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An international team of researchers has made CRISPR technology more accessible and standardized by simplifying its complex implementation. The simpler, faster CRISPR, which is presented in the journal Nature Communications, offers a broad platform for off-the shelf genome engineering that may lower the barrier of entry for this powerful technology.
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NEW YORK (GenomeWeb) – A team of researchers in Belgium and Texas have developed a CRISPR editing approach that takes advantage of a common genetic element present in Escherichia coli, making the genome editing process faster and scarless.
Genome editing normally requires the creation of CRISPR constructs that include unique guide RNAs (gRNA), which target a gene for modification. But by generating a gRNA against this common genetic element, called the flippase recognition target (FRT) site, the CRISPR-FRT circumvents this design constraint and obviates the need for unique gRNAs, according to the researchers.
"In E. coli, efficient genome editing using CRISPR and homology-directed repair requires induction of the CRISPR components (Cas9 and gRNA), induction of λ phage recombinase genes, and a rescue DNA template with the desired mutation," the authors, led by the University of Leuven's Jan Michiels and Baylor College of Medicine's Olivier Lichtarge, wrote in Nature Communications today. "Here we make CRISPR more accessible and standardized with a simple solution that simultaneously avoids cloning of new gRNAs, circumvents complex design of rescue templates, and provides an easy phenotypic screen for positive clones."
The team showed that the CRISPR-FRT method directs a gRNA to an FRT sequence present in each knockout mutant of the E. coli strains in the Keio collection. In the arrayed Keio collection of 3,884 deletion mutants, each non-essential E. coli gene has been replaced by a kanamycin-resistance (KanR) cassette flanked on each end by FRT sites. Instead of designing and cloning a unique gRNA for each gene, a single gRNA-FRT can target any gene in this collection, the researchers said.
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APPLES, mushrooms and pork sounds a promising recipe for a kebab, but the average barbecuer might balk at adding strawberries. According to John Gordon of IBM, however, the result is delicious. Dr Gordon is one of the leaders of that firm’s cognitive-computing team, responsible for a machine called Watson which is able to digest and analyse large amounts of English text and then draw inferences from it. When, in March, Watson was fed reams of recipes and texts about food, it reasoned that these four ingredients would complement each other, based on their sharing a number of flavoursome chemical compounds. And Dr Gordon, at least, thinks Watson’s suggestion is a winner. ...
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Assigning function to genes remains a big challenge in biology. Researchers often turn to gene or protein networks to infer the role of a particular gene. Local network analysis identifies the function of a network node by existing annotations, which can be insufficient. Global network analysis looks for relatedness over an entire network and is therefore more sensitive, but it is also more computationally expensive and thus restricted to networks of no more than several thousand nodes. Lisewski et al. circumvent this limitation by using a compression scheme that eliminates redundancies between and within networks. This allowed them to analyze networks of genes from hundreds of genomes. As demonstration, they identified the function of a Plasmodium falciparum antigen with potential as a drug target.
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IBM has unveiled a new application for Watson — the Jeopardy winning super-computing system — designed to help academic researchers rapidly process scientific literature.
During a Thursday event at New York’s Museum of Art and Design, IBM researchers announced that the application, called the Watson Discovery Advisor, is now available to companies as an Internet-cloud based service.
The service can process large volumes of academic literature in a few hours, according to IBM Watson Group vice president and healthcare leader Rob Merkel. A genetic scientist might ask Watson which two genes are likely to occur together, and Watson would churn through thousands of journal articles — both in that particular institution’s library, and whatever information is publicly available — to identify common pairs. ...
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Watch out, Sherlock, there's a new Dr. Watson in town. IBM's Watson, the computer that famously won the quiz show 'Jeopardy!', is now helping researchers make scientific discoveries.
The artificially intelligent computer system is moving beyond answering known questions into a new realm, pushing the boundaries of science by testing hypotheses. The new system, known as the Watson Discovery Advisor, could accelerate the scientific process by sifting through massive amounts of information and visualizing patterns in the data. ...
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Sometimes, figuring out the right question is harder than finding the answer. Just ask Watson.
Watson’s claim to fame rests on beating human champions in the question-and-answer game “Jeopardy!” In the three years since, IBM has been working to move Watson into the marketplace, step by step. The next step came on Thursday, when the company made a Watson technology, Discovery Advisor, available for companies and research organizations to use as a cloud service. ...
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For the early part of its existence, IBM’s Watson supercomputer was a bit of a carnival act. It could perform feats of computational magic, win on Jeopardy, and whip up crazy burrito recipes at SXSW. But Watson is designed to become IBM’s money-making, Big Data platform, earning its keep across a variety of industries. In New York, the company announced that a Watson-enabled group of researchers was able to speed the process of discovery to uncover new targets for cancer research.
“We’re moving from a time where Watson helps answer questions to one where it tackles the questions that don’t have answers,” says IBM vice president John Gordon, Watson’s boss. ...
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Research and development, by definition, comes along with extraordinary risk. Entire industries and investment portfolios are colored by the simple fact that scientific and medical research takes huge upfront spending, patience, a high tolerance for losses.
What if all that changed thanks to big data analytics? Much of the estimated $600 billion spent by the world's top 1,000 research companies last year -- not to mention the time of their researchers -- would be up for reallocation. ...
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WASHINGTON: International Business Machines Corp on Wednesday launched a computer system that can quickly identify patterns in massive amounts of data, an ability that IBM said should hasten breakthroughs in science and medical research.
The computer system, Watson Discovery Advisor, understands chemical compound interaction and human language and can visually map out connections in data, the company said in a statement. ...
Press Release
Watch out, Sherlock, there's a new Dr. Watson in town. IBM's Watson, the computer that famously won the quiz show 'Jeopardy!', is now helping researchers make scientific discoveries.
The artificially intelligent computer system is moving beyond answering known questions into a new realm, pushing the boundaries of science by testing hypotheses. The new system, known as the Watson Discovery Advisor, could accelerate the scientific process by sifting through massive amounts of information and visualizing patterns in the data. ...
Press Release
When IBM’s advanced artificial intelligence program Watson beat Jeopardy champion Ken Jennings in 2011, it was an impressive feat for a computer–but still, it was only processing information that humans already knew in order to answer trivia questions.
As IBM attempts to turn Watson into a new line of business and make it useful in a wide range of industries that are dealing lately with an overwhelming amount of data, it’s now working to push the software, which excels at learning and interpreting human language, forward into the realm of the unknown. ...
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Two new studies present methods to explore how host and parasite transcriptomes interact with one another. Yamagishi and colleagues describe a new approach to analyse human and parasite RNA expression profiles simultaneously, and Lisewski and colleagues demonstrate the feasibility of compressing biological networks by eliminating redundant evolutionary relationships to enable functional predictions.
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WASHINGTON (Reuters) - International Business Machines Corp on Wednesday launched a computer system that can quickly identify patterns in massive amounts of data, an ability that IBM said should hasten breakthroughs in science and medical research.
The computer system, Watson Discovery Advisor, understands chemical compound interaction and human language and can visually map out connections in data, the company said in a statement. ...
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IN MAY last year, a supercomputer in San Jose, California, read 100,000 research papers in 2 hours. It found completely new biology hidden in the data. Called KnIT, the computer is one of a handful of systems pushing back the frontiers of knowledge without human help.
KnIT didn’t read the papers like a scientist – that would have taken a lifetime. Instead, it scanned for information on a protein called p53, and a class of enzymes that can interact with it, called kinases. Also known as “the guardian of the genome”, p53 suppresses tumours in humans. KnIT trawled the literature searching for links that imply undiscovered p53 kinases, which could provide routes to new cancer drugs. ...
