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Content Tagged "metagenomics"

Overcoming short-read genome sequence assembly challenges

The genome assembly challenges posed by short sequence reads from sequencing platforms such as 454/Roche and Illumina are well-documented; the lack of reference genome data can hinder attempts to put together the myriad of short DNA sequences. Researchers from the Georgia Institute of Technology and the DOE JGI wanted to determine the impact of short… [Read More]

Analysis of a TCE-degrading metagenome

Groundwater sites contaminated with compounds such as trichloroethene (TCE), a pervasive organic groundwater pollutant often used by industry as cleansers or degreasers.Dehalococcoidesbacteria, often found in a community of other microorganisms at groundwater sites contaminated with these compounds, can break down TCE and convert it into ethene, a harmless chemical compound often used to help ripen… [Read More]

DOE JGI Genomics of Energy and Environment Meeting coverage by GenomeWeb

Purdue University’s Jody Banks kicked off the scientific sessions at the US Department of Energy Joint Genome Institute’s 7th annual User Meeting in Walnut Creek, Calif., this week with her talk on the Selaginella genome and how sequencing diverse species could help researchers understand plant evolution. Read more at GenomeWeb [Read More]

Bioinformatics challenges for metagenomic analyses

There are more microbes in, on and around the planet than there are stars in the sky. However, the vast majority of these microorganisms have not yet been studied, in part because many of them do not thrive when moved out of their natural environment. A spoonful of soil contains a complex and diverse microbial… [Read More]

Elucidating bacteria’s roles in ant fungal gardens

Leafcutter ants cultivate fungal gardens that serve as their primary food source. Working toward the goal of harnessing novel enzymes for breaking down plant biomass to produce cellulosic biofuels, Great Lakes Bioenergy Research Center (GLBRC) researchers have been studying the process by which the fungi break down the plant leaves harvested by the ants and… [Read More]

Permafrost study referenced in ScienceNews

In Nature in December, a team of researchers at the Department of Energy’s Joint Genome Institute in Walnut Creek, Calif., and colleagues reported one such microbe’s draft genome — put together from DNA acquired from the semifrozen dirt in an Alaskan black spruce forest. The Alaskan microbe carries genes tuned to transform organic matter into methane, a finding that… [Read More]

Permafrost metagenome study on VOA Special English report

The researchers say one gram of the soil could contain thousands of different kinds of microbes and billions of cells. They say these organisms had never before been cultured in a laboratory. JANET JANSSON:  “So more than ninety percent of those bacteria and other microorganisms in permafrost, we had no idea what they were.” Read… [Read More]

New tools for the IMG/M analysis system

Since the initial release of the Integrated Microbial Genomes with Microbiome samples (IMG/M) system in 2007 to support the comparative analysis of metagenomic data sets, DOE JGI researchers have made several updates in order to keep pace with the rapid increase in data set generation due to advances in sequencing technologies. As reported by researchers… [Read More]

DOE JGI research featured in io9

Last month I was lucky enough to visit one of the biggest genomics labs in the world. At the Joint Genome Institute (JGI) in Walnut Creek, CA, huge rooms full of genome sequencing machines work 24/7 to crunch the codes that create life. And the research here, funded by the US Department of Energy, has… [Read More]

Microbial response to the thawing Arctic

The frozen Arctic soils keep an estimated 1,672 billion metric tons of carbon out of the Earth’s atmosphere, more than 250 times the amount of greenhouse gas emissions attributed to the United States in the year 2009. Rising global temperatures have led to increasing concerns on the potential impacts of thawing permafrost upon the carbon… [Read More]