Category Archives: Genome

Aquamarine Fukushima

An African coelacanth, photographed using a Remotely Operated Vehicle off the coast of Tanga, Tanzania.

By John Roach, Contributing Writer, NBC News

The genome of the coelacanth, an ancient-looking lobed-finned fish, has been sequenced and is already providing insight to the evolutionary changes that allowed the first four-limbed animals, called tetrapods, to crawl out of the water and on to land.

The sequence and preliminary analysis, reported Thursday in the journal Natureby a team spanning 40 research institutions and 12 countries,is a "massive piece of work," Xiaobo Xu, a paleontologist at Kean University who was not involved in the effort, told NBC News in an email.

"The paper really provides rare and valuable genomic data for offering heavy-weight opinions on issues bearing on the fish (to) tetrapod transition," he said.

It also settles a debate that has long raged amongst evolutionary biologists: what fish is the closest relative of tetrapods: the coelacanth or the equally odd-looking lobed-finned lungfish. The winner, according to analysis of the newly-published genome, is the lungfish.

"We think we have definitively shown it now," Jessica Alfldi, a research scientist at the Broad Institute of MIT and Harvard and co-first author of the paper, told NBC News. "They are very close, which is why it took so much data to figure it out."

Slow evolving genes Scientists thought coelacanths went extinct about 70 million years ago, during the Late Cretaceous period. That changed when a fish trawler off the South African coast delivered a fresh-caught coelacanth to a local natural history museum in 1938, proving that the fish are alive and well.

The coelacanths' odd, ancient-looking looks raised eyebrows and earned it the nickname "living fossil" much to the chagrin of evolutionary biologists, noted Alfldi. ("It makes people think there was no evolution," she explained.)

Read more:
Genome of ancient-looking fish gives clues to first limbed landlubbers

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

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. Credit: Gary Cot

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."

More information: The "fossilized" mitochondrial genome of Liriodendron tulipifera: Ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate, Aaron O Richardson, Danny W Rice, Gregory J Young, Andrew J Alverson and Jeffrey D Palmer, BMC Biology 2013, 11:29 doi:10.1186/1741-7007-11-29

Commentary: Mitochondrial genomes as living 'fossils', Ian Small, BMC Biology 2013, 11:30 doi:10.1186/1741-7007-11-30

Provided by BioMed Central

Link:
The tulip tree reveals mitochondrial genome of ancestral flowering plant

Ion Torrent via YouTube

A researcher initializes an Ion Proton system at the Baylor College of Medicine Human Genome Sequencing Center in Houston. Ion Torrent says the benchtop device is designed to sequence a human genome in a day for less than $1,000.

By Tanya Lewis, LiveScience

This month marks the 10-year anniversary of the Human Genome Project, a 13-year international effort to determine the sequence of the 3 billion "letters" in a human being's DNA.

The $3 billion project, led by the U.S. Department of Energy and the National Institutes of Health, began in 1990 and was completed on April 14, 2003. In the decade since then, scientists have achieved many important milestones in using genomic discoveries to advance medical knowledge.

Sequencing technology has vastly improved in recent years. Sequencing the first human genome cost about $1 billion and took 13 years to complete; today it costs about $3,000 to $5,000 and takes just one to two days.

But just knowing the sequence would be meaningless without a way to interpret it. So researchers found ways to study the genomes function, by sequencing the genomes of 135 other organisms and surveying the global variation among human genomes. [Unraveling the Human Genome: 6 Molecular Milestones]

Researchers compared the genome sequences of other animals, such as chimpanzees and platypuses, as well as other eurkaryotic organisms (those whose cells have a nucleus), such as yeast and flat worms. From this comparison, scientists could identify stretches of DNA that have remained largely unchanged over the course of evolution. Five to 8 percent of the human genome has been unchanged for thousands of years.

One of the more surprising findings is how little of the human genome (only 1.5 percent) actually encodes proteins, the molecular building blocks that perform most of the critical functions inside cells.

To probe this mystery, more than 400 researchers from 32 labs worldwide created the ENCyclopedia Of DNA Elements (ENCODE) consortium. In 2012, they published many important findings about how the human genome functions. These include locations in the genome that may be genetic "switches" to turn genes on and off, as well as demonstrating that more than 80 percent of the genome that was once called "junk DNA" actually does serve a function.

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Human Genome Project marks 10 years

This month marks the 10-year anniversary of the Human Genome Project, a 13-year international effort to determine the sequence of the 3 billion "letters" in a human being's DNA.

The $3 billion project, led by the U.S. Department of Energy and the National Institutes of Health, began in 1990 and was completed on April 14, 2003. In the decade since then, scientists have achieved many important milestones in using genomic discoveries to advance medical knowledge.

Sequencing technology has vastly improved in recent years. Sequencing the first human genome cost about $1 billion and took 13 years to complete; today it costs about $3,000 to $5000 and takes just one to two days.

Probing genome function

But just knowing the sequence would be meaningless without a way to interpret it. So researchers found ways to study the genomes function, by sequencing the genomes of 135 other organisms and surveying the global variation among human genomes. [Unraveling the Human Genome: 6 Molecular Milestones]

Researchers compared the genome sequences of other animals, such as chimpanzees and platypuses, as well as other eurkaryotic organisms (those whose cells have a nucleus), such as yeast and flat worms. From this comparison, scientists could identify stretches of DNA that have remained largely unchanged over the course of evolution. Five to 8 percent of the human genome has been unchanged for thousands of years.

One of the more surprising findings is how little of the human genome (only 1.5 percent) actually encodes proteins, the molecular building blocks that perform most of the critical functions inside cells.

To probe this mystery, more than 400 researchers from 32 labs worldwide created the ENCyclopedia Of DNA Element (ENCODE) consortium. In 2012, they published many important findings about how the human genome functions. These include locations in the genome that may be genetic "switches" to turn genes on and off, as well as demonstrating that more than 80 percent of the genome that was once called "junk DNA" actually does serve a function.

Other research has focused on measuring the variation among human genomes. Preliminary studies during the Human Genome Project indicated that human genomes differ by just one-tenth of a percent. Investigating the limited variation that does exist is key to understanding human health and disease.

In sickness and in health

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Human Genome Project Marks 10th Anniversary

Sequencing the Human Genome

By: gatechhonor

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Sequencing the Human Genome - Video

AGRC1020 Resurrection of DNA Function In Vivo from an Extinct Genome
A draft for AGRC1020 Applied Animal Biology assessment 2013. Article can be found here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.00...

By: Hannah Russell

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AGRC1020 Resurrection of DNA Function In Vivo from an Extinct Genome - Video

Public release date: 11-Apr-2013 [ | E-mail | Share ]

Contact: Kim Newman sciencenews@einstein.yu.edu 718-430-3101 Albert Einstein College of Medicine

April 11, 2013 (BRONX, NY) Albert Einstein College of Medicine of Yeshiva University will join the New York Genome Center (NYGC) as its twelfth Institutional Founding Member (IFM). A collaboration among leading academic medical centers, research universities and commercial organizations, NYGC aims to transform medical research and clinical care by creating one of the largest genomics research facilities in North America.

"Einstein is pleased to join other leading biomedical research institutions as a founding member," said Allen M. Spiegel, M.D., the Marilyn and Stanley M. Katz Dean. "Working together, we can significantly improve our understanding of genetics and help transform biomedical research with the goal of better understanding disease and improving patient care."

NYGC represents an unprecedented sharing of data and resources among premier institutions, which will pave the way for advances in personalized medicine, accelerate the development of new diagnostics and treatments for human diseases, and provide an engine for life science commercialization in the region.

"Albert Einstein College of Medicine has been involved with the New York Genome Center since its very inception," said Robert B. Darnell, M.D., Ph.D., president & scientific director of NYGC. "We are thrilled to formalize our relationship with this prestigious institution and have its researchers participate in the vibrant life of the center."

NYGC's other IFMs include: Cold Spring Harbor Laboratory, Columbia University, Cornell University/Weill Cornell Medical College, The Jackson Laboratory, Memorial Sloan-Kettering Cancer Center, Mount Sinai Medical Center, NewYork-Presbyterian Hospital, New York University/NYU School of Medicine, North Shore-LIJ Health System, The Rockefeller University, and Stony Brook University.

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About Albert Einstein College of Medicine

Albert Einstein College of Medicine of Yeshiva University is one of the nation's premier centers for research, medical education and clinical investigation. In 2012, Einstein received over $160 million in awards from the NIH for major research centers at Einstein in diabetes, cancer, liver disease, and AIDS, as well as other areas. Through its affiliation with Montefiore Medical Center, the University Hospital for Einstein, and six other hospital systems, the College of Medicine runs one of the largest residency and fellowship training programs in the medical and dental professions in the United States. For more information, please visit http://www.einstein.yu.edu and follow us on Twitter @EinsteinMed.

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Einstein joins the New York Genome Center as 12th institutional founding member

A decade after completion of the Human Genome Project on April 14, 2003, a top official of the National Institutes of Health surveyed the rarefied view from that mountaintop:

Admitting, "we have a long way to go to deliver on the promise of genomic medicine," Eric D. Green, director of the institute devoted to this research, still stressed that progress in some areas has been "amazing."

Scientists have obtained the full genetic script of a woman's unborn baby, and the federal government is already preparing for a future in which all babies will have their genomes sequenced at birth.

Doctors now know the genetic underpinnings of almost 5,000 rare diseases, more than twice as many as a decade ago.

We have learned that humans are more than 99.9% alike in their DNA, and yet so vast is the script - a sequence of almost 3.2 billion chemical bases - that our genome is "astonishing in the depth and breadth of its variation," Green said.

Researchers have also overturned a major foundation of genetics by showing that large portions of the script, up to 80% once dismissed as "junk DNA," actually turn out to have specific biological functions.

To a degree few had expected in the 1990s, the speed of genome sequencing has increased and the cost has dropped. Green pointed out that the first human genome took six to eight years to complete at a cost of roughly $1 billion. On the day it was finished in 2003, scientists were already able to sequence the second human in about three to four months at a cost of $30 million to $50 million.

Today, sequencing a genome takes just one or two days and costs about $5,000; what was once a national scientific quest is now well on its way to becoming a common procedure like an MRI.

And then there are the patients such as Wisconsin youngster Nic Volker, whose genes were sequenced in 2009 and used to diagnose and treat a disease that had never been seen before. Across the country, there has been just a trickle of similar success stories.

However, information from the genetic script is already allowing doctors to treat different cancers with greater precision. By sequencing cancer patients, doctors can figure out what medications will and will not work for them.

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Science of genome-sequencing has rocketed forward in 10 years