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NIH, Venter Center, ABI, US Department of Energy, CLC Bio

Sequencing Projects Among Eight NIH Awards for Cancer Genome Atlas
The National Institutes of Health said this week that it has awarded eight two-year awards worth a total of $3.4 million to support the development of new technologies — including sequencing-based approaches — for the Cancer Genome Atlas pilot program.
The Cancer Genome Atlas, a joint initiative of the National Cancer Institute and the National Human Genome Research Institute that kicked off in late 2005, aims to "test the feasibility of a large-scale, systematic approach to identifying the changes that occur in the genomes of cancer cells," NIH said in a statement.
"The goal is to generate genomic information that the research community can use to develop new and improved strategies for detecting, treating and, ultimately, preventing cancer," NIH said.
The following investigators and institutions will use the NIH funds for a number of studies that will generate large amounts of data focused on cancer genomics:
  • Baylor College of Medicine's Aleksandar Milosavljevic will receive $413,000 to develop methods based on next-generation sequencing platforms to investigate structural variations in the genomes of cancer cells.
  • City of Hope/Beckman Research Institute's Gerd Pfeifer will receive $465,000 to study DNA methylation in cancer genomes.
  • Benjamin Tycko, of Columbia University, will receive $443,000 to use high-density oligonucleotide arrays to characterize genomic aberrations and DNA methylation.
  • Timothy Bestor, also at Columbia University, will receive $362,000 to develop methods for high-throughput analysis of DNA methylation.
  • Johns Hopkins University's Andrew Feinberg will use $464,000 to develop new approaches for investigating allele-specific gene expression patterns.
  • Nimblegen Systems will use a $415,000 grant to use high-density oligonucleotide arrays to select genomic regions for DNA sequence analysis.
  • Stanford University's Ronald Davis will receive $429,000 to develop methods for high-throughput isolation of genomic regions for DNA sequence analysis.
  • Peggy Farnham of the University of California, Davis, will use $418,000 to develop ChIP-chip assays to study cancer-associated changes in genomic regions that are important in gene regulation, using small fragments of cancer tissue.

Venter Center Successfully Transplants Genome of One Bacteria into Another
Researchers at the J. Craig Venter Institute have transplanted an entire genome from one bacterial cell into the cell of another bacterium in what could be a significant milestone in synthetic genomics.
In a conference call with reporters last week, Venter and JCVI colleagues described how they transferred the genome, a breakthrough that could eventually lead to the creation of new and man-made organisms.
The research is part of Venter’s plan to use such custom-made organisms as constituents of new biofuels.
In the experiment, published in last week’s Science, the JCVI researchers stripped all proteins from M. mycoides and transplanted the resulting naked DNA into M. capricolum, a highly similar bacterium and one without a cell wall to prohibit the transfer. Both bugs are goat pathogens. M. mycoides has around 1,214,067 base pairs.
The researchers sequenced the bacterial genomes and used their reactions to an antibiotic to determine if the transplants were successes or failures. 
The experiment raised many questions. For instance, among the cells in which the transplant took hold, what caused them to “boot up,” as Venter put it, and become the other organism? Also, there is a question about what exactly happens to the replaced DNA, and what controls its destination.
“We don’t have any idea yet really how widely applicable this would be,” according to JCVI researcher Clyde Hutchison. “Our hunch is one could make it work for other systems, but you could think of another barriers.”
Though “synthetic biology has yet to be proven,” Venter said the bacterial transplant is “a step closer to knowing it’s provable.”
Of course there will be barriers in progressing from the transplant of this simple organism's genome into another, and the development of designer bacteria with particular functions, said researcher Hamilton Smith, group leader in the JCVI’s synthetic biology division.
But “once that first barrier is passed we think what’s taken several years to get to this point will take only months to get to the next stages,” Smith added.
The genome transplant report came a few days after the Kavli Foundation, a research-focused nonprofit in California, made a public call for an international effort to push synthetic genomics, which the foundation called a coming “revolution in biology.”
"We face daunting problems of climate change, energy, health, and water resources,” the joint statement said. “Synthetic biology offers solutions to these issues: microorganisms that convert plant matter to fuels or that synthesize new drugs or target and destroy rogue cells in the body."
The group called for greater efforts to create new hardware and new software and an increased push in nanotechnologies, as well as enhanced social involvement with the life sciences, and synthetic biology in particular.
The complete Kavli report can be seen here
— Matt Jones

ABI Contributes Sequencer, Other Tools to Help Egypt, Discovery Channel Identify Mummies
Applied Biosystems has provided technology and training to the government of Egypt to help it outfit a lab aimed at using DNA tools to identify mummies.
ABI said last week that it stocked the lab with DNA analysis instruments, reagents, and software. Among the technologies supplied by ABI are a 9700 thermocycler, a 3130 Genetic Analyzer, and a PCR amplification kit.
Based in the Egyptian Museum of Cairo, the lab will use the technologies to identify the mummy of Hatshepsut, a powerful Egyptian queen and pharaoh of the 15th Century BC.
The lab, which has been running tests on the instruments since April, will also seek to identify other mummies that have been removed from their tombs, and to “clarify familial relationships within and between Egypt’s ancient dynasties.”
In a statement, Nicola Oldroyd, an ABI senior forensic specialist, said that “initial results are very promising as both nuclear and mitochondrial DNA have been retrieved and amplified for these mummies.”
ABI was enlisted for the project by the Discovery Channel, which will air a two-hour special, called “Secrets of Egypt’s Lost Queen,” in July that documents the search for Hatshepsut and the quest to positively identify her remains.
Hatsepshut’s death and the possible disappearance of her remains have long posed a mystery to Egyptologists.

DOE Awards $375M to Three Systems Bio Biofuel Research Centers
The US Department of Energy plans to award as much as $375 million to help create three Bioenergy Research Centers that will use biomolecular technology, including genomic tools, to develop cost-effective biofuels from cellulosic ethanol, the DOE said last week.
The three centers will be: the Bioenergy Science Center at Oak Ridge National Laboratory in Oak Ridge, Tenn.; the Joint Bioenergy Institute at Lawrence Berkeley National Laboratory in Berkeley, Calif.; and the Great Lakes Bioenergy Research Center at the University of Wisconsin in Madison. Each facility will receive $125 million over five years.
These university-affiliated labs also will partner with more than 15 other universities, seven national laboratories, and an undisclosed number of corporations, the DOE said. 
A major focus of the centers will be to understand how to “reengineer biological processes to develop new, more efficient methods for converting the cellulose in plant material into ethanol or other biofuels that serve as a substitute for gasoline,” the DOE said.
Timothy Donohue, who will lead the ethanol study efforts at the Great Lakes center, said the main thrust of the joint project is to use genomics and genome-based computational methods to “remove the bottlenecks” that limit the production of bioenergy, particularly the production of ethanol.
Jay Keasling, leader of the JBEI’s Physical Biosciences Division, said his team will focus on enzymatic processes involved in cellulose biology, development, and in bioenergy production. Keasling also said JBEI could pursue microbial metabolomics studies.
Donohue also suggested the development of new strains of plants “that will not look like the food you have in the supermarket,” which may be used in bioenegy and biomass production.
The centers are expected to begin work in 2008 “subject to the finalization of contract terms and congressional appropriations,” DOE said.
Additional information can be found here.

CLC Bio Software to Support South American Biodiversity Database Project
A South American effort to create a database of sequence data from the continent’s “vast biodiversity” will use CLC Bio’s software, data-analysis tools, training, and other services, the company said last week.
The database project, called Patrimonio Genomico y Saberes Locales (PGSL) — roughly translated to mean “Genomic Heritage and Local Wisdom” — kicked off with a recent inaugural meeting in Ecuador.
The goal of the PGSL is to harvest and preserve sequence data from species throughout the continent and build a database similar to GenBank, EMBL, and DDBJ, CLC Bio said.
The project also intends to investigate and preserve traditional therapeutic healthcare substances that native civilizations in South America have used for thousands of years.
Another important issue for PGSL is to minimize “bio-piracy” — the act of non-native scientists harvesting and using genetic materials from South America for copyrighted products.
CLC Bio said it is supporting the program via a new educational software package and consultancy services.
Founding partners include Pontificia Universidad Católica del Ecuador; Universidad Politecnica Salesiana, Ecuador; Instituto de Biomedicina of Universidad Central del Ecuador; Pontificia Universidad Javieriana, Colombia; Sociedad Peruana de Derecho Ambiental, Peru; Universidad Catolica Andres Bello, Venezuela; and others. 

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.