Category Archives: Genome

The document, carefully described as Landers personal view, argues that Utah-based Myriad has patented products of nature, which are ineligible for such protection. The patents, Lander argues, are an insurmountable barrier to studying the DNA, with serious repercussions for medical progress.

Although the brief is filed in support of neither party, it is a strong critique of the reasoning that has been used to protect the gene patents that Myriad holds on BRCA1 and BRCA2, breast cancer risk genes for which it sells a diagnostic test. In his brief, Lander proposes a thought experiment, asking the court to consider what would have occurred if such restrictive patents had been taken on HIV.

The patent holder would have been legally entitled to use his patent to block anyone from observing, characterizing or analyzing the virus by any means whatsoever. Scientists would not have been able to rapidly learn the secrets of this insidious virus; drug developers would not have been able to develop life-saving drugs; technologists would not have been able to develop effective diagnostics; and patients would not have been able to know their HIV status, Lander wrote. To their credit, the discoverers of HIV obtained appropriately narrow patents that do not exclude others from observing, characterizing and analyzing naturally occurring HIV.

To build his argument, Lander gets back to basic biology. The federal Circuit Court, which ruled in favor of Myriads patents, had reasoned that the isolated DNA fragments of the human genome patented by Myriad were not products of nature because they required human intervention to be cleaved out of the chromosome.

Lander, however, notes that for three decades, scientists have known that isolated DNA fragments occur naturally. Every time a cell dies, chromosomal DNA is broken into fragments. DNA fragments are found in cells, urine, spit, and stool. They are found in the blood of people with cancer, viral infections, stroke, or traumaand even in samples taken from people who exercise excessively. Analyzing such fragments in a pregnant womans blood is already used as a prenatal test to flag chromosomal disorders in fetuses. Fragments that contain the exact breast cancer genes on which Myriad holds patents were found in two studies, Lander notes.

He goes on to argue that understanding the genome, such as the risks conferred by a gene, is not an invention, but rather is more akin to discovery of a law of Nature.

The Myriad case is due to be heard before the Supreme Court in April. The biotechnology industry argues that if the patents arent upheld, such a decision could erode much of the foundation for a wide array of businesses that range from pharmaceutical companies to agricultural companies. Scientific organizations and patient groups have argued that the patents impede research, and even patients ability to know their own risks.

Lander suggests that the court could rule carefully on the Myriad case without endangering the broader industry. The court could rule as invalid patents on fragments of the human genome, while allowing patents on DNA obtained through a process that involves reverse- engineering a DNA blueprint from other genetic material that produces proteins.

Science is the systematic and cumulative study of the natural world, Lander wrote. For scientific progress to proceed, scientists must have the ability to study the handiwork of Nature.

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Eric Lander, human genome project leader, weighs in on Supreme Court gene patenting case

This network is a visual representation of something I have jokingly begun calling the MLS Player Genome Project.

Using statistics from the Opta's MLS chalkboards and a heavy amount of number crunching, each player (having played at least the minimum minutes required by the high lord sample size) is compared to every other player in MLS. Their positional tendencies and statistical dispositions are each carefully compared and contrasted.

During this process, each pair of players is assigned a similarity score. If this score is above a certain threshold, the representative nodes of the two similar players are connected. Then, using different visual clustering techniques, this enormous matrix of player comparisons is untangled into the visualization seen above.

Complete Central Winger archive

The results are impressive. Forwards are clustered together in blue on the bottom left. Connected to the forwards are attack-minded midfielders in green. The left side of the green cluster seems to be more flank players, while the right side of the cluster seems to have a few more central players.

Moving from the green midfielders, we connect to the red cluster which seems to be home to some more conservative midfielders. And, as expected, this conservatism grows as you move from left to right until you find a handful of prototypical defensive midfielders in Dax McCarty and Kyle Beckerman at the extreme. The fullbacks have their own cluster, featuring players that almost exclusively play wing back. And the goalkeepers, as expected, were pretty easy to statistically pluck out of the crowd.

While these player connections are far from perfect (they are roughly based on mathematical concepts that online dating websites use for personal matching and what Pandora uses for deciphering your musical taste), much value can be gleaned from looking at MLS in this perspective. Strikers and fullbacks, for example, clearly still have very distinct and specific roles. The modern midfield on the other hand is becoming ever more nebulous, to the point that there is no separate cluster for flank midfielders.

Is that a surprise? Not really, since the traditional left and right midfielders commonly featured in a prototypical 4-4-2 are replaced with hybrid attacking wingers more commonly seen in a modern 4-3-3.

As North American soccer continues to grow and improve, I expect this network to become even more illuminating. The tactical game inside the game becomes increasingly sophisticated, so the types of roles that will be required will become even more distinct. A soccer game, after all, is never decided by players playing their positions on a whiteboard; its a series of actions and reactions.

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Central Winger: Sifting through Opta data to sequence the soccer genome

Moso bamboo. Credit: Wikipedia, Creative Commons

Published: Feb. 26, 2013 at 8:55 PM

BEIJING, Feb. 26 (UPI) -- Chinese scientists report they have decoded the genome for a variety of bamboo in hopes of improving it and using the plant as an alternative to wood.

The results of the study of moso bamboo, a giant timber bamboo that can grow to more than 90 feet tall, have been published in the journal Nature Genetics.

Jiang Zehui, leader of the researchers responsible for decoding the genome, said the team began their work on the moso bamboo, the most common species used in the bamboo textile industry of China, in 2007, China's state-run Xinhua News Agency reported.

China is the world's biggest grower and user of bamboo with 9.5 million acres of moso bamboo, which accounts for 72 percent of the country's bamboo-planting area.

One of the fastest-growing plants in the world, moso bamboo can grow 40 inches in just 24 hours if conditions are favorable.

The decoded genome will allow scientists to modify the species and find new uses for it, Han Bin, a senior genetics researcher at the Chinese Academy of Sciences, said.

The decoded genome will also help alleviate food shortages for giant pandas, Han said.

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Genome of Chinese bamboo decoded

Human Genome Sprapp (HGS) Episode #4 "Searching for Genes"
Genes are sequences of DNA Nucleobases distributed in various places along the 23 pairs of Human Chromosomes. In this episode I developed some formulas that support searching for small parts of genes (less than 51 bases). This Proof of Concepts can be scaled up to support actual gene sequences which can run thousands if not millions of bases long. For more info of the Human Genome Pivot Table Experiment - check out Ken #39;s Talk.com

By: Ken Braverman

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Human Genome Sprapp (HGS) Episode #4 "Searching for Genes" - Video

LAS CRUCES Are you ready for a vanilla dessert chile pepper? How about pepper plants with leaves and stems as brilliantly colored (and maybe even as spicy) as their spectacular fruits?

Nobody has to tell those of us in the Chile Capital of the World that our favorite pepper is something special.

But mapping the entire genome of the chile pepper has brought us new information about just how unique chiles are, along with some exciting new potentials, Paul Bosland reported at the Chile Pepper Institutes 2013 New Mexico Chile Leaders Dinner earlier this month.

This puts NMSU and the , Chile Pepper Institute on the cutting edge with a new level of research, said Bosland, a New Mexico State University Regents professor and director of the Chile Pepper Institute.

It might even be argued that chiles are more sophisticated and complex than the humans who eat them.

Weve now determined that the chile pepper has approximately 3.5 billion base pairs, which are the building blocks that make up the DNA double helix, compared to tomatoes which have about 950 million (homo sapiens have about 3 billion). The Human Genome Project determined we have about 20,000 genes. Chile peppers have about 37,000 genes.

Whether that means chiles are more evolved than we are, I dont know, quipped Bosland.

The chile genome project, a cooperative effort with a leading South Korea university laboratory, could have some very serious benefits.

To complete the first-ever high-resolution draft of the chile pepper genome, the institute sent NMSU graduate student Greg Reeves to Seoul National University in South Korea last summer to work with professor Doil Choi and his Illumina sequencer.

Its a very expensive, incredibly advanced machine that only takes a few days to do the same amount of genetic processing work that previously took 600 machines 10 years to accomplish, Bosland reported.

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Chile genome project explores complexity

Human Genome Sprapp (HGS) Episode #3 - Scratching the Surface
Episode #3 in the 2013 quest to sequence my entire genome in Microsoft Excel and analyze using Pivot Tables and Charts. This episode dives into molecular mass, density, hydrogen bonds, and small sequencing patterns for the nucleobases found in DNA. For more info on the progress check out Ken #39;s Talk.com.

By: Ken Braverman

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Human Genome Sprapp (HGS) Episode #3 - Scratching the Surface - Video

Feb. 24, 2013 Scientists at the Marine Biological Laboratory (MBL) have identified several genes linked to human neurological disorders, including Alzheimer's disease, Parkinson's disease and spinal cord injury, in the sea lamprey, a vertebrate fish whose whole-genome sequence is reported this week in the journal Nature Genetics.

"This means that we can use the sea lamprey as a powerful model to drive forward our molecular understanding of human neurodegenerative disease and neurological disorders," says Jennifer Morgan of the MBL's Eugene Bell Center for Regenerative Biology and Tissue Engineering. The ultimate goals are to determine what goes wrong with neurons after injury and during disease, and to determine how to correct these deficits in order to restore normal nervous system functions.

Unlike humans, the lamprey has an extraordinary capacity to regenerate its nervous system. If a lamprey's spinal cord is severed, it can regenerate the damaged nerve cells and be swimming again in 10-12 weeks.

Morgan and her collaborators at MBL, Ona Bloom and Joseph Buxbaum, have been studying the lamprey's recovery from spinal cord injury since 2009. The lamprey has large, identified neurons in its brain and spinal cord, making it an excellent model to study regeneration at the single cell-level. Now, the lamprey's genomic information gives them a whole new "toolkit" for understanding its regenerative mechanisms, and for comparing aspects of its physiology, such as inflammation response, to that of humans.

The lamprey genome project was accomplished by a consortium of 59 researchers led by Weiming Li of Michigan State University and Jeramiah Smith of the University of Kentucky. The MBL scientists' contribution focused on neural aspects of the genome, including one of the project's most intriguing findings.

Lampreys, in contrast to humans, don't have myelin, an insulating sheath around neurons that allows faster conduction of nerve impulses. Yet the consortium found genes expressed in the lamprey that are normally expressed in myelin. In humans, myelin-associated molecules inhibit nerves from regenerating if damaged. "A lot of the focus of the spinal cord injury field is on neutralizing those inhibitory molecules," Morgan says.

"So there is an interesting conundrum," Morgan says. "What are these myelin-associated genes doing in an animal that doesn't have myelin, and yet is good at regeneration? It opens up a new and interesting set of questions, " she says. Addressing them could bring insight to why humans lost the capacity for neural regeneration long ago, and how this might be restored.

At present, Morgan and her collaborators are focused on analyzing which genes are expressed and when, after spinal cord injury and regeneration. The whole-genome sequence gives them an invaluable reference for their work.

Morgan, Bloom, and Buxbaum collaborate at the MBL through funding by the Charles Evans Foundation. Bloom is based at the Feinstein Institute for Medical Research/Hofstra North Shore-Long Island Jewish in New York. Buxbaum is from Mount Sinai School of Medicine in New York.

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Scientists find genes linked to human neurological disorders in sea lamprey genome

Protein Function on a Genome - Analysis of Molecular Networks
Understanding Protein Function on a Genome - scale through the Analysis of Molecular Networks

By: hats0fyou

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Protein Function on a Genome - Analysis of Molecular Networks - Video

Nabsyss technology could provide the positional accuracy missing from current DNA sequencing methods.

Nabsys, a DNA technology startup, showed off today its solid-state gene sequencing machine at the Advances in Genome Biology and Technology conference in Marco Island, Florida. The company says that later this year it will begin selling its machine, which will allow researchers to determine the structural organization of long stretches of DNA. This differs from most existing sequencing methods, which read DNA in short snippets that are later stitched together by software. The new system will, at first, complement existing methods, but it could eventually offer cheaper and faster sequencing than other approaches.

Understanding the overall order of DNA sequence on a chromosome is important for studying disease and treating patients, but this big picture can be difficult to get because of the short-snippet approach of most sequencing. Because these methods cannot always figure out how to arrange long repetitive sequences, they can fail to recognize missing sequences, additional sequences, or repeated sequences, all of which can lead to disease.

If you encounter these [repetitive] regions in traditional sequencing where DNA is chopped up, it is very hard to know how many times it was repeated, says Jens Gundlach, a physicist who heads the University of Washingtons Nanopore Physics Lab.

Oncology, in particular, could benefit from Nabsyss approach because the genomic changes that occur in cancer cells often include large, structural rearrangements. In a tumor, you need to characterize the mixture of [genetic variation] in your sample at different length scales, says Barrett Bready, CEO of Nabsys.

There are other technologies that can provide the kind of long-range mapping information that Nabsys promises. Opgen, for example, has developed a technique that visually measures the length of DNA in between known sequences (see A Map of the Whole Genome Tracks Outbreaks), but the optical technique cant provide the resolution that the Nabsys technology promises. Groups such as Oxford Nanopore (see Nanopore Sequencing), which introduced its technology a year ago at the same conference, and Gundlachs lab are developing nanopore technologies as another method for getting long sequences, but so far no nanopore technology has made it to the market. These systems use a biological pore as the site of DNA analysis, which limits the speed at which DNA can be read.

Nabsyss technology also passes DNA through a pore, but instead of the protein pore approach that Oxford Nanopore and others are taking, Nabsys uses a pore cut into a solid-state chip. According to the journalBiotechniques, Oxford Nanopores system can process DNA at a maximum rate of 400 bases per second. Nabsys claims its system can read up to a million nucleotides per second. Such speed could be critical in clinical settings, where fast diagnoses are needed to make treatment choices.

The Providence, Rhode Island-based company uses premade short stretches of DNA called probes that can be detected on Nabsyss chip when bound to a single molecule of DNA under study. Each probe consists of a short combination of the four DNA bases that will stick to matching sections of the larger DNA under study. The Nabsys technology detects where a probe is bound by watching an electric current change as the DNA complex snakes through a pore on the solid-state chip. Thousands of probes of different combinations of letters would be needed to map the whole genome. But by combining the position of many probes of different DNA sequences, the company can re-create a map of long stretches of DNA.

The Nabsys technology isnt a DNA reader per se, says Gundlach. Its a more complex process to look for certain regions on a piece of DNA, he says, that is complementary to the existing sequencing techniques and helps them in providing contiguity.

The company will initially focus on being a complementary technology to existing next-generation sequencers, but its technology can provide full-sequence information if more probes are used to analyze a sample.

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Solid-State Sequencer Debuts at Genome Conference

Feb. 20, 2013 A study combining genetic data with brain imaging, designed to identify genes associated with the amyloid plaque deposits found in Alzheimer's disease patients, has not only identified the APOE gene -- long associated with development of Alzheimer's -- but has uncovered an association with a second gene, called BCHE.

A national research team, led by scientists at the Indiana University School of Medicine, reported the results of the study in an article in Molecular Psychiatry posted online February 19. The study is believed to be the first genome-wide association study of plaque deposits using a specialized PET scan tracer that binds to amyloid.

The research also is believed to be the first to implicate variations in the BCHE gene in plaque deposits visualized in living individuals who have been diagnosed with Alzheimer's disease or are at-risk for developing the disease. The enzyme coded by the BCHE gene has previously been studied in post-mortem brain tissue and is known to be found in plaques.

"The findings could recharge research efforts studying the molecular pathways contributing to amyloid deposits in the brain as Alzheimer's disease develops and affects learning and memory," said Vijay K. Ramanan, the paper's first author and an M.D./Ph.D. student at the IU School of Medicine.

The BCHE gene finding "brings together two of the major hypotheses about the development of Alzheimer's disease," said Andrew J. Saykin, Psy.D., Raymond C. Beeler Professor of Radiology and Imaging Sciences at IU and principal investigator for the genetics core of the Alzheimer's Disease Neuroimaging Initiative.

Scientists have long pointed to the loss of an important brain neurotransmitter, acetylcholine, which is depleted early in the development of the disease, as a key aspect of the loss of memory related neurons. The BCHE gene is responsible for an enzyme that breaks down acetylcholine in the brain. The other major Alzheimer's hypothesis holds that the development of the amyloid plaques is the primary cause of the disease's debilitating symptoms. As it turns out, the enzyme for which the BCHE gene codes is also found in significant quantities in those plaques.

"This study is connecting two of the biggest Alzheimer's dots," said Dr. Saykin, director of the Indiana Alzheimer Disease Center and the IU Center for Neuroimaging at the IU Health Neuroscience Center.

"The finding that BCHE gene variant predicts the extent of plaque deposit in PET scans among people at risk for Alzheimer's disease is likely to reinvigorate research into drugs that could modify the disease by affecting the BCHE enzyme or its metabolic pathway," he said. Some existing drugs inhibit this enzyme, but it is unclear whether this influences plaque deposits.

Overall, the results appear to offer scientists new potential targets for drugs to slow, reverse or even prevent the disease. Alzheimer's disease affects an estimated 5.4 million Americans and has proven resistant to treatments that do more than temporarily slow the worsening of symptoms.

Amyloid plaque deposits build up abnormally in the brains of Alzheimer's patients and are believed to play an important role in the memory loss and other problems that plague patients.

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Genome-wide imaging study identifies new gene associated with Alzheimer's plaques