Wednesday, April 16, 2008

They've Sequenced James Watson, and They Did it in 4 Months!


With the plethora of genome sequences from lots of different organisms now being generated, it's almost an afterthought on the news when a new genome arrives. The dog has been sequenced! The horse has been sequenced! Campylobacter jejuni has been sequenced!

See here for my blog on DNA and genomes if you need a ... primer.

A few years ago they finally sequenced the human genome. It was a vast undertaking of many different labs that took 13 years (1990 - 2003) to sequence the 3 billion nucleotide base pairs in our 46 chromosomes. To put it bluntly, the technology that existed in 1990 was not up to that task. To give an example of what needed to happen to achieve this goal, let's compare it to putting a person on the moon.

When John F. Kennedy in 1961 swore to put a man on the moon by the end of that decade, huge resources went into research and development to make it happen. Rockets were designed, space ships were made air tight, and oxygen delivery systems were built. Dehydrated food and drink was made. What happened was an era of huge technological breakthroughs that culminated in Apollo 11 landing on the moon in July of 1969.

More recently, in the late 1980's-early 1990's, scientists started talking about sequencing the human genome. You have to understand what it was like to sequence DNA at this point in history. It was a very long, painstaking procedure. I sequenced DNA by those methods. You got sequence, but you worked hard for not very much. You can't get 3 billion nucleotides of sequence when you have to read sequence by the naked eye and can only achieve, if your lucky, a couple thousand nucleotides a day. (Some pictures of old-style sequence gels here)

Similar to what happened in the moon race, DNA sequencing technology changed dramatically during the drive to sequence the human genome. Dedicated machines designed solely to generate sequence data that is read by computers changed the field (see picture at the top for an example of a computer generated sequence trace). Along the way, the genomes of many other organisms (said dogs, horses, Campylobacter jejuni, for example) were completed as well. And more continue to be completed every month.

And the technology continues to evolve.

Today I open the table of contents to the new issue of Nature, and I see that they've sequenced the genome of James Watson, a Nobel Prize winner who had a hand in discovering the sequence of DNA back in 1953. And they did it in 4 months! From 13 years to 4 months! Yup, the next generation of sequencing technology can do it in a fraction of the time at 1% of the cost of the previous technology.

I could have used that sequencing technology when I was in grad school!

But like any good scientific achievement, the ability to sequence a genome results in a lot of answers, but opens up an enormous amount of questions. Ok, so you know the sequence of the genes. How do they work? Some fascinating work going on in that department that I hope to address in future entries.

Thursday, April 10, 2008

Frogs Without Lungs!

But it's true! Here's the link to the story in the San Francisco Chronicle. It has no lungs, and breathes through its skin. They also say it kind of resembles a small version of Jabba the Hut from Star Wars. But it's well adapted to the streams it lives in, which is cold, rapidly moving streams that are rich in oxygen.

Maybe the lack of lungs keeps it less buoyant so that it isn't swept away in the current.

Evolutionarily it is related to other frogs that DO have lungs, and the biologists think that this may be an example of extreme evolutionary change in response to an environment.