Tuesday, March 18, 2014

We've moved!

Effective March 17, 2014, this blog has migrated to the DOE Joint Genome Institute's website at http://jgi.doe.gov/. Track our Science Highlights at http://jgi.doe.gov/category/science-highlights/

Friday, February 21, 2014

DOE Science Highlights: Biofuels from a floating water weed

The recently sequenced genome of Spirodela polyrhiza showcases why the plant makes an excellent raw source for biofuels

The Science

Duckweed is one of the smallest and fastest-growing flowering plants that can be a hard-to-control weed in ponds and small lakes. Sequencing the genome of Greater Duckweed (Spirodela polyrhiza) has provides clues about how the tiny plant can be used as an efficient biofuel raw material. It turns out to have one of the smallest plant genomes and is missing many genes, including those for plant maturation and production of cellulose and lignin. It has more genes than comparable plants for starch production.

The Impact

Duckweed shows great promise as a biofuel feedstock. Private companies are already exploring using duckweed to produce fuel. Because of duckweed’s many unique traits (low cellulose and lignin production and high starch production) and life cycle, insights from its genome can tell us a lot about the genes are involved in production of cellulose and lignin. Removing these woody materials from feedstock has been a major challenge in biofuel production. Moreover, S. polyrhiza’s high starch content is also a desirable trait in biofuel feedstock.
Duckweed is a relatively simple plant with fronds that float on the surface of the water and roots that extend into the water. In the flask on the left, you can see the dormant phase, turions, that have dropped to the bottom. Photo by Wenquin Wang

Friday, February 14, 2014

DOE Science Highlights: Feeding at the biofuel trough

Researchers are using “experimental evolution” to develop bacteria that are more efficient at decomposing biomass

The Science

Clostridium phytofermentans is a soil-dwelling bacterium that helps decompose leaf litter. Researchers grew successive generations of bacteria on different woody material that make up plant cell walls (cellulose, cellobiose and xylan) and found that the bacteria adapted and became more efficient over generations. Genetic analysis found that mutations were in regions of DNA that coded for or regulated genes that were involved with carbohydrate (simple sugars) use or transport.

The Impact

This is the first experiment to use an “experimental evolution” approach with a microbe that feeds on cellulose, following generations of bacteria as they adapt to different living environments. The findings suggest that it may be possible to find key genes and mutations that can be used in pinpointing genes that can be used to efficiently break down biomass feedstock, the raw material of biofuels.

The bacteria in this study, Clostridium phytofermentans, were isolated near the Quabbin Reservoir in Massachusetts. The bacteria live in the soil and help break down leaf litter on the forest floor. (Image by Philip Halling via Wikimedia Commons)

Thursday, February 6, 2014

DOE Science Highlights: A cool glass of clean drinking water

A new system called ScanDrop could revolutionize how we identify pathogens in drinking water

The Science

Researchers from Lawrence Berkeley National Laboratory (the Joint BioEnergy Institute and the DOE Joint Genome Institute) and Northeastern University and the Massachusetts General Hospital/Harvard Medical School) have developed a portable, network-enabled system for testing drinking water contamination. The system, called ScanDrop, developed by Tania Konry's group (NEU/MGH/HMS), uses droplet based microfluidics and bead based assay technologies with integrated portable optics to detect bacteria in water. This ScanDrop system was combined with automated microscope control software (PR-PR) and cloud-based networking, developed by Nathan Hillson's (LBNL/JBEI/JGI) group, to scan water samples for pathogens and transmit the data remotely.

The Impact

Testing drinking water supplies for disease-causing pathogens requires several days to test a water sample in a laboratory. This study serves as a proof-of-concept for a method of testing for pathogens in drinking water that is faster than current options and cheap enough that it could be deployed in many poor countries. The system could also potentially be set up to test for several pathogens at once or to test for other kinds of contaminants, including environmental sampling for bacteria that impact the global carbon cycle or are used for bioremediation.

On the left, a graphic demonstrating how droplets of oil move through ScanDrop’s microfluidic chip. On the right, the arrows indicate single bacteria cells inside a droplet of oil. (Image courtesy of N. Hillman)

Tuesday, January 28, 2014

DOE Science Highlights: Faster, bigger, stronger: improvements to two of JGI’s genome databases

Capacities for DOE JGI’s twin genome analysis systems, IMG and IMG/M have both been expanded in the last two years.

The Science

The DOE Joint Genome Institute maintains the Integrated Microbial Genomes (IMG) data warehouse, which contains a rich collection of genomes from all three domains of life. IMG/M provides a similar collection of microbial communities (metagenomes). Both have recently been upgraded to deal with the uptick in genome sequencing and provide more options for users.

The Impact

One major challenge for users of IMG and IMG/M has been the swiftly growing number of genomes and metagenomes available for analysis. Both data systems have been cited in hundreds of publications and are also used by students learning genomics. Improvements in both systems have expanded their capacity and added new tools.

The IMG system has new tools to analyze RNA sequencing results

Friday, January 17, 2014

DOE Science Highlights: Fresh water and marine SAR11 bacteria – distant relatives and different lives

Fresh water lineages of an abundant marine microbe have a distinctly divergent history

The Science

Researchers assembled genomes from several single-cell isolates of the SAR11 group of Alphaproteobacteria and found that they form microclusters within the freshwater clade. They are also much less genetically diverse than the marine clades of SAR11, although they retain highly variable regions (HVR) of DNA that researchers believe help SAR11 bacteria evade viral infection.

The Impact

Researchers are only beginning to understand the successful strategies that the SAR11 group of bacteria uses to survive in nearly every kind of ocean environment. They feed on organic carbon and release carbon dioxide in the process. Because there are so many of them – they make up an estimated half of all marine surface microbes – they exert a large influence on the global carbon cycle. These are the first genomes sequenced for the freshwater clades of this bacterial group. The surprising lack of genetic diversity in this clade provides a useful comparison for the highly diverse marine clades.
Lake Mendota, in Madison, Wis., is one of three lakes from which isolates of the SAR11 clade were collected.  Image via Wikimedia Commons

Friday, January 10, 2014

DOE Science Highlights: ENVO brings structure to biological “environments”

New tool aims to help life science researchers formalize naming conventions for the environments they study

The Science

Biological and biomedical research is increasingly referencing and compiling data from environmental samples, leading to a growing need for a formal and standardized approach to describing those environments. The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open-access project headed by the Berkeley Bioinformatics Open-source Projects (BBOP) group at the Lawrence Berkeley National Laboratory. Its goal is to specify a wide range of environments relevant to several life science disciplines and accommodate the terminologies that those disciplines use.

The Impact

ENVO has already been used on several projects including one related to marine microbes and another cataloguing grass species. As ENVO is adopted by a larger group of researchers, it will provide an even more extensive archive of environmental data.

In the paper describing ENVO, researchers describe an example of a sperm whale swimming on a rocky marine reef and provides one way of describing the biome, environmental feature and environmental material.

Monday, January 6, 2014

DOE Science Highlights: Out with the old, in with the new, improved Genome Portal

The newest iteration of the DOE Joint Genome Institute’s and analytical tools sports improved user interface and infrastructure

The Science

The DOE Joint Genome Institute’s massive genomic database and data management system, the Genome Portal (http://genome.jgi.doe.gov), has recently been upgraded with a more robust infrastructure to manage the torrent of genomic data available and a variety of ways for users to access that information.

The Impact

The amount of data now being generated by DOE JGI and its collaborators falls squarely in the big data category. The ramped-up supply and complexity of data means that the Genome Portal now needs a computational structure to keep pace. The details of those upgrades were outlined in an article in the January 1, 2014 issue of the journal, Nucleic Acids Research.

The revised homepage of the DOE JGI's Genome Portal

Friday, December 20, 2013

DOE Science Highlights: Surprising finds in a rare plant’s mitochondrial genome

Rare and ancient plant gobbles up entire mitochondria from other plants and holds onto them for eons

The Science

One of the oldest flowering plants, Amborella trichopoda, split off from the lineage of other flower plants about 200 million years ago. Analysis reveals that it has a record-setting amount of foreign DNA in its mitochondria, the powerhouse organelles that essentially make it possible for all living things to breathe. Amborella mitochondria have absorbed whole genomes of mitochondria from six other plant species, including one moss and three algae and two other flowering plants. The researchers propose a “mitochondrial fusion” model to explain this near-whole genome retention.

The Impact

Sequencing the entire mitochondrial genome of Amborella, initiated under the DOE JGI’s Community Sequencing Program, was an effort that took eight years. But the effort has yielded several surprising insights, from the size of the genome (3.9 megabases) to the mechanism by which mitochondrial DNA transfer occurs.

Friday, December 13, 2013

DOE Science Highlights: One big family: Understanding the Polyporales phylogenetic and phylogenomic trees

Looking at a combination of whole genomes and gene databases suggests a new way to examine this fungus family tree

The Science

Researchers reviewed 10 currently available whole genomes, comparing them to known gene datasets. They reported family trees for several taxonomic subgroupings called clades. They also analyzed several single-copy genes to assess them for their potential as markers of relationships between members of this group.

The Impact

The phylogenetic trees reported in this paper refine the taxonomic relationships for members of this family and in the words of the researchers, “can now be used to select target species for the next round of whole genome sequencing.”