Free Newsletters - Space - Defense - Environment - Energy - Solar - Nuclear
..
. Earth Science News .




FLORA AND FAUNA
DNA Sequenced for Parrots' Ability to Parrot
by Staff Writers
Durham NC (SPX) Jul 05, 2012


This male budgie from the Fort Worth Zoo is like the parrots Erich Jarvis uses to study vocal learning behaviors. Credit: Jerry Tillery.

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 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.

.


Related Links
Duke University
Darwin Today At TerraDaily.com






Comment on this article via your Facebook, Yahoo, AOL, Hotmail login.

Share this article via these popular social media networks
del.icio.usdel.icio.us DiggDigg RedditReddit GoogleGoogle




Memory Foam Mattress Review
Newsletters :: SpaceDaily :: SpaceWar :: TerraDaily :: Energy Daily
XML Feeds :: Space News :: Earth News :: War News :: Solar Energy News





FLORA AND FAUNA
Do the world's smallest flies decapitate tiny ants?
Lanham MD (SPX) Jul 05, 2012
A new species of phorid fly from Thailand is the smallest fly ever discovered. At just 0.40 millimeters in length, it is 15 times smaller than a house fly and five times smaller than a fruit fly. The tiny fly, Euryplatea nanaknihali, is also the first of its genus to be discovered in Asia, and it belongs to a fly family (Phoridae) that is known for "decapitating" ants. Some species i ... read more


FLORA AND FAUNA
Fukushima was 'man-made' disaster: Japanese probe

Aussie patrol boats are 'under pressure'

Japan Diet to publish Fukushima disaster probe

Jakarta, Canberra boost asylum cooperation

FLORA AND FAUNA
Expert defends China's rare earth policy

Running on empty

Deep-sea rare earths found in Japan

Toshiba fined in US antitrust case

FLORA AND FAUNA
China's Three Gorges Dam at full capacity: Xinhua

Natural climate change shut down Pacific reefs: study

Laos vows to address Mekong dam fears

Britain's urban rivers bounce back

FLORA AND FAUNA
Argentina court upholds glacier protections against mining

Study: Wrong diet doomed 1912 polar try

Scientists to produce first 3-D models of Arctic sea ice

Canada builds up arctic region defenses

FLORA AND FAUNA
US drought hits global grain outlook: FAO

Vertical farm in abandoned pork plant turns waste into food

Screening horticultural imports: New models assess plant risk through better analysis

Scientists urge new approaches to plant research

FLORA AND FAUNA
Nine killed, four missing in Turkey floods

Northeast India floods kill 79, displace two million

Shallow 6.3-magnitude quake hits northwest China

Floods swamp eastern India, 1.3 million displaced

FLORA AND FAUNA
S.African game farmer jailed for 8 years over rhino horn

Chimpanzees cleared after mauling American in S.Africa: park

Rwanda gorillas prosper despite guerrillas next door

Kenyan army hunts kidnappers of four foreign aid workers

FLORA AND FAUNA
Seabirds studied for clues to human aging

Hong Kong's land shortage forces bereaved to sea

Diet of early human relative Australopithecus shows surprises

Outside View: 18th-century words for today




The content herein, unless otherwise known to be public domain, are Copyright 1995-2014 - Space Media Network. AFP, UPI and IANS news wire stories are copyright Agence France-Presse, United Press International and Indo-Asia News Service. ESA Portal Reports are copyright European Space Agency. All NASA sourced material is public domain. Additional copyrights may apply in whole or part to other bona fide parties. Advertising does not imply endorsement,agreement or approval of any opinions, statements or information provided by Space Media Network on any Web page published or hosted by Space Media Network. Privacy Statement