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Source: http://twitter.com/Moonbootica/statuses/220601768462135296
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Wednesday, July 4, 2012
'Shift'in Russia, China positions on Syria: Annan
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Source: http://news.yahoo.com/russia-china-shifting-syria-annan-spokesman-113247002.html
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DNA sequenced for parrot's ability to parrot
ScienceDaily (July 2, 2012) ? Scientists say they have assembled more completely the string of genetic letters that could control how well parrots learn to imitate their owners and other sounds.
The research team unraveled the specific regions of the parrots' genome using a new technology, single molecule sequencing, and fixing its flaws with data from older DNA-decoding devices. The team also decoded hard-to-sequence genetic material from corn and bacteria as proof of their new sequencing approach.
The results of the study appeared online July 1 in the journal Nature Biotechnology.
Single molecule sequencing "got a lot of hype last year" because it generates long sequencing reads, "supposedly making it easier to assemble complex parts of the genome," said Duke University neurobiologist Erich Jarvis, a co-author of the study.
He is interested in the sequences that regulate parrots' imitation abilities because they could give neuroscientists information about the gene regions that control speech development in humans.
Jarvis began his project with collaborators by trying to piece together the genome regions with what are known as next-generation sequencers, which read chunks of 100 to 400 DNA base pairs at a time and then take a few days to assemble them into a draft genome. After doing the sequencing, the scientists discovered that the read lengths were not long enough to assemble the regulatory regions of some of the genes that control brain circuits for vocal learning.
University of Maryland computational biologists Adam Phillippy and Sergey Koren -- experts at assembling genomes -- heard about Jarvis's sequencing struggles at a conference and approached him with a possible solution of modifying the algorithms that order the DNA base pairs. But the fix was still not sufficient.
Last year, 1000 base-pair reads by Roch 454 became available, as did the single molecule sequencer by Pacific Biosciences. The Pacbio technology generates strands of 2,250 to 23,000 base pairs at a time and can draft an entire genome in about a day.
Jarvis and others thought the new technologies would solve the genome-sequencing challenges. Through a competition, called the Assemblathon, the scientists discovered that the Pacbio machine had trouble accurately decoding complex regions of the parrot, Melopsittacus undulates, genome. The machine had a high error rate, generating the wrong genetic letter at every fifth or sixth spot in a string of DNA. The mistakes made it nearly impossible to create a genome assembly with the very long reads, Jarvis said.
But with a team, including scientists from the DOE Genome Science Institute and Cold Spring Harbor in New York, Phillippy, Koren and Jarvis corrected the Pacbio sequencer's errors using shorter, more accurate codes from the next-generation devices. The fix reduces the single-molecule, or third-generation, sequencing machine's error rate from 15 percent to less than one-tenth of one percent.
"Finally we have been able to assemble the regulatory regions of genes, such as FoxP2 and egr1, that are of interest to us and others in vocal learning behavior," Jarvis said.
He explained that FoxP2 is a gene required for speech development in humans and vocal learning in birds that learn to imitate sounds, like songbirds and parrots. Erg1 is a gene that controls the brain's ability to reorganize itself based on new experiences.
By being able to decode and organize the DNA that regulates these regions, neuroscientists may be able to better understand what genetic mechanism causes birds to imitate and sing well. They may also be able to collect more information about genetic factors that affect a person's ability to learn how to communicate well and to speak, Jarvis said. He and his team plan to describe the biology of the parrot???s genetic code they sequenced in more detail in an upcoming paper.
Jarvis added that as more scientists use the hybrid sequencing approach, they could possibly decode complex, elusive genes linked to how cancer cells develop and to the sequences that control other brain functions.
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The above story is reprinted from materials provided by Duke University. The original article was written by Ashley Yeager.
Note: Materials may be edited for content and length. For further information, please contact the source cited above.
Journal Reference:
- Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis, Adam M Phillippy. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology, 2012; DOI: 10.1038/nbt.2280
Note: If no author is given, the source is cited instead.
Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.
Source: http://www.sciencedaily.com/releases/2012/07/120702210229.htm
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Yemen says smashes three al Qaeda-linked cells
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Source: http://news.yahoo.com/yemen-says-smashes-three-al-qaeda-linked-cells-133233495.html
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Researchers from Penn, Michigan and Duke study how cooperation can trump competition in monkeys
![[ Back to EurekAlert! ]](https://lh3.googleusercontent.com/blogger_img_proxy/AEn0k_suexoMh9WTcTo4DMCdy154gjIcTZSI9F0keaoECGZclQwgjnksgJ4QRh4NnIpMV7RcfWZnUVjv1FTX1RwwAQWDMf7rafQE4bQGwGF2U6g=s0-d){kind=small}
Public release date: 3-Jul-2012[ | E-mail |
Share ] Contact: Evan Lerner
elerner@upenn.edu
215-573-6604
University of Pennsylvania
PHILADELPHIA Being the top dog or, in this case, the top gelada monkey is even better if the alpha male is willing to concede at times to subordinates, according to a study by researchers from the University of Pennsylvania, the University of Michigan and Duke University.
Alpha male geladas who allowed subordinate competitors into their group had a longer tenure as leader, resulting in an average of three more offspring each during their lifetimes.
The findings, collected from data during a five-year period ending in January 2011 through the University of Michigan Gelada Research Project, were published in the Proceedings of The Royal Society.
The research was conducted by Noah Snyder-Mackler, then a graduate student in the Department of Psychology in Penn's School of Arts and Sciences. He collaborated with Thore Bergman, assistant professor of psychology at Michigan, and Susan Alberts, professor of biology at Duke.
Cooperation is surprisingly common among wild animals, the researchers said. While it makes evolutionary sense for animals to help their kin, it is harder to explain cases where competitors especially unrelated adult males join forces. This conundrum is particularly hard to explain because mating is generally a zero-sum game in which males can only reproduce by stealing mating opportunities from each other.
Why would an alpha male allow other males to be a part of his unit, if they will inevitably decrease the probability that he will pass on his own genes? The researchers felt there must be a reason since this kind of behavior is observed in many species.
"For example, in some species unrelated males will sometimes tolerate the presence of one another and, in rare cases, form bonds and even appear to cooperate," Snyder-Mackler said.
To understand why potential rivals might team up, researchers compared the fitness consequences for dominant male gelada monkeys living in single- or multi-male groups. They found that, although subordinate males father some of the offspring in multi-male groups, dominant males gain a lifetime fitness benefit because the subordinate aids in defense of the group from other males, thus extending the dominant male's reproductive career.
Even more tantalizing is evidence that the subordinate males that are allowed to mate stay around in the group for much longer.
"This suggests," Bergman said, "that the alpha males may allow the subordinate to reproduce as a 'staying incentive' for defending the group, a payment for their services."
While it is not yet clear that a willing exchange is occurring subordinate males may simply "steal" some chances at reproduction the evidence is strong that subordinates confer some benefit to the leader.
"These findings demonstrate a benefit of forming multi-male groups in a predominantly single-male system, an important step in the evolution of sociality among unrelated competitors," Bergman said.
In studying wild geladas in the Simien Mountains National Park in Ethiopia, researchers identified the leader and follower males, noted the numbers of females in all units; tracked individuals involved in unit takeovers; and noted all new births. They used non-invasively collected genetic samples to conduct paternity analysis to determine the identities of the fathers.
Researchers saw that the dominant and subordinate males cooperatively defended their females by fending off unattached bachelor males intent on taking their females, the likely mechanism leading to the increased tenure of the dominants.
Even though geladas primarily form single-male groups, researchers showed a benefit to forming multi-male groups. Multi-male units had fewer takeovers (a rate of 0.27) per year from other competitors and longer tenure (3.7 years as leader) compared with single-male units (0.35 takeovers per year and 2.86 years as leader.)
"Overall, this means that, just because animals appear to be in direct competition for a limited resource, they may still benefit from the relationship overall," Snyder-Mackler said.
Thus, cooperation can evolve among competitors through a variety of mechanisms. In the study, researchers chronicled how it can evolve in the context of reproductive sharing.
"More comparative research on other species will give us a better understanding of how and under what circumstances cooperation among unrelated individuals may have evolved," Snyder-Mackler said.
###
The research was funded by the National Science Foundation, Leakey Foundation and National Geographic Society.
Synder-Mackler is now a postdoctoral fellow at Duke.
[ | 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.
Public release date: 3-Jul-2012[ | E-mail |
Share ] Contact: Evan Lerner
elerner@upenn.edu
215-573-6604
University of Pennsylvania
PHILADELPHIA Being the top dog or, in this case, the top gelada monkey is even better if the alpha male is willing to concede at times to subordinates, according to a study by researchers from the University of Pennsylvania, the University of Michigan and Duke University.
Alpha male geladas who allowed subordinate competitors into their group had a longer tenure as leader, resulting in an average of three more offspring each during their lifetimes.
The findings, collected from data during a five-year period ending in January 2011 through the University of Michigan Gelada Research Project, were published in the Proceedings of The Royal Society.
The research was conducted by Noah Snyder-Mackler, then a graduate student in the Department of Psychology in Penn's School of Arts and Sciences. He collaborated with Thore Bergman, assistant professor of psychology at Michigan, and Susan Alberts, professor of biology at Duke.
Cooperation is surprisingly common among wild animals, the researchers said. While it makes evolutionary sense for animals to help their kin, it is harder to explain cases where competitors especially unrelated adult males join forces. This conundrum is particularly hard to explain because mating is generally a zero-sum game in which males can only reproduce by stealing mating opportunities from each other.
Why would an alpha male allow other males to be a part of his unit, if they will inevitably decrease the probability that he will pass on his own genes? The researchers felt there must be a reason since this kind of behavior is observed in many species.
"For example, in some species unrelated males will sometimes tolerate the presence of one another and, in rare cases, form bonds and even appear to cooperate," Snyder-Mackler said.
To understand why potential rivals might team up, researchers compared the fitness consequences for dominant male gelada monkeys living in single- or multi-male groups. They found that, although subordinate males father some of the offspring in multi-male groups, dominant males gain a lifetime fitness benefit because the subordinate aids in defense of the group from other males, thus extending the dominant male's reproductive career.
Even more tantalizing is evidence that the subordinate males that are allowed to mate stay around in the group for much longer.
"This suggests," Bergman said, "that the alpha males may allow the subordinate to reproduce as a 'staying incentive' for defending the group, a payment for their services."
While it is not yet clear that a willing exchange is occurring subordinate males may simply "steal" some chances at reproduction the evidence is strong that subordinates confer some benefit to the leader.
"These findings demonstrate a benefit of forming multi-male groups in a predominantly single-male system, an important step in the evolution of sociality among unrelated competitors," Bergman said.
In studying wild geladas in the Simien Mountains National Park in Ethiopia, researchers identified the leader and follower males, noted the numbers of females in all units; tracked individuals involved in unit takeovers; and noted all new births. They used non-invasively collected genetic samples to conduct paternity analysis to determine the identities of the fathers.
Researchers saw that the dominant and subordinate males cooperatively defended their females by fending off unattached bachelor males intent on taking their females, the likely mechanism leading to the increased tenure of the dominants.
Even though geladas primarily form single-male groups, researchers showed a benefit to forming multi-male groups. Multi-male units had fewer takeovers (a rate of 0.27) per year from other competitors and longer tenure (3.7 years as leader) compared with single-male units (0.35 takeovers per year and 2.86 years as leader.)
"Overall, this means that, just because animals appear to be in direct competition for a limited resource, they may still benefit from the relationship overall," Snyder-Mackler said.
Thus, cooperation can evolve among competitors through a variety of mechanisms. In the study, researchers chronicled how it can evolve in the context of reproductive sharing.
"More comparative research on other species will give us a better understanding of how and under what circumstances cooperation among unrelated individuals may have evolved," Snyder-Mackler said.
###
The research was funded by the National Science Foundation, Leakey Foundation and National Geographic Society.
Synder-Mackler is now a postdoctoral fellow at Duke.
[ | 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.
Source: http://www.eurekalert.org/pub_releases/2012-07/uop-rfp070312.php
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Tuesday, July 3, 2012
Programmable DNA scissors found for bacterial immune system
Monday, July 2, 2012
Genetic engineers and genomics researchers should welcome the news from the Lawrence Berkeley National Laboratory (Berkeley Lab) where an international team of scientists has discovered a new and possibly more effective means of editing genomes. This discovery holds potentially big implications for advanced biofuels and therapeutic drugs, as genetically modified microorganisms, such as bacteria and fungi, are expected to play a key role in the green chemistry production of these and other valuable chemical products.
Jennifer Doudna, a biochemist with Berkeley Lab's Physical Biosciences Division and professor at the University of California (UC) Berkeley, helped lead the team that identified a double-RNA structure responsible for directing a bacterial protein to cleave foreign DNA at specific nucleotide sequences. Furthermore, the research team found that it is possible to program the protein with a single RNA to enable cleavage of essentially any DNA sequence.
"We've discovered the mechanism behind the RNA-guided cleavage of double-stranded DNA that is central to the bacterial acquired immunity system," says Doudna, who holds appointments with UC Berkeley's Department of Molecular and Cell Biology and Department of Chemistry, and is an investigator with the Howard Hughes Medical Institute (HHMI). "Our results could provide genetic engineers with a new and promising alternative to artificial enzymes for gene targeting and genome editing in bacteria and other cell types."
Doudna is one of two corresponding authors of a paper in the journal Science describing this work titled "A programmable dual RNA-guided DNA endonuclease in adaptive bacterial immunity." The second corresponding author is Emmanuelle Charpentier of the Laboratory for Molecular Infection Medicine at Sweden's Ume? University. Other co-authors of the paper were Martin Jinek, Krzysztof Chylinski, Ines Fonfara and Michael Hauer.
Bacterial and archaeon microbes face a never-ending onslaught from viruses and invading circles of nucleic acid known as plasmids. To survive, the microbes deploy an adaptive-type nucleic acid-based immune system that revolves around a genetic element known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. Through the combination of CRISPRs and associated endonucleases, called CRISPR-associated ? "Cas" ? proteins, bacteria and archaeons are able to utilize small customized crRNA molecules (for CRISPR-derived RNA) to target and destroy the DNA of invading viruses and plasmids.
There are three distinct types of CRISPR/Cas immunity systems. Doudna and her colleagues studied the Type II system which relies exclusively upon one family of endonucleases for the targeting and cleaving of foreign DNA, the Cas9 proteins.
"For the Type II CRISPR/Cas system, we found that crRNA connects via base-pairs with a trans-activating RNA (tracrRNA), to form a two-RNA structure," Doudna says. "These dual RNA molecules (tracrRNA:crRNA) direct Cas9 proteins to introduce double-stranded DNA breaks at specific sites targeted by the crRNA-guide sequence."
Doudna and her colleagues demonstrated that the dual tracrRNA:crRNA molecules can be engineered as a single RNA chimera for site-specific DNA cleavage, opening the door to RNA-programmable genome editing.
"Cas9 binds to the tracrRNA:crRNA complex which in turn directs it to a specific DNA sequence through base-pairing between the crRNA and the target DNA," Doudna says. "Microbes use this elegant mechanism to cleave and destroy viruses and plasmids, but for genome editing, the system could be used to introduce targeted DNA changes into the genome.
Doudna notes that the "beauty of CRISPR loci" is that they can be moved around on plasmids.
"It is well-established that CRISPR systems can be transplanted into heterologous bacterial strains," she says. "Also, there is evidence to suggest that CRISPR loci are horizontally transferred in nature."
Doudna and her colleagues are now in the process of gathering more details on how the RNA-guided cleavage reaction works and testing whether the system will work in eukaryotic organisms including fungi, worms, plants and human cells.
"Although we've not yet demonstrated genome editing, given the mechanism we describe it is now a very real possibility," Doudna says.
###
DOE/Lawrence Berkeley National Laboratory: http://www.lbl.gov
Thanks to DOE/Lawrence Berkeley National Laboratory for this article.
This press release was posted to serve as a topic for discussion. Please comment below. We try our best to only post press releases that are associated with peer reviewed scientific literature. Critical discussions of the research are appreciated. If you need help finding a link to the original article, please contact us on twitter or via e-mail.
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Source: http://www.labspaces.net/121382/Programmable_DNA_scissors_found_for_bacterial_immune_system
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Monday, July 2, 2012
Get Ready for Amazon Maps [Video]
Source: http://feeds.gawker.com/~r/gizmodo/full/~3/tuew-a7NdK4/get-ready-for-amazon-maps
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