National Institute of Biology, Slovenia
At A Glance:
Name: Katarina Cankar
Title: Researcher, National Institute of Biology, Slovenia
Background: Katarina Cankar is a researcher and PhD student at the National Institute of Biology in Ljubljana, Slovenia who has also worked at the RIKILT Institute of Food Safety in The Netherlands and L'Institut de la Recherche Agronomique in Versailles, France.
When people talk about the "holy grail" for microarray-developed applications, they tend to think in vitro diagnostics, not potatoes. But the reality is that in markets with stringent food safety regulations such as the European Union and Japan, microarray-based research is getting significant state-funding to create new methods for assessing the content and safety of foods. One such program is Safe Foods, an EU-funded consortium founded last year through the EU's Sixth Framework Programme that is investing resources into using arrays to do just that, and one of the first projects out of the consortium has been creating arrays for diagnosing pathogens and identifying genetic modifications in different varieties of potatoes.
BioArray News first learned of the project at the BioScience 2005 conference held in Glasgow, UK last month, and spoke with Katarina Cankar, a researcher at the Slovenia's National Institute of Biology, last week to learn more about the project.
Can you give me some background about the National Institute of Biology in Slovenia and what you are doing there?
Our group is the group of plant pathology and biotechnology. We are working on two subjects, one is the detection of plant pathogens and also [interactions] between pathogens and plants. The other part of our work is work on genetically modified organisms. We are doing detection for customers and we are also involved in the European network of these laboratories, so we are also developing new techniques for detection and we are involved in safety evaluations for the effort.
Out of all the different areas that you are focused on to which does this 'potato microarray' belong?
We are using potato microarrays in two fields. One is the plant pathogen interactions, and we are using it mostly to study potato virus Y. And the array that was presented in Glasgow was done in The Netherlands, and the purpose of this array is to use it for food safety evaluation. So for this array, several institutes have contributed clones; The Scottish Crop Research Institute, the RIKILT Institute from The Netherlands, and our institute. We are using this array on potato samples that are grown under different conditions. So the final aim of this project is to use microarrays as a tool for safety analysis.
How did you create the arrays? Were they printed externally or internally?
We were printing them internally. We prepared the clones with subtractive hybridizations and then we were printing them ourselves. We all [contributed] the clones and they were printed in Wageningen in The Netherlands at the RIKILT Institute.
Where is the funding coming from for this project?
Actually it's coming from a European project which is called "Safe Foods." The aim of this project is to prepare better techniques for food safety evaluation. And the idea is that instead of having only compositional analysis of novel foods that we could also use new profiling techniques that are not targeted because at the moment, in novel foods there's only compositional analysis going on so we know the targets that we are looking for. But if there are unintended effects in the novel plant varieties, we don't pick them up in targeted approaches. So using profiling techniques could help us to see whether there are some unintentional changes in these novel plant varieties. Besides microarrays, they are also trying metabolomics and proteomics.
How involved is Safe Foods in the actual project?
Every half a year we have a meeting, and these results are presented. So another lab inside this project is running proteomics on the same set of samples, some other lab is responsible for distributing the samples, another lab is helping with statistical analysis. This is all done within this project. The Safe Foods project started one year ago, and working with microarrays was one of the aims of this project. And we are cooperating with another project, Quality Low-Input Food, but they are not interested in arrays. They are interested in yield, and the presence of different minerals and so on. And we are interested in the differences in gene expression or protein content.
How great is the demand for this knowledge right now?
Food safety is a big issue. Also the new varieties that are coming out, they need to be fully evaluated. That's why it's so important that we are also developing new techniques in this field.
But how long will it take before Safe Foods is using your array to evaluate different foods for food safety? Will they use it anytime soon?
Safe Foods is just a project that is developing all these techniques. But later, if they are proven useful, they will be probably used in safety evaluation procedures across Europe.
Is there a any information on this particular food that has been generated using microarray analysis?
There are some articles and reports already written on this.
So how does your study fit into the work that has already been done?
Our study is the first study where we, on a large scale, have looked at different production techniques. Actually there are two studies. Experiment one and experiment two. So we are looking at different varieties of potato that are treated with different types of fertilizers and genetic treatments. In other experiments we are looking at the different between conventional and organic agricultural techniques. This is the first time that such a large scale analysis was done. Because we ran experiments on approximately 180 arrays and we would like to see whether with the microarray techniques we can see differences in gene expression between different agricultural methods. So in this way we would have an idea whether we could identify which kinds of genes are involved and respond to these kinds of agricultural practices.
So what is the next step for your group?
After analyzing these results there will also be experiments done comparing genetically modified and non-genetically modified varieties and other things, and inside of Safe Foods they will start applying microarray technology to other plants.