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Broad Institute, Solexa, ABI, Covaris, Translational Genomics Research Institute, Wageningen University and Research Center, Roche, Nestlé, Kluyver Centre for Genomics of Industrial Fermentation, Eurofins Group, NHGRI, NIAID, Decode Genetics, 23andMe, FDA

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Broad Analyzes Three TB Strains Using Solexa/ABI Sequencing
 
As part of an international research project to sequence the genomes of drug-resistant tuberculosis bacterial strains, the Broad Institute has sequenced the genomes of three strains of M. tuberculosis, using a combination of Solexa and ABI sequencing.
 
According to the Broad’s website, the researchers created “12X Solexa/ABI assemblies” for the three strains, isolated from patients in the KwaZulu-Natal province of South Africa.
 
One strain, the so-called XDR strain of Mycobacterium tuberculosis, was linked to more than 50 deaths in a recent outbreak in the region.
 
The researchers said in a press release that they released the data in advance of publication due to the danger of the disease. Initial comparisons of the genome sequences indicate that the drug-resistant and drug-sensitive strains differ “at only a few dozen locations” along the 4-megabase genome. The analysis revealed some known drug-resistance genes as well as some additional genes that may also be important to the spread of TB, they said.
 
"By looking at the genomes of different strains, we can learn how the tuberculosis microbe outwits current drugs and how new drugs might be designed,” said Megan Murray of the Harvard School of Public Health in a statement.
 
Murray also said the research could enable the future development of a rapid diagnostic test for TB that would help prevent the spread of the most virulent strains.
 
Data from the project is available here.
 

 
ABI Tested Covaris DNA Shearing Instrument for 9 Months Prior to Deal
 
ABI tested and evaluated Covaris’ S2 sample prep system for about nine month prior to deciding to sell the instrument along with its SOLiD sequencer, according to an ABI spokesperson (see In Sequence 11/13/2007).
 
“It was determined that the [Covaris’] Adaptive Focused Acoustic technology would bring speed and efficiency to biological and chemical sample preparation that would help SOLiD System customers take advantage of emerging applications for next-gen sequencing and help ensure they receive quality data,” the spokesperson told In Sequence by e-mail.
 
Scientists at Agencourt Personal Genomics used Covaris’ instrument even prior to APG’s acquisition by ABI, Covaris president and CEO Jim Laugharn told In Sequence by e-mail.
 
The list price of the Covaris S2 instrument, which is included in ABI’s $600,000 SOLiD system, is $40,000.
 
Customers of other sequencing platforms can also buy an instrument directly from Covaris and use it for DNA shearing purposes, according to Laugharn.
 
The Covaris S2 instrument shears genomic DNA into short fragments with uniform and consistent size fractions, with a target range between 100 and 200 base pairs for SOLiD fragment libraries.
 
The instrument can also be used for lysing cells and tissues, and to micronize particulates and solvate molecules for chemical samples, such as nanoparticles, according to Laugharn. 
 
Like sonicators, the Covaris technology uses acoustic energy, but it precisely controls and efficiently delivers mechanical energy in a non-contact, isothermal, and rapid manner, he said. The technology is a combination of diagnostic imaging ultrasound signal processing and high intensity, therapeutic ultrasound technologies. 
 

 
TGen Lands $300K Grant to Study Genome of Valley Fever Fungus
 
The Translational Genomics Research Institute said this week that it will use a $300,000 grant from the Arizona Biomedical Research Commission to study the genome of the fungus that causes Valley Fever, a respiratory illness that is estimated to infect around 100,000 people each year.
 
The ABRC awarded the funding to the Phoenix-based institute and the Arizona Department of Health Services. TGen said it will work on the project in concert with its sister branch, TGen North, which is located in Flagstaff and focuses on pathogen genomics.
 
TGen hopes the project will lead to a rapid diagnostic test for the disease and to possible treatments.
 
Valley Fever, which also is called Coccidioides, is caused by inhaling fungal spores that inhabit the desert soil.
 
TGen also said that it expects to receive an undisclosed amount of funding for the project from the Valley Fever Center for Excellence, located in Tucson.
 

 
Wageningen University and Research Center Buys 454 FLX System for Plant Research
 
Wageningen University and Research Center, based in the Netherlands, has purchased a 454 FLX sequencer from Roche to help it study plant genomics, the company said this week.
 
The sequencer will be installed next month at the Bioscience business unit of Plant Research International.
 
The center, known as Wageningen UR, is a collaboration between Wageningen University, Van Hall Larenstein School of Higher Professional Education, and the specialized research institutes of the Dutch Ministry of Agriculture.
 

 
Nestlé Research Center Joins Dutch Microbial Genomics Consortium
 
The nutrition research arm of Swiss food and confection giant Nestlé has joined the Kluyver Centre for Genomics of Industrial Fermentation, a Dutch group that studies microbial genomics and systems biology.
 
The Nestlé Research Center said it became a member to help it “better understand fermentation techniques using beneficial bacteria” in its food-processing business. Located in Lausanne, Switzerland, the NRC said that such knowledge can enable it to develop “novel and better fermented food products by classical techniques.”
 
The Kluyver Centre, which is a Center of Excellence of the Netherlands Genomics Initiative, uses microbial genomics “to improve microorganisms for use in industrial fermentation processes.” The center said one of its goals is to help produce renewable feedstock, food products and ingredients, beverages, pharmaceutical compounds, nutraceuticals, and fine and bulk chemicals.
 
The center is a consortium of Delft University of Technology, Wageningen University and Research Centre, the universities of Leiden and Utrecht, Radboud University Nijmegen, TNO, Wageningen Centre for Food Sciences, Agrotechnology and Food Sciences Group, and NIZO food research.
 
Members of the alliance include Akzo Nobel Diosynth, Applikon, Bird Engineering, DSM, Friesland Foods, Heineken, PURAC, Royal Nedalco, and Tate & Lyle.
 

 
Eurofins Buys Three DNA-Synthesis, -Analysis, and Proteomic Services Shops
 
Eurofins Group this week said it has acquired three undisclosed companies in Germany, Japan, and the US that deal in custom DNA synthesis, analysis, and proteomic services.
 
Though Eurofins did not name the firms, it said together they employ around 200 people and generated more than €20 million ($30 million) in 2006. The company said the acquisitions “should contribute positively” to the company’s financials “from 2008 onwards.”
 
“Through these acquisitions we will, together with our new partners, improve our market penetration in the area of molecular-biological research,” Eurofins CEO Gilles Martin said in a statement.
 
Financial terms of the acquisitions were not disclosed.
 
Eurofins provides testing and support services to the pharmaceutical, food, environmental, and consumer-products industries and to governments.
 
The company generates around $600 million in annual revenues. It employs 7,000 people across 100 sites in 27 countries.
 
At the beginning of this year, Eurofins Medigenomix took over the sequencing business of MWG Biotech.
 

 
NHGRI, NIAID Set Aside $30M in RFAs to Finish Human Microbiome DNA Sequences
 
The National Human Genome Research Institute and the National Institute of Allergy and Infectious Diseases have set aside around $30.5 million in a request for applications for a project that aims to finish compiling a reference set of DNA sequences for the Human Microbiome Project, the National Institutes of Health said last week.
 
The aim of the 4-year project is “to support continued generation of sequenced microbial genomes isolated from the human body … through metagenomic sequencing of the microbial flora at a set of designated anatomical sites of the human body,” according to the NIH.
 
The project, which is part of the NIH Roadmap and is open only to NHGRI and NIAID awardees of large-scale sequencing centers, is expected to fund five awards.
 
“The purpose of this limited competition RFA is to solicit applications for projects for continued large-scale, state-of-the-art production of genomic sequence to generate sequenced, assembled, and annotated microbial genomes isolated from the human body and to explore, through metagenomic sequencing of the microbial flora at a set of designated body sites, the complexity of the human microbiome,” the NIH said in its RFA.
 
The project plans to sequence the genomes of culturable and potentially unculturable bacteria, archaea, fungi, parasites, and viruses from anatomical sites such as the mouth, gastrointestinal and urogenital tracts, and skin.
 
The goal of the HMP is to “extensively characterize the human microbiome and create a technological and data research resource that will enable in-depth study of its variation … and its influence on health and disease,” the NIH said.
 
Besides generating the reference set of genome sequences, the project also aims to perform “initial metagenomic studies that will generate an initial estimate of the complexity of the microbial community at each site, providing initial answers to the questions of whether there is a ‘core’ microbiome at each site and whether variation in the microbiome can be systematically studied; to determine whether variation in the microbiome at a site can be related to human phenotypes, notably disease; to develop new technologies, informatics capabilities, and resources to help develop the field of metagenomics; and to analyze relevant potential ethical, legal, and social issues.”
 
Letters of intent for this RFA are due April 22, 2008, and applications are due May 22. The RFA expires May 23.
 
The project is expected to start April 1, 2009.
 
Additional information can be found here.
 

 
New Consumer Genomic Services Raise Questions About FDA Regulation
 
The recent debut of consumer genomics services from Decode Genetics and 23andMe have raised questions about whether the US Food and Drug Administration will get involved in regulating the services, and if so, to what extent.
 
An FDA official said last week that while the agency is following these new services with interest, it cannot comment further at this time.
 
Officials from Decode, whose service debuted Nov. 16, and 23andMe, which launched its service three days later, stressed that they are not offering consumers genetic tests — such as those offered to consumers by DNA Direct.
  
“We can’t really speak to how the FDA is going to respond, but what we can tell you is that we feel very strongly that we also … are very aligned with the FDA and that we want to do things that are for the good of society and for the benefit of genetic research,” said Linda Avey, co-founder of 23andMe.
 
She added that the firm would remain close to “all of the stakeholders in this area” to try and ensure it is “aligned with all of the objectives and the principles of these bodies.”
 
Likewise, the DecodeMe website tells potential subscribers that the service is not offering genetic tests.
 
“We strongly encourage you not to use this to make medical decisions,” Decode CEO Kari Stefansson said during a recent webcast. “If there is something that raises concerns when you look at your result … you can ask a question that will be answered by our experts.”
 
The firm may also refer subscribers to a genetic counselor.
 
However, genetic testing, and direct-to-consumer genetic testing in particular, has come under increased scrutiny over the past year and a half. Last year, the FDA, the US Federal Trade Commission, and the US Centers for Disease Control and Prevention issued a joint statement warning consumers of some of the pitfalls of at-home genetic testing — including DTC pharmacogenomic testing.
 
Although the statement acknowledged that DTC companies’ pharmacogenomic claims are based on trustworthy science, it warned consumers not to act on that information alone. At-home tests that can give information about a person’s response to certain drugs “are not a substitute for a physician’s judgment and clinical experience,” the agencies said.
 
— Ed Winnick, editor of BioCommerce Week, an In Sequence sister publication.
 

 
Rite-Aid's West Coast Stores to Sell Sorenson's Paternity Test Kit
 
Sorensen Genomics said this week that Rite Aid stores in California, Washington, and Oregon will sell the firm’s Indentigene DNA Paternity Test Kit.
 
According to Sorenson, this marks the first time a DNA test kit has been made available to the public in a retail store.
 
The kit includes a swab to collect cells from the inside of the mouth. The customer then sends the sample, consent forms, and lab fee to Identigene, which is a subsidiary of Sorenson. Results of the test are available three to five business days after Identigene receives the sample and can be obtained via fax, e-mail, or mail.
 
Testing and analysis for the kits is performed by Sorenson in its ISO-accredited testing laboratory.
 
Sorenson said the suggested retail price of the kit is $29.99, and the lab processing fee is $119.
 

 
Metagenomic Study of Termite's 'Bioreactor' Hindgut Shows Promise for Biofuel Apps
 
Researchers working with the US Department of Energy’s Joint Genome Institute published a metagenomic study of the content of the termite hindgut last week.
 
A group led by the DOE’s Joint Genome Institute and the California Institute of Technology conducted metagenomic shotgun sequencing of the hindgut content of a species of tree-dwelling Costa Rican worker termites, and found 12 different phyla of bacteria inhabiting the area.
 
These bacteria are essential to the termite’s ability to digest cellulose and lignite, which impede the use of plants as fuel sources.
 
The JGI and Caltech researchers collaborated with biofuels company Verenium, the National Biodiversity Institute of Costa Rica, and IBM’s Thomas J. Watson Research Center on the study, which they published in last week’s Nature.
 
JGI used Sanger sequencing to generate around 71 million base pairs from 165 specimens, which were computationally reassembled to identify around a dozen different phyla.
 
The research team identified two major bacterial lineages, treponemes and fibrobacters, in the hindgut. Treponemes were known to inhabit the termite gut, “but fibrobacters were an exciting new find," said co-author Phil Hugenholtz, head of DOE JGI's Microbial Ecology Program, in a statement. These bacteria are related to species in cow rumen that are known to degrade cellulose, he said, noting that the combination of microbes makes the termite “a mobile miniature bioreactor."
 
Over 500 genes were located in the hindgut that are related to enzymatic deconstruction of cellulose and hemicellulose. That information has been placed on JGI’s metagenome data management and analysis system for public review.
 
While the studies of the termite gut have identified structures that could be useful in biofuel production, turning that information into an industrial-scale system will be “far from easy,” said JGI director Eddy Rubin.
 
"Termites can efficiently convert milligrams of lignocellulose into fermentable sugars in their tiny bioreactor hindguts. Scaling up this process so that biomass factories can produce biofuels more efficiently and economically is another story,” Rubin added.
 
”To get there, we must define the set of genes with key functional attributes for the breakdown of cellulose, and this study represents an essential step along that path.”

The Scan

Should've Been Spotted Sooner

Scientists tell the Guardian that SARS-CoV-2 testing issues at a UK lab should have been noticed earlier.

For Martian Fuel

Researchers have outlined a plan to produce rocket fuel on Mars that uses a combination of sunlight, carbon dioxide, frozen water, cyanobacteria, and engineered E. coli, according to Gizmodo.

To Boost Rapid Testing

The Washington Post writes that new US programs aim to boost the availability of rapid at-home SARS-CoV-2 tests.

PNAS Papers on Strawberry Evolution, Cell Cycle Regulators, False-Positive Triplex Gene Editing

In PNAS this week: strawberry pan-genome, cell cycle-related roles for MDM2 and MDMX, and more.