Saturday, September 20, 2008

The DNA Network

The DNA Network

Win prizes and trips for studying the brain! [Discovering Biology in a Digital World]

Posted: 20 Sep 2008 08:08 PM CDT

Hey high school teachers! Are your students interested in the brain?

Who isn't?

Three winners will win all-expense-paid trips to present their work in a poster session in Seattle at the 2009 Annual Meeting of the American Academy of Neurology. Their teachers get to come too! I can tell you, Seattle is a fun place to visit.


Low tide at Golden Gardens, July 2008

Plus, three student winners will get $1000 in cash in addition to the trip.

Find out more at

Read the comments on this post...

You are free to say what I want to hear [Mailund on the Internet]

Posted: 20 Sep 2008 09:17 AM CDT

I just read this post at Gene Expression.

The opening paragraph is:

You might have heard that Richard Dawkins’ website has been blocked in Turkey because of that moron Harun Yahya (H/T Thabet). Here’s the justification:

His press assistant, Seda Aral, said: “We are not against freedom of speech or expression but you cannot insult people. We found the comments hurtful. It was not a scientific discussion. There was a line and the limit has been passed. We have used all the legal means to stop this site. We asked them to remove the comments but they did not.”

(emphasis from the link).

I don’t know what to say to that, really. You have freedom of expression, but you cannot say anything that is insulting?

Recreating the Spanish flu [Mailund on the Internet]

Posted: 20 Sep 2008 09:01 AM CDT

Bayblab posted on this news story:

The body of an aristocrat who died nearly 90 years ago has been exhumed in the hope that it will help scientists combat a future flu pandemic.

Didn’t they already do roughly the same thing back in 2005?

Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus
Tumpey et al. Science 310(5745) pp. 77 - 80, 2005

The pandemic influenza virus of 1918–1919 killed an estimated 20 to 50 million people worldwide. With the recent availability of the complete 1918 influenza virus coding sequence, we used reverse genetics to generate an influenza virus bearing all eight gene segments of the pandemic virus to study the properties associated with its extraordinary virulence. In stark contrast to contemporary human influenza H1N1 viruses, the 1918 pandemic virus had the ability to replicate in the absence of trypsin, caused death in mice and embryonated chicken eggs, and displayed a high-growth phenotype in human bronchial epithelial cells. Moreover, the coordinated expression of the 1918 virus genes most certainly confers the unique high-virulence phenotype observed with this pandemic virus.

The Spanish flu

The Spanish flu is a nasty virus. It’s an influenza that from 1918 to 1920 killed between 20 and 100 million people worldwide.  In comparison, only about 20 million were killed in the entire First World War, so if you look at deaths per year in the early 20th century, it is the Spanish flu that will show a spike, more than the war.

It was a truly global epidemic.  It is called the Spanish flu because the Spanish press wrote about it (most other countries had the press censored during the war, but Spain wasn’t involved in the war), but really it was found everywhere across the globe, with as much as 20% of the world population infected and killing 2.5-5% of the worldwide population.

With the danger of sounding like a mad scientist, I am really fascinated by this epidemic.

Digging up victims, to try to recreate the flu, might not be the brightest idea ever, but the reason people want to do this is to learn more about influenza epidemics.  With all the scare about the bird flu, we might need all the knowledge about influenza we can get.

There is absolutely nothing preventing a new worldwide epidemic like the Spanish flu, and we really want to be prepared if that happens.

Reconstructing the Spanish flu

I’m not sure exactly what the plan is for Sir Mark Sykes — the guy they are digging up now — but what they did in the Science paper was to re-create the Spanish flu virus from the samples they got there.

They managed to get the sequence of the Spanish flu virus genome and then combine it with (the modern) H1N1 virus, to get viruses with more or less of the Spanish flu in them.  These they then grew to learn about the virus.

Knowing the sequence of the Spanish flu will let us analyse the evolution of it and maybe tell us where it came from (jumping from another species; recombining or mutating to that particular variant; etc.)

Actually growing the virus lets us experiment with it, learn how deadly it really is and how it works (see e.g. this story), maybe develop vaccines (not that that would be much help against a new epidemic variant, but we might learn something from it).

T. M. Tumpey, Christopher F. Basler, Patricia V. Aguilar, Hui Zeng, Alicia Solórzano, David E. Swayne, Nancy J. Cox, Jacqueline M. Katz, Jeffery K. Taubenberger, Peter Palese, Adolfo García-Sastre (2005). Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus Science, 310 (5745), 77-80 DOI: 10.1126/science.1119392

Grave-robbing for Science [Bayblab]

Posted: 20 Sep 2008 06:17 AM CDT

The Spanish Flu killed an estimated 20 to 100 million people across the globe in the years 1918-1920. Towards the end of the pandemic soldier and diplomat Sir Mark Sykes was killed by the virus and buried in a lead coffin.

With lingering fears of a possible bird flu (H5N1) pandemic, and with a dearth of samples from Spanish flu (a subtype of avian flu H1N1), he has recently been exhumed by scientists -- paging Dr. Frankenstein!

Taking tissues from his body, well preserved by his lead casket, the team is trying to learn more about the Spanish flu and how it killed him in the hope of transferring that knowledge to the understanding and treatment of H5N1. His body was re-interred after removing samples in a special laboratory, airtight to avoid any risk of contamination.

The future of mobile devices [Mailund on the Internet]

Posted: 20 Sep 2008 06:12 AM CDT

There’s a very interesting post on Google’s blog: The Future of Mobile.

Where is the mobile phone heading? How will it change the future?

How much for that genome? [Mailund on the Internet]

Posted: 20 Sep 2008 04:24 AM CDT

It is a quiet Saturday morning.  I am slightly hung over.  My scripts are scanning through a genome and I am just sitting here waiting for them to finish with nothing much to do.

So I started thinking.  How much does it actually cost to get a new genome, these days? If I wanted my own genome sequenced, how much would I have to pay and how long would it take to get it?

The (first) human genome project cost about $3 billion (about $300 million for Celera) and took about 10 years (1990 to 2000 for the first assembly, then three more years for completion, but let’s just say 10 here).

Now they want to sequence 1000 humans in three years for $30-50 million. Next generation sequencing techniques lowered the cost of that project by a factor of 10. Of course, it helps a lot to have the original genome to assemble up against as well.

I’ve asked Roald about the price for the first “arab genome”, but I haven’t gotten an answer yet.  I guess he doesn’t work Saturday mornings ;-)

The genomics age

Some people say we are in the “post genomic” age, but really we are just in the middle of the genomics age if anything.  We are seeing an explosion in new genomes sequenced.

From GOLD you can download some statistics on genome projects. Plotting the total number of genomes published against years, you clearly see the explosive increase in data:

It is even more impressive when you consider all genome projects and not just the published genomes so far:

Statistics at NCBI says we have 22 complete Eukaryote genomes, 161 with a draft assembly and 176 in progress. For Prokaryotes the numbers are 749 complete, 540 draft and 676 in progress.

It doesn’t say anything about the cost of sequencing genomes, though, so I don’t know how much the price has dropped over time.

I was a bit surprised to learn that the only mammals considered complete are mouse and man. There are 22 mammals with draft assemblies and another 26 in progress.  Will the draft genomes be completed any time soon?

I don’t want a 23andMe — I want the real genetic tests [Think Gene]

Posted: 19 Sep 2008 11:01 PM CDT

Our friendly government lists some available genetic tests: these are the real deal, high penetrance tests for things you already have or conditions you will get.

Unlike Sergey Brin, I don’t particularly care about a mutation that gives me a slightly increased risk for a disease. That’s not significant, though if the placebo effect of a 23andMe test gets you to exercise more, congratulations.

However, if I knew I was bound to get Huntington’s Disease, I would really live my life differently with the moral superiority provided by knowing that my time on this earth was sadly limited by my genetics. I would just take things so much more seriously than all those suckers blissfully unaware of the cold, cruel nature of reality.

For now, it’s prohibitively expensive to get every single genetic test. With how much I would have to spend today to get 50 patented tests I would be better off waiting a year and getting my genome sequenced, then analyzing the data myself to (illegally?) check for every high penetrance mutation.

Interfacial phenomena [business|bytes|genes|molecules]

Posted: 19 Sep 2008 07:19 PM CDT

Zooming interfaces are cool. This week I have had a chance to see Zoomii in action, a Microsoft Surface, and of course, I use the multitouch zooming of the iphone quite regularly.

In an interview with Jon Udell, Kristin Tolle, who works on biomedical computing at Microsoft Research had this to say

Yeah, and we have these cool technologies. I think the WorldWide Telescope could be redeployed in many environments, and I think healthcare is one of those killer applications. We were talking with the National Cancer Institute, and one of the things they’d like to do is take a slice out of the liver while the patient is still on the table and be able to zoom in and zoom out — it’s the same technology.

This was in response to a question on our abilities to make sense of complex data. I am very curious about how futuristic, or should we say modern since they’re here, will help our abilities to manipulate data, visualize it, etc. We have already seen the Google Maps API utilized to build genome browsers, and there is the stuff that Andrew has done. I have had the chance to see some very excellent visualizations, but they tend to have poor UIs and interaction models. That’s where I suspect we are going to see the most innovation in the coming years.

Reblog this post [with Zemanta]

MIA? [business|bytes|genes|molecules]

Posted: 19 Sep 2008 07:10 AM CDT

No, contrary to popular belief no aliens are involved in my longest blog silence in a long time. Thanks to a hectic road trip, mostly at Web 2.0 Expo, haven’t had much of a chance to write about anything.

In the meantime, the internet stayed up, the financial markets are in a mess, AWS made a huge announcement, and Tim O’Reilly gave a rather though provoking talk that I have to blog about soon.

Oh, and the new Zemanta is sweet. Got a chance to meet Jure this week too :).

Reblog this post [with Zemanta]

No comments: