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HudsonAlpha involved in cacao genome project

Excerpted from EurekAlert!: “Mockaitis, a biochemist-turned-genomicist, joined the project in early 2009, and quickly set to work with her collaborators to tackle the challenge of sequencing and accurately pasting together the approximately 400 million base pairs of the tree’s genome. Mockaitis’ Cacao Genome Group partners at the U.S. Department of Agriculture’s Subtropical Horticulture Research Station… [Read More]

New clues for understanding a novel cellulolytic process

Fibrobacter succinogenes is an anaerobic bacterium that breaks down plant cell wall biomass in ruminants and converts the cellulose into glucose. Sequenced at the DOE JGI for the Great Lakes Bioenergy Research Center (GLBRC), the 3.8 million base genome was completed and the information submitted to the National Center for Biotechnology Information in late 2009…. [Read More]

Bacterial lessons in rare metal recovery

One of the goals of the DOE’s Genomics:GTL Program is understanding how microbes and microbial communities perform the functions that have helped them thrive in a wide variety of environments and which have applications in the DOE mission areas of bioenergy, carbon cycling and biogeochemistry. British scientists applied information gleaned from Desulfovibrio genomes sequenced by… [Read More]

Brachypodium genome project on The Warsaw Voice

Brachypodium distachyon, commonly called purple false brome, is a model grass that enables researchers to more easily and thoroughly study temperate cereals, such as wheat, barley, rye and oats. These grasses are one of the most important groups of domesticated plants. The sequencing of the nuclear genome of Brachypodium is a big step towards intensified… [Read More]

Sponge genome project on Cosmos magazine

It’s just a blob, with no eyes, no nervous system, no muscle, no gut, no circulatory system, no tissues of any sort really – just cells embedded in a jelly matrix. They’re not even considered true animals. Yet according to the Nature report the sponge genome, which was read by researchers at the University of… [Read More]

Standardizing metagenomic classifications

A five-tier metagenome classification system would  enable genomic researchers to better extract and understand data. (Image from Ivanova et al. Env Microbiol. 2010: 12(7):1803-1805.) Studying the genomes of microbial communities, or metagenomics, has been facilitated in the last few years by advances in sequencing technologies. However, as the DOE JGI’s Natalia Ivanova, Susannah Tringe, Dino… [Read More]

A bacterium for biohydrogen production

Breaking down organic wastes typically involves microbial communities of bacteria and archaea working in concert with methanogens, which remove the hydrogen generated during the degradation process. The interactions between these syntrophic communities are being studied to understand the roles these microbes play individually and and as whole. In the August 2010 issue of the journal… [Read More]

Sponge genome project on Inside Science

According to the new study, which was based on a species of sponge found on the Great Barrier Reef off the coast of Australia, the creature has some 18,000 genes. This is fewer than the number of genes humans possess (currently estimated at about 20,500 genes) — but not far off. A few years ago,… [Read More]

Updating Genomics and Bioinformatics Courses for Undergraduates

Responding to the National Research Council of the National Academies’ call to “involve students in working with real data and tolls that reflect the nature of life sciences research in the 21st century,” the DOE JGI’s Education Program, headed by Cheryl Kerfeld, collaborated with faculty members from several universities around the country to develop bioinformatics… [Read More]

Syntrophic communities sequencing project on SciGuru

In work published in the advanced online version of the International Society for Microbial Ecology (ISME)’s Journal on August 5, an international team of scientists including DOE JGI researchers report the first metagenome analysis of a microbial community grown in an anaerobic methanogenic (methane producing) bioreactor. The microbial community is syntrophic, i.e., certain organisms live… [Read More]