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Syngenta, Genomining, Prevas Bioinformatics, GeneData, University of California, San Diego

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Syngenta to Share Rice Genome Data with IRGSP

Japan’s National Institute of Agrobiological Sciences (NIAS) and Syngenta signed an agreement last week to share the Syngenta rice genome draft sequence data with the International Rice Genome Sequencing Project (IRGSP).

Currently, Syngenta allows academic researchers to access up to 100 kb of data per week with no reach-through rights. It also provides the full assembly on CD-ROM for those willing to sign an agreement. According to the company, more than 700 researchers have already accessed the data.

The company said it would now transfer its assembled sequence, underlying sequence files, and chromosome assignment information to the NIAS and The Institute for Genomic Research. The IRGSP consortium, which has split up its sequencing work by chromosome, plans to use the data to improve its own efforts.

Syngenta’s draft, created with the whole-genome shotgun method, is estimated to be 99.8 percent accurate. The IRGSP plans to publish its version once it is 99.99 percent accurate.

 

Genomining Completes Decrypthon Grid Project

Paris-based bioinformatics firm Genomining said last week that it had completed the calculation phase of the “Decrypthon” grid computing project it began in December.

Genomining, along with Platform Computing, the French Myopathy Association (AFM), and IBM, used the computational power of 75,000 PCs to compare more than 500,000 proteins using a modified version of the Smith-Waterman algorithm. The company said it would validate and format the resulting database, and make it publicly available to researchers by September.

Each computer contributed up to 133 hours, or 10 million hours of calculations. According to Genomining, a single computer would have required almost 1,170 years to perform the same calculation. In addition, 21 IBM servers hosted the data throughout the operation.

 

Prevas Wins Consulting Contract with Alpha Helix

Prevas Bioinformatics of Uppsala, Sweden, said it has signed a consulting contract with Alpha Helix, also of Uppsala, to develop bioinformatics approaches to improve the company’s PCR technology.

Alpha Helix is developing a new, rapid PCR thermocycler technology called SuperConvection. A bioinformatics consultant from Prevas will work with Alpha Helix for “at least six months” to implement and evaluate algorithms to analyze data from the instrument.

 

GeneData to Collaborate with University of Wuerzburg on Pathogenic Genomics

GeneData of Basel, Switzerland, said last week that it had entered a research collaboration with the “Competence Network Pathogenomik” based at the University of Wuerzburg to study the genomics of pathogenic bacteria.

Under the agreement, the Competence Network Pathogenomik will use components of GeneData’s Phylosopher and Expressionist computational platforms for genome and mRNA profile analysis.

The Competence Network Pathogenomik was established by the German Federal Ministry of Education and Research in 2001 and is funded with 10 million ($9.2 million) for three years.

 

UCSD Computational Method Gives Mobility to Molecular Targets

Andrew McCammon and his colleagues at the University of California, San Diego, have developed a new computational technique to model drug targets as flexible structures rather than as rigid objects.

The method, reported in the May 22 Journal of the American Chemical Society, “both verifies and competes with costly lab methods that rely on thousands of trials of nearly similar molecules,” said McCammon in a statement. In addition, he said, the technique eliminates the need to synthesize and purify proteins and is not limited by the sizes of the molecules.

Many docking programs have accounted for ligand flexibility, but according to McCammon, most still treat the receptors as rigid objects.

The “relaxed-complex” method they developed draws from two other popular techniques: the “SAR by NMR” method and the “tether” method. It samples the motions of receptor molecules, then determines how ligands bind to an “ensemble” of receptor conformations. According to the researchers, this accounts for the fact that ligands may exhibit better binding when the receptor is in a stretched or curled position that is very different from the original crystal conformation.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.