Tuesday, September 9, 2008

The DNA Network

The DNA Network

Obama's economist sees healthcare spending as GDP driver rather than drain [biomarker-driven mental health 2.0]

Posted: 09 Sep 2008 07:32 PM CDT

ALBUQUERQUE, NM - FEBRUARY 01:  Economic advis...Image by Getty Images via Daylife A recent article in "Technology Review" profiles Austan Goolsbee, a professor at the University of Chicago School of Business & senior economic advisor to Barack Obama. I was surprised by a comment he made suggesting that as healthcare spending continues to expand, he can see it becoming a central driver of economic growth, if not, a major foundation of economic growth. Indeed, the end product of all this bioscience is much more valuable than a new car or big-screen LCD television. I'm hoping we'll hear more on this new perspective in the coming months (and 4 years).
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Blogs getting a bit more respect at UC Davis [The Tree of Life]

Posted: 09 Sep 2008 06:17 PM CDT

Well, to go along with the FreindFeed discussions I have been having recently here is a tidbit of interest. Blogs keep getting a bit more respect at UC Davis. First, there was Egghead, a blog about research at Davis sponsored by the College of Biological Sciences. And now there is "UC Davis Blogs" a web site with details about blogs by UC Davis people. And here is the current list:

Behind the Lens by Karin Higgins

Arts and humanities

Business and law

Science and agriculture

Social science

They have left out a few including one of my favorites: "Mario's Entangled Bank" by Mario Pineda-Krch but the listing by UC Davis is a good thing.

The Center of Science in the Public Interest answers questions about GE crops [Tomorrow's Table]

Posted: 09 Sep 2008 04:47 PM CDT

I recently posted "10 things about GE crops to scratch from your worry list"

Today I learned that the Center for Science Policy in the Public Interest has posted a similar list in their answers to frequently asked questions.

This is the group that campaigned for a federal law requiring nutrition labeling of packaged foods and a ban on deceptive health claims. They also led the effort to win passage of a federal law defining "organic" food.

CSPI does not take a dime from industry or government, so if you would like additional information, free from conflicts of interest, this list is for you.

Are We Losing the War on Cancer? [adaptivecomplexity's column]

Posted: 09 Sep 2008 04:11 PM CDT

Imagine that instead of setting out to invent a better lightbulb, Thomas Edison had announced his intention to invent a light-emitting diode that you could use to illuminate your kitchen. This isn't completely far-fetched: the first examples of light-emitting diodes (LEDs) began to appear as early as 1907. But it wasn't until the 1960's and 70's that useful, visible-spectrum LEDs began to appear, and LEDs haven't been used to light kitchens until very recently. Thomas Edison, had he set out to make a useful, household LED, would have been doomed to failure beacause it would be years before basic science made the necessary technologies possible.

When Richard Nixon declared the conquest of cancer "a national crusade" in 1971, cancer researchers were inevitably set up to be viewed as failures. Although at the time the recent molecular biology revolution led people to think that disease conquest was just around the corner, now we can look back and see that the War on Cancer had no hope of achieving its goals in the 1970's. Scientists are being punished for that hubris now, in the form of misguided news pieces such as Newsweek's current exposé: "We Fought Cancer...And Cancer Won".


The "when does human life begin" debate is the wrong debate [Mary Meets Dolly]

Posted: 09 Sep 2008 12:57 PM CDT

It is unfortunate that I feel compelled to write this entry at all.  The rhetoric surrounding Roe vs. Wade has crippled us in this discussion.  It has confused biological fact with questions that cannot be answered by science.

Let me be very clear.  The debate IS NOT when human life begins.  A new human life identifiable by his or her unique DNA is created at conception. 

What we are REALLY discussing is whether or not that life has VALUE

Now, that IS a question worth debating.  If you think that a human embryo does not deserve protection under the law then say so.  It does no one any good trying to assert that a human embryo or fetus is not a human life.  Focusing on the wrong debate really gets us nowhere.

Picking on the "genetically defective" kid [Mary Meets Dolly]

Posted: 09 Sep 2008 12:24 PM CDT

I have had it. The assault on Sarah Palin for her apparent crime of bringing Trig, a child with Down syndrome, into the world has gotten out of control. I was standing in line at the grocery store and was sickened by the headlines that repeated over and over again that Trig was "afflicted" with Downs. This piece by
Vanity Fair is particulaly disgusting. It questions Trig's parentage, suggesting that Bristol, Palin's pregnant 17 year-old, is really Trig's mother.

So much for our compassionate and inclusive society that embraces our "differences." It is apparently fine to be different as long as you are not "genetically defective." Then you are fair game. The media can say you are "afflicted" and drag your mother and sister through the mud and it is perfectly acceptable.

Forget about commending the Palins for loving their child. No, that would be wrong. Because in the back of every one of these media bigots' mind is the thought that Trig should have been aborted. The only explanation I can come up with for assaulting little Trig is that in the liberal media's eyes, Trig's crime isn't that his mother is running for Vice President, it is that he was born with an extra chromosome 21. Disgusting.

Has anyone even thought of Trig? What about his feelings? What about how this sickening media blitz is affecting his world, his family, his life? It is like a big bully and a group of his degenerate friends picking on the "slow" kid. Vanity Fair should hang their heads in shame.

Poo Identification [Bayblab]

Posted: 09 Sep 2008 12:04 PM CDT

It's been some time since we had a scatalogical post - which is odd considering how often it comes up at lunch. Last month, Adventures in Ethics and Science had a "name that poo" challenge, calling on readers to identify the feces of several circus animals. Check it out and tell us how you did. Use this flowchart if you must. Answers are here. No cheating!

Darwin on the Wall [The Tree of Life]

Posted: 09 Sep 2008 12:00 PM CDT

Lots of other bloggers posting about this but I got to put it out there too.  Check out the remarkable story of the Darwin Shaped Wall Stain and how it is galvanizing the evolution community - See Evolutionists Flock To Darwin-Shaped Wall Stain.  It is from the Onion.  One of my favorite "news" sources.  Hat tip to many many people for pointing this out.

How many building blocks do you expect in a cell? [Reportergene]

Posted: 09 Sep 2008 10:57 AM CDT

ResearchBlogging.org Expectations that defined variation in the DNA blueprint would serve to pinpoint our whole inner biology was completely unfulfilled by the genome projects. To date, under the light of system biology, we can conceive at least 68 omics disciplines - would say Jamey Marth (HHMI) - DNA is just one character and there are 68 molecules that contribute to the synthesis and primary structures of the 4 fundamental macromolecular components of all cells (nucleic acids, proteins, glycans and lipids).

We need to take care of our 68 players in defining conceptual frameworks for biology. We are writing our periodic table of cell's building blocks.

Jamey D. Marth (2008). A unified vision of the building blocks of life Nature Cell Biology, 10 (9), 1015-1015 DOI: 10.1038/ncb0908-1015

Predicting the future (for molluscs) [The Tree of Life]

Posted: 09 Sep 2008 08:55 AM CDT

As many of you know, I spend a decent amount of my blogging time trying to come up with funny evolution or genomics related posts. Well, if you like that type of thing, you really have to check out this new site:

The Molluskan Zodiac

The site states
"While most people are familiar with western astrology and with the Chinese zodiac, much less is known about the 'molluskan zodiac' (sometimes known as the mariners zodiac). But ask any fisherman, and they will tell you instantly which of the ten signs of the molluskan zodiac they were born under."
It is very very funny. And real of course. Kudos to Keith Bradnam, who happens to be from the UC Davis Genome Center (where I work) for revealing the inner secrets of these wonderful invertebrates. And while you are checking out the Zodiac, check out Bradnam's new PLoS One paper on intron length which he authored with Ian Korf. Science humor, invertebrates, and Open Access publishing. Now what could be better than that?

Where's my 600 dollar refund? [The Gene Sherpa: Personalized Medicine and You]

Posted: 09 Sep 2008 08:07 AM CDT

In a not so surprising move the NY Times reports that 23 and Me will be lowering their prices from 999 USD to a whopping 399 USD. That is no joke. There are some market reports out there that push...

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Epigenetic findings nearly tread on Central Dogma, but yield clues to suicide [biomarker-driven mental health 2.0]

Posted: 09 Sep 2008 08:02 AM CDT

Lamarck, late in life.Image via Wikipedia The "Central Dogma" of molecular biology rightfully points out a somewhat one-way transfer of information from DNA to RNA to protein. This mechanism has obvious implications for evolution insofar as you are issued a newly shuffled genome at birth and must make the best of it - no cheating allowed by receiving the acquired levels of fitness of your parents - since these cannot be transmitted via the bare thread of DNA. This being the case, however, it is, of course, fun to encounter ways in which mother nature skirts the rules. The term 'mother' is particularly apt to the work of Michael Meaney and colleagues in Montreal, who have for many years been teasing apart mechanisms underlying maternal care in mammals. It seems that when a female rat has been deprived of good mothering (copious licking & grooming are the traits of a good rat mom) they, themselves, also demonstrate poor mothering skills (sadly, daughters DO grow up to be their mothers). The Meany group provide a great review of the mechanisms of this seeming example of "inheritance of acquired characteristics" in their review, "Epigenetic Programming of Phenotypic Variations in Reproductive Strategies in the Rat Through Maternal Care" [DOI: 10.1111/j.1365-2826.2008.01725.x]. Apparently, this mode of inheritance is dependent on the early development of neuro-endocrine circuits that regulate emotional responsivity and are dependent on early, neonatal environmental stimulation (licking & grooming activate these developing circuits) - and is not dependent on the sperm/egg-bourne passage of a particular stretch of DNA. Interestingly though, the team demonstrates that genomic CpG hypermethylation of the estrogen receptor might serve as a mechanism to maintain the effect - at the level of the genome - of the mother's poor parenting. Mom's who were poorly cared for as infants may have a hypermethylated estrogen receptor and therefore are more likely to demonstrate poor parenting in adulthood as a result of the maintainence of this methylated (transcriptionally repressed) estrogen receptor. More interestingly, the team has recently begun to investigate this mechanism in humans, and reported that in post-mortem analysis of hippocampal tissue from individuals who experienced early life neglect and, tragically, suffered death from suicide, that there seems to be a similar type of hypermethylation. Their PLoS ONE article, "Promoter-Wide Hypermethylation of the Ribosomal RNA Gene Promoter in the Suicide Brain" [DOI: 10.1371/journal.pone.0002085] provides an analysis of promoters of rRNA genes in the hippocampus - a brain region whose development and structure is negatively affected by environmental stress and neglect. This is a line of research that is interesting on many levels - from Lamarck to Freud. As a parent, the work shows how important it is to understand & appreciate the role of parenting and social welfare in mental health.

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23andMe Lowers Price to $399 and Adds More Genealogical SNPs [The Genetic Genealogist]

Posted: 09 Sep 2008 06:08 AM CDT

logo 23andMe just announced that the price of their service has dropped from $999 to $399.  According to an article in the San Francisco Chronicle, the company lowered the price of testing to attract more customers and increase the size of their database.  The article maintains that 23andMe will still bring in profit from the lower membership price, which is made possible by a “new, higher-density gene-scanning chip made by Illumina Inc. of San Diego.”  From the press release:

“The new Beadchip, called the HumanHap550-Quad+, makes use of a four-sample format. 23andMe also has added improved custom content to the new Beadchip, which will include a broader range of Single Nucleotide Polymorphism (SNP) variations and rare mutations not found on the previous Beadchip, thereby providing more relevant data on published associations, as well as maternal and paternal ancestry.”

Since 23andMe launched nearly a year ago, I’ve said that genealogists are a huge potential market for 23andMe’s services.  Undoubtedly, the company has recognized the value of marketing their product to genealogists.  Indeed, 23andMe’s blog, the Spittoon, announced today that the company has partnered with Ancestry.com to provide ancestry-related content from 23andMe to customers who have their DNA analyzed by Ancestry.com:

“We're also very pleased to announce a new partnership between 23andMe and Ancestry.com, the world's largest online source of family history information. As part of this arrangement, customers who have their DNA analyzed for genealogical purposes by Ancestry.com will also have access to ancestry-related content from 23andMe.”

You can learn more about the partnership by reading 23andMe’s press release.  As of Tuesday morning, I don’t see any press release at Ancestry.com or DNA Ancestry.

This lower price is only slightly more than many current genetic genealogy tests (some of which only sequence a few thousand bases rather than the 1,000,000+ SNPs tested by 23andMe’s SNP Chip). Will this lower price spur you to sign up for 23andMe’s services?  Will other companies such as deCODEme lower their prices in response?  What do you think?

Long introns delay transcriptional time [Reportergene]

Posted: 09 Sep 2008 01:55 AM CDT


In a negative feedback loop, does intron lenght affects gene expression? Yan Swinburne and colleagues (Harward) answered this question by engineering a gene network and modifying only intron length between clonal variants. What they observed was such network (with delayed autoinhibition) exhibiting pulses of reporter expression that were correlating with intron length. A successive simulation with mathematical models suggested that fluorescence bursting (Venus fast-maturing variant of yellow fluorescent protein) accumulated during transcription elongation.

Note in the construct diagram the presence of PEST and ARE used to destabilize both protein and mRNA: destabilization is fundamental to limit reporter accumulation and so to gain time-resolution. (Swinburne et al, Genes and Development 2008)

The delay of transcriptional machine by introns may be important in many contexts (somitogenesis during development, NF-kb patterns). Undoubtedly, this work further evidences that reporter genes are instrumental to the goals of system biology.

I. A. Swinburne, D. G. Miguez, D. Landgraf, P. A. Silver (2008). Intron length increases oscillatory periods of gene expression in animal cells Genes & Development, 22 (17), 2342-2346 DOI: 10.1101/gad.1696108

Your personal health: 23andme v2 [business|bytes|genes|molecules]

Posted: 09 Sep 2008 12:23 AM CDT

Image representing 23andMe as depicted in Crun...Image via CrunchBase, source unknown Did 23andme just cut prices?

Update: Apparently they did

A new blog post suggests that they’ve dropped prices to $399 (unless I am being completely dense and that’s an upsell). That information is part of the launch of 23andme v2.

With the introduction of v2, our next-generation analytical platform, 23andMe customers will have access to an even more powerful set of the SNPs we use to probe their unique genetic composition.

Can anyone with a 23andme account, or in the know, tell me what the potential and scope of the “analytical platform” is. I also suspect that v2 is on the 1M chip.. From the press release, it appears they are using the new Quad+ Beadchips

The price reduction is largely made possible following technological advancements by Illumina — a leading provider of genetic analysis technologies — to its DNA Analysis Beadchips, which 23andMe uses to genotype customers. The new Beadchip, called the HumanHap550-Quad+, makes use of a four-sample format. 23andMe also has added improved custom content to the new Beadchip, which will include a broader range of Single Nucleotide Polymorphism (SNP) variations and rare mutations not found on the previous Beadchip, thereby providing more relevant data on published associations, as well as maternal and paternal ancestry.

Need to dig into this more, but just saw the post and decided to throw it out there.

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Collect, analyze, re-mix, re-purpose [business|bytes|genes|molecules]

Posted: 08 Sep 2008 11:51 PM CDT

The Cutting EdgeImage via Wikipedia

Science was always about mashing up, taking one result and applying it to your [work] in a different way. The question is 'Can we make that as effective [for] samples [of] data and analysis as it [is] for a map and set of addresses for a coffee shop?' That is the vision. — Cameron Neylon

Those words, found on a great post at the Science Commons blog, have been stuck in my head since I saw them.

I’ve talked about mashing up science many times. In my time in the bioinformatics industry, the need to do “integrative genomics” comes up again and again, yet the approaches we adopt to solve those problems are either too heavy and complex, or simply abandoned due to the inherent gaps in our data.

Mashups, e.g. the ones with Google Maps that we are all used to, are not trivial. They are enabled by some very cool technology at the back end, but we’ve managed to abstract away the complexity and enable creativity and utility. We need innovators in the life sciences, people who will build the backend infrastructure and enable creativity. The Biogang and many others in the community would be so much more effective given the right tools. We end up locking too much away in proprietary software, in complexity, or in paradigms written for a different era, but I think we’re making slow progress. Increasingly people are becoming aware of what can be achieved in today’s web-scale world. There are people who are at the cutting edge, but don’t quite look as cutting edge as they might have a few years ago.

I would like to throw down the challenge to commercial providers of life science software. Join the web of data. Architect for innovation. Think about new business models, cause I am not sure the traditional ones are sustainable, and innovation is limited (with some notable exceptions). Help people not only collect and analyze data, but re-mix and re-purpose.

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