A scientist is studying an emergent yeast species that has become a particular danger to infants. Dick Ahlstrom reports.
A common but little-known yeast is a real danger to newborn and premature babies because of its ability to form a thin coating known as a biofilm. Now a researcher at University College Dublin using advanced genetic technologies hopes to find the yeast genes responsible, which could produce information that would lead to new kinds of treatments.
"The biofilms are drug-resistant and are a particular problem for premature neonates," says Dr Geraldine Butler, senior lecturer in UCD's department of biochemistry.
Also involved in UCD's Conway Institute of Biomolecular and Biomedical Research, Butler recently won a four-year Science Foundation Ireland investigator award worth almost 1 million.
She will use this to study a pathogenic yeast, Candida parapsilosis, an "emergent" yeast that causes an increasing number of infections.
C parapsilosis is related to the more familiar C albicans, but although C albicans has come in for extensive study and its genome has been sequenced, very little is known about C parapsilosis, despite its new importance as a cause of disease, says Butler.
It is responsible for half of all infant infections and a quarter of general infections associated with the candida organism, she says. "C parapsilosis is not sequenced at all. There is almost no sequence information for it."
She will use her award to correct that situation, carrying out a "genome sequence survey" of C parapsilosis. "It is not a full sequence, it is a survey of the genome," she says.
"What I am trying to get is partial information of a lot of genes. It will tell us quite a lot about the genome structure."
The full genome has between 26 and 30 million steps, or base pairs, and an estimated 6,500 genes. Her survey will provide a rapid overview of the yeast's genome and help identify where the genes are without a full sequence. "I would hope to identify a third of them," she says.
Her targets are the genes linked to the yeast's ability to form biofilms, colonies of individual yeasts that join together to coat medical implants, catheters and other devices. They are resistant to drugs in this form and often cause blood infections that force the removal of what might be a life-sustaining implant.
The survey will involve chopping up the yeast's genome into about 5,000 fragments. The team will then sequence only 400 to 500 bases at either end of the fragments, data that help identify the genes quickly.
The next step is to find genes that are associated with biofilms.
"What I really want to do is try and understand why this organism makes biofilms, because this is why it is a problem organism," she explains.
"No one really knows what makes cells develop in this way. We are trying to find out which genes are switched on to form films rather than when the organism is free-living."
She and team members Dr Mary Kelly and Sean Laffey will prepare an "expression pattern" for genes, comparing biofilm and free-living yeasts to see which genes are on or off.
They will use micro arrays that can confirm the presence or absence of thousands of proteins, the substances produced by the genes, in a single sample.
This in turn will give a wealth of information about the genes linked to the formation of biofilms, she says. A better understanding of the process should throw up new ways to treat the biofilms and prevent infections without having to remove the medical implants.