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NY Botanical Garden s Dennis Stevenson On New Plant Research Methods, Tools

Dr. Dennis W. Stevenson
Vice President and Rupert Barneby Curator for
Botanical Science
The New York Botanical Garden

Last week, the Bronx-based New York Botanical Garden held a ceremony to celebrate the erection of the steel structure that will contain the new $23 million, 26,000-square-foot Pfizer Plant Research Laboratory facility set to open in 2006.

The lab building will house more than a dozen plant scientists of different disciplines, graduate student and post-docs, and new research tools for the garden, which is a founding member of the Plant Genomics consortium, a collaboration with Cold Spring Harbor, the Department of Biology at New York University, and the American Museum of Natural History.

BioCommerce Week recently spoke with Dennis Stevenson, vice president of botanical science for the garden, to learn about the science being planned for the facility, and the tools that will be needed to conduct it.

What are the molecular biology research efforts at the lab?

We are doing two projects: one, in comparative genomics, where you compare what the genes are doing that lead to the development of structures in different species; and two, functional genomics, the functions of the genes, which is investigating Guam Dementia, research conducted by Oliver Sacks. [Click here for abstract: Cox, P.A., and O.W. Sacks. 2002. Cycad neurotoxins, consumption of flying foxes and ALS-PDC disease in Guam. Neurology 58(March 26):956-959]

Basically, the story is that this compound, BMAA, apparently induces precocious Lou Gehrig's disease, Alzheimer's, and Parkinson's — neurological disorders. The latest finding is that these people in Guam have been eating bats, which eat the seeds of cycads. This bioconcentrates the [BMAA] compound in the bat. The people eat the bats and have been coming down with these neurological disorders.

We have been looking at that because the way that your nerves work is through glutamate receptors. Very simply, glutamate attaches to the receptor, and it tells the neuron to do something, and is then released back into the glutamate pool. But when you get this BMAA, in your system, it's a glutamate agonist. It goes to the glutamate receptors instead of glutamate and your neurons keep firing, and firing, and eventually die. Basically, as we get old, we lose a neuron a day. But what happens in these people is that they are losing a neuron and a half a day, so that when they are 45 years old, they are more like they are 80, neurologically. So, the question becomes this: if a plant makes a glutamate agonist, but plants themselves have glutamate receptors, how does it live? We think that by understanding a plant's solution to a problem, then maybe we can use that solution to understand human health issues.

The other side of it is, cycads are the most primitive living seed plants, so they have a fossil history that is 300 million years old. They are ancient and they still look that way. Since they are the earliest seed plants, we are interested in what genes are functional in cycads in terms of having seeds develop, and are those the same genes that are being used in the flowering plants? In other words, how have those genes changed through time to give us different kinds of seeds? One of the reasons you might want to use that is that the seeds and the flowering plants, of course, are where all the cereal grains come from, so they are economically important.

The other thing that we do at the Botanical Garden is the Lewis B. and Dorothy Cullman program in molecular systematics. Basically, in that program, scientists take three, four, five, or six genes across many, many species to try and reveal the family tree within a plant family. Once you have that phylogenetic tree as a diagram, you can then begin to use that to kick out which species you can study in a genomic sense. In other words, which evolutionary lineage do they represent? If you know that, you can then compare lineages. It's a circle. You build a family tree, which you use to begin to look at the evolution of seeds, then the information you get about that, like the genes involved in seeds, and feed that back into your system, to test your original hypothesis on the evolutionary relationships of the species by adding more data to your analysis.

So, how does this lab move you forward?

The current lab was state-of-the-art when it was opened in 1957. It was ahead of its time, but 50 years later, we have outgrown it in terms of not having enough space for our programs. And, it's in bad need of retrofit. That's because we have changed the way we function, the way we do power supplies. It's like when your car engine gets so bad, you just replace it, you don't repair it. So, we decided to build a new state-of-the-art lab to last the next 50 years that more than doubles the existing space we have and gives us room to grow for the future.

What are the disciplines housed there?

There will be 15 scientists in the facility, but the garden also has a graduate program with local universities with about 40 graduate students, plus five or six visitors, and five or six postdocs. Some of our scientists are what we call evo-devo — for evolution and development — and they work on comparative genomics. Some do molecular systematics. Some do functional genomics. The lab also has another function besides molecular investigation. We do structural botany, and some phytochemistry, or plant chemistry, that is oriented toward identifying the unique chemicals that occur in plants that have potential for medicinal use, but also studying chemicals that plants have developed in response the environment. An example would be anti-herbivores, things that plants use to keep things from eating on them. The structural botany is looking at the anatomy of the plant as it grows. In that case, we use scanning electron microscopes. That is all part of the laboratory. And, you need that. If you are going to look at the evolutionary development of seed, you need to be able to do the anatomy at the same time.

One of the current trends accelerating biological research is that the joining of different disciplines in new facilities helps facilitate new ideas.

What we do is bring together people who work with plants, but from many different points of view. That was the idea behind the consortium. The New York Botanical Garden, one, can grow plants; two, we know where to go in the world to get plants; and three, we can develop these molecular systematic phylogenic type trees. Cold Spring Harbor, on the other hand, isn't going to grow a stand of Ginko trees for experimental purposes, but they have high-throughput sequencing. NYU biologists are plant molecular biologists, hard core ones. So they bring that expertise. So, what we have built is something that no one of us can do individually. It would be pointless for NYU to duplicate our library, or our herbarium's 7 million collections. And, it would be stupid for us to put in a sequencing facility that Cold Spring Harbor has. The success of this collaboration is shown in that we just got this very large grant, $5 million from NSF, to do a seed project.

What equipment are you going to have?

In getting ready to build the lab, I started thinking it would be nice to have a lab, but if you don't have a program, that is kind of dumb. I have delayed some of our equipment purchases until we got the program going for a lot of reasons: One, I didn't want to move the equipment; and two, the technology moves so quickly.

The things that we are going to add to our repertoire are: confocal microscopes, Affymetri- type chip-readers. We are going to want to read gene chips for tomato and potato and other species. We will be also be adding banks of ABI sequencers, and we will be upgrading our equipment, replacing our electron microscope, which is 12 years old, rather than moving it. The old one we made trade in, or give it to a local college.

If you have this collaboration with Cold Spring Harbor, why have sequencers?

We don't do a lot of sequencing. We do some for molecular systematics. But part of that will be to have them here for training. Because of our history in Latin America, many of our students are from there. Part of our teaching is to train them in all the things you can do in a lab, so that when they return they have that expertise.

What is your budget?

The equipment budget is going to be close to $2 million.

Will you be using any mass spectrometry?

We used to do some HPLC here, but not any more. I have hooked up with the chemistry department at NYU and I've discovered that collaboration is the way to go on these things.

What kind of informatics support will you have?

Our informatics backbone is very basic. But, as part of our membership in the consortium, we are associated with the Courant Institute of Mathematical Sciences at NYU. They are a part of that informatics backbone, and some of the work is done at Cold Spring Harbor, and another chunk of data analysis is done the American Museum of Natural History, especially problems in molecular biology about paralogs versus orthologs. We are in the process of developing what we call ortholog ID.

Was there anything you were not able to get for the lab?

We don't know yet. We are satisfied programmatically. We have a couple of NFS grants to buy equipment so we will see what happens. Most of the NSF equipment grants are matching funds, from 30 percent to 50 percent is matched, and the institution will fund-raise for that. This lab building was built with state money, federal money, private individual donors and corporate donors.

Where do you think this facility will fit in the plant research world?

What we are doing in terms of genomics is unique for a botanical garden, right now. There just aren't any botanical gardens with genomics programs in them. Some of them do molecular systematics, like Kew Gardens in London. But, if you have the goals for science of understanding the diversity of life, and how it got that way, these are the techniques you now use. In the old days, you ground up a plant and tried to look at the chemicals in it to try to unravel the tree of life. Now we use molecular methodologies to do that. We still have microtomes, and we still grind plants because we do these bioprospecting projects with Merck. But, now, once we have the compounds we are interested in, we would begin to follow up on investigating what are the genes and the pathways involved, from a function point of view. And, that is what this BMAA is about. And, what is nice about that is that taxonomically, BMAA is what defines the cycads, no other plant makes it. What we would like to know are its pathways, and we would like to use it in neurobiology. And part of that is functional genomics: What are the genes that make the stuff and what are the genes that protect the plant from it with its own compounds?

One of the things that people haven't used enough is this idea: If plants make toxic compounds, like nicotine and caffeine, then that plant has to have developed a system to work with that. If you can figure that out, then you can go back and understand how they work in human health. Like how do antioxidants work in plants? If we can find out how they work there, we might find out how they work in us. That is why this BMAA is so interesting to us.

And, the science fiction part of that is: if we can find a gene that causes resistance to glutamate agonists, because evolution made one for that plant species, then you could put that in stem cells. When people die from Lou Gehrig's disease, three or four years after they get the disease, it's their bodies that cause this to happen. So, you could generate a new nervous system for them from stem cells, but you would have the same problem again. But not if you could program those stem cells to be resistant by sticking the gene from the plant that had developed its own resistance to this. It's a new way of thinking. It's not: 'I'm going to go out and eat and plant and get a cure.' It's: 'I'm going to use the plant to understand the biology.'

 

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