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Short Reads: Jan 6, 2009

Helicos to Pay Down $10M from Loan
Helicos BioSciences said in a regulatory filing last week that it planned to make a $10 million pre-payment on a $20 million loan from GE Capital on or before Dec. 31, 2008.
The pre-payment is part of a third amendment to the loan and security agreement, originally signed Dec. 2007 between Helicos, “certain lenders,” and GE Capital.
The third amendment allows Helicos to make the $10 million pre-payment without incurring any penalties. In connection with the payment, Helicos will pay a fee equal to 2 percent of the initial $10 million term loan — in lieu of the 4 percent final payment fee related to the pay down amount — which is payable either on Jan. 31, 2011, or on the maturity date for the subsequent term loan made to Helicos pursuant to the second amendment in June 2008, whichever is earlier.
Under that second amendment, Helicos received the second $10 million from the lenders. It also paid GE Capital a fee of $150,000 to serve as agent for the credit facility, and issued warrants for the rights to acquire up to 110,000 shares of its common stock for an exercise price of $4.80 per share.
Under the third amendment filed last week, Helicos’ obligations under the loan agreement are no longer secured by a cash amount of $10 million. Such obligations are secured by “substantially all of the company's personal property, including the pledge of the stock of the company's wholly-owned subsidiary, and proceeds of any intellectual property, but not by the company's intellectual property,” according to the filing.

NSF Pledges $12M in '09 for Research to Fill in Tree of Life
The National Science Foundation wants to continue to fund studies that will help use the “flood of information” from genome studies to fill in the Tree of Life, NSF said two weeks ago.
NSF will spend $12 million in 2009 to continue funding the “Assembling the Tree of Life” program, which is focused on supporting the long-term goal of constructing “evolutionary history for all species of life.”
To that end, the NSF plans to back between three and six awards with up to $3 million for up to five years for “innovative research that will resolve evolutionary relationships for large groups of organisms throughout the history of life,” according to the NSF’s program announcement.
Researchers also may receive funding for projects including data acquisition, analysis, algorithm development, and computational phylogenetics and phyloinformatics.
Assembling a phylogeny for all 1.7 million described species will require “a magnified effort, often involving large teams working across institutions and disciplines,” NSF said.
More information about the NSF’s “Tree of Life” funding program is available here.

DNAVision Expands Facilities with Plans for Adding Next-Gen Sequencing and Other New Services
Belgian applied genetics and genomics services company DNAVision announced this week that it has doubled its laboratories and office space in Charleroi-Gosselies, Belgium, adding five new laboratory areas dedicated to cell culture and nucleic acid extraction.
The move is aimed at augmenting the company’s RNA- and DNA-based analytical techniques, expanding its biopharmaceutical services portfolio, and providing new GMP- certified assays.
DNAVision said that its DNAVision AgriFood subsidiary, a spin-off of the University of Liège, will move to a new facility at the end of this month. Along with biosafety level 3 laboratory services, DNAVision said it will also provide a range of new services, including next-generation sequencing, though it did not provide details on the sequencing platform it plans to use.
In a statement this week, DNAVision CEO Jean-Pol Detiffe said that the firm’s revenues increased more than 50 percent in 2008. He also noted that the company plans to launch consumer genetic services this year.
DNAVision, a spin-out of the University of Brussels, provides nucleic acid extraction and purification services. Most of these extraction services are accredited by the Belgian accreditation body BELAC.

$17M EU Project to Study Dog Genomes to Gain Insight into Human Disease
The European Commission has awarded €12 million ($16.9 million) to a consortium of European research centers through 2012 to conduct genome-wide association studies on several dog breeds in hopes of gaining a better understanding of human diseases.
The program, called Lupa, is funded under the EC’s Seventh Framework Program. It involves 20 veterinary schools in 12 European countries that will collect 10,000 DNA samples from purebred dog species that have genetic diseases and from healthy dogs.
The researchers will compare the genomes of healthy and sick dogs within single breeds to identify SNPs that could help target genes responsible for any of 18 different diseases, including cancer and heart disease, inflammatory disorders, and neurological disorders.
“We have decided to focus on certain areas and to standardize the characterization of these diseases,” Uppsala University Professor Leif Andersson said in a statement from the EC.
Some of the breeds involved in the project include the Golden Retriever and German Shepherd for cancer studies, the English Cocker Spaniel for aggressive behavior, the Doberman and Boxer for hypothyroid diseases, Great Danes and Irish Wolfhounds for cardiovascular disorders, and the Greyhound and Collie as part of a monogenic disorders package.

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.