Wednesday, November 19, 2008

Woolly Mammoth Genome Sequenced


Scientists at Penn State are leaders of a team that is the first to report the genome-wide sequence of an extinct animal, according to Webb Miller, professor of biology and of computer science and engineering and one of the project's two leaders. The scientists sequenced the genome of the woolly mammoth, an extinct species of elephant that was adapted to living in the cold environment of the northern hemisphere. They sequenced four billion DNA bases using next-generation DNA-sequencing instruments and a novel approach that reads ancient DNA highly efficiently.

"Previous studies on extinct organisms have generated only small amounts of data," said Stephan C. Schuster, Penn State professor of biochemistry and molecular biology and the project's other leader. "Our dataset is 100 times more extensive than any other published dataset for an extinct species, demonstrating that ancient DNA studies can be brought up to the same level as modern genome projects."

The researchers suspect that the full woolly-mammoth genome is over four-billion DNA bases, which they believe is the size of the modern-day African elephant's genome. Although their dataset consists of more than four-billion DNA bases, only 3.3 billion of them -- a little over the size of the human genome -- currently can be assigned to the mammoth genome. Some of the remaining DNA bases may belong to the mammoth, but others could belong to other organisms, like bacteria and fungi, from the surrounding environment that had contaminated the sample. The team used a draft version of the African elephant's genome, which currently is being generated by scientists at the Broad Institute of MIT and Harvard, to distinguish those sequences that truly belong to the mammoth from possible contaminants.

"Only after the genome of the African elephant has been completed will we be able to make a final assessment about how much of the full woolly-mammoth genome we have sequenced," said Miller. The team plans to finish sequencing the woolly mammoth's genome when the project receives additional funding.

The team sequenced the mammoth's nuclear genome using DNA extracted from the hairs of a mammoth mummy that had been buried in the Siberian permafrost for 20,000 years and a second mammoth mummy that is at least 60,000-years-old. By using hair, the scientists avoided problems that have bedeviled the sequencing of ancient DNA from bones because DNA from bacteria and fungi, which always are associated with ancient DNA, can more easily be removed from hair than from bones. Another advantage of using hair is that less damage occurs to ancient DNA in hair because the hair shaft encases the remnant DNA like a biological plastic, thus protecting it from degradation and exposure to the elements.


Wow. Read the rest.

3 comments:

  1. Anonymous1:32 PM

    I was just about to e-mail you this.

    My (future) kids might be able to see a live Wolly Mammoth before they graduate High School.

    Wow.

    We do live in interesting times.

    Mind you, there is nothing particularly _useful_ about doing that, which reminds me of a certain timeline;

    Housing Bubble burst,

    Iraq War going better than most thought possible in 2006 (making future interventions not look so bad),

    Spending and national debt increasing at dramatic rates,

    Financial criss and recession/depression,

    . . . is it just me or do we seem right on track for the Semper Fi TL?

    http://finance.yahoo.com/career-work/article/105959/Next-Victim-of-Turmoil-Your-Salary;_ylt=AkhXRhaaTWbD1re3k_HRnxK7YWsA

    "Income for the median household — the one in the dead middle of the income distribution — will probably be lower in 2010 than it was, amazingly enough, a full decade earlier. That hasn't happened since the 1930s. Already, median pay today is slightly lower than it was in 2000, and by 2010, could end up more than 5 percent lower than its old peak.

    If you look back at poll results over the last few decades, you will see that nothing predicts the public mood quite like income growth."

    You know, no one under about 50 has real adult memories of a bad long lasting recession in the US. 26 years is historically a _damn_ good run without a long recession so if we're honest, we've both been lucky to have been alive during such a long prosperous time, but still most people don't judge things by anything other than their own experiences. I think me and my wife are pretty secure in our jobs, and we have a nice chunk of change saved, but sometimes you roll two 1's in a role, and if that happens am I really going to be comforted by saying, "Well, at least things aren't as bad as the 1830's"?

    Time will tell of course. This could turn out to be a short correction. The Dot Com Bubble bursting looked pretty scary too.

    Cheers,
    Mike

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  2. We might be headed for Semper Fi, but it really depends on what happens with convergence for that TL to come about. What happens with China's banking industry and the reduction in export demand will tell us whether or not that has stalled. or not. I doubt they're going to melt down completely, but they might stall because of this.

    AS for the length of the recession. Two more years, I bet. Two more years, late 2010 to early 2011, is my guess. I doubt it'll be short because the housing market (and its waaaaaaaay overvaluation) hits a lot, a lot of people.

    Now. The mammoth. There's a lot between here with the genome map and being able to make a mammoth. A lot. Maybe in 20 years. Probably not before.

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  3. >Two more years, I bet.

    That's around my guesstimate as well.

    Did I ever mention that the business I work out just finished a 10 figure new building? Half of my job over the last two years has been working with the contractors and the city dotting the i's and crossing the t's.

    Two years and a half years ago when the big bosses were talking about weather to go with a small expansion or a HUGE expansion (which is what we did), I approached one them and said something like, "You know, and I know, that the housing bubble is going to burst sometime. It could be next year it could be in five, but it's going to happen. What are we going to do if we get done with this huge investment just when a recession hits?" The look on his face told me that he never really considered that possibility and I never felt like I got a good answer.

    Now the building is pretty much all done and we're ready to deal with an explosion of new customers.
    So. Yea . . .

    >Maybe in 20 years. Probably not before.<

    Well, plans are plans, but the earliest the wife and I are planning on starting to try and have a kid is 2010, which means that we probably won't have one earlier than 2011, which means they will still be in High School in 2018. So that's 20 years from now.

    And you want to know what the _weirdest_ thing is? 20 years doesn't seem an eternity to me anymore. It's a ways away, of course, but it doesn't feel like something that is incredibly far away like it did just ten or even five years ago.

    Has anyone looked into if time is speeding up? ;)

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