The Department of Energy’s Joint Genome Institute has already churned out over 40 trillion bases of sequence data this year, using a variety of next-generation sequencers for applications including de novo whole genome sequencing, RNA-seq, ChIP-seq, methylation sequencing, and even some single cell sequencing.While the majority of its work is currently in whole genome sequencing,…
Protein studies offer clues on how palm worms can take the heat
Hydrothermal vents behave like geysers at a national park, except that they erupt deep underwater in the Pacific and Atlantic Oceans. Though the water that shoots out of these vents can reach temperatures as high as 300°C (572°F), many animals and other organisms thrive in the surrounding area. Two such extremophiles are “palm worms,” named…
DOE JGI’s IMG/M data system in Berkeley Lab’s release on the Human Microbiome Project
Berkeley Lab’s role in mapping the human microbiome revolves around big data, both analyzing it and making it available for scientists to use worldwide…. Berkeley Lab scientists developed and maintain a comparative analysis system called the Integrated Microbial Genomes and Metagenomes for the Human Microbiome Project (IMG/M HMP). It allows scientists to study the human microbiome…
Dekkera yeast project in Science Daily
The yeast Dekkera bruxellensis plays an important role in the production of wine, as it can have either a positive or a negative impact on the taste. Researchers at Lund University in Sweden, among others, have analyzed the yeast’s genome sequenced by the US Department of Energy Joint Genome Institute, giving wine producers the possibility to take…
Comparative genomics method to tag novel nitrogen-fixation genes
Nitrogen is crucial for plant growth but plants cannot harness it directly from the atmosphere. In the United States, legume crops such as soybeans and peas rely on nitrogen fertilizers to boost yields; in 2007, 13 million tons of industrially-produced fertilizers were applied. Soil bacteria such as Sinorhizobiummeliloti have a symbiotic relationship with plant hosts…
Kbase and DOE’s Susan Gregurick in GenomeWeb’s BioInform
Kbase is currently in alpha release and is targeted for full production release in early 2013.The community-driven and scalable open-source system is intended to provide a framework for evidence-based functional annotation of genome sequences. It will also enable the creation of metabolic and regulatory models that may be used to generate scientific hypotheses; as well…
Lessons from the adaptive strategies of a fungal pathogen
by ressaure Coniferous forests in Europe and North America have suffered several hundred million dollars in damages annually from the fungal pathogen Heterobasidion annosum. Aside from the economic losses, scientists are concerned by the white rot fungus that not only breaks down the wood for nutrients, but also releases the carbon dioxide trapped in the…
Foxtail Millet Genome an Improved Reference for Switchgrass
The DOE is interested in switchgrass as a prospective biofuels feedstock, but its genome is complicated because it has multiple copies of its chromosomes. As the world leader in sequencing plants and other organisms for their relevance to DOE missions, the JGI has sequenced switchgrass and several other plants that are candidate plant feedstocks; other…
Foxtail millet project in GenomeWeb Daily News
From Genomics in the Journals: “Bennetzen and colleagues from the University of Georgia, the HudsonAlpha Institute, the Department of Energy’s Joint Genome Institute, and elsewhere used Sanger sequencing complemented by high-throughput sequencing methods to generate a high-quality, 400 million base reference genome for foxtail millet. “ Read more at GenomeWeb Daily News
Foxtail millet project in Biofuels Digest
In an attempt to piece together the switchgrass genome, the DOE Joint Genome Institute (JGI) in an international partnership with includes the DOE BioEnergy Science Center (BESC) and the DOE Joint BioEnergy Institute (JBEI) has sequenced plant genomes of related candidate bioenergy crops such as sorghum and the model grass Brachypodium but may have found the missing…