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 Discovery of a Key Regulatory Gene in Cardiac Valve Formation
24.05.2017 | Universität Basel

nachricht Carcinogenic soot particles from GDI engines
24.05.2017 | Empa - Eidgenössische Materialprüfungs- und Forschungsanstalt

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: A quantum walk of photons

Physicists from the University of Würzburg are capable of generating identical looking single light particles at the push of a button. Two new studies now demonstrate the potential this method holds.

The quantum computer has fuelled the imagination of scientists for decades: It is based on fundamentally different phenomena than a conventional computer....

Im Focus: Turmoil in sluggish electrons’ existence

An international team of physicists has monitored the scattering behaviour of electrons in a non-conducting material in real-time. Their insights could be beneficial for radiotherapy.

We can refer to electrons in non-conducting materials as ‘sluggish’. Typically, they remain fixed in a location, deep inside an atomic composite. It is hence...

Im Focus: Wafer-thin Magnetic Materials Developed for Future Quantum Technologies

Two-dimensional magnetic structures are regarded as a promising material for new types of data storage, since the magnetic properties of individual molecular building blocks can be investigated and modified. For the first time, researchers have now produced a wafer-thin ferrimagnet, in which molecules with different magnetic centers arrange themselves on a gold surface to form a checkerboard pattern. Scientists at the Swiss Nanoscience Institute at the University of Basel and the Paul Scherrer Institute published their findings in the journal Nature Communications.

Ferrimagnets are composed of two centers which are magnetized at different strengths and point in opposing directions. Two-dimensional, quasi-flat ferrimagnets...

Im Focus: World's thinnest hologram paves path to new 3-D world

Nano-hologram paves way for integration of 3-D holography into everyday electronics

An Australian-Chinese research team has created the world's thinnest hologram, paving the way towards the integration of 3D holography into everyday...

Im Focus: Using graphene to create quantum bits

In the race to produce a quantum computer, a number of projects are seeking a way to create quantum bits -- or qubits -- that are stable, meaning they are not much affected by changes in their environment. This normally needs highly nonlinear non-dissipative elements capable of functioning at very low temperatures.

In pursuit of this goal, researchers at EPFL's Laboratory of Photonics and Quantum Measurements LPQM (STI/SB), have investigated a nonlinear graphene-based...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Marine Conservation: IASS Contributes to UN Ocean Conference in New York on 5-9 June

24.05.2017 | Event News

AWK Aachen Machine Tool Colloquium 2017: Internet of Production for Agile Enterprises

23.05.2017 | Event News

Dortmund MST Conference presents Individualized Healthcare Solutions with micro and nanotechnology

22.05.2017 | Event News

 
Latest News

Physicists discover mechanism behind granular capillary effect

24.05.2017 | Physics and Astronomy

Measured for the first time: Direction of light waves changed by quantum effect

24.05.2017 | Physics and Astronomy

Marine Conservation: IASS Contributes to UN Ocean Conference in New York on 5-9 June

24.05.2017 | Event News

VideoLinks
B2B-VideoLinks
More VideoLinks >>>