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Director?and actor Ron Howard, who was just 5 when he first played Sheriff Andy Taylor's son, Opie, on "The Andy Griffith Show," talked to msnbc's Andrea Mitchell Tuesday about Griffith's death.
Howard, who went on to play Richie Cunningham on "Happy Days" and then to an acclaimed directorial career in the movies, said that Griffith "created an environment on that set that was very creative, very playful, but extremely disciplined."
Griffith's character evolved from a broader country-bumpkin type into a more nuanced man as the show progressed, Howard told Mitchell.
"The character became a much greater reflection of Andy," he said, noting that as a child actor he was allowed to witness discussions of which jokes were appropriate for the characters and which jokes "were perhaps undercutting the integrity of the characters."
Howard said that on his own films he tries to create a comfortable setting where actors and crew can feel confident and?do their best possible work, and says, "Without getting up and making speeches, I try to create that environment, as Andy did."
The actor and director also said he hopes fans will remember?the star's?entire body of work, including not just "The Andy Griffith Show," but 1980s legal drama "Matlock," the 1957 movie "A Face in the Crowd," and his music, for which Griffith won a Grammy.
"There's a reason that he's so impactful in so many different?mediums and styles," Howard told Mitchell. "And that's because he cared about what he was doing."
Share your memories of Andy Griffith's many roles on Facebook.
The Lotka-Volterra equations describe population dynamics between competing species. Criminologists have now shown they also describe gang turf boundary formation and violence hot spots. Evelyn Lamb reports.
July 2, 2012
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The same mathematical models used to study the hunting range of lions have many other applications?they describe the flight patterns of honeybees. And now researchers say these math models can help explain the stability of gang territories and patterns of between-gang violence. The work is in the journal Criminology. [Jeffrey Brantingham et al, The Ecology of Gang Territorial Boundaries]
Researchers used the models to draw new maps of gang territories in east LA. What are known as the competitive Lotka-Volterra equations describe population dynamics between species competing for resources. They take into account the effect each population has on the other.
The researchers generated maps of gang territories using the Lotka-Volterra equations rather than police reports or urban geographical features. After creating maps, researchers analyzed data about between-gang shootings and found that violence clusters along the gang boundaries predicted by their model.
The researchers think that their work also demonstrates that a gang?s turf forms in part based on competitive interactions with other gangs. The hope is that understanding patterns of between-gang violence can help police prevent more of it.
An error-eliminating fix overcomes big problem in '3rd-gen' genome sequencingPublic release date: 1-Jul-2012 [ | E-mail | 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.
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.
[ | E-mail | 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 sequencingPublic release date: 1-Jul-2012 [ | E-mail | 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.
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.
[ | E-mail | 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.
Marilyn Golias, right, looks at the remains of a utility pole which fell across the street from her house in Falls Church, Va., Saturday, June 30, 2012. Millions across the mid-Atlantic region sweltered Saturday in the aftermath of violent storms that pummeled the eastern U.S. with high winds and downed trees, killing at least 13 people and leaving 3 million without power during a triple-digit heat wave. (AP Photo/Cliff Owen)
Marilyn Golias, right, looks at the remains of a utility pole which fell across the street from her house in Falls Church, Va., Saturday, June 30, 2012. Millions across the mid-Atlantic region sweltered Saturday in the aftermath of violent storms that pummeled the eastern U.S. with high winds and downed trees, killing at least 13 people and leaving 3 million without power during a triple-digit heat wave. (AP Photo/Cliff Owen)
A worker uses a chainsaw to clear a tree that fell onto the 14th fairway at Congressional Country Club in Bethesda, Md., Saturday, June 30, 2012, after a strong storm blew through overnight. The AT&T National golf tournament was postponed to allow workers to clear the course. (AP Photo/Patrick Semansky)
In this Friday, June 29, 2012 photo, a car sits damaged from where a brick wall fell on it from the second story of a store in Columbus Grove, Ohio. The bricks fell on and crushed two vehicles as strong winds tore through the region Friday afternoon. (AP Photo/The Lima News, Jay Sowers)
A pedestrian helps a bicyclist navigate a sidewalk blocked by a fallen tree that also damaged a parked vehicle in the Dupont Circle neighborhood of Washington, Saturday, June 30, 2012. Violent evening storms following a day of triple-digit temperatures wiped out power to more than 2 million people across the eastern United States. (AP Photo/Pablo Martinez Monsivais)
Robert St. Denny plays with his daughter, 9-month-old Lily St. Denny, as his wife Kelly Reyes sits at right, at a Red Cross shelter at Northwestern High School gym Saturday, June 30, 2012, in Hyattsville, Md. The apartment complex the St. Denny's live in was damaged by violent evening storms following a day of triple-digit temperatures that also wiped out power to more than 2 million people across the eastern United States. (AP Photo/Alex Brandon)
Violent storms swept across the eastern U.S., killing at least 13 people and knocking out power to millions of people on a day when temperatures across the region reached triple-digits.
The Mid-Atlantic region had already been experiencing 100-degree temperatures before Friday evening's violent storms. More than 3 million were left without power ? and without air conditioning ? as crews work to clear downed tree limbs and restore electricity.
The storms caused damage from Indiana to New Jersey, although the bulk of it was in West Virginia, Washington and suburban Virginia and Maryland. At least six of the dead were killed in Virginia, including a 90-year-old woman asleep in bed when a tree slammed into her home. Two young cousins in New Jersey were killed when a tree fell on their tent while camping. Two were killed in Maryland, one in Ohio, one in Kentucky and one in Washington.
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