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WFRC s Maureen Purcell on Using Microarrays to Increase Fishery Productivity

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At A Glance

Name: Maureen Purcell

Educational Background: MS 1997 University of Maine, Orono; BS 1993 Washington State University.


SEATTLE — Fishing is deeply rooted in Pacific Northwest culture, and both Atlantic salmon and rainbow trout are traditionally thought of as regional "cash crops." It is unsurprising, then, that in a state where the governor has set up a special commission to protect salmon, microarrays have finally made their way into research that aims to increase the productivity of the region's fisheries.

Researchers at the Western Fisheries Research Center in Seattle in particular have been hard at work analyzing the biological response of rainbow trout to a rhabdoviral-encoding glycoprotein used to vaccinate the fish against infectious hematopoietic necrosis virus (IHNV), a deadly pathogen that threatens fisheries in the region. These researchers have turned to using microarrays to measure genetic response to the vaccine.

Maureen Purcell, a doctoral student at the University of Washington in Seattle and one of the researchers involved in the project, presented the findings of her group at the Northwest Gene Expression Conference held here last week, and BioArray News sat down with her after her presentation to learn more about how microarrays can help the fisheries of the Pacific Northwest.

So what got you interested in fish?

I just actually kind of fell into it. It's just really an interesting system because there are a lot of unanswered questions; a lot of interesting questions to ask. For awhile I was working on [and] looking at QTLs controlling diseases like atherosclerosis. It was interesting but it was kind of fun to think that I could come back to working on fish and sort of apply the same sort of principles.

You have said that IHNV has a negative effect on Atlantic salmon and rainbow trout. Can you describe what it does to the fish that it creates such a negative effect?

The main industry that's had a problem with it is rainbow trout — that's really where it has had its big impact. It primarily kills them, or they may survive but then they are deformed, which makes them unmarketable.

What do you mean by 'deformed'?

They develop some sort of skeletal abnormalities and various things.

So you wouldn't want to eat them.

It's certainly not a benefit to the people who are trying to sell the fish as a product. Because people like to buy whole fish that look nice. It's a problem certainly in aquaculture, but it's also present in wild populations of salmon. We think it's probably just part of their normal lifecycle.

So you are saying that every salmon might get this disease?

All animals evolve with their pathogens. There [are] pathogens involved in every natural ecosystem. Some people believe that pathogens actually control to some extent ecological dynamics. So one thing is that we don't want to focus so much on aquaculture, because people tend to think that, "This is a problem that aquaculture has," and that there's a risk in giving it to wild populations. But in fact it's just the opposite. They are acquiring this from wild populations. But it's a priority pathogen for the US Department of Agriculture. It's one of their primary pathogens for aquaculture.

They have a list?

There are four pathogens, and this is really the one for rainbow trout.

So who created the vaccine, and how is it injected into the fish?

Eric Anderson made the first vaccine and then he came to the [Western Fisheries Research Center] and worked with Gail Kurath and they made a second-generation vaccine. You can use something called a gene gun [to inject the fish], which bombards the skin. It's kind of how DNA vaccines are delivered in other systems — interdermally. There's a lot of interest in that because it's easier to apply.

But how do you apply that to a large population?

That's the problem with this vaccine. This vaccine is not approved for commercial use. The main problems are delivery. There's no way to mass deliver it. To my knowledge there hasn't been a DNA vaccine commercialized for this industry, and so I think there's a little bit of reluctance to approve it. There definitely are some regulatory issues, but really I think it's a delivery problem.

Why did you decide to use gene expression profiling to determine how the fish were responding to the vaccine?

Well, we were just interested in using it as a discovery tool, because we had a couple genes that we thought were important. We started to accumulate other genes that we thought might be important. But with the microarrays we could demonstrate that they are regulated. In a single experiment we could look at many genes — just like any microarray experiment. So what we wanted to do was to test the hypothesis, which is that we knew that interferons were important [in how the fish responded to the vaccine] and so we wanted to see if they were up-regulated, and it turns out that many of them were. So it was actually a really good way to validate the pathways and what the mechanisms of the immunity were.

Where did you get the arrays [for rainbow trout and Atlantic salmon] from?

From GRASP. It's the Genomic Research on Atlantic Salmon Project. It's at the University of Victoria [in British Columbia] and they've done a really fantastic job of making this chip and delivering it to the research community for a small fee. They have annotated it. They have 15,000 genes and so it's sort of a first half. And they are in the process of re-annotating. But what we need is just the different files. What I'd like to have is the functional annotation so that you can look at different functional pathways. It would be nice to do those sorts of analyses, but we are just not there. And I don't think these are hard barriers. They are all doable. We just need the people to do them. We need some dedicated bioinformatics people working on this. I mean I am not a bioinformaticist, I am a biologist. So it's a lot of work for me to do this stuff.

So you have the systems, but you are in need of the talent.

This is actually something the whole rainbow trout community struggles with. But to that end there are groups of people that have written to the USDA, and tried to get their support for bioinformatics capabilities for rainbow trout. But a lot of things that I need for this study are things that an undergraduate could help me do. Just write programs and process data and various things.

You mentioned that you found some genes were up-regulated and some were down-regulated during your presentation. Which genes were up-regulated and which genes were down-regulated?

For down-regulated, they were primarily genes that [are] functioning [in] the normal metabolism. These are genes that are normally expressed in a normal muscle cell on a day-to-day basis. Those go down and what goes up are genes associated with inflammation, things like strep proteins. The interferon genes and interferon-inducible genes go up, and quite a lot of other genes.

So what's the next step for your research?

Well, most of the next step is to just sort of validate a lot of these findings. What I would like to do is to validate this model conclusively by looking at genes using another platform, which will probably be quantitative PCR. The other thing is that we'd like to really show that the glycoprotein product really is capable of affecting the immune system, because that's all it is, a glycoprotein — there is no virus. So that's where we are going. A lot of what we've gotten out of this microarray study is just markers. [We are looking for] a way to fast-track markers that have a high probability of being informative.

How will this be applied commercially?

I don't think this is really going to help with the vaccine development. But if somebody wanted to look at a different delivery strategy, they would now have a series of biomarkers where they could look for a response instead of having to use bits of live virus because those experiments are a bit more difficult to do. But giving them the vaccine a different way, and looking at the response from the molecular biomarkers? It's much easier.

 

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