Tuesday, July 3, 2012

Oh, baby! A young star flaunts its X-ray spots in McNeil's Nebula

Oh, baby! A young star flaunts its X-ray spots in McNeil's Nebula [ Back to EurekAlert! ] Public release date: 3-Jul-2012
[ | E-mail | Share Share ]

Contact: Susan Gawlowicz
smguns@rit.edu
585-475-5061
Rochester Institute of Technology

RIT astronomers on team announcing the rapidly spinning protostar

X-ray observations have revealed something curious about the young star that illuminates McNeil's Nebula, a glowing jewel of cosmic dust in the Orion constellation: The object is a protostar rotating once a day, or 30 times faster than the sun. The stellar baby also has distinct birthmarkstwo X-ray-emitting spots, where gas flows from a surrounding disk, fueling the infant star.

The young star, V1647 Orionis, first made news in early 2004, when it erupted and lit up McNeil's Nebula, located 1,300 light years away in a region of active star formation within the constellation of Orion. The initial outburst died down in early 2006, but then V1647 Ori erupted again in 2008, and has since remained bright.

More recently, astronomers combined 11 observations of V1647 Ori from NASA's Chandra X-ray Observatory, the Japan-led Suzaku satellite, and the European Space Agency's XMM-Newton to determine the source of the high-energy emission. The team began monitoring the star shortly after its eruption in 2004 and continued to keep watch through 2010, a period covering both eruptions.

Strong similarities among X-ray light curves captured over this six-year period allowed the lead author on the study, Kenji Hamaguchi, astrophysicist at NASA's Goddard Space Flight Center, to identify cyclic X-ray variations. Hamaguchi and the rest of the team determined the star is rotating once per day, making V1647 among the youngest stars whose spin has been determined using an X-ray-based technique. Results from the study will appear in the paper "X-raying the Beating Heart of a Newborn Star: Rotational Modulation of High-energy Radiation from V1647 Ori," in the July 20 issue of The Astrophysical Journal.

"The observations give us a look inside the cradle at a very young star," says co-author Joel Kastner, a professor of imaging science and astronomical sciences and technology at Rochester Institute of Technology. "It's as though we're able to see its beating heart. We're actually able to watch it rotate. We caught the star at a point where it is rotating so fast as it gains material that it's barely able to hold itself together. It's rotating at near break-up speed."

The team identified V1647 Ori as a protostar in formation. "Based on infrared studies, we suspect that this protostar is no more than a million years old, and probably much younger," Hamaguchi says.

V1647 Ori presently feeds on gas channeled from a surrounding disk and will likely continue to do sothough not nearly so rapidlyfor millions of years. At that point it will finally be able to generate its own energy by fusing hydrogen into helium in its core like the sun and other mature stars.

Hamaguchi's analysis focused on repetitive behavior found in the data from all three of the X-ray observatories. By combining data, he pieced together a picture showing the daily rotation of two X-ray-emitting spots on V1647 Ori that are thousands of times hotter than the rest of the star.

The hot spots are located at opposite sides of the star, with the southerly one five times brighter than its companion. Each spot is about the diameter of the sun. In comparison, the low density of V1647 Ori bloats the star itself to nearly five times the size of the sun.

"We think these spots are showing us X-ray-emitting regions that are very tightly constrained to a couple positions on the star by magnetic fields," says Kastner, director of the Laboratory for Multiwavelength Astrophysics in RIT's Chester F. Carlson Center for Imaging Science. "For six years, through two different eruptions, we've seen it rotate like this. That means the magnetic field configurationthe overall geometry between the disk and the staris very stable. At the same time, the local disruption of magnetic fields probably generates the X-rays."

"One attractive possibility for driving such high-speed matter involves magnetic fields that are undergoing a continual cycle of shearing and reconnection in mass accretion," says co-author David Weintraub, professor of astronomy at Vanderbilt University.

In this picture, X-ray outbursts result from interplay of the magnetic fields belonging to the star and the disk. The star spins faster than the disk and winds up the magnetic fields until they snap like rubber bands. The pent up energy creates a powerful blast when the tangled magnetic fields fall back into place. The process, called magnetic reconnection, also powers X-ray flares on the sun.

During the outbursts, the star's luminosity varied at optical and infrared wavelengths. The astronomers associated this to changes in the protostar's main energy source, the inflow of matter onto the star. Because changes in the X-ray brightness of V1647 Ori closely followed those in the optical and infrared, the team established that its higher-energy emission is also closely linked to accretion.

"V1647 Ori gave us the first direct evidence that a protostar surges in X-ray activity as its rate of mass accretion rises," says co-author Nicolas Grosso, an astrophysicist of the French National Center for Scientific Research at the Strasbourg Astronomical Observatory.

The finding that an accretion burst could be accompanied a surge of high-energy X-rays during the formation of a young star was originally announced by essentially the same study team, led by Kastner, in a paper published in Nature in 2004. In that paper, the team first argued that X-rays emitted by V1647 Ori were coming from material falling onto the star from a surrounding disk.

Up until then, the more widely accepted mechanism for producing X-rays from protostars was thought to be via coronae that are far more powerful than the sun's, Kastner explains. Signatures in X-ray observations of a handful of stars in formative stages had led to the hunch that accretion might also contribute to or even dominate protostellar X-ray emission. The eruptions of V1647 Ori and a few other young stars that were accompanied by elevated X-ray emission levels have since underscored this connection, Kastner notes.

"The exciting and unexpected thing about our fresh look at the whole set of X-ray data for V1647 Ori is that this is the first time we've seen a star in such an early stage of formation with a regular rotation that you can measure in X-rays," Kastner says.

Kastner and team hope to confirm the X-ray study's findings at infrared wavelengths using NASA's Spitzer Space Telescope.

###

Additional co-authors on the study include Michael Richmond, professor of physics at RIT; David Principe, a doctoral candidate in RIT's Astrophysical Sciences and Technology program; and William Teets, a recent doctoral recipient in physics and astronomy from Vanderbilt University.


[ Back to EurekAlert! ] [ | E-mail | Share Share ]

?


AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.


Oh, baby! A young star flaunts its X-ray spots in McNeil's Nebula [ Back to EurekAlert! ] Public release date: 3-Jul-2012
[ | E-mail | Share Share ]

Contact: Susan Gawlowicz
smguns@rit.edu
585-475-5061
Rochester Institute of Technology

RIT astronomers on team announcing the rapidly spinning protostar

X-ray observations have revealed something curious about the young star that illuminates McNeil's Nebula, a glowing jewel of cosmic dust in the Orion constellation: The object is a protostar rotating once a day, or 30 times faster than the sun. The stellar baby also has distinct birthmarkstwo X-ray-emitting spots, where gas flows from a surrounding disk, fueling the infant star.

The young star, V1647 Orionis, first made news in early 2004, when it erupted and lit up McNeil's Nebula, located 1,300 light years away in a region of active star formation within the constellation of Orion. The initial outburst died down in early 2006, but then V1647 Ori erupted again in 2008, and has since remained bright.

More recently, astronomers combined 11 observations of V1647 Ori from NASA's Chandra X-ray Observatory, the Japan-led Suzaku satellite, and the European Space Agency's XMM-Newton to determine the source of the high-energy emission. The team began monitoring the star shortly after its eruption in 2004 and continued to keep watch through 2010, a period covering both eruptions.

Strong similarities among X-ray light curves captured over this six-year period allowed the lead author on the study, Kenji Hamaguchi, astrophysicist at NASA's Goddard Space Flight Center, to identify cyclic X-ray variations. Hamaguchi and the rest of the team determined the star is rotating once per day, making V1647 among the youngest stars whose spin has been determined using an X-ray-based technique. Results from the study will appear in the paper "X-raying the Beating Heart of a Newborn Star: Rotational Modulation of High-energy Radiation from V1647 Ori," in the July 20 issue of The Astrophysical Journal.

"The observations give us a look inside the cradle at a very young star," says co-author Joel Kastner, a professor of imaging science and astronomical sciences and technology at Rochester Institute of Technology. "It's as though we're able to see its beating heart. We're actually able to watch it rotate. We caught the star at a point where it is rotating so fast as it gains material that it's barely able to hold itself together. It's rotating at near break-up speed."

The team identified V1647 Ori as a protostar in formation. "Based on infrared studies, we suspect that this protostar is no more than a million years old, and probably much younger," Hamaguchi says.

V1647 Ori presently feeds on gas channeled from a surrounding disk and will likely continue to do sothough not nearly so rapidlyfor millions of years. At that point it will finally be able to generate its own energy by fusing hydrogen into helium in its core like the sun and other mature stars.

Hamaguchi's analysis focused on repetitive behavior found in the data from all three of the X-ray observatories. By combining data, he pieced together a picture showing the daily rotation of two X-ray-emitting spots on V1647 Ori that are thousands of times hotter than the rest of the star.

The hot spots are located at opposite sides of the star, with the southerly one five times brighter than its companion. Each spot is about the diameter of the sun. In comparison, the low density of V1647 Ori bloats the star itself to nearly five times the size of the sun.

"We think these spots are showing us X-ray-emitting regions that are very tightly constrained to a couple positions on the star by magnetic fields," says Kastner, director of the Laboratory for Multiwavelength Astrophysics in RIT's Chester F. Carlson Center for Imaging Science. "For six years, through two different eruptions, we've seen it rotate like this. That means the magnetic field configurationthe overall geometry between the disk and the staris very stable. At the same time, the local disruption of magnetic fields probably generates the X-rays."

"One attractive possibility for driving such high-speed matter involves magnetic fields that are undergoing a continual cycle of shearing and reconnection in mass accretion," says co-author David Weintraub, professor of astronomy at Vanderbilt University.

In this picture, X-ray outbursts result from interplay of the magnetic fields belonging to the star and the disk. The star spins faster than the disk and winds up the magnetic fields until they snap like rubber bands. The pent up energy creates a powerful blast when the tangled magnetic fields fall back into place. The process, called magnetic reconnection, also powers X-ray flares on the sun.

During the outbursts, the star's luminosity varied at optical and infrared wavelengths. The astronomers associated this to changes in the protostar's main energy source, the inflow of matter onto the star. Because changes in the X-ray brightness of V1647 Ori closely followed those in the optical and infrared, the team established that its higher-energy emission is also closely linked to accretion.

"V1647 Ori gave us the first direct evidence that a protostar surges in X-ray activity as its rate of mass accretion rises," says co-author Nicolas Grosso, an astrophysicist of the French National Center for Scientific Research at the Strasbourg Astronomical Observatory.

The finding that an accretion burst could be accompanied a surge of high-energy X-rays during the formation of a young star was originally announced by essentially the same study team, led by Kastner, in a paper published in Nature in 2004. In that paper, the team first argued that X-rays emitted by V1647 Ori were coming from material falling onto the star from a surrounding disk.

Up until then, the more widely accepted mechanism for producing X-rays from protostars was thought to be via coronae that are far more powerful than the sun's, Kastner explains. Signatures in X-ray observations of a handful of stars in formative stages had led to the hunch that accretion might also contribute to or even dominate protostellar X-ray emission. The eruptions of V1647 Ori and a few other young stars that were accompanied by elevated X-ray emission levels have since underscored this connection, Kastner notes.

"The exciting and unexpected thing about our fresh look at the whole set of X-ray data for V1647 Ori is that this is the first time we've seen a star in such an early stage of formation with a regular rotation that you can measure in X-rays," Kastner says.

Kastner and team hope to confirm the X-ray study's findings at infrared wavelengths using NASA's Spitzer Space Telescope.

###

Additional co-authors on the study include Michael Richmond, professor of physics at RIT; David Principe, a doctoral candidate in RIT's Astrophysical Sciences and Technology program; and William Teets, a recent doctoral recipient in physics and astronomy from Vanderbilt University.


[ Back to EurekAlert! ] [ | E-mail | Share Share ]

?


AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.


Source: http://www.eurekalert.org/pub_releases/2012-07/riot-oba070312.php

drop dead gorgeous ticket city bowl 2011 nfl playoff schedule cowboys vs giants ndaa timberwolves weight watchers

Monday, July 2, 2012

Feds propose $3.7M penalty for Mich. oil spill

FILE- In this July 29, 2010, file photo, a worker monitors water in Talmadge Creek in Marshall Township, Mich., near the Kalamazoo River as oil from a ruptured pipeline, owned by Enbridge Inc., is attempted to be trapped by booms. On Monday, July 2, 2012, federal regulators proposed a $3.7 million civil penalty against the Canadian owner of the ruptured pipeline which dumped more than 800 million gallons of oil into the river. (AP Photo/Paul Sancya, File)

FILE- In this July 29, 2010, file photo, a worker monitors water in Talmadge Creek in Marshall Township, Mich., near the Kalamazoo River as oil from a ruptured pipeline, owned by Enbridge Inc., is attempted to be trapped by booms. On Monday, July 2, 2012, federal regulators proposed a $3.7 million civil penalty against the Canadian owner of the ruptured pipeline which dumped more than 800 million gallons of oil into the river. (AP Photo/Paul Sancya, File)

(AP) ? Federal regulators proposed a $3.7 million civil penalty Monday against the Canadian owner of a pipeline that ruptured in 2010, dumping more than 800,000 gallons of oil into a southwestern Michigan river.

The U.S. Department of Transportation's Pipeline and Hazardous Materials Safety Administration said the penalty against Enbridge Inc. would be the largest it has imposed. In a letter to the company, the agency listed 24 violations of hazardous liquid pipeline regulations, including failure to fix corrosion problems in the damaged pipe joint discovered as far back as 2004.

It also said the company had failed to detect the rupture for 17 hours after it happened during a scheduled shutdown July 25, 2010. Instead, Enbridge personnel twice restarted the line despite receiving multiple alarms and "indications of abnormal operating conditions" in its control center.

More than 680,000 gallons of crude was injected into the pipe during that period, "causing the total spill volume to greatly exceed Enbridge's worst case discharge scenario for this location," said the letter signed by David Barrett, director of PHMSA's central region office. The oil leaked into the Kalamazoo River and a tributary creek.

"We will hold pipeline operators accountable if they do not follow proper safety procedures to protect the environment and local communities," U.S. Transportation Secretary Ray LaHood said.

Enbridge, based in Calgary, Alberta, has 30 days to respond. It could accept the agency's findings and pay the penalty or request a hearing before an administrative judge.

The company said it was cooperating with investigators and would not provide detailed comment until analyzing the agency's letter.

"Enbridge appreciates the hard work and due diligence that PHMSA has put into this investigation," said Stephen Wuori, president for liquid pipelines. He said the company had improved its control center operations and training since the Michigan spill.

The National Transportation Safety Board is expected to issue a report next week on what caused the rupture in the 30-inch pipeline extending from Griffith, Ind., to Sarnia, Ontario.

Barrett's letter said the break happened on the day Enbridge was conducting the latest in a series of inspections, using a tool that was left inside the line until after it was restarted more than two months later.

Enbridge's control center in Edmonton, Alberta, was undertaking what was supposed to be a 10-hour shutdown of the pipe when the failure occurred around 6 p.m. EDT, setting off alarms, Barrett's letter said. Instead of implementing procedures for dealing with emergencies and suspected leaks, operators left the line idle.

Around 4 a.m. on July 26, 2010, a different crew restarted the line and soon received alarms and troubling messages: Pressure at the Marshall pumping station wasn't rising as expected and there was a significant imbalance between the volume of oil being pumped into the line and the volume it was delivering.

Still, personnel took no emergency actions and kept the oil flowing for an hour, sending more than 439,000 gallons of heavy crude into the pipe. After evaluating the situation they again started the line. Despite receiving more alarms, they injected nearly 243,000 additional gallons over a half-hour before shutting it down again.

"By this time the prospects of a suspected leak had been openly discussed by various ... personnel, yet the Enbridge procedures for a suspected leak were not executed," Barrett said.

At 11:18 a.m., nearly 17 hours after the failure, a natural gas worker with Consumers Energy notified Enbridge that oil had been spotted in a creek near Marshall. Only then did the control center close remotely operated valves, isolating a 3-mile-long stretch of line that including the rupture.

Outlining specific regulatory violations, Barrett said Enbridge inspections in 2004 had turned up corrosion problems along the weld seam of the pipe joint that eventually would fail. In 2005, "crack-like anomalies" were found on the same joint. No repairs were made. The agency assessed the largest portion of the penalty ? $1 million ? for that alleged failure.

Most of the other violations drew $100,000 penalties.

Despite the largest fine ever levied by PHMSA, the $3.7 million total is much less than what companies have paid out for other large spills. Officials have yet to determine the fine against BP PLC for Clean Water Act violations from the Gulf of Mexico spill, but they could range from $5.4 billion to $21.1 billion.

Anthony Swift, attorney for the Natural Resources Defense Council, said the pipeline agency lacks authority to impose meaningful punishment.

"With projects this big, a fine of less than $4 million becomes a minimal cost of doing business rather than a real motivator to follow safety standards," Swift said.

Enbridge has estimated it cleanup costs at about $700 million.

Associated Press

Source: http://hosted2.ap.org/APDEFAULT/f70471f764144b2fab526d39972d37b3/Article_2012-07-02-Michigan%20Oil%20Spill/id-7fcab10f2abb4019a0c64ad6a40468d8

front door alyssa bustamante protandim weightless ellen degeneres jcpenney yeardley love nba all star reserves

Freedom, the Cure For Poverty (Powerlineblog)

Share With Friends: Share on FacebookTweet ThisPost to Google-BuzzSend on GmailPost to Linked-InSubscribe to This Feed | Rss To Twitter | Politics - Top Stories News, RSS Feeds and Widgets via Feedzilla.

Source: http://news.feedzilla.com/en_us/stories/politics/top-stories/236686494?client_source=feed&format=rss

meet the press steelers vs broncos chris herren jay z patsy cline pierre thomas beyonce gives birth

Genes may play role in educational achievement

ScienceDaily (July 2, 2012) ? Researchers have identified genetic markers that may influence whether a person finishes high school and goes on to college, according to a national longitudinal study of thousands of young Americans.

The study is in the July issue of Developmental Psychology, a publication of the American Psychological Association.

"Being able to show that specific genes are related in any way to academic achievement is a big step forward in understanding the developmental pathways among young people," said the study's lead author, Kevin Beaver, PhD, a professor at the College of Criminology and Criminal Justice at Florida State University.

The three genes identified in the study -- DAT1, DRD2 and DRD4 -- have been linked to behaviors such as attention regulation, motivation, violence, cognitive skills and intelligence, according to the study. Previous research has explored the genetic underpinnings of intelligence but virtually none has examined genes that potentially contribute to educational attainment in community samples, said Beaver.

He and his colleagues analyzed data from the National Longitudinal Study of Adolescent Health, also known as Add Health. Add Health is a four-wave study of a nationally representative sample of American youths who were enrolled in middle or high school in 1994 and 1995. The study continued until 2008, when most of the respondents were between the ages of 24 and 32. The participants completed surveys, provided DNA samples and were interviewed, along with their parents. The sample used for this analysis consisted of 1,674 respondents.

The genes identified in this research are known as dopamine transporter and receptor genes. Every person has the genes DAT1, DRD2 and DRD4, but what is of interest are molecular differences within the genes, known as alleles, according to Beaver. Subjects who possessed certain alleles within these genes achieved the highest levels of education, according to the findings.

Dopamine transporter genes assist in the production of proteins that regulate levels of the neurotransmitter dopamine in the brain, while dopamine receptor genes are involved in neurotransmission. Previous research has shown that dopamine levels play a role in regulating impulsive behavior, attention and intelligence.

The presence of the alleles alone did not guarantee higher levels of education, the study found. Having a lower IQ was more strongly associated with lower levels of education. Also, living in poverty and essentially "running with a bad crowd" resulted in lower levels of education despite the genetic effects.

Even though the genetic variants were found to be associated with educational levels, having a specific allele does not determine whether someone will graduate from high school or earn a college degree, according to Beaver. Rather, these genes work in a probabilistic way, with the presence of certain alleles simply increasing or decreasing the likelihood of educational outcomes, he said. "No one gene is going to say, 'Sally will graduate from high school' or 'Johnny will earn a college degree,'" he said. "These genetic effects operate indirectly, through memory, violent tendencies and impulsivity, which are all known predictors of how well a kid will succeed in school. If we can keep moving forward and identify more genetic markers for educational achievement, we can begin to truly understand how genetics play a role in how we live and succeed in life."

Share this story on Facebook, Twitter, and Google:

Other social bookmarking and sharing tools:


Story Source:

The above story is reprinted from materials provided by American Psychological Association (APA).

Note: Materials may be edited for content and length. For further information, please contact the source cited above.


Journal Reference:

  1. Kevin M. Beaver, John Paul Wright, Matt DeLisi, Michael G. Vaughn. Dopaminergic polymorphisms and educational achievement: Results from a longitudinal sample of americans.. Developmental Psychology, 2011; DOI: 10.1037/a0026313

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

Source: http://www.sciencedaily.com/releases/2012/07/120702172737.htm

lra eric johnson eric johnson big east tournament ashley olsen new apple tv sun flare

An error-eliminating fix overcomes big problem in '3rd-gen' genome sequencing

An error-eliminating fix overcomes big problem in '3rd-gen' genome sequencing [ Back to EurekAlert! ] Public release date: 1-Jul-2012
[ | E-mail | Share Share ]

Contact: Peter Tarr
tarr@cshl.edu
917-435-5068
Cold Spring Harbor Laboratory

Hybrid error-correction approach boosts accuracy of 'long reads' to 99.9 percent

Cold Spring Harbor, NY The next "next-gen" technology in genome sequencing has gotten a major boost.

A quantitative biologist at Cold Spring Harbor Laboratory (CSHL) and collaborators today published results of experiments that demonstrate the power of so-called single-molecule sequencing, which was recently introduced but whose use has so far been limited by technical issues.

The team, led by CSHL Assistant Professor Michael Schatz and Adam Phillippy and Sergey Koren of the National Biodefense Analysis and Countermeasures Center and the University of Maryland (UMD), has developed a software package that corrects a serious problem inherent in the new sequencing technology: the fact that every fifth or sixth DNA "letter" it generates is incorrect. The high error rate is the flip side of the new method's chief virtue: it generates much longer genome "reads" than other technologies currently used, up to 100 times longer, and thus can provide a much more complete picture of genome structure than can be obtained with current, "2nd-gen" sequencing technology.

Using mathematical algorithms, Schatz and the team have preserved the great advantage of the "3rd-gen" method while all but eliminating its chief flaw. They have reduced the error rate from about 15% or greater to less than one-tenth of one percent. This mathematical "fix" which has been published in open-source code to the World Wide Web greatly increases the practical utility of 3rd-gen sequencing for the entire biomedical research community.

The team demonstrates the breadth of potential applications of single-molecule sequencing by applying their fix to sequencing tasks ranging from the tiny bacteriophage virus at one end of the difficulty scale to the large and vastly more complex genome of the parrot, at the other. The parrot genome is more than a third the size of the human genome and is published online today with the team's paper in Nature Biotechnology. The parrot sequence is "far superior to that of any previously sequenced bird genome," Schatz says.

To understand why it is better is to appreciate the advantages of 3rd-gen sequencing. The main advantage has to do with the average length of each "read" (i.e., genome segments read by a sequencer). The individual sequences are assembled into "contigs" -- shorthand for contiguous sequences -- much the way pieces in a jigsaw puzzle are assembled. In currently used 2nd-gen technology, the contigs are very small, and are massively redundant. A "consensus" version of each segment, representing the results of many layered reads, tends to be extremely accurate. But the small size of puzzle pieces prevents accurate assembly of certain genome portions, like those containing long repetitive sequences.

Obtaining superior versions of complete genomes was the objective that motivated Schatz and his collaborators, who also include HHMI Investigator Erich D. Jarvis of Duke University and CSHL Professor W. Richard McCombie, a sequencing pioneer, among others.

Combining the best of both generations

With single-molecule sequencing, the assembled contigs are much longer affording a much better picture of relatively larger genome segments, including those occupied by lengthy repeats. This is what Schatz and his team wanted to preserve, while at the same time boosting the error-free rate. They did so by effectively taking the best of both 2nd- and 3rd-gen technologies.

"We call our approach 'hybrid error correction,'" Schatz explains.

The team's major insight was to take advantage of the long-read data offered by a 3rd-gen machine like that used in their experiments, a Pacific Biosciences RS sequencer, and mixing in highly accurate short reads obtained from a separate 2nd-gen sequencer. The two data types were run through an open-source genome assembly program called Celera Assembler to generate a clean final assembly that has proven 99.9% error-free and composed of contigs whose median size is at least double that obtainable with 2nd-gen "short-read" sequencers. Contig sizes are expected to increase appreciably in subsequent iterations of the hybrid approach as single molecule long-read sequencing improves.

High-quality genome assemblies are especially important for genome annotation and comparative genome analyses. Many microbial genome analyses depend on finished genomes, but their cost is prohibitive using older technologies. High-quality analysis of the genomes of higher organisms depends upon continuous sequences that capture long stretches of DNA that spell out genes. Discoveries in recent years of spontaneously occurring structural changes in genomes called copy number variations -- such as those made by CSHL Professor Mike Wigler and his team in their research on schizophrenia and autism make clear the importance of being able to obtain clean and accurate pictures of the entire genomes of affected individuals.

With hybrid error correction, Schatz and his colleagues have "demonstrated that high error rates associated with long reads need not be a barrier to genome assembly," he summarizes. "High-error long reads can be efficiently assembled in combination with complementary short reads to produce assemblies not previously possible."

###

"Hybrid error correction and de novo assembly of single-molecule sequencing reads" appears online in Nature Biotechnology July 1, 2012. The authors are: Sergey Koren, Michael C. Schatz, Brian P. Walenz, Jeffrey Martin, Jason Howard, Ganeshkumar Ganapathy, Zhong Wang, David A. Rasko, W. Richard McCombie, Erich D. Davis and Adam M. Phillippy. the paper can be obtained online using doi: xxxxxxxxxxxxxxxx.

About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory (CSHL) has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. CSHL is ranked number one in the world by Thomson Reuters for impact of its research in molecular biology and genetics. The Laboratory has been home to eight Nobel Prize winners. Today, CSHL's multidisciplinary scientific community is more than 360 scientists strong and its Meetings & Courses program hosts more than 12,500 scientists from around the world each year to its Long Island campus and its China center. Tens of thousands more benefit from the research, reviews, and ideas published in journals and books distributed internationally by CSHL Press. The Laboratory's education arm also includes a graduate school and programs for undergraduates as well as middle and high school students and teachers. CSHL is a private, not-for-profit institution on the north shore of Long Island. For more information, visit www.cshl.edu.


[ Back to EurekAlert! ] [ | E-mail | Share Share ]

?


AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.


An error-eliminating fix overcomes big problem in '3rd-gen' genome sequencing [ Back to EurekAlert! ] Public release date: 1-Jul-2012
[ | E-mail | Share Share ]

Contact: Peter Tarr
tarr@cshl.edu
917-435-5068
Cold Spring Harbor Laboratory

Hybrid error-correction approach boosts accuracy of 'long reads' to 99.9 percent

Cold Spring Harbor, NY The next "next-gen" technology in genome sequencing has gotten a major boost.

A quantitative biologist at Cold Spring Harbor Laboratory (CSHL) and collaborators today published results of experiments that demonstrate the power of so-called single-molecule sequencing, which was recently introduced but whose use has so far been limited by technical issues.

The team, led by CSHL Assistant Professor Michael Schatz and Adam Phillippy and Sergey Koren of the National Biodefense Analysis and Countermeasures Center and the University of Maryland (UMD), has developed a software package that corrects a serious problem inherent in the new sequencing technology: the fact that every fifth or sixth DNA "letter" it generates is incorrect. The high error rate is the flip side of the new method's chief virtue: it generates much longer genome "reads" than other technologies currently used, up to 100 times longer, and thus can provide a much more complete picture of genome structure than can be obtained with current, "2nd-gen" sequencing technology.

Using mathematical algorithms, Schatz and the team have preserved the great advantage of the "3rd-gen" method while all but eliminating its chief flaw. They have reduced the error rate from about 15% or greater to less than one-tenth of one percent. This mathematical "fix" which has been published in open-source code to the World Wide Web greatly increases the practical utility of 3rd-gen sequencing for the entire biomedical research community.

The team demonstrates the breadth of potential applications of single-molecule sequencing by applying their fix to sequencing tasks ranging from the tiny bacteriophage virus at one end of the difficulty scale to the large and vastly more complex genome of the parrot, at the other. The parrot genome is more than a third the size of the human genome and is published online today with the team's paper in Nature Biotechnology. The parrot sequence is "far superior to that of any previously sequenced bird genome," Schatz says.

To understand why it is better is to appreciate the advantages of 3rd-gen sequencing. The main advantage has to do with the average length of each "read" (i.e., genome segments read by a sequencer). The individual sequences are assembled into "contigs" -- shorthand for contiguous sequences -- much the way pieces in a jigsaw puzzle are assembled. In currently used 2nd-gen technology, the contigs are very small, and are massively redundant. A "consensus" version of each segment, representing the results of many layered reads, tends to be extremely accurate. But the small size of puzzle pieces prevents accurate assembly of certain genome portions, like those containing long repetitive sequences.

Obtaining superior versions of complete genomes was the objective that motivated Schatz and his collaborators, who also include HHMI Investigator Erich D. Jarvis of Duke University and CSHL Professor W. Richard McCombie, a sequencing pioneer, among others.

Combining the best of both generations

With single-molecule sequencing, the assembled contigs are much longer affording a much better picture of relatively larger genome segments, including those occupied by lengthy repeats. This is what Schatz and his team wanted to preserve, while at the same time boosting the error-free rate. They did so by effectively taking the best of both 2nd- and 3rd-gen technologies.

"We call our approach 'hybrid error correction,'" Schatz explains.

The team's major insight was to take advantage of the long-read data offered by a 3rd-gen machine like that used in their experiments, a Pacific Biosciences RS sequencer, and mixing in highly accurate short reads obtained from a separate 2nd-gen sequencer. The two data types were run through an open-source genome assembly program called Celera Assembler to generate a clean final assembly that has proven 99.9% error-free and composed of contigs whose median size is at least double that obtainable with 2nd-gen "short-read" sequencers. Contig sizes are expected to increase appreciably in subsequent iterations of the hybrid approach as single molecule long-read sequencing improves.

High-quality genome assemblies are especially important for genome annotation and comparative genome analyses. Many microbial genome analyses depend on finished genomes, but their cost is prohibitive using older technologies. High-quality analysis of the genomes of higher organisms depends upon continuous sequences that capture long stretches of DNA that spell out genes. Discoveries in recent years of spontaneously occurring structural changes in genomes called copy number variations -- such as those made by CSHL Professor Mike Wigler and his team in their research on schizophrenia and autism make clear the importance of being able to obtain clean and accurate pictures of the entire genomes of affected individuals.

With hybrid error correction, Schatz and his colleagues have "demonstrated that high error rates associated with long reads need not be a barrier to genome assembly," he summarizes. "High-error long reads can be efficiently assembled in combination with complementary short reads to produce assemblies not previously possible."

###

"Hybrid error correction and de novo assembly of single-molecule sequencing reads" appears online in Nature Biotechnology July 1, 2012. The authors are: Sergey Koren, Michael C. Schatz, Brian P. Walenz, Jeffrey Martin, Jason Howard, Ganeshkumar Ganapathy, Zhong Wang, David A. Rasko, W. Richard McCombie, Erich D. Davis and Adam M. Phillippy. the paper can be obtained online using doi: xxxxxxxxxxxxxxxx.

About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory (CSHL) has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. CSHL is ranked number one in the world by Thomson Reuters for impact of its research in molecular biology and genetics. The Laboratory has been home to eight Nobel Prize winners. Today, CSHL's multidisciplinary scientific community is more than 360 scientists strong and its Meetings & Courses program hosts more than 12,500 scientists from around the world each year to its Long Island campus and its China center. Tens of thousands more benefit from the research, reviews, and ideas published in journals and books distributed internationally by CSHL Press. The Laboratory's education arm also includes a graduate school and programs for undergraduates as well as middle and high school students and teachers. CSHL is a private, not-for-profit institution on the north shore of Long Island. For more information, visit www.cshl.edu.


[ Back to EurekAlert! ] [ | E-mail | Share Share ]

?


AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert! system.


Source: http://www.eurekalert.org/pub_releases/2012-07/cshl-aef062812.php

jim yong kim michael bush the host trailer whitney houston cause of death marquette university marquette hilary duff

Saturday, May 5, 2012

Friday, May 4, 2012

53-year-old knocks out opponent half his age

Let's hear it for the old guys! 53-year-old Tim Karaker showed up at Fire Extreme in Bourbonnais, Ill. last week and was asked to fight. He said yes, and knocked out 21-year-old Brandon Frey. Watch his MMA debut here, and skip to the 2:30 mark for the KO. UFC fighter Stephan Bonnar narrates and lets a few NSFW words slip.

Apparently, the medical personnel who is supposed to be at that fight were out for a walk, because they weren't too quick in responding to Frey on the ground. Nonetheless, congratulations to Karaker. You're now the hero of Bonnar as well as every man over the age of 50 who wanted to throw some leather at a youngun but couldn't actually get in a cage with him.

--

Follow Cagewriter on Twitter and Facebook.

bcs standings bcs standings douglas fir jim boeheim jim boeheim bill of rights toys r us