there isn't a lot of nutrients.
But even still, when there isn't a lot of phosphate, for instance, then the plant root will send out the signal like, help, I want to recruit microbes that will help me uptake phosphate.
And so, it generally sends out the signal as plant hormone, that called strigalactone.
But anyways, to convince our muscular mycorrhizal fungi, which can help.
[46:51] Which can help bring phosphate into the plant. So that's the signal that it produces, because it wants the root to interact with these herbuscular mycorrhizal fungi to get morephosphate.
Striga Hijacking the Process
[47:04] And then strigas hijack that process. So striga, when it perceives that.
Strigalactone signal and parasitic plant-host root interaction
[47:35] Strigalactone signal, It looks kind of like, it's like a flat paddle, kind of.
And then that structure is able to penetrate the root, it'll attach and then it'll penetrate the root.
And then it will form connections between the parasitic plants and the host root. So, it'll form these xylem-xylem connections, which basically means that it can suck up all the water andall the mineral nutrients from the plant.
And then it'll just grow along in its merry way.
And the sorghum can't access anything anymore because the striga is sucking it all up.
So, the goal of that project is to identify microbes that interfere with that interaction.
And then those microbes can ideally then be applied as ways to reduce that interaction between sorghum and striga so that these farmers can grow sorghum and get sufficient yield.
Keller:
[48:38] And once that interaction happens, like initial connection after the paddle is connected, at that point, is it kind of like done? Is there any way to reverse the connection at that point?
Siobhan:
[48:51] Yeah, that's one of the things that we're interested in, like using the cell types. So it comes back to the cell types.
[48:57] So we would love to, and we think we found ways that you can have the paddle go into the root, but then it'll hit a barrier. So it'll like hit a wall and that it'll hit that wall before ithits the xylem.
And then once that hits, once it hits that wall, then it'll stop.
The other way that we found this to work is by, so remember when we talked about flooding?
Again, it comes back to certain cell types. That's really nice.
So in the cortex, we also talked about the cortex, in a flooding tolerant species, what they do is they produce these holes in the cortex.
So in a really targeted way when there's really low oxygen like from flooding, the plant will start this.
[49:43] Process where it'll basically tell its cells to commit suicide.
And so then we'll have just these holes in the cortical cells where they can keep oxygen for their use later on.
And so we've identified, or one of the ways in which you can interfere with this interaction is to have the microbiome produce somehow these holes in the root, in the cortex.
And so we think that that means that like the paddle, like the Hastoria will move into the roots and then it'll hit these holes and then it just won't do anything else because it's like, what'sthe point? Why am I bothering?
Physical barriers in xylem and other cell layers to block striga
[50:23] That's all speculation. But yeah, but we can definitely, we've definitely shown that these holes are correlated with reduced striga infection. Yeah.
Brent:
[50:32] Okay. So if you're talking about the physical barrier one, would that be like having the xylem cells produce like more the lignin to then block it.
Siobhan:
[50:40] Ooh, nice. That was good. That was very good. So it could also take place at lignin in the xylem.
We also want to see if we can have it take place in another like neighboring cell before it gets to the vascular tissue where the xylem is, so called the endodermis.
And then it could even do so at the exodermis, which is this other cell layer that we talked about.
So there's lots of different places where these walls made of lignin or subarin could be put up.
Brent:
[51:10] Okay, that's very interesting.
Keller:
[51:12] And how damaging are these witchweeds to the plant yield, like more in a more broad sense?
Siobhan:
[51:16] Devastating.
Keller:
[51:17] Devastating?
Siobhan:
[51:18] Devastating. I can't remember, I have actual numbers, but yeah, just devastating.
You can have, you know, year upon year upon year of like, you know, essentially zero harvest.
And so the farmers are out there like weeding, hand weeding, but because there's like so many striga seeds, it's almost futile, right?
Keller:
[51:42] Yeah.
Brent:
[51:43] So the ultimate goal is to like hopefully make food a lot more secure if we can get the sorghum to be protected against the weed.
Siobhan:
[51:53] Exactly. Yeah, you've got it.
Keller:
[51:56] And we kind of touched on this earlier, but with the editing of those different genes, is there like definable criteria that make a certain edit expressionable, or is that kind of like wetalked about, it has to really just depend on what you're doing with the environment and all those different factors.
Siobhan:
[52:13] All right, so.
Again, this is like my general knowledge of what I understand.
So editing as determined by the US Department of Agriculture has to hit particular requirements.
So you're just editing the gene in its natural environment, like its natural genomic context. You're not introducing any new sequence.
You're just making mutations in sequence that you could get just by natural mutation within within a population.
That'll occur just like regular. There's lots of mutation occurring all the time in genomes.
And then the second piece is that you cannot have a foreign gene or protein be within the plant species. And so that's this protein called Cas9.
And Cas9 is this protein that makes the mutations.
And so, you have to have that Cas9 be removed from the plant.
So, those are the two basic requirements that you have to meet.
And so, but any plant species or any plant line that's produced, that's released into the field has to undergo these USDA reviews.
Foreign genetics and the removal of Cas9 protein
Brent:
[53:33] Yeah.
Sioban:
[53:35] So if you can't add foreign genetics, so- It doesn't mean that you can't, it just means that like, because the US has lots of cases in which it does allow, in which it does allow likecases where you can have foreign DNA.
But but it goes through an independent review process. And that review process is really lengthy.
So the CRISPR edited plants, they don't require any of that like really laborious review.
Brent:
[54:11] Because the Cas9 gets removed.
Siobhan:
[54:12] And there's nothing foreign in there anymore.
Brent:
[54:14] Okay, and would foreign be defined as like human-made genetics, or like if we figured out the mechanism for rice to become very tolerant of flooding, and we could take that andput it into a different plant, is that now foreign to that plant because it's rice?
Siobhan:
[54:27] That's my understanding. Okay.
Brent:
[54:29] Yeah. So then that would have to go through the longer review process?
Siobhan:
[54:33] Correct. Yeah.
Brent:
[54:34] Interesting.
Siobhan:
[54:35] Which is why you kind of want to take like with our, like the SURF project, the submergence upregulated gene families, we want to identify genes which are conserved in theresponse across all plant species, and then try to find a way in which you can change the response so that with, with a gene that's already existing, and then you can just find ways to makeit it like more active or change it so it can do it better.
Brent:
[54:59] It's kind of tapping into a genetic memory.
Siobhan:
[55:02] Oh, well, that's a whole nother thing. But tapping into like the genetic or the gene pool that's already there. Memory is different.
Memory is like changes to.
There's like specific modifications made to the DNA that isn't actually changing the DNA sequence.
That's like called epigenetics and that's associated with memory.
Keller:
[55:25] So yeah.
Siobhan:
[55:26] So like in that case, like for surfs, there'd be like, I think it was like 82 or that 82 plants that have that gene in them. There's 82 genes that were found across all of those plants.
Keller:
[55:38] Okay. So then like within those plants, those 82 are free game to be that initial review.
But but then if you stepped out of that, okay. Correct, yeah.
And with this research is like when it's going through the review process, are they looking into like the nutritional makeup of these plants after they've been mutated?
Sioban:
[55:56] So for the cases where you're introducing foreign DNA, that's my understanding that they do.
But for the CRISPR edited lines where you weren't changing anything, again, as far as I understand, they aren't doing anything.
Because any changes that it would make would, it could change the nutritional status, but in a way that would just happen in nature anyways.
Brent:
[56:16] Okay. So, where do you see the future of your work going?
Transitioning to a new stage of lab research
Siobhan:
[56:22] Yeah. Also a good question, because I'm kind of in this transition point now in my lab's research. I have a bunch of people who found great positions that are moving on, and so it'slike a new stage of my lab's research.
I am super excited about ways in which cell types respond to the environment and ways in which they mount these programs that change the way that they look or change the types ofbarriers that they produce.
There's so many exotic ways that they do this in.
And you can just look at that textbook by Catherine Esau.
I mentioned Catherine Esau before and she has a textbook. You can just look at these images that have been around for centuries, and sometimes they're drawings that they've been aroundfor centuries, and there's just such a variety of the ways that these plants can do it.
And so I really want to.
Exploring Climate Change and Plant Stressors
[57:36] Understand the different ways in which a beneficial outcome.
And then I'm really interested in climate change and finding a way to use those.
Uh, to protect plants from those stressors that are more extreme or different than what these plants have over, you know, time evolved, um, to respond to.
Or like where they, they haven't evolved in order to respond to those stresses.
Keller:
[58:03] P.S. Oh yeah, I could see so many different applications that are really inspiring.
And I kind of want to touch on, you talked about like your lab and people kind of shifting out. C.S. Yeah. P.S. I saw you had something on lab culture.
Siobhan:
[58:14] C.S.
Keller:
[58:15] Yes. The importance of building that up. Could you talk about that?
Siobhan:
[58:17] Yeah. So this was a perspective or a commentary piece that came out of this international conference on Arabidopsis research.
It was actually organized by this woman Joanna Friesner who was a former UC Davis graduate student.
So in this conference, So actually this woman named Jackie Monahan and Heather McFarland, who are both Canadian, because I'm Canadian, that's very exciting.
So they approached myself and Sonali Roy and Elizabeth Haswell, and I think also Benjamin Schwesinger, who are from different labs across the world.
And we all contributed seminars to talk about how we think about developing a lab culture that's sustainable, that is balanced, that is set up really intentionally, where you really thinkabout what you want your lab environment to be.
[59:27] The steps that you can take to make it such that you're going to accomplish your goals in the short term and not be burnt out yourself or have your lab members be burnt out in thelong term.
So that's where it came from.
And so we each, yeah, we each contributed our pieces with respect to that.
And in my particular case, I talked about how to think about developing your area of research for your lab when you're a new professor, and how to think about that process.
But I think more generally in that paper, or in that commentary piece, we all value having a lab where we think about our culture and how we want students and postdocs and scientists inthat lab to really like live their work life while they're in your lab for this period of time.
Brent:
[1:00:31] That's amazing. And could you expand a bit more on like how people should go about finding what gonna research? Yeah.
Finding Research Opportunities and Developing Research Skills
Siobhan:
[1:00:40] Practice, right? And so, we also talked about this when you approached me initially about this podcast.
You two, for instance, as an example, are really interested in research.
Probably the most interested of anybody in terms of like your diverse interests that I've ever met before, but you need to hopefully secure labs where you can get practice with research, sodoing a research internship.
And so that's ideally what you should do, and in my opinion, you should start doing it as soon as possible.
Than later because like if you approach a professor for instance about doing your research and you're in your last quarter of your undergraduate career, there isn't as much, you know, likeyou would train somebody but you can't learn a ton in just a quarter.
So anyway, so just approaching professors and identifying different and really diverse types of research projects where you can like actually go into the lab and learn how they're doingtheir research that you can get more experience.
There's also a lot of like, you know, you can get undergraduate internships that are advertised on, I can't remember the name of it, but there's like a website where these opportunities areadvertised.
Keller:
[1:02:09] The ICC. The ICC. We'll find it, we'll link it.
Siobhan:
[1:02:12] Okay, thank you. And then there's also just like lots of ads that go up, like for instance, research experience for undergraduates.
So, we have one of those where it's like, okay, it's May 15th, I have to really advertise it, where the government gives you funding to have students, undergraduate students do research inyour lab for the summer, but they have to be undergraduates and they're given stipends and they're involved in hopefully training not just in the research, but also in like science as aprofessional career.
So there's opportunities like that. But again, if you start earlier on in your undergraduate career, then you'll have more time to get more experience and then you'll be more attractive toother professors as you move through your academic career so that you can get more experiences, more diverse experiences.
Brent:
[1:03:01] Yeah, and then with those experiences, I'm sure you'll learn to ask your own questions and find the next way. Exactly.
Siobhan:
[1:03:08] You want to have.
A number of experiences, but if you want to also really have the more concrete way of doing research, you should hopefully have one experience where you're doing like a year or so or ayear and a half of research within one lab so that you can begin to develop your own independent questions and start to answer them by doing research in a way that's appropriate for yourlevel as an undergrad researcher.
Brent:
[1:03:43] That makes sense.
Keller:
[1:03:44] And with all that being said, do you happen to have any openings in your research?
Siobhan:
[1:03:48] I will have a research experience for undergraduates open, and I am the limiting factor in that because my graduate student, Kevin, has made the ad.
I will be advertising it, and I would love to have an undergraduate who hopefully is at the end of their sophomore year.
So if you're interested, contact me. There's a stipend associated with it too, right? So it can be like, so it'll give you enough to survive, like, you know, to be able to pay foraccommodations and food.
And we have an awesome lab. I have a really great, vibrant set of graduate students and postdocs who are pretty friendly.
We're a good team. So if you're interested, contact me.
Brent:
[1:04:29] Perfect.
Keller:
[1:04:30] And then kind of one last thing is do you have any advice aside from research just to students broadly that are interested in plant science and plant biology?
Siobhan:
[1:04:40] Just be passionate about about learning new things just like the world outside is so beautiful right like just go out into the arboretum like right now and you know just go and lookat the plants and just think about how they actually live in these different environments, how they produce these different forms, their colors, you know, like the type, like look at theground and think about what they have to do to be able to like live in that ground.
Just be amazed by nature itself, right?
Like we use nature to kind of calm and center ourselves, but also think about like just how that nature came about, like what's happening at those individual cells that make them look likethat. That would be my advice.
Keller:
[1:05:34] Thank you so much, Professor Brady.
Siobhan:
[1:05:35] Okay, thank you so much for doing this. It's a really great resource. Thank you. Thank you.