Take millions of puzzle pieces containing partial words and put them back together into full words, sentences, paragraphs and chapters until the book these random parts came from is rebuilt.
That daunting process in not unlike sequencing an organism's genome, says University of Oregon biologist Eric A. Johnson, a member of the UO Institute of Molecular Biology. His lab developed a patent-pending technology for discovering differences between genomes called restriction-site associated DNA markers, or RAD. They have now shown that RAD can also be used to help put a genome sequence together.
The original RAD technique, unveiled in 2005, led to the UO spinoff company Floragenex, which uses the technology in plant genetics. More recently, Johnson and UO colleague William A. Cresko used it to identify genetic differences in threespine stickleback, a fish, which evolved separately after environmental conditions had isolated some of the saltwater fish into freshwater habitats.
Now, after three years of research, adapting it along the way as sequencing tools advanced, Johnson, Cresko and three UO colleagues provide a proof-of-principle paper in the April issue of PLoS One, a publication of the Public Library of Science. The National Institutes of Health-funded research documents that the new method, called RAD paired-end contigs, works and provides accurate sequencing results.
"The RAD sequence is a placeholder that identifies one small region of a genome," Johnson said. "We showed that this technique lets us gather together appropriate nearby sequences and piece them together." In just seconds, a section is completed, he said. In a matter of hours, he added, an entire genome's sequence emerges.
Using the book analogy, Johnson said: "We first asked if we can piece together one short sentence at a time instead of ordering all the words in the whole book at once. Next, can we put together one paragraph at a time? That's like going from, say, 1,000 letters of the genome in a row to 5,000 at a time. Here, we show that we can do this. We can put the book back together."
A RAD marker in the book analogy might be a word at the start of each sentence. Using that marker as an anchor, the rest of the words in the sentence are easily separated from all the words in the book, and then the words in the sentence are put in the right order, on an on until all the content is organized correctly, Johnson said. The end product, he added, contains few, if any, leftover or unexplained fragments, a problem occurring with current technologies that rely on clusters of computers, requiring extensive memory, to complete sequencing projects.
RAD technology can be applied to study the genetics of organisms for which genomes have not been completed, Johnson said.
The PLoS One paper detailed how RAD works on stickleback and the bacterium e-coli. Both involve small and rather simple genomes. There already is interest in its potential application in human genome sequencing, Johnson said.
At about the same time the PLoS One paper was being published, Johnson, who also is the chief scientific officer of Floragenex, was part of a company-sponsored, one-day RAD Sequencing and Genomics Symposium in Portland, Ore., on April 19. Nine researchers from five institutions (UO, Oregon State University, University of British Columbia, University of Tennessee and University of Washington) described how they are applying RAD in their sequencing projects.
"It was quite gratifying to hear them speak about this technology and how it is working for them," Johnson said.
RAD technology also is being used in a three-year project -- funded by a $1 million grant from the W.M. Keck Foundation and led by Cresko and UO colleague Hui Zong -- to identify genetic changes that occur from the formation of a single mutation to full-fledged cancer. The project could lead to a new generation of molecular diagnostics to detect cancers in their earliest stages.
Co-authors of the PLoS One paper with Johnson and Cresko were Paul D. Etter, a postdoctoral researcher, and doctoral student Jessica L. Preston, both of Johnson's lab, and Susan Bassham, a postdoctoral researcher in Cresko's lab.
About the University of Oregon
The University of Oregon is among the 108 institutions chosen from 4,633 U.S. universities for top-tier designation of "Very High Research Activity" in the 2010 Carnegie Classification of Institutions of Higher Education. The UO also is one of two Pacific Northwest members of the Association of American Universities.
Source: Eric A. Johnson, associate professor of biology, 541-346-5183, email@example.com
Jim Barlow | EurekAlert!
Meadows beat out shrubs when it comes to storing carbon
23.11.2017 | Norwegian University of Science and Technology
Migrating Cells: Folds in the cell membrane supply material for necessary blebs
23.11.2017 | Westfälische Wilhelms-Universität Münster
Heat from the friction of rocks caused by tidal forces could be the “engine” for the hydrothermal activity on Saturn's moon Enceladus. This presupposes that...
The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.
Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases....
The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.
Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...
Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.
That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...
Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.
During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....
15.11.2017 | Event News
15.11.2017 | Event News
30.10.2017 | Event News
23.11.2017 | Information Technology
23.11.2017 | Physics and Astronomy
23.11.2017 | Life Sciences