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Applied Biosystems, Stanford University, University of Queensland, Cogenics, 454 Life Sciences, Limagrain, Febit, USDA, Integrated Genomics, TMO, Promega, 23andMe, Washington University, University of Colorado at Boulder, Research Triangle Institute, Univ

Australian, US Teams Publish First Studies Involving ABI SOLiD Platform
Two research teams, from the US and Australia, have independently published the first peer-reviewed studies involving Applied Biosystems’ SOLiD sequencing technology.
The first study, published online last month in Genome Research by Andrew Fire at Stanford University School of Medicine and his colleagues, used the technology to generate a high-resolution map of more than 44 million putative nucleosome cores in C. elegans.
The other study, published online in Nature Methods last week by a team led by Sean Grimmond from the University of Queensland in Australia, used the SOLiD platform to profile the transcriptomes of undifferentiated mouse embryonic stem cells and embryoid bodies.
Both studies also involved researchers from Applied Biosystems.

Cogenics, 454, Limagrain Collaborate to Discover SNPs in Crops
Cogenics, 454 Life Sciences, and French plant breeder Limagrain Verneuil Holding will collaborate to develop methods for large-scale SNPs discovery that could be used to engineer better crops, 454 and Cogenics’ parent company Clinical Data said this week.
The first project will focus on wheat. Cogenics will develop a genome complexity reduction assay to select gene-rich portions of a crop genome across multiple variants of the species. The company will then “work in close concert with” 454 to sequence 2 gigabases of the wheat genome using the GS-FLX sequencer.
The project, which will be conducted by a unit of Cogenics in France, is the first step in a two-stage process, through which the companies plan to identify molecular markers that are linked with desirable characteristics. Later, Cogenics plans to offer its complexity reduction assay to other groups.
The second stage, which involves large-scale genotyping, will be managed by Limagrain.

Febit Receives US Patent for Genome Capture Method
Febit has received a US patent for a microfluidic microarray-based method to extract DNA and RNA, the Heidelberg, Germany-based company said last week.
The patent, No. 7320862, forms the basis for a method called hybselect for selecting DNA regions from the genome.
The new method can be used in conjunction with new high-throughput sequencing methods, according to the company.
Similar patents in Europe and other countries will follow soon, Febit said.

USDA Releases Genomic Data from 150 Bird Flu Viruses
The United States Department of Agriculture has released the complete genome sequences of 150 different avian influenza viruses through GenBank.
The USDA said last week that the sequencing data is part of the federal government’s initiative on avian influenza, and that this information will be combined with studies that compare the viruses’ ability to infect poultry such as chickens, turkeys, and domestic ducks.
The research that generated the data was conducted by the USDA’s Agricultural Research Service’s Southeast Poultry Research Laboratory, the University of Georgia, Ohio State University, the University of Delaware, and the University of Alaska-Fairbanks.
"The project's ultimate goal is to sequence 900 avian influenza viruses from the SEPRL repository," David Suarez, a researcher with SEPRL, said in a statement. "These include avian influenza viruses collected from both poultry and wild bird species in the United States and around the world.
"This sequence information, deciphered by our large team, will help researchers better understand virus biology and improve diagnostic tests for avian influenza viruses," Suarez added.
Houston-based SeqWright provided sequencing services for the project.

Integrated Genomics Extends Software License to Biofuel Firm TMO
Integrated Genomics has extended a license agreement with TMO Renewables for IG’s ERGO software for use in a cellulosic ethanol development program.
Under the agreement, TMO will use IG’s software to identify pathways that can be used to upgrade TMO’s cellulosic ethanol program. Initially, the company plans to focus on its membrane transport proteins in its thermophilic strain.
The software is used to integrate biological data from genomics research, gene expression studies, genetics, and from sources in literature.
TMO’s ethanol production uses “high-temperature process organisms capable of producing bioethanol quickly and efficiently from a wide diversity of sustainable cellulosic feedstocks,” said Kirstin Eley, external program manager at TMO.
The ERGO software contains over 1,350 genomes that are in various stages of completion and more than 6,000 networked metabolic and non-metabolic pathways.

Promega Gets CE Mark for DNA Purification System
Promega said last week that its Maxwell 16 system for DNA-based tests has received the CE Mark, enabling it to be marketed for diagnostic use throughout the European Union.
Madison, Wis.-based Promega said that the CE Mark would be particularly helpful for European labs conducting molecular pathology and transplant HLA to be compliant with in vitro diagnostic directives in their countries. The firm noted that the system already meets general purpose medical device requirements in the US.
The Maxwell 16 system can purify up to 16 DNA samples simultaneously in about 30 minutes with higher yield and greater consistency than similar methods, according to Promega. The instrument is a small bench-top unit that is roughly the size of an open laptop computer, the company said.

23andMe Offers Customers Participation in Research Project
23andMe said last week that it has launched 23andWe, a program under which its customers can enroll in company-directed research projects.
According to the firm, the goal of the program is “to conduct large-scale studies powered by a web-based community of diverse individuals who are willing to share information, on a confidential basis, about their health and other personal traits.”
Under the program, 23andMe will collect genetic and phenotypic information through DNA analysis and online surveys for genome-wide association studies.
23andMe will evaluate and approve research proposals for inclusion in the 23andWe program. Company researchers will then develop online surveys for collecting phenotypic information from customers who want to participate in the study. 23andMe researchers will analyze the data to determine the genetic bases for certain traits or diseases.
The company will provide study participants with regular updates about 23andWe projects and information about how they can become further involved in genetic research.
23andMe will conduct one of the first studies in partnership with the Parkinson’s Institute of Sunnyvale, Calif. The company expects to add more initiatives on a regular basis.

WUSTL, UC Boulder to Study Microbes Involved in Inflammatory Bowel Disease
Researchers at Washington University in St. Louis and at the University of Colorado at Boulder will partner with the Crohn’s and Colitis Foundation of America to study how microbes in the human gut contribute to inflammatory bowel disease, the foundation said last week.
The foundation’s Gut Microbiome Initiative will use metagenomic sequencing and informatics to develop new tools that can be used in the development of cures for chronic digestive diseases.
Jeffrey Gordon, director of Washington University’s Center for Genome Sciences, will serve as principal investigator on the project, which will focus on identical and fraternal twins and their mothers first, and then on IBD patients.
Gordon said in a statement that "knowing how to rapidly and accurately define the nature and operations of the gut microbiome should help investigators develop new insights about the mechanisms that lead to IBD, better ways to diagnose and categorize IBD, new therapeutic approaches, and ultimately, new ways to prevent these disorders in susceptible individuals.”
University of Colorado’s Rob Knight will lead a group developing data-mining and statistical and visualization tools that can handle the “complex and massive datasets” the genomics research will generate.
The tools and the gut microbiome datasets will be made publicly available in order to be of use to other researchers, CCFR said.
CCFR also said it expects the efforts will help in the development of new molecular diagnostics.

RTI Wants Researchers Involved in Developing GWAS Measures
The Research Triangle Institute plans at the end of June to release a survey for genomics researchers, healthcare specialists, and a range of other experts, which it will use as part of a collaboration with the National Human Genome Research Institute to develop consensus measures that can be used in genome-wide association studies.
RTI said last week that it is working with the NHGRI, through $6.8 million in grant funding over three years, to identify up to 20 research disciplines that are significant for research and public health, and will develop 15 standard measures for each of these disciplines. The goal is to obtain information about phenotypes and relationships about genetics, environment, health, and disease for use in GWA studies and other large-scale genomics research programs.
The collaboration aims to improve the ability of research groups to combine data and to increase the size of their population samples and enhance the ability to detect genes that are associated with common, complex disease.
The first of these PhenX (Phenotypes and eXposures) surveys will present proposed measures for a domain focused on demographic characteristics of interest such as age, sex, ethnicity, ancestry, education, income, and employment status. But the surveys will not be the only way the PhenX program develops specifications for the measures; these decisions also will be made through working groups and a steering committee.
"The participation and collaboration of experts from diverse scientific and health disciplines are essential to making this project a success," Carol Hamilton, who is director of Bioinformatics at the North Carolina-based RTI and principal investigator on the project, said in a statement.
"The ability to combine the results of these studies is critical to furthering our knowledge of the many complex relationships between genetics, environmental factors, health and disease," said Jonathan Haines, who chairs the PhenX steering committee.

Metagenomics Uncovers Unexpected Sea Floor Microbial Diversity
There are more microbes on the sea floor than in the waters above, new research suggests.
In a paper published online last week in Nature, a group of researchers from across the country used quantitative PCR, metagenomics, and phylogenetic analysis to quantify the microbial diversity in unsedimented mid-ocean ridges in the Pacific Ocean and near Hawaii. Based on these samples, the researchers concluded that there are thousands to tens-of-thousands of times more bacteria residing on the sea floor than in the vast sea above.
The region — a seam of glassy basalt rock in the mid-ocean that’s some 37,000 miles long — represents “potentially the largest surface area for microbes to colonize on Earth,” senior author Katrina Edwards, a geomicrobiologist at the University of Southern California, said in a statement.
“These scientists used modern molecular methods to quantify the diversity of microbes in remote deep-sea environments,” said David Garrison, director of the National Science Foundation’s biological oceanography program, who was not involved in the study. “As a result, we know that there are many more such microbes than anyone had guessed.”
Previous research indicated that there was microbial life on the sea floor. But until now, no one had quantified these microbial communities. To quantify these microbes, Edwards and her colleagues sampled basalt sea floor lava that was up to 20,000 years old, using qPCR to determine the bacterial and archeal population densities in different samples.
This data, combined with the team’s catalyzed reporter deposition-fluorescent in situ hybridization experiments suggested that bacteria outnumbered archea on the sea floor. Meanwhile, 16S ribosomal RNA profiles helped the team tease out the specific taxonomic groups present in the sea floor bacterial communities.
The researchers found more than 20 taxonomic groups from sea floor basalt. The Proteobacteria phylum was particularly well represented, although the team also detected sequences from Plantomycetes, Actinobacteria, Bacteroidetes, Acidobacteria, Verrucomicrobia, and other phyla.
Their results suggested that the East Pacific Rise contained more “bacterial richness” than other marine habitats. For instance, they estimated that the bacterial diversity was similar to that found in soil microbial communities. The team found similar bacterial richness in samples collected from the sea floor lava offshore from Hawaii’s big island.
Initially though, it was unclear how the bugs manage to eke out enough energy to survive in that environment, where there is very little organic carbon. The team speculated that the basalt on which the microbes grow may provide them with energy through so-called alteration reactions, in which the basalt is exposed to oxidation and hydration. Indeed, laboratory measurements of basalt chemical reactions seemed to be consistent with that notion.
And, the team says, the findings may inform future studies of everything from the carbon cycle under the sea to evolution. For instance, many have proposed that early life began in shallow water. But these results raise the possibility that life emerged deep in the ocean.
In the future, Edwards and her team plan to set up a microbial observatory some 15,000 feet below sea level to investigate microbes on and below the sea floor. “It is my hope that people turn their heads and notice that there’s life down there,” Edwards said.

Ancient Human Hair Exposes Bits of Greenland's Population History
Researchers have sequenced the entire mitochondrial genome of an ancient human and, in so doing, have gotten a glimpse into the history of early populations living in the far North.
In a paper published online last week in Science, researchers from the University of Copenhagen and elsewhere extracted and decoded mitochondrial DNA from a mass of human hair that had been hidden in Greenland’s permafrost for thousands of years. The results suggest that the Saqqaq, the earliest known culture in Greenland and the extreme American North, were not related to present day Native Americans or Greenlanders. Rather, the group appears to have originated from islands in and around the Bering Sea.
“The Saqqaq probably weren’t Native Americans and they probably weren’t the ancestors of modern Greenlanders,” lead author Tom Gilbert, an evolutionary biologist at the University of Copenhagen, told In Sequence’s sister publication GenomeWeb Daily News last week.
There is evidence that humans lived in Greenland and the New World’s distant north at least 4,000 years ago. Since then, there have been distinct populations of ancient humans, termed “Paleo-Eskimos,” in this region at different moments in history. But for the most part these cultures are known only from cultural artifacts excavated in the North, Gilbert explained. Consequently, there has been heated debate over how many times people populated the North and where each of these populations originated.
For instance, some speculated that the Saqqaq were related to Native Americans, while others thought they were related to the Siberian population that gave rise to modern Greenlanders, Gilbert said. Still others believed the group was distinct from both Native Americans and Siberians.
Adding to the mystery was the fact that no Saqqaq human remains were discovered in Northern Canada or Greenland. That changed in the 1980’s, when a handful of bones and a clump of human hair — preserved in permafrost for some 3,400 to 4,500 years — was discovered in the Disko Bay fjords in the north-west part of Greenland. But the bones were poorly preserved, Gilbert said, and it took several years before researchers turned their attention to the soda can-sized chunk of hair.
Initial experiments suggested that the samples hadn’t been contaminated by modern human DNA. Rather, based on the mitochondrial hypervariable sequence, the Saqqaq individual appeared to be unrelated to modern European and Greenland Inuit populations.
Although there was some DNA fragmentation in the hair sample, Gilbert said, there was enough DNA to do genetic analysis. For this study, Gilbert and his colleagues sequenced the entire mitochondrial genome to about 10.7 times coverage using 454 Life Sciences’ FLX sequencer.
Overall, the researchers noted that the Saqqaq mitochondrial genome differed from the latest Cambridge Reference Sequence at 40 SNPs. Although some of these seem to represent damaged DNA, most seemed to correspond to genuine sequence differences. The sequence also contained a previously unrecognized heteroplasmic site.
To get a better idea of how the ancient Saqqaq individual was related to living populations, if at all, the team compared the mitochondrial sequence with those from other populations. To do this, they sequenced mtDNA from 14 modern Greenlanders and relied on available sequence data for other populations, such as Native Americans and northeast Asians.
Based on this comparison, Gilbert and his colleagues concluded that the Saqqaq haplogroup was different from that of Native Americans and from that of the so-called “Neo-Eskimo” populations living in the far North for the last 1,000 years or so.
“It’s never been observed in Native Americans and it’s never been observed in Greenlanders,” Gilbert said. “It’s a completely different mitochondrial group.”
Gilbert was quick to acknowledge the possibility that the groups are related and that present day Native Americans or Greenlanders have lost the Saqqaq genetic signature. But, based on the information available at this time, the ancient Saqqaq individual seems to be most closely related to Aleut populations in the Commander Islands and a sub-set of the Sireniki Yuit, a population in Siberia.
Even so, Gilbert noted, it’s difficult to draw firm conclusions about entire populations based on one individual. And because the team looked strictly at mitochondrial sequence for this study, it can only predict Saqqaq maternal lineage. In the future, the group plans to do further genetic analysis, including Y chromosome sequencing that will give them a better handle on Saqqaq paternal lineage as well.
— By Andrea Anderson; originally published by GenomeWeb Daily News

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.