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NSF, Merck, Institute for Genomics Research, Cepheid, Idaho Tech

NSF Awards $14M for Plant Comparative Genomics
The money will go to several programs focused on “economically important plants” and will study their genome sequences, genetic markers, maps, and expressed sequence collections, the NSF said.
Sharing the cash will be Iowa State University, whose researchers plan to study polyploidy in cotton; the University of Missouri, which will look into Brassica species such as Brussels sprouts and canola; and the University of Georgia and the University of Arizona, which will develop sequence resources to further popular grain research.
The studies will also study weeds, which not only compete with crops for nutrients but are also related to some crops. For instance, Washington University will study the genome of red rice, a weed that greatly reduces yields of cultivated rice, to find out its relation to domesticated rice.
Also, researchers at Michigan State University will study gene expression in weedy and cultivated radishes to learn how plants become either weedy or invasive.
James Collins, assistant director for biological sciences at the NSF, said these projects will “provide the mortar” to build upon the “bricks” laid down by the Plant Genome Research Program, a program supported by the US Department of Agriculture and the National Agriculture Library program that began in 1998.
Collins said the program will “tie together studies of the evolution of gene structure, function and regulation across the whole plant kingdom.”
A full list of awards is available here.

Merck KgaA Subsidiary to Market BioServe Biotechnologies Products in India
Merck Specialties, an Indian subsidiary of Merck KGaA, will market and distribute BioServe Biotechnologies’ DNA and RNA purification reagents and DNA sequencing, oligonucleotide synthesis, and molecular biology teaching kits, BioServe said last week.
BioServe said the companies plan to extend the deal throughout Asia later in 2007.
BioServe has offices in Hyderabad, India, and in Laurel, Md.
Financial terms of the agreement were not released.

Scientists Sequence Surprisingly Large Genome of STD Parasite T. vaginalis
Led by the Institute for Genomics Research, an international team of scientists has published the draft genome of a parasite that causes trichomoniasis, a common sexually transmitted disease.
The 160-megabase genome of Trichomonas vaginalis, published in the Jan. 12 issue of Science, contains nearly 26,000 predicted genes. The scientists said they were surprised by its size.
Jane Carlton, an associate professor in the department of medical parasitology at New York University School of Medicine and a co-author on the paper, noted that “parasites generally have smaller amounts of DNA than non-parasitic organisms, but in this case, there was 10 times as much DNA than we originally thought.”
 About two-thirds of the genome is made up of repeats and transposable elements, which “reflects a recent massive expansion of genetic material,” according to the authors. They suggest this sudden expansion may have happened when the parasite adapted from life in the intestines to one in the urogenital region.
The researchers found more than 150 instances of bacterial genes transferring into the T. vaginalis genome, and also found 800 genes for surface proteins that may enable the parasite to stick to cells in the urinary and genital tracts.
The scientists also managed to analyze proteins they believe may be connected to the parasite’s hydrogenosome organelle, which also is the target of two drugs used to treat trichomoniasis. They also discovered possible ways the parasite may develop resistance to those medications. 
According to the Centers for Disease Control and Prevention, there are roughly 7.4 million new cases of trichomoniasis in men and women in the US each year. The disease causes vaginal irritation and other symptoms in women, and irritation and other symptoms in the urethra in men. The disease also heightens the risk of contracting HIV.

Cepheid Pays Idaho Tech $3.5M to Settle PCR Patent Suit, Pens Cross-Licensing Pact
Cepheid said last week that it has paid Idaho Technology $3.5 million and penned a cross-licensing agreement to settle a patent-infringement suit related to PCR technology.
Terms of the settlement call for the companies to pay license fees and enable them to continue to make and sell their respective lines for products.
Idaho Technology sued Cepheid in 2005 for allegedly infringing three patents that cover "rapid polymerase chain reaction methods and instrumentation, use of SYBR Green I in PCR reactions, and certain methods of analysis of real-time PCR data,” Cepheid said.
Cepheid said the settlement “resolves all claims” made by Idaho Tech and its licensor, University of Utah Research Foundation, and resulted in a dismissal of the case.
Idaho Technology, based in Salt Lake City, makes instruments for pathogen detection, reagents, and thermocyclers.

The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.