Archive

Our Science
Home › Science Highlights

A mechanism for de novo intron insertion

Introns are the parts of a gene sequence that are not expressed in the protein. In the August 30 issue of Nature Communications, a team led by DOE JGI’s Eukaryote Program head Dan Rokhsar and Uffe Hellsten describe a potential mechanism by which introns have been added to a genome sequence since what they refer… [Read More]

A “meraculous” way to conduct whole-genome assemblies

The dramatic shift in sequencing technologies that allows genome researchers to generate the equivalent of a single human genome in days rather than the decades it took multiple organizations to complete a single one has also shifted the bottleneck from sequence production to sequence assembly. For example, the Sanger platform routinely produced reads 700 basepairs… [Read More]

Toward a Better Understanding of Soil-Microbe Interactions

In the August 2011 issue of the Journal of Bacteriology, a team of researchers led by DOE JGI’s Patrick Chain at Los Alamos National Laboratory focused on a microbe that can help or harm as the case may be. Ochrobactrum anthropi thrives in a variety of habitats including polluted soil, plants and even higher mammals…. [Read More]

Another Brown Mercury Producer Genome Sequenced

In the August edition of The Journal of Bacteriology, a group of scientists including several DOE JGI researchers and longtime collaborator Judy Wall of the University of Missouri described the genome for Desulfovibrio africanus, a sulfate-reducing bacterium isolated from Namibia that doesn’t require oxygen for its survival. Like the Desulfovibrio species sequenced as recently as… [Read More]

Sweetening the Biofuels Production Process

Currently, converting cellulosic biomass into biofuels is inefficient and costly.  One of the barriers to reducing costs and yields is that xylose, a five-carbon sugar that represents nearly half of available sugars in plant (in the form of hemicellulose), is extremely difficult and time-consuming to break down using enzymes sourced from conventional yeast strains. In… [Read More]

Ethanol Contaminant Could Assist Production Efficiency

An Ethanol plant in Bairstown, Iowa (Courtesy of USDA) In the August edition of The Journal of Bacteriology, researchers led by long-time collaborator David Mills of the University of California Davis, and including DOE JGI’s Alex Copeland, Olga Chertkov and Lynne Goodwin, announced the completed genome sequence of Lactobacillus buchneri and has now been made… [Read More]

Destroyer of Houses Harnessed for Biofuel Production

Although people rarely see the positives when their wooden houses begin to rot, scientists at the DOE JGI have found a silver lining in this destructive phenomenon. Through DNA sequencing and a comparative analysis with other fungi that DOE JGI has characterized, researchers have homed in on the mechanisms that the brown rot, Serpula lacrymans,… [Read More]

Efficiency Improvements in Biofuels Production

To overcome the difficulties of converting cellulosic biomass into high energy-content fuel, researchers have been seeking to improve various stages of the process. One big obstacle that stands in the way is that most enzymes are inefficient at breaking down biomass when in the presence of ionic liquids, solvents that have proven effective at treating the… [Read More]

Consortium Drives Genome Standards

As technology for sequencing genomes has become cheaper and more widely accessible, there is a greater urgency to institute a standardized, comprehensive language for researchers to share their findings. The Genomic Standards Consortium (GSC), an open-membership organization, is building a culture of collaboration to achieve greater efficiencies by spending less time combing through and interpreting inconsistent… [Read More]

GreenCut2: Algorithm to ID Plant Protein Functions

Researchers use genome sequencing to inform various cellular processes in land plants and algae, including the details of photosynthesis.  Despite the access to an increasing number of plant genomes (most of which have been generated by the DOE JGI), it remains difficult to correlate protein information with function, until now.  For example, identifying the role… [Read More]