Aim of international project: To reconstruct evolutionary history
Chang Ai-Lien, Straits Times 21 Nov 09;
HE IS a scientist whose hunting grounds span the high seas, whose collaborators are fishermen, and whose dissection centre can be a chopper and makeshift table at the roadside.
Fish expert Byrappa Venkatesh, of the Institute of Molecular and Cell Biology (IMCB), has spent decades searching out and studying the weird and wonderful of the fish world. These include the deadly pufferfish, with skin and organs 20 times more poisonous than cyanide; and the oddball elephant shark, which last shared an ancestor with humans 500million years ago.
Now, he has been selected to lead part of an international team which aims to decode the genetic make-up of 10,000 animals - the most ambitious endeavour since the Human Genome Project mapped the DNA of humans in 2003.
The latest project, Genome 10K, will allow scientists to see evolution in action by comparing animal and human genomes to reconstruct their evolutionary history, as well as predicting how animals will respond to challenges such as climate change and pollution.
Professor Venkatesh's chance involvement happened during a visit earlier this year by Dr Stephen O'Brien to the Agency for Science, Technology and Research institute. Dr O'Brien, chief of the genomic diversity laboratory at the US National Cancer Institute, was one of three scientists behind Genome 10K, and when he learnt of Prof Venkatesh's role in decoding genomes of key fish, he made an immediate decision.
'He told me, you're the person I'm looking for,' said Prof Venkatesh, who is the only person from Asia chairing a section of the project. He will lead the charge to put the genomes of 4,000 fish under the microscope.
The US$50 million (S$69 million) international effort is expected to start in two years, after enough money has been raised, and taking into consideration that the costs of genetic sequencing will plummet.
Prof Venkatesh, part of the team that won the National Science Award in 2004 for pioneering work in identifying and sequencing the fugu genome, explained that the cost of sequencing a genome has shrunk from US$300 million to US$4,400 in less than a decade as techniques have improved.
The project is expected to yield invaluable information in areas such as animal physiology, adaptation and conservation.
'It will help all aspects of biology. Just like the human genome revolutionised medicine, this is going to revolutionise biology.'
He has set his sights on creatures like the primitive bichir, whose lineage gave rise to all fishes. Other candidates include the largest bony fish - the simple mola mola, a giant silver disc which is basically brains, stomach and gonads; and fish with extreme adaptive features such as the seahorse, which mates for life, with the male bearing young.
To collect such samples, his travels have taken him to the seas off South Africa, Japan and Tasmania, for example. And just like any other angler, he wakes up at 5am to set off with fishermen, only to sometimes spend days shivering in freezing weather and coming up empty.
When his net is full however, he needs to act fast before the fish DNA degrades. Hence, the trained zoologist also has to have some of the talents of a sashimi chef. He generally sets up shop the moment the boat reaches shore, skilfully carving out slices of liver, heart and other organs, as well as drawing blood. The specimens are immediately dipped by chopstick into liquid nitrogen in a flask to preserve them.
Lucky catches, as well as tissue donated by museums, researchers and aquariums have added up to several hundred precious DNA samples in his freezers, carefully frozen at minus 80 deg C.
Another surprising treasure trove has proven to be fish shops here, which have yielded rare species such as the air-breathing lungfish and the salamander.
When contacted, the Agri-Food and Veterinary Authority said the sale of such creatures was prohibited, and that shops could be fined and prosecuted if caught during its spot checks and inspections.
The animal-loving 56-year-old has even ventured beyond fish in his genomic adventures, saving a baby python caught at his institute, and releasing it at Bukit Timah Nature Reserve after drawing some blood for sequencing.
Formerly a fisheries development officer in India, he came to Singapore in 1987 as a zoology research scholar and joined the IMCB four years later.
He and his wife Mangala, 49, a housewife, are originally from Bangalore, although both are now Singapore permanent residents.
His love of science has also been inherited by his only child, a Singapore citizen. Daughter Aparna Venkatesh, 24, won a scholarship to the University of Milan in Italy to do her PhD in immunology, he let on proudly.
Recounting one hair-raising experience in his 18-year career at IMCB, he said he had been collecting pufferfish in Japan when he was bitten. The fish is notorious for its poisonous organs and skin which are lethal if ingested.
'I panicked and tried to tell the fisherman, who spoke no English,' he said.
'Finally he understood and gestured that the toxin is not in the teeth. Nonetheless, I felt a tingling sensation on my finger where I was bitten.'
But it's not once bitten twice shy for the professor, who is currently on an expedition in Hokkaido, Japan.
He is there to search for the hagfish - a primitive slime-producing creature with an eel-like body which has four hearts and two brains.
$69m project to decode 10,000 species
Straits Times 21 Nov 09;
THE Genome 10K project is a massive international effort which aims to sequence the genomes of 10,000 vertebrate species - one in six of all known creatures with backbones. The US$50 million (S$69 million) project has roped in 68 scientists and is split into six groups - mammals, birds, reptiles, amphibians, fish, and policy decisions.
Capturing the genetic diversity will create an unprecedented resource for the life sciences and for worldwide conservation efforts, say researchers. The results will be freely available to researchers.
Genome 10K aims to compare the vast database from the upcoming genetic zoo with that of humans. This will help in the understanding of human diseases and allow species' evolutionary history to be reconstructed.
