Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Innovation via genetic ‘googling’

05.10.2009
Intelligent search engines called PosMed and PosMed-plus make it easier for researchers to identify candidate genes for cloning

Many diseases are caused by genetic mutations. Researchers can use a technique called linkage analysis to identify rough intervals on the chromosome that might have mutated to cause each condition; however, these intervals often contain tens or hundreds of genes.

Rather than laboriously testing each gene, it is useful for researchers to acquire as much knowledge as possible about the condition in question, so that they can narrow down their choice to the most likely candidate genes.

Now, Tetsuro Toyoda and co-workers at RIKEN’s Bioinformatics And Systems Engineering (BASE) division in Yokohama have developed intelligent search engines that can identify candidate genes from huge genetic databases and over 17 million medical and biological documents1,2. The programs could not only help researchers to identify the genes responsible for diseases, but also highlight useful mutations that make crops more robust.

Toyoda explains some of the motivation behind his team’s work: “The RIKEN Genomic Sciences Center promoted a project to generate genetically mutated mice on a large scale. The disadvantage is that the locations of the mutation that confer the phenotypes, such as diseases, were difficult to identify [using] a conventional genetics approach.”

The BASE team worked alongside researchers at RIKEN’s BioResource Center in Ibaraki to develop their search engine, called PosMed (Positional Medline), which accesses vast amounts of information on the genetics of humans, mice and rats. They also collaborated with RIKEN’s Plant Science Center to develop a similar system for plants, called PosMed-plus (Positional Medline for plant upgrading science), which so far includes thale cress (Arabidopsis thaliana) and rice (Oryza sativa).

A researcher using PosMed or PosMed-plus can choose their species of interest, then type in a simple phrase representing a phenotype or function, for example ‘diabetes’ or ‘drought tolerance’. The program then searches through text in existing literature databases and assesses the strength of each gene’s connection to the phenotype in question. It can also highlight other genes that are expressed at the same times or places, or cited in the same papers, and even find similar genes in other species.

“Since the invention of the PosMed system, many mutations have been easily identified, because a researcher can prioritize the genes that need to be investigated with direct sequencing,” says Toyoda.

The researchers hope to add more species to their databases soon. For example, Toyoda says: “Recently we are focusing on plants that are useful for green technologies—to combat climate change.”

The corresponding author for this highlight is based at the RIKEN Bioinformatics And Systems Engineering division

1. Yoshida, Y., Makita, Y., Heida, N., Asano, S., Matsushima, A., Ishii, M., Mochizuki, Y., Masuya, H., Wakana, S., Kobayashi, N. & Toyoda, T. PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. Nucleic Acids Research 37, W147–W152 (2009).

2. Makita, Y., Kobayashi, N., Mochizuki, Y., Yoshida, Y., Asano, S., Heida, N., Deshpande, M., Bhatia, R., Matsushima, A., Ishii, M. et al. PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants. Plant Cell Physiology 50, 1249–1259 (2009).

Saeko Okada | Research asia research news
Further information:
http://www.rikenresearch.riken.jp/eng/research/6046
http://www.researchsea.com

More articles from Life Sciences:

nachricht A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht On the way to developing a new active ingredient against chronic infections
18.08.2017 | Deutsches Zentrum für Infektionsforschung

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

A Map of the Cell’s Power Station

18.08.2017 | Life Sciences

Engineering team images tiny quasicrystals as they form

18.08.2017 | Physics and Astronomy

Researchers printed graphene-like materials with inkjet

18.08.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>