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…
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…
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…
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,…
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…
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…
Sponge genome project on Cell Daily News Aggregator
The sponge, which was not recognized as an animal until the 19th century, is now the simplest and most ancient group of animals to have their genome sequenced.In a paper appearing in the August 5 issue of the journal Nature, a team of researchers led by Daniel Rokhsar of the University of California, Berkeley, and…
Sponge genome project on U Wire
A team of scientists – led by Daniel Rokhsar, UC Berkeley professor of molecular cell biology and physics and program head for computational genomics at the U.S. Department of Energy’s Joint Genome Institute – assembled a draft genome sequence of the Amphimedon queenslandica, a sponge native to the Great Barrier Reef, which researchers said provides…
DNA Sequencing Reveals Complex Microbial Quid Pro Quo for Managing Carbon and Waste Streams
WALNUT CREEK, CA—Microbial communities drive many of the important processes on the planet and DNA sequencing is emerging as a powerful tool for shedding light on their complex dynamics. Applications abound, ranging from rendering plant biomass into biofuel, to understanding how carbon is managed in the land, sea, and atmosphere, to how these communities can…
Sponge genome project on Astrobiology magazine
Sponges are an ancient group, with fossils dating back at least 650 million years. They are thought to have been the first group of animals to branch from all the others. Therefore, genes shared by sponges and other animals must have been present in the common ancestor of all metazoans. This ancestor would have evolved…