Saturday, August 2, 2008

The DNA Network

The DNA Network

Copy number variation carries the day - and the risk of mental illness [biomarker-driven mental health 2.0]

Posted: 02 Aug 2008 07:30 PM CDT

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A pair of Nature papers (here and here) find that mapping the risk of schizophrenia to the genome is more readily achieved when examining structural variation (insertions, deletions, duplications etc.). This is welcome news given the sparse success of SNP screening, although it would be reasonable to assume that SNPs can modify such structural variants (here for the most recent schizophrenia SNP association study). The pair of papers found similar sites, which is pretty amazing given that many structural variants are rare (see the 2006 survey report). The Copy Number Variation Project provides more details on this important class of variation.

Prevalence of obesity in multi-racial vs. mono-racial individuals [Yann Klimentidis' Weblog]

Posted: 02 Aug 2008 03:40 PM CDT

Despite the weird sounding title (why "ethnic admixture adults "? ... why not: "ethnically admixed adults" or something like that?) this paper (see below) examines quite an interesting question.
Do mixed-race individuals have a higher prevalence of obesity than single-race individuals?
First off, they mention that there is a high proportion (20%) of individuals who report two or more ethnicities in Hawaii, compared to the rest of the US (2%).
The introduction does not state why they expect to see the difference that they are looking for.
They have a humongous sample size (n=215,000), but the data is based on self-report which may bias the results.
The highest prevalence of overweight was for Hawaiian/Latino men (88%,) and black/Latina women (74.5%). The highest prevalence of obesity occurred in Hawaiian/Latino men (53.7%) and Hawaiian women (39.2%). The prevalence of obesity in men and women with Asian/white, Hawaiian/white, Hawaiian/Asian, Latina/white, and Hawaiian/Asian/white ethnic admixtures was significantly higher (P less than 0.0001) than the average prevalence of the ethnic groups with whom they share a common ethnicity/race.
and the money line:
Across all of the ethnic admixtures, the prevalences for both overweight and obesity were similar to or higher than the average of the prevalence estimates for their shared ethnicities; in contrast, none of the admixture prevalences were less than the average of their component ethnicities.
I can't believe they don't provide very much discussion about some of the potential mechanisms that would underlie their findings. They do find that:
"a high caloric intake (e.g., calories from fat and alcohol) and exercise did modestly decrease this difference" (referring to difference in prevalence between ethnic admixturesand monorace adults)"
There might be social and psychological factors that bi-racials experience more often than mono-racials, and this may negatively influence their health.
Nevertheless, this study is interesting and the finding merits future exploration.

The Prevalence of Obesity in Ethnic Admixture Adults
Cheryl L. Albright, Alana D. Steffen, Lynne R. Wilkens, Brian E. Henderson and Laurence N. Kolonel
Obesity (2008) 16 5, 1138–1143. doi:10.1038/oby.2008.31
Abstract: Objective: To determine whether the prevalence of obesity in ethnic admixture adults varies systematically from the average of the prevalence estimates for the ethnic groups with whom they share a common ethnicity.Methods and Procedures: The sample included 215,000 adults who reported one or more ethnicities, height, weight, and other characteristics through a mailed survey.Results: The highest age-adjusted prevalence of overweight (BMI 25) was in Hawaiian/Latino men (88% ; n = 41) and black/Latina women (74.5% ; n = 79), and highest obesity (BMI 30) rates were in Hawaiian/Latino men (53.7% ; n = 41) and Hawaiian women (39.2% , n = 1,247). The prevalence estimates for most admixed groups were similar to or higher than the average of the prevalences for the ethnic groups with whom they shared common ethnicities. For instance, the prevalence of overweight/obesity in five ethnic admixtures—Asian/white, Hawaiian/white, Hawaiian/Asian, Latina/white, and Hawaiian/Asian/white ethnic admixtures—was significantly higher (P less than 0.0001) than the average of the prevalence estimates for their component ethnic groups.Discussion: The identification of individuals who have a high-risk ethnic admixture is important not only to the personal health and well-being of such individuals, but could also be important to future efforts in order to control the epidemic of obesity in the United States.

Polynesian chickens in the pre-Columbian Americas...maybe not, after all [Yann Klimentidis' Weblog]

Posted: 02 Aug 2008 11:13 AM CDT

see here for the post about this from last year.

Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA
Jaime Gongora, Nicolas J. Rawlence, Victor A. Mobegi§, Han Jianlin, Jose A. Alcalde, Jose T. Matus, Olivier Hanotte, Chris Moran, Jeremy J. Austin, Sean Ulm, Atholl J. Anderson, Greger Larson, and Alan Cooper
PNAS
Abstract: European chickens were introduced into the American continents by the Spanish after their arrival in the 15th century. However, there is ongoing debate as to the presence of pre-Columbian chickens among Amerindians in South America, particularly in relation to Chilean breeds such as the Araucana and Passion Fowl. To understand the origin of these populations, we have generated partial mitochondrial DNA control region sequences from 41 native Chilean specimens and compared them with a previously generated database of ≈1,000 domestic chicken sequences from across the world as well as published Chilean and Polynesian ancient DNA sequences. The modern Chilean sequences cluster closely with haplotypes predominantly distributed among European, Indian subcontinental, and Southeast Asian chickens, consistent with a European genetic origin. A published, apparently pre-Columbian, Chilean specimen and six pre-European Polynesian specimens also cluster with the same European/Indian subcontinental/Southeast Asian sequences, providing no support for a Polynesian introduction of chickens to South America. In contrast, sequences from two archaeological sites on Easter Island group with an uncommon haplogroup from Indonesia, Japan, and China and may represent a genetic signature of an early Polynesian dispersal. Modeling of the potential marine carbon contribution to the Chilean archaeological specimen casts further doubt on claims for pre-Columbian chickens, and definitive proof will require further analyses of ancient DNA sequences and radiocarbon and stable isotope data from archaeological excavations within both Chile and Polynesia.

The Latest Technology May Not Have Transformed Your Health, But It Has Changed Science [adaptivecomplexity's column]

Posted: 02 Aug 2008 06:09 AM CDT

New advances in DNA sequencing technology have been receiving a lot of press, but mostly in the context of how DNA sequencing is going to make personalized medicine possible. Your physician will some day be able to prescribe drugs and give you advice on disease prevention, all based on a reading of your DNA. Obviously that day is not here quite yet; however, the amazing power of next-generation DNA sequencing is already transforming what goes on in a biology lab.

To see this, we can take a look at an old technology and look at the changes it has gone through, from its pre-genome-era state in the 80's and 90's, to its transformation into a genome-scale tool around the turn of the millennium, to its latest incarnation during this emerging era of massive, cheap DNA sequencing. This technology, called chromatin immunoprecipitation (or ChIP), has been a critical tool in studies of how genes are regulated. ChIP, in its current, next-generation DNA sequencing form, is opening up some stunning new approaches to studying gene regulation.

Read More...

New Harry Potter Trailer [Sciencebase Science Blog]

Posted: 02 Aug 2008 05:00 AM CDT

My son used to be sooooo into Harry Potter and I’m sure he’ll go to see Harry Potter and the Half-Blood Prince when it shows in the UK, in fact when I mentioned this post he was only too keen to see the trailer. Of course, sadly, long gone are the days when all go to the cinema together as a family, so I’m going to have to content my self with a cinematic surprise for Saturday, at least until it makes it to DVD (just in time for Christmas). So here’s the Harry Potter teaser, trailer, trail, what you will, complete with young Voldemort (played by Ralph Fiennes nephew, no less, thanks Zath)

So, what you may ask, is the science connection with today’s post? Well, there is none. It’s Saturday, it should be a day of fun. Of course, if you want to a connection between science, technology and magic, then you only have to turn to the inimitable Arthur C Clarke book of quotes:

Any sufficiently advanced technology is indistinguishable from magic

This quote was turned on its head by science fiction author and astrophysicist Gregory Benford:

Any technology that is distinguishable from magic is not sufficiently advanced

And, to quote Robert Persig from one of my favourite books (Zen and the Art of Motorcycle Maintenance), in which the word technology might be switched for magic to bring us full circle in today’s Harry Potter theme:

There is an evil tendency underlying all our technology - the tendency to do what is reasonable even when it isn’t any good

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New Harry Potter Trailer

Live Webcams: Hospitals and Labs [ScienceRoll]

Posted: 02 Aug 2008 02:17 AM CDT


Would you like to watch live what’s happening at a hospital or in a lab? Here are some options:

The lab at night

Would you like to be watched all day long?

What’s on the web? (2 August 2008) [ScienceRoll]

Posted: 02 Aug 2008 01:25 AM CDT


~ Pre-Blog: Del.icio.us is a what ? Now: Many people are much better at meta-tagging than I am, and all of us can view their hand-picked sites.

~ Pre-Blog: Didn't use RSS readers such as Bloglines or Google Reader to 'collect' blogs of professional or personal interest. Now: It is a most convenient way to see what others are buzzing about online, check out trends, read about who is covering what.

~ Pre-Blog: YouTube is a source of entertainment. Now: Recognize that it is an essential reference source. Where else could I find all those medical student videos?

~ Pre-Blog: Little use or interest in virtual environments such as Second Life. Now: Realize that a great deal of quality learning and instruction can take place in virtual environments, which represent a democratic, efficient, equalized way to distribute information or share knowledge regardless of physical location, geography, socioeconomic status, level of education or physical limitations.

~ Pre-Blog: Blogging is easy. Now: Nope, blogging is not easy. It is time-consuming.

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