Tuesday, October 21, 2008

The DNA Network

The DNA Network

Recall: Melamine Nipple Spread [Bayblab]

Posted: 21 Oct 2008 07:37 PM CDT

On our upcoming podcast we discuss the melamine tainted milk scandal and some of the affected products. The average Bayblab reader probably hasn't been affected, until now: The recalls continue, and just this past weekend The Guardian reported that thousands of novelty chocolate products were being pulled from shelves because they contained up to 100 times the allowable limit.
"The Food Standards Agency issued an alert over chocolate willy spread, a related nipple spread and a novelty pen set, which contains a chocolate-flavoured body pen, all of which were imported from a Chinese manufacturer called Le Bang.

Food safety experts detected levels of melamine were up to 100 times greater than limits set by the European commission."
I guess I'll be sticking with butterscotch.

SecA/SecY - The subject of a thousand colorful metaphors [The Daily Transcript]

Posted: 21 Oct 2008 07:12 PM CDT

Yesterday I wrote to you about the great work that came out of the Rapoport lab describing how the SecA motor pumps secreted proteins across the protein conducting channel, SecY (aka the translocon). Today I would like to make a couple of remarks on the publication of these results in the last issue of Nature.

First, let's start off with the cover.

Now what in the world were they thinking when they chose that title? Channel hopping??? For any non-Brits, "channel hopping" is slang for crossing the English Channel ... get it? And yes, I realize that Nature is a British rag, but this title is just too cute and UNINFORMATIVE - why do all the journals do this? Just look at Cell's Pop-art covers - are the science journals overrun with new PR-type gurus who think that they can sell more issues by snazzy-ing up the appearance of these magazines? Are they trying to emulate People? When I pick up Nature and read a random title like that, it does not entice me to read the featured article. In fact, it elicits no response from me at all.

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Abiogenesis in a flask [Bayblab]

Posted: 21 Oct 2008 03:06 PM CDT

I'm a bit late on this one but the Miller-Urey experiment has produced some more data. This is the classic experiment, conducted in 1953, where possible conditions of the early earth were simulated in a flask. This flask was then subjected to arcs of electricity (to simulate lightening) and allowed to fester. After 1 week (he let it rest on Sunday) 10-15% of the carbon in the system was present in organic molecules, most notably 11 amino acids. Now in 2008, some of the original samples from this and similar experiments have been reanalyzed using modern, more sensitive equipment. Turns out another similar experiment resulted in the production of 22 amino acids. This again validates the strong possibility of the presence of the building blocks of life, as we know it, on many earth-like planets.
Also if your interested check out this fun/funny Miller-Urey Experiment simulator. Note: it's pretty easy to make it blow up.

A question for Sen. Obama: Can I live? [Mary Meets Dolly]

Posted: 21 Oct 2008 12:29 PM CDT

I think I have posted this video before, but this time I could not help seeing all the children asking Senator Obama, "Can I live?"

Fish odour syndrome [Bayblab]

Posted: 21 Oct 2008 12:12 PM CDT

I found this story on the interwebs about a woman who smelled like rotten fish, and was finally diagnosed at age 41 with a condition known as Trimethylaminuria. From the article:

"Trimethylaminuria is a genetic mutation that causes the body to produce too much trimethylamine, a compound found in fish. Particular foods, medication and hormones can exacerbate the condition."

This unusual condition is caused by a mutation in the FMO3 gene, and leads to an accumulation of trimethylamine because it cannot be converted to trimethylamine N-oxide. trimethylamine is a pungent compound found abundantly in fish.

However there exist milder variant polymorphisms, and even "normal" woman can be subject to the fish smell during menstruation and have transient trimethylaminuria because of a decrease in FMO3 activity (perhaps an evolutionary deterrent for mating?):

"In comparison, three healthy control subjects that harbored heterozygous polymorphisms for [Glu158Lys; Glu308Gly] FMO3 or homozygous for wild FMO3 showed normal (> 90%) metabolic capacity, however, on days around menstruation the FMO3 metabolic capacity was decreased to ~60-70%. CONCLUSION: Together, these results indicate that abnormal FMO3 capacity is caused by menstruation particularly in the presence, in homozygous form, of mild genetic variants such as [Glu158Lys; Glu308Gly] that cause a reduced FMO3 function"

Like a few other syndromes (such as maple syrup urine), trimethylamineuria can be diagnosed a a simple whiff of body odours, but it may be confused with halitosis. Thankfully this group from Philadelphia produced a better diagnostic protocol to distinguish the two:

"Because of our basic research into the nature of human body odors, our lab has received referrals of people with idiopathic malodor production, from either the oral cavity or body. We developed a protocol to help differentiate individuals with chronic halitosis from those with the genetic, odor-producing metabolic disorder trimethylaminuria (TMAU)."

Hispanics and Alzheimer's: article in New York Times [Yann Klimentidis' Weblog]

Posted: 21 Oct 2008 11:52 AM CDT

It looks like Hispanics have a disproportionately high prevalence of Alzheimer's and tend to develop it earlier, according to research cited in this New York Times article.
Genetic reasons are not favored, at least according to what the author of the article, Pam Belluck has gleaned:
"It is not that Hispanics are more genetically predisposed to Alzheimer's, say experts, who say the diversity of ethnicities that make up Hispanics or Latinos make a genetic explanation unlikely."
...and what this researcher has found:
Dr. Rafael A. Lantigua, a professor of clinical medicine at Columbia University Medical School, said, "There's no gene at this point that we can say this is just for Latinos." Dr. Lantigua added that one gene that increased Alzheimer's risk was less prevalent in Latinos than non-Hispanic whites.
More favored explanations are SES, "cultural dislocation", and depression.
The author goes on to describe several studies that have examined the etiology of population differences in Alzheimer's, one of them finding that higher acculturation to American society among Mexican Americans was associated with higher Alzheimer's risk.

G-Day, Episode I [genomeboy.com]

Posted: 21 Oct 2008 10:35 AM CDT

Thanks to all who emailed me about the New York Times article. Amy Harmon did her usual stellar job. And in case you’re wondering: yes, skin biopsies hurt.

I have to say, this whole extravaganza felt more like a walk-through or a dress rehearsal. Several of us did not get our sequence data yesterday and those who did got very rough, low-coverage data. So besides the fact that assembling the ten of us is like herding cats, what was the point? I think there were two: First, to demonstrate that the PGP is indeed a community. While personal genomics is finally about the individual, if we are ever to to destigmatize this information, then I think it’s critical that we start to move away from the Venter and Watson “me me me” models. There are now 5000 people in the queue to be PGP participants. Which brings me to the second point: even though we are hardly the first to make our SNP data public, my hope is that our collective example might nudge still more folks in that direction.

A note on my still-to-come sequence data: As loudly as I’ve agitated for public release of genomic data on this blog, I have reserved the right to redact any or all of my sequence data and my Coriell EBV-transformed cell line. I am alone among the PGP-10 in doing this and I feel a little sheepish about it, but I am unapologetic. I have two young daughters. Yes, genomic information is probabilistic information and my genome is not theirs. But I have what I imagine every other loving father has: a fierce instinct to protect his children. If I carry a known mutation in a highly penetrant mendelian disorder, I want them to find that out from me and my wife, not from the internet or from some precocious classmate.

My public profile is here. I am bracing myself for the SSRI spam.

My SNP and sequence data will eventually be there as well. My SNP data will appear on SNPedia very soon.

A New Dawn For Bitesize Bio [Bitesize Bio]

Posted: 21 Oct 2008 08:29 AM CDT

Finally, after a lot of blood, sweat and tears, the new Bitesize Bio has arrived. And, as you can see, there have been a few changes around here!

Of course, the site looks much better and is easier to navigate. So, we hope you’ll want to stick around more. It’s now so easy to scan through our most recent articles, browse our archives and watch Bitesize Bio TV… why would you ever want to leave?

But what we really want is to make this site a community. That’s why we have added the Bitesize Bio Bistro, which is a virtual meeting place for bio researchers.

Unlike most bio forums, The Bistro is cosy and welcoming, uncomplicated and the software is lightweight, which means a very fast loading site.

Our article discussions will now all take place in the Bistro, but you can, of course, also start your own discussions on whatever you like.

Whether you are having a problem with your cloning or your boss, you want to know whether anyone has tried out a particular kit, or whatever, just start a new discussion and our writers, and other members of the community will be there to participate and hopefully offer advice.

To encourage everyone to sign up, we have teamed up with MoBio Laboratories to set up a prize draw into which everyone who signs up before the end of November will be included. Up for grabs are a 16GB iPod Nano, 2 Kensington wireless presenters and 3 vouchers or Starbucks or Amazon.

It only takes 30 seconds to sign up, so click here to do it!

Finally, this is just the beginning of the improvements we have in mind for Bitesize Bio. We intend to make more additions to the site over the coming year that we hope you will find very useful.

To do this, and keep the site going, we depend on your support. As well as reading our articles and participating in the Bistro, there are a number of other simple things you can do to help out. We have listed them here, so please be sure to take a look!

That’s enough for me - Happy browsing, and I’ll catch up with you in the Bistro. :)

Brain Doping April 1 Joke still getting some press [The Tree of Life]

Posted: 21 Oct 2008 03:48 AM CDT

Well, my April 1 collaborative joke on brain doping is still getting some press. See El Pais which reports
Como muestra, algo que empezó como una broma. "Los centros del NIH (los Institutos de Salud de Estados Unidos) pedirán a todos los científicos que quieran optar a sus ayudas y subvenciones a que pasen pruebas antidopaje para comprobar que no han tomado estimulantes cognitivos para aumentar su rendimiento intelectual". Una supuesta World Anti-Brain Doping Authority (WABDA) se encargaría de los análisis. Es el mensaje de una nota de prensa falsa. Una fake lanzada en Internet el pasado 1 de abril, el día de los inocentes en Estados Unidos, por Jonathan Eisen, biólogo evolucionista de la Universidad de California. Comenzó como una travesura, pero el rumor acabó por extenderse por la red.

La broma apunta, sin embargo, a un debate abierto entre la comunidad científica. Si se controla el dopaje en deportes como el ciclismo, ¿por qué no controlarlo en la comunidad científica, donde también compite el intelecto por conseguir becas, ayudas e incluso premios en reconocimiento de su inteligencia? Esa era la reflexión original que, según explica Eisen, le llevó a colgar su broma de Internet. Sin embargo, también afirma que nunca aceptaría que se realizasen ese tipo de controles.

Practical triple stores [business|bytes|genes|molecules]

Posted: 21 Oct 2008 01:26 AM CDT

The standard streams for input, output, and errorImage via WikipediaEver wondered what you might want to use a triple store for? Well, wonder no more. Toby Segaran has put one to good use to essentially capture his personal stream for the month of September. That stream includes phone records, email history, contacts, calendar and Facebook friends. Of course, being Toby, it’s not just about getting the data in there, but also doing something with it. At this time, it involves some clustering, and seeing the groupings of the connections.

Toby’s right. We have lots of applications which, rightly so, are optimized to do a certain task well, but few ways of capturing information across applications. In a world where you can output data streams in XML or JSON, or RDF, or whatever easily parsable format we choose, we need approaches that allow us to reconcile all that information. To some extent that is what something like Friendfeed enables, but not in the programmatic, data-mining ready approach that Toby has adopted. As he writes

I now have code to keep my triple-store synced with my friend network, my contacts, my phone records, my email and my calendar. I can construct queries across all of this (who did I forget to call on their birthday? Who have I seen recently who went to Stanford?). I'll be sharing this code at some point, but I want to see how far I can take this. I'm also interested in hearing from anyone who has tried similar experiments and wants to collaborate.

I love when people do seemingly obvious and simple, but in reality non-trivial things like Toby just did. The great thing is, as our APIs get better at making information available, as we move towards more linked data, and platforms (like Talis, Freebase and the likes) that allow us to put data in, and then query across data streams, we’ll all be capable of doing what Toby did, and not just with our personal information streams, but other kinds of data streams, like data from multiple research projects, or assay types. Not trivial, but definitely doable given the right data types and information content.

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DTC says "Steal your baby's genome....it's fun!" [The Gene Sherpa: Personalized Medicine and You]

Posted: 20 Oct 2008 11:48 AM CDT

One of the big things 23andMe has emphasized in the past is that their data is not to be used to make medical decisions..... "23andMe's services are not medical ... they are educational," argues...

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Uh Oh......the FDA sets the bar [The Gene Sherpa: Personalized Medicine and You]

Posted: 19 Oct 2008 05:19 PM CDT

In an editorial from the Lancet, Medical groups have expressed doubts about the validity, effectiveness, and clinical usefulness of direct-to-consumer genetic testing. More harm than good is done,...

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