Daily Archives: April 16, 2013

This past Sunday marked the 10th anniversary of the sequencing of the human genome. Many remember the peaceable celebration between two rivals on the project, Francis Collins, who ran the government-backed component of the project, and Craig Venter, whose private venture threatened to embarrass the whole effort by doing things much faster with his shotgun sequencing approach. Both men have now moved on to other projects. Venter among other pursuits, likes to sail around the world sampling the waters for new life forms to sequence, while Collins is now tasked with running the new BRAIN Initiative for Obama.

Now that a little time has passed, it makes sense to take stock of what the project has done for us. For the average person, probably not a whole lot. Having an example DNA sequence on file for analysis has slowly trickled out blips of insight for those who look at things like, for example, subtle varieties of various functional genes, or tracing the remnant repeats of viruses that have integrated into the sequence over time. Of particular interest has been how many times they have copied themselves, and spread throughout the genome. However, the main area that sequence technology gives its greatest benefit is medicine in particular, cancer treatment.

When Steve Jobs was diagnosed with pancreatic cancer, he paid around $100,000 to have his genome sequenced in an effort to gain any information he could about his cancer, and possible treatments for it. Unfortunately there wasnt a whole lot that could be done with that information even just a few years ago. Today however, depending on the type of cancer you have, everything from the invasiveness of your particular brand of tumor, its response to any of a host of drugs in your treatment cocktail, and even how your body metabolizes, excretes, or otherwise unravels in allergic response to those drugs, can be assessed.

Regrettably, at the moment at least, the tests for those various factors are still given piecemeal, kind of like paying $32 to read a journal article for 24 hours when a years subscription is only $120. With the cost of sequencing a genome shrinking to $1000 or less, it will soon make sense for everyone to subscribe.

Nowhere has genetic analysis of cancer patients become more of an issue than for breast cancer. This week the courts began deliberations on the right of one company, Myriad Genetics, to patent your genes in particular a gene known as BRCA-1. A better way to put that, may be to say that the courts began deliberations on your right to pursue genetically-informed treatments in a timely and affordable manner without the now present monopoly on information that should be in the public domain, regardless of efforts spent to obtain it. It is absurd to live under a system that says just because someone spends resource to solve a problem you happen to have, you have no right to seek relief from any other source. Right now if woman wants to know if she has mutations in two common breast cancer genes, she has little or no choice of where she can be tested, for her own gene. Myriad controls that, and virtually the entire market with it.

Immediate issues aside, we have a long way to go towards learning the function of all the genes we have now sequenced. Even more important than knowing these functions, is how all of the genome is organized in the nucleus to define each of our cells, and by implication, our entire organism. The neat pictures of chromosomes packaged into neat little x-shapes is not a picture of a nucleus as it normally exists. The operational structure of nucleus is what we want to understand now.

Beyond that, having a fully-clickable genome, not only for the fertilized egg from which we were conceived, but from any important cell in our bodies at the time it was sequenced, would would be invaluable towards understanding our current health and future prognosis. Each major hit of radiation, or of any of a host of other natural insults we receive in the course of life, leaves its mark. Depending on the health of repair mechanisms, faults might be repaired, or they can slip away unnoticed to cause problems at a latter date.

The legacy of the understanding of our genomes has just begun. As more people arm themselves with knowledge of their genes, this information will continue to grow in collective value. To share this information openly with others and learn from them in response is a privilege. To fear sharing that knowledge on the weak pretense of abuse will be seen looking back not only as cowardice, but ingratitude.

Now read: Your complete genome can now be sequenced from a single cell

Read more:
Human Genome Project is 10 years old, what’s next?

Apr. 15, 2013 The extraordinary level of conservation of the tulip tree (Liriodendron tulipifera) mitochondrial genome has redefined our interpretation of evolution of the angiosperms (flowering plants), finds research in biomed Central's open access journal BMC Biology. This beautiful 'molecular fossil' has a remarkably slow mutation rate meaning that its mitochondrial genome has remained largely unchanged since the dinosaurs were roaming the Earth.

Evolutionary studies make used of mitochondrial (powerhouse) genomes to identify maternal lineages, for example the human mitochondrial Eve. Among plants, the lack of genomic data from lineages which split away from the main evolutionary branch early on has prevented researchers from reconstructing patterns of genome evolution.

L. tulipifera is native to North America. It belongs to a more unusual group of dicotyledons (plants with two seed leaves) known as magnoliids, which are thought to have diverged early in the evolution of flowing plants.

By sequencing the mitochondrial genome of L. tulipifera, researchers from Indiana University and University of Arkansas discovered that its mitochondrial genome has one of the slowest silent mutation rates (ones which do not affect gene function) of any known genome. Compared to humans the rate is 2000 times slower -- the amount of genomic change in a single human generation would take 50,000 years for the tulip tree. The rate is even slower for magnolia trees, taking 130,000 years for the same amount of mitochondrial genomic change.

Ancestral gene clusters and tRNA genes have been preserved and L. tulipifera still contains many genes lost during the subsequent 200 million years of evolution of flowering plants. In fact one tRNA gene is no longer present in any other sequenced angiosperm.

Prof Jeffrey Palmer who led this study explained, "By using the tulip tree as a guide we are able to estimate that the ancestral angiosperm mitochondrial genome contained 41 protein genes, 14 tRNA genes, seven tRNA genes sequestered from chloroplasts, and more than 700 sites of protein editing. Based on this, it appears that the genome has been more-or-less frozen in time for millions and millions of years."

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The above story is reprinted from materials provided by BioMed Central Limited, via AlphaGalileo.

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Tulip tree reveals mitochondrial genome of ancestral flowering plant