New Zealand Biotech Industries News
2004/11/09

New Zealand bioinformatics company Biomatters has recruited some Elvish agents to search DNA databases for genetic treasure, while biologists get on with more important work.

Daniel Batten, CEO of the Auckland-based software company believes Biomatters’ new iSeek software platform, launched last week, represents the future of bioinformatics, and will help usher in the age of personalized medicine.

Batten is at Ausbio2004 in Brisbane promoting the technology to Australian biotechnology researchers.

Like the shoemaking elves of fairytale fame, iSeek’s software agents work in the background, comparing gene sequences from different individuals, seeking tiny differences that may influence a person’s risk of developing cancer, cardiovascular disease, diabetes and other diseases.

The estimated 25-30,000 human genes in the human genome are peppered with thousands of single-letter differences, called single-nucleotide polymorphisms (SNPs, or “snips”).

SNPs are the ultimate source of individual genetic differences – or genetic variability – in the world’s 6 billion-plus individuals. SNPs may not only influence an individual’s susceptibility to disease, but their response to therapeutic drugs. An oncologist’s choice of a chemotherapy drug, and the dose, could pivot on whether a cancer patient has a particular SNP in a key gene.

Batten says personalized medicine has remained a dream because computer science has not kept pace with the rate at which DNA sequence data is cascading into international genetic databases.

Until now, molecular biologists have had to manually program their software to compare gene sequences in international databases. Batten said these first-generation bioinformatics tools, many of them developed in-house, are time-consuming to use, and are not interoperable.

He said iSeq provides a framework where bioinformatics tools can talk to each other, hiding much of the complexity of genome analysis behind a single, user-intuitive interface that any molecular geneticist can use.

ISeek can perform local searches on downloaded DNA sequences, or go hunting on line in large public databases, automatically comparing, extracting, aligning and annotating gene-sequence information.

With current methods, the information retrieved may be months out of date by the time a search is completed – the volume of data is growing by 50 per cent a year. ISeek’s “elves” can be programmed to monitor new sequence data flowing into international databases, for variation in genes of interest.

Batten said iSeek promises to save biologists large amounts of valuable research time that is currently wasted on laborious and time-consuming searches.

Science in Public, 9 November 2004

New Zealand researchers have successfully harnessed insect smell receptors to detect fruit smells. They plan to create handheld devices that could instantly identify critical odours, such as dangerous explosives or the best fruit.

The HortResearch New Zealand team have extracted genes for the receptor compounds used by insects to detect odours such as fruit smells. These genes have successfully been inserted into cell lines in the laboratory and manipulated to ‘light up’ in response to the fruity smells. The next step will be to incorporate insect smell receptors into an artificial membrane, and use them as a switch to trigger an electronic system.

“We want to develop a hand-held device, which you can use to take instantaneous readings,” says Dr Richard Newcomb, who heads the laboratory. “Ultimately we could go to the airport and sniff for drugs or fruit across bags, or build a sensor into a production line to detect spoilt food on the go. There’s machinery around that can do this kind of stuff, but not instantly and it is not miniaturised for convenience.” He hopes the group will have demonstrated proof of concept within two years and have built prototypes of their biosensor within five years.

Newcomb’s team has rapidly become a world leader in the study and application of olfaction. At HortResearch the group also is working on projects to enhance the tastes of fruits and match them to particular markets, as well as to control insect and mammal pests by disrupting their olfactory communication.

The work has built upon the decade of smell research since 2004 Nobel Prize winners for Medicine, Dr Richard Axel and Dr Linda Buck, first identified the receptors which respond to odour molecules in humans. “As genomes are being sequenced,” says Newcomb, “we can readily pull out the receptors that detect smells, and we can start to get a handle on what receptors are detecting what compounds.”
To develop the biosensor, the Hortresearch Molecular Olfaction Laboratory have joined forces with Australian researchers from Monash University in Melbourne and CSIRO Entomology in Canberra.

It’s a good example of how Australia and New Zealand can work together to form a biotechnology hub in the Asia Pacific region, Newcomb says.

Science in Public, 9 November 2004

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